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1. Targeted RNAseq assay incorporating unique molecular identifiers for improved quantification of gene expression signatures and transcribed mutation fraction in fixed tumor samples

Author: Chunxiao Fu, Michal Marczyk, Michael Samuels, Alexander J. Trevarton, Jiaxin Qu, Rosanna Lau, Lili Du, Todd Pappas, Bruno V. Sinn, Rebekah E. Gould, Lajos Pusztai, Christos Hatzis, and W. Fraser Symmans
Subjects: Targeted RNAseq, Unique molecular identifiers, Assay development, Breast cancer, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract: Abstract Background Our objective was to assess whether modifications to a customized targeted RNA sequencing (RNAseq) assay to include unique molecular identifiers (UMIs) that collapse read counts to their source mRNA counts would improve quantification of transcripts from formalin-fixed paraffin-embedded (FFPE) tumor tissue samples. The assay (SET4) includes signatures that measure hormone receptor and PI3-kinase related transcriptional activity (SETER/PR and PI3Kges), and measures expression of selected activating point mutations and key breast cancer genes. Methods Modifications included steps to introduce eight nucleotides-long UMIs during reverse transcription (RT) in bulk solution, followed by polymerase chain reaction (PCR) of labeled cDNA in droplets, with optimization of the polymerase enzyme and reaction conditions. We used Lin’s concordance correlation coefficient (CCC) to measure concordance, including precision (Rho) and accuracy (Bias), and nonparametric tests (Wilcoxon, Levene’s) to compare the modified (NEW) SET4 assay to the original (OLD) SET4 assay and to whole transcriptome RNAseq using RNA from matched fresh frozen (FF) and FFPE samples from 12 primary breast cancers. Results The modified (NEW) SET4 assay measured single transcripts (p
Published: 2021
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2. Genome-enabled insights into the biology of thrips as crop pests

Author: Dorith Rotenberg, Aaron A. Baumann, Sulley Ben-Mahmoud, Olivier Christiaens, Wannes Dermauw, Panagiotis Ioannidis, Chris G. C. Jacobs, Iris M. Vargas Jentzsch, Jonathan E. Oliver, Monica F. Poelchau, Swapna Priya Rajarapu, Derek J. Schneweis, Simon Snoeck, Clauvis N. T. Taning, Dong Wei, Shirani M. K. Widana Gamage, Daniel S. T. Hughes, Shwetha C. Murali, Samuel T. Bailey, Nicolas E. Bejerman, Christopher J. Holmes, Emily C. Jennings, Andrew J. Rosendale, Andrew Rosselot, Kaylee Hervey, Brandi A. Schneweis, Sammy Cheng, Christopher Childers, Felipe A. Simão, Ralf G. Dietzgen, Hsu Chao, Huyen Dinh, Harsha Vardhan Doddapaneni, Shannon Dugan, Yi Han, Sandra L. Lee, Donna M. Muzny, Jiaxin Qu, Kim C. Worley, Joshua B. Benoit, Markus Friedrich, Jeffery W. Jones, Kristen A. Panfilio, Yoonseong Park, Hugh M. Robertson, Guy Smagghe, Diane E. Ullman, Maurijn van der Zee, Thomas Van Leeuwen, Jan A. Veenstra, Robert M. Waterhouse, Matthew T. Weirauch, John H. Werren, Anna E. Whitfield, Evgeny M. Zdobnov, Richard A. Gibbs, and Stephen Richards
Subjects: Thysanoptera, Western flower thrips, Hemipteroid assemblage, Insect genomics, Tospovirus, Salivary glands, Biology (General), QH301-705.5
Abstract: Abstract Background The western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set. Results We report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~ 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta. Conclusions Analysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species.
Published: 2020
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3. Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest

Author: Michael E. Sparks, Raman Bansal, Joshua B. Benoit, Michael B. Blackburn, Hsu Chao, Mengyao Chen, Sammy Cheng, Christopher Childers, Huyen Dinh, Harsha Vardhan Doddapaneni, Shannon Dugan, Elena N. Elpidina, David W. Farrow, Markus Friedrich, Richard A. Gibbs, Brantley Hall, Yi Han, Richard W. Hardy, Christopher J. Holmes, Daniel S. T. Hughes, Panagiotis Ioannidis, Alys M. Cheatle Jarvela, J. Spencer Johnston, Jeffery W. Jones, Brent A. Kronmiller, Faith Kung, Sandra L. Lee, Alexander G. Martynov, Patrick Masterson, Florian Maumus, Monica Munoz-Torres, Shwetha C. Murali, Terence D. Murphy, Donna M. Muzny, David R. Nelson, Brenda Oppert, Kristen A. Panfilio, Débora Pires Paula, Leslie Pick, Monica F. Poelchau, Jiaxin Qu, Katie Reding, Joshua H. Rhoades, Adelaide Rhodes, Stephen Richards, Rose Richter, Hugh M. Robertson, Andrew J. Rosendale, Zhijian Jake Tu, Arun S. Velamuri, Robert M. Waterhouse, Matthew T. Weirauch, Jackson T. Wells, John H. Werren, Kim C. Worley, Evgeny M. Zdobnov, and Dawn E. Gundersen-Rindal
Subjects: Brown marmorated stink bug genome, Pentatomid genomics, polyphagy, chemoreceptors, odorant binding proteins, opsins, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract: Abstract Background Halyomorpha halys (Stål), the brown marmorated stink bug, is a highly invasive insect species due in part to its exceptionally high levels of polyphagy. This species is also a nuisance due to overwintering in human-made structures. It has caused significant agricultural losses in recent years along the Atlantic seaboard of North America and in continental Europe. Genomic resources will assist with determining the molecular basis for this species’ feeding and habitat traits, defining potential targets for pest management strategies. Results Analysis of the 1.15-Gb draft genome assembly has identified a wide variety of genetic elements underpinning the biological characteristics of this formidable pest species, encompassing the roles of sensory functions, digestion, immunity, detoxification and development, all of which likely support H. halys’ capacity for invasiveness. Many of the genes identified herein have potential for biomolecular pesticide applications. Conclusions Availability of the H. halys genome sequence will be useful for the development of environmentally friendly biomolecular pesticides to be applied in concert with more traditional, synthetic chemical-based controls.
Published: 2020
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4. Gene content evolution in the arthropods

Author: Gregg W. C. Thomas, Elias Dohmen, Daniel S. T. Hughes, Shwetha C. Murali, Monica Poelchau, Karl Glastad, Clare A. Anstead, Nadia A. Ayoub, Phillip Batterham, Michelle Bellair, Greta J. Binford, Hsu Chao, Yolanda H. Chen, Christopher Childers, Huyen Dinh, Harsha Vardhan Doddapaneni, Jian J. Duan, Shannon Dugan, Lauren A. Esposito, Markus Friedrich, Jessica Garb, Robin B. Gasser, Michael A. D. Goodisman, Dawn E. Gundersen-Rindal, Yi Han, Alfred M. Handler, Masatsugu Hatakeyama, Lars Hering, Wayne B. Hunter, Panagiotis Ioannidis, Joy C. Jayaseelan, Divya Kalra, Abderrahman Khila, Pasi K. Korhonen, Carol Eunmi Lee, Sandra L. Lee, Yiyuan Li, Amelia R. I. Lindsey, Georg Mayer, Alistair P. McGregor, Duane D. McKenna, Bernhard Misof, Mala Munidasa, Monica Munoz-Torres, Donna M. Muzny, Oliver Niehuis, Nkechinyere Osuji-Lacy, Subba R. Palli, Kristen A. Panfilio, Matthias Pechmann, Trent Perry, Ralph S. Peters, Helen C. Poynton, Nikola-Michael Prpic, Jiaxin Qu, Dorith Rotenberg, Coby Schal, Sean D. Schoville, Erin D. Scully, Evette Skinner, Daniel B. Sloan, Richard Stouthamer, Michael R. Strand, Nikolaus U. Szucsich, Asela Wijeratne, Neil D. Young, Eduardo E. Zattara, Joshua B. Benoit, Evgeny M. Zdobnov, Michael E. Pfrender, Kevin J. Hackett, John H. Werren, Kim C. Worley, Richard A. Gibbs, Ariel D. Chipman, Robert M. Waterhouse, Erich Bornberg-Bauer, Matthew W. Hahn, and Stephen Richards
Subjects: Arthropods, Genome assembly, Genomics, Protein domains, Gene content, Evolution, Biology (General), QH301-705.5, Genetics, QH426-470
Abstract: Abstract Background Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods. Results Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception. Conclusions These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity.
Published: 2020
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5. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome

Author: Kristen A. Panfilio, Iris M. Vargas Jentzsch, Joshua B. Benoit, Deniz Erezyilmaz, Yuichiro Suzuki, Stefano Colella, Hugh M. Robertson, Monica F. Poelchau, Robert M. Waterhouse, Panagiotis Ioannidis, Matthew T. Weirauch, Daniel S. T. Hughes, Shwetha C. Murali, John H. Werren, Chris G. C. Jacobs, Elizabeth J. Duncan, David Armisén, Barbara M. I. Vreede, Patrice Baa-Puyoulet, Chloé S. Berger, Chun-che Chang, Hsu Chao, Mei-Ju M. Chen, Yen-Ta Chen, Christopher P. Childers, Ariel D. Chipman, Andrew G. Cridge, Antonin J. J. Crumière, Peter K. Dearden, Elise M. Didion, Huyen Dinh, Harsha Vardhan Doddapaneni, Amanda Dolan, Shannon Dugan, Cassandra G. Extavour, Gérard Febvay, Markus Friedrich, Neta Ginzburg, Yi Han, Peter Heger, Christopher J. Holmes, Thorsten Horn, Yi-min Hsiao, Emily C. Jennings, J. Spencer Johnston, Tamsin E. Jones, Jeffery W. Jones, Abderrahman Khila, Stefan Koelzer, Viera Kovacova, Megan Leask, Sandra L. Lee, Chien-Yueh Lee, Mackenzie R. Lovegrove, Hsiao-ling Lu, Yong Lu, Patricia J. Moore, Monica C. Munoz-Torres, Donna M. Muzny, Subba R. Palli, Nicolas Parisot, Leslie Pick, Megan L. Porter, Jiaxin Qu, Peter N. Refki, Rose Richter, Rolando Rivera-Pomar, Andrew J. Rosendale, Siegfried Roth, Lena Sachs, M. Emília Santos, Jan Seibert, Essia Sghaier, Jayendra N. Shukla, Richard J. Stancliffe, Olivia Tidswell, Lucila Traverso, Maurijn van der Zee, Séverine Viala, Kim C. Worley, Evgeny M. Zdobnov, Richard A. Gibbs, and Stephen Richards
Subjects: Phytophagy, Transcription factors, Gene structure, Lateral gene transfer, RNAi, Gene family evolution, Biology (General), QH301-705.5, Genetics, QH426-470
Abstract: Abstract Background The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. Results The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. Conclusions With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus’s strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.
Published: 2019
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6. The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water

Author: David Armisén, Rajendhran Rajakumar, Markus Friedrich, Joshua B. Benoit, Hugh M. Robertson, Kristen A. Panfilio, Seung-Joon Ahn, Monica F. Poelchau, Hsu Chao, Huyen Dinh, Harsha Vardhan Doddapaneni, Shannon Dugan, Richard A. Gibbs, Daniel S. T. Hughes, Yi Han, Sandra L. Lee, Shwetha C. Murali, Donna M. Muzny, Jiaxin Qu, Kim C. Worley, Monica Munoz-Torres, Ehab Abouheif, François Bonneton, Travis Chen, Li-Mei Chiang, Christopher P. Childers, Andrew G. Cridge, Antonin J. J. Crumière, Amelie Decaras, Elise M. Didion, Elizabeth J. Duncan, Elena N. Elpidina, Marie-Julie Favé, Cédric Finet, Chris G. C. Jacobs, Alys M. Cheatle Jarvela, Emily C. Jennings, Jeffery W. Jones, Maryna P. Lesoway, Mackenzie R. Lovegrove, Alexander Martynov, Brenda Oppert, Angelica Lillico-Ouachour, Arjuna Rajakumar, Peter Nagui Refki, Andrew J. Rosendale, Maria Emilia Santos, William Toubiana, Maurijn van der Zee, Iris M. Vargas Jentzsch, Aidamalia Vargas Lowman, Severine Viala, Stephen Richards, and Abderrahman Khila
Subjects: Water striders, Genome sequence, Water surface locomotion, Evolution, Adaptation, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract: Abstract Background Having conquered water surfaces worldwide, the semi-aquatic bugs occupy ponds, streams, lakes, mangroves, and even open oceans. The diversity of this group has inspired a range of scientific studies from ecology and evolution to developmental genetics and hydrodynamics of fluid locomotion. However, the lack of a representative water strider genome hinders our ability to more thoroughly investigate the molecular mechanisms underlying the processes of adaptation and diversification within this group. Results Here we report the sequencing and manual annotation of the Gerris buenoi (G. buenoi) genome; the first water strider genome to be sequenced thus far. The size of the G. buenoi genome is approximately 1,000 Mb, and this sequencing effort has recovered 20,949 predicted protein-coding genes. Manual annotation uncovered a number of local (tandem and proximal) gene duplications and expansions of gene families known for their importance in a variety of processes associated with morphological and physiological adaptations to a water surface lifestyle. These expansions may affect key processes associated with growth, vision, desiccation resistance, detoxification, olfaction and epigenetic regulation. Strikingly, the G. buenoi genome contains three insulin receptors, suggesting key changes in the rewiring and function of the insulin pathway. Other genomic changes affecting with opsin genes may be associated with wavelength sensitivity shifts in opsins, which is likely to be key in facilitating specific adaptations in vision for diverse water habitats. Conclusions Our findings suggest that local gene duplications might have played an important role during the evolution of water striders. Along with these findings, the sequencing of the G. buenoi genome now provides us the opportunity to pursue exciting research opportunities to further understand the genomic underpinnings of traits associated with the extreme body plan and life history of water striders.
Published: 2018
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7. Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum

Author: Amelia R. I. Lindsey, Yogeshwar D. Kelkar, Xin Wu, Dan Sun, Ellen O. Martinson, Zhichao Yan, Paul F. Rugman-Jones, Daniel S. T. Hughes, Shwetha C. Murali, Jiaxin Qu, Shannon Dugan, Sandra L. Lee, Hsu Chao, Huyen Dinh, Yi Han, Harsha Vardhan Doddapaneni, Kim C. Worley, Donna M. Muzny, Gongyin Ye, Richard A. Gibbs, Stephen Richards, Soojin V. Yi, Richard Stouthamer, and John H. Werren
Subjects: Chalcidoidea, Wolbachia, Comparative genomics, Parthenogenesis, Symbiosis, Biological control, Biology (General), QH301-705.5
Abstract: Abstract Background Trichogrammatids are minute parasitoid wasps that develop within other insect eggs. They are less than half a millimeter long, smaller than some protozoans. The Trichogrammatidae are one of the earliest branching families of Chalcidoidea: a diverse superfamily of approximately half a million species of parasitoid wasps, proposed to have evolved from a miniaturized ancestor. Trichogramma are frequently used in agriculture, released as biological control agents against major moth and butterfly pests. Additionally, Trichogramma are well known for their symbiotic bacteria that induce asexual reproduction in infected females. Knowledge of the genome sequence of Trichogramma is a major step towards further understanding its biology and potential applications in pest control. Results We report the 195-Mb genome sequence of Trichogramma pretiosum and uncover signatures of miniaturization and adaptation in Trichogramma and related parasitoids. Comparative analyses reveal relatively rapid evolution of proteins involved in ribosome biogenesis and function, transcriptional regulation, and ploidy regulation. Chalcids also show loss or especially rapid evolution of 285 gene clusters conserved in other Hymenoptera, including many that are involved in signal transduction and embryonic development. Comparisons between sexual and asexual lineages of Trichogramma pretiosum reveal that there is no strong evidence for genome degradation (e.g., gene loss) in the asexual lineage, although it does contain a lower repeat content than the sexual lineage. Trichogramma shows particularly rapid genome evolution compared to other hymenopterans. We speculate these changes reflect adaptations to miniaturization, and to life as a specialized egg parasitoid. Conclusions The genomes of Trichogramma and related parasitoids are a valuable resource for future studies of these diverse and economically important insects, including explorations of parasitoid biology, symbiosis, asexuality, biological control, and the evolution of miniaturization. Understanding the molecular determinants of parasitism can also inform mass rearing of Trichogramma and other parasitoids for biological control.
Published: 2018
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8. Synchronous delivery of oxygen and photosensitizer for alleviation of hypoxia tumor microenvironment and dramatically enhanced photodynamic therapy

Author: Xiaomeng Guo, Jiaxin Qu, Chunqi Zhu, Wei Li, Lihua Luo, Jie Yang, Xiaoyi Yin, Qingpo Li, Yongzhong Du, Dawei Chen, Yunqing Qiu, Yan Lou, and Jian You
Subjects: tumor hypoxia, photodynamic therapy, oxygen, hemoglobin, photosensitizer, Therapeutics. Pharmacology, RM1-950
Abstract: Photosensitizer, proper laser irradiation, and oxygen are essential components for effective photodynamic therapy (PDT) in clinical cancer therapy. However, native hypoxic tumoral microenvironment is a major barrier hindering photodynamic reactions in vivo. Thus, we have prepared biocompatible liposomes by loading complexes of oxygen-carrier (hemoglobin, Hb) and photosensitizer (indocyanine green, ICG) for enhanced PDT against hypoxic tumor. Ideal oxygen donor Hb, which is an oxygen-carried protein in red blood cells, makes such liposome which provide stable oxygen supply. ICG, as a photosensitizer, could transfer energy from lasers to oxygen to generate cytotoxic reactive oxygen species (ROS) for treatment. The liposomes loading ICG and Hb (LIH) exhibited efficient tumor homing upon intravenous injection. As revealed by T2-weighted magnetic resonance imaging and immunohistochemical analysis, the intratumoral hypoxia was greatly alleviated, and the level of hypoxia inducible factor-1α (HIF-1α) and vascular endothelial growth factor (VEGF) in tumor was obviously down-regulated. A weak PDT efficiency was found in cells incubated in simulated hypoxia condition in vitro, while PDT effect was dramatically enhanced in LIH treated hypoxia cells under near-infrared (NIR) laser, which was mainly attributed to massive generation of ROS with sufficient oxygen supply. ROS trigger oxidative damage of tumors and induce complete suppression of tumor growth and 100% survival rate of mice, which were also in good health condition. Our work highlights a liposome-based nanomedicine that could effectively deliver oxygen to tumor and alleviate tumor hypoxia state, inducing greatly improved efficacy compared to conventional cancer PDT and demonstrates the promise of modulating unfavorable tumor microenvironment with nanotechnology to overcome limitations of cancer therapies.
Published: 2018
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9. Correction to: Genome-enabled insights into the biology of thrips as crop pests

Author: Dorith Rotenberg, Aaron A. Baumann, Sulley Ben-Mahmoud, Olivier Christiaens, Wannes Dermauw, Panagiotis Ioannidis, Chris G. C. Jacobs, Iris M. Vargas Jentzsch, Jonathan E. Oliver, Monica F. Poelchau, Swapna Priya Rajarapu, Derek J. Schneweis, Simon Snoeck, Clauvis N. T. Taning, Dong Wei, Shirani M. K. Widana Gamage, Daniel S. T. Hughes, Shwetha C. Murali, Samuel T. Bailey, Nicolas E. Bejerman, Christopher J. Holmes, Emily C. Jennings, Andrew J. Rosendale, Andrew Rosselot, Kaylee Hervey, Brandi A. Schneweis, Sammy Cheng, Christopher Childers, Felipe A. Simão, Ralf G. Dietzgen, Hsu Chao, Huyen Dinh, Harsha Vardhan Doddapaneni, Shannon Dugan, Yi Han, Sandra L. Lee, Donna M. Muzny, Jiaxin Qu, Kim C. Worley, Joshua B. Benoit, Markus Friedrich, Jeffery W. Jones, Kristen A. Panfilio, Yoonseong Park, Hugh M. Robertson, Guy Smagghe, Diane E. Ullman, Maurijn van der Zee, Thomas Van Leeuwen, Jan A. Veenstra, Robert M. Waterhouse, Matthew T. Weirauch, John H. Werren, Anna E. Whitfield, Evgeny M. Zdobnov, Richard A. Gibbs, and Stephen Richards
Subjects: Biology (General), QH301-705.5
Abstract: An amendment to this paper has been published and can be accessed via the original article.
Published: 2020
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10. The house spider genome reveals an ancient whole-genome duplication during arachnid evolution

Author: Evelyn E. Schwager, Prashant P. Sharma, Thomas Clarke, Daniel J. Leite, Torsten Wierschin, Matthias Pechmann, Yasuko Akiyama-Oda, Lauren Esposito, Jesper Bechsgaard, Trine Bilde, Alexandra D. Buffry, Hsu Chao, Huyen Dinh, HarshaVardhan Doddapaneni, Shannon Dugan, Cornelius Eibner, Cassandra G. Extavour, Peter Funch, Jessica Garb, Luis B. Gonzalez, Vanessa L. Gonzalez, Sam Griffiths-Jones, Yi Han, Cheryl Hayashi, Maarten Hilbrant, Daniel S. T. Hughes, Ralf Janssen, Sandra L. Lee, Ignacio Maeso, Shwetha C. Murali, Donna M. Muzny, Rodrigo Nunes da Fonseca, Christian L. B. Paese, Jiaxin Qu, Matthew Ronshaugen, Christoph Schomburg, Anna Schönauer, Angelika Stollewerk, Montserrat Torres-Oliva, Natascha Turetzek, Bram Vanthournout, John H. Werren, Carsten Wolff, Kim C. Worley, Gregor Bucher, Richard A. Gibbs, Jonathan Coddington, Hiroki Oda, Mario Stanke, Nadia A. Ayoub, Nikola-Michael Prpic, Jean-François Flot, Nico Posnien, Stephen Richards, and Alistair P. McGregor
Subjects: Parasteatoda tepidariorum, Genome, Centruroides sculpturatus, Gene duplication, Evolution, Hox genes, Biology (General), QH301-705.5
Abstract: Abstract Background The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. Results We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication. Conclusions Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes.
Published: 2017
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11. Unique features of a global human ectoparasite identified through sequencing of the bed bug genome

Author: Joshua B. Benoit, Zach N. Adelman, Klaus Reinhardt, Amanda Dolan, Monica Poelchau, Emily C. Jennings, Elise M. Szuter, Richard W. Hagan, Hemant Gujar, Jayendra Nath Shukla, Fang Zhu, M. Mohan, David R. Nelson, Andrew J. Rosendale, Christian Derst, Valentina Resnik, Sebastian Wernig, Pamela Menegazzi, Christian Wegener, Nicolai Peschel, Jacob M. Hendershot, Wolfgang Blenau, Reinhard Predel, Paul R. Johnston, Panagiotis Ioannidis, Robert M. Waterhouse, Ralf Nauen, Corinna Schorn, Mark-Christoph Ott, Frank Maiwald, J. Spencer Johnston, Ameya D. Gondhalekar, Michael E. Scharf, Brittany F. Peterson, Kapil R. Raje, Benjamin A. Hottel, David Armisén, Antonin Jean Johan Crumière, Peter Nagui Refki, Maria Emilia Santos, Essia Sghaier, Sèverine Viala, Abderrahman Khila, Seung-Joon Ahn, Christopher Childers, Chien-Yueh Lee, Han Lin, Daniel S. T. Hughes, Elizabeth J. Duncan, Shwetha C. Murali, Jiaxin Qu, Shannon Dugan, Sandra L. Lee, Hsu Chao, Huyen Dinh, Yi Han, Harshavardhan Doddapaneni, Kim C. Worley, Donna M. Muzny, David Wheeler, Kristen A. Panfilio, Iris M. Vargas Jentzsch, Edward L. Vargo, Warren Booth, Markus Friedrich, Matthew T. Weirauch, Michelle A. E. Anderson, Jeffery W. Jones, Omprakash Mittapalli, Chaoyang Zhao, Jing-Jiang Zhou, Jay D. Evans, Geoffrey M. Attardo, Hugh M. Robertson, Evgeny M. Zdobnov, Jose M. C. Ribeiro, Richard A. Gibbs, John H. Werren, Subba R. Palli, Coby Schal, and Stephen Richards
Subjects: Science
Abstract: The bed bug, Cimex lectularius, is a ubiquitous human ectoparasite with global distribution. Here, the authors sequence the genome of the bed bug and identify reductions in chemosensory genes, expansion of genes associated with blood digestion and genes linked to pesticide resistance.
Published: 2016
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12. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.

Author: Ariel D Chipman, David E K Ferrier, Carlo Brena, Jiaxin Qu, Daniel S T Hughes, Reinhard Schröder, Montserrat Torres-Oliva, Nadia Znassi, Huaiyang Jiang, Francisca C Almeida, Claudio R Alonso, Zivkos Apostolou, Peshtewani Aqrawi, Wallace Arthur, Jennifer C J Barna, Kerstin P Blankenburg, Daniela Brites, Salvador Capella-Gutiérrez, Marcus Coyle, Peter K Dearden, Louis Du Pasquier, Elizabeth J Duncan, Dieter Ebert, Cornelius Eibner, Galina Erikson, Peter D Evans, Cassandra G Extavour, Liezl Francisco, Toni Gabaldón, William J Gillis, Elizabeth A Goodwin-Horn, Jack E Green, Sam Griffiths-Jones, Cornelis J P Grimmelikhuijzen, Sai Gubbala, Roderic Guigó, Yi Han, Frank Hauser, Paul Havlak, Luke Hayden, Sophie Helbing, Michael Holder, Jerome H L Hui, Julia P Hunn, Vera S Hunnekuhl, LaRonda Jackson, Mehwish Javaid, Shalini N Jhangiani, Francis M Jiggins, Tamsin E Jones, Tobias S Kaiser, Divya Kalra, Nathan J Kenny, Viktoriya Korchina, Christie L Kovar, F Bernhard Kraus, François Lapraz, Sandra L Lee, Jie Lv, Christigale Mandapat, Gerard Manning, Marco Mariotti, Robert Mata, Tittu Mathew, Tobias Neumann, Irene Newsham, Dinh N Ngo, Maria Ninova, Geoffrey Okwuonu, Fiona Ongeri, William J Palmer, Shobha Patil, Pedro Patraquim, Christopher Pham, Ling-Ling Pu, Nicholas H Putman, Catherine Rabouille, Olivia Mendivil Ramos, Adelaide C Rhodes, Helen E Robertson, Hugh M Robertson, Matthew Ronshaugen, Julio Rozas, Nehad Saada, Alejandro Sánchez-Gracia, Steven E Scherer, Andrew M Schurko, Kenneth W Siggens, DeNard Simmons, Anna Stief, Eckart Stolle, Maximilian J Telford, Kristin Tessmar-Raible, Rebecca Thornton, Maurijn van der Zee, Arndt von Haeseler, James M Williams, Judith H Willis, Yuanqing Wu, Xiaoyan Zou, Daniel Lawson, Donna M Muzny, Kim C Worley, Richard A Gibbs, Michael Akam, and Stephen Richards
Subjects: Biology (General), QH301-705.5
Abstract: Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.
Published: 2014
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13. Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology.

Author: Adam C English, Stephen Richards, Yi Han, Min Wang, Vanesa Vee, Jiaxin Qu, Xiang Qin, Donna M Muzny, Jeffrey G Reid, Kim C Worley, and Richard A Gibbs
Subjects: Medicine, Science
Abstract: Many genomes have been sequenced to high-quality draft status using Sanger capillary electrophoresis and/or newer short-read sequence data and whole genome assembly techniques. However, even the best draft genomes contain gaps and other imperfections due to limitations in the input data and the techniques used to build draft assemblies. Sequencing biases, repetitive genomic features, genomic polymorphism, and other complicating factors all come together to make some regions difficult or impossible to assemble. Traditionally, draft genomes were upgraded to "phase 3 finished" status using time-consuming and expensive Sanger-based manual finishing processes. For more facile assembly and automated finishing of draft genomes, we present here an automated approach to finishing using long-reads from the Pacific Biosciences RS (PacBio) platform. Our algorithm and associated software tool, PBJelly, (publicly available at https://sourceforge.net/projects/pb-jelly/) automates the finishing process using long sequence reads in a reference-guided assembly process. PBJelly also provides "lift-over" co-ordinate tables to easily port existing annotations to the upgraded assembly. Using PBJelly and long PacBio reads, we upgraded the draft genome sequences of a simulated Drosophila melanogaster, the version 2 draft Drosophila pseudoobscura, an assembly of the Assemblathon 2.0 budgerigar dataset, and a preliminary assembly of the Sooty mangabey. With 24× mapped coverage of PacBio long-reads, we addressed 99% of gaps and were able to close 69% and improve 12% of all gaps in D. pseudoobscura. With 4× mapped coverage of PacBio long-reads we saw reads address 63% of gaps in our budgerigar assembly, of which 32% were closed and 63% improved. With 6.8× mapped coverage of mangabey PacBio long-reads we addressed 97% of gaps and closed 66% of addressed gaps and improved 19%. The accuracy of gap closure was validated by comparison to Sanger sequencing on gaps from the original D. pseudoobscura draft assembly and shown to be dependent on initial reference quality.
Published: 2012
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14. A hybrid algorithm for drone routing problem with time windows.

Author: Jiaxin Qu, Tao Jia 0003, and Dong Lei
Published: 2023
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15. Unravelling the nature of the active species as well as the Mn doping effect over gamma-Al2O3 catalyst for eliminating AsH3 and PH3

Author: Bowen Xu, Jiaxin Qu, Xueqian Wang, Langlang Wang, Yu Pu, Ping Ning, Yibing Xie, Yixing Ma, and Qiang Ma
Subjects: Environmental Engineering, Environmental Chemistry, General Medicine, General Environmental Science
Published: 2024

16. Intelligent Monitoring Method of Helmet Wearing Identification in Power Plants

Author: Xingke Li, Yikai Wang, Jiaxin Qu, Wei Wang, Xingming Xu, Shisong Jin, Yunhao Wu, and Yingjian Li
Published: 2023

17. Targeted RNAseq assay incorporating unique molecular identifiers for improved quantification of gene expression signatures and transcribed mutation fraction in fixed tumor samples

Author: Jiaxin Qu, Chunxiao Fu, Rebekah Gould, Todd Pappas, Lili Du, W. Fraser Symmans, Christos Hatzis, Lajos Pusztai, Michal Marczyk, Rosanna Lau, Michael Samuels, Bruno Valentin Sinn, and Alexander J. Trevarton
Subjects: 0301 basic medicine, Targeted RNAseq, Cancer Research, Tissue Fixation, lcsh:RC254-282, law.invention, Specimen Handling, 03 medical and health sciences, 0302 clinical medicine, Breast cancer, law, Complementary DNA, Formaldehyde, Neoplasms, Gene expression, Genetics, Biomarkers, Tumor, Humans, Gene, Polymerase chain reaction, Polymerase, Messenger RNA, Paraffin Embedding, biology, Chemistry, Sequence Analysis, RNA, Gene Expression Profiling, Assay development, Prognosis, lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens, Molecular biology, Reverse transcriptase, 030104 developmental biology, Concordance correlation coefficient, Oncology, Technical Advance, 030220 oncology & carcinogenesis, Mutation, biology.protein, Transcriptome, Unique molecular identifiers
Abstract: Background Our objective was to assess whether modifications to a customized targeted RNA sequencing (RNAseq) assay to include unique molecular identifiers (UMIs) that collapse read counts to their source mRNA counts would improve quantification of transcripts from formalin-fixed paraffin-embedded (FFPE) tumor tissue samples. The assay (SET4) includes signatures that measure hormone receptor and PI3-kinase related transcriptional activity (SETER/PR and PI3Kges), and measures expression of selected activating point mutations and key breast cancer genes. Methods Modifications included steps to introduce eight nucleotides-long UMIs during reverse transcription (RT) in bulk solution, followed by polymerase chain reaction (PCR) of labeled cDNA in droplets, with optimization of the polymerase enzyme and reaction conditions. We used Lin’s concordance correlation coefficient (CCC) to measure concordance, including precision (Rho) and accuracy (Bias), and nonparametric tests (Wilcoxon, Levene’s) to compare the modified (NEW) SET4 assay to the original (OLD) SET4 assay and to whole transcriptome RNAseq using RNA from matched fresh frozen (FF) and FFPE samples from 12 primary breast cancers. Results The modified (NEW) SET4 assay measured single transcripts (pER/PR (p=0.002) more reproducibly in technical replicates from FFPE samples. The modified SET4 assay was more precise for measuring single transcripts (Rho 0.966 vs 0.888, pER/PR (Rho 0.985 vs 0.968) or PI3Kges (Rho 0.985 vs 0.946) in FFPE, compared to FF samples. It was also more precise than wtRNAseq of FFPE for measuring transcripts (Rho 0.986 vs 0.934, pER/PR (Rho 0.993 vs 0.915, p=0.004), but not PI3Kges (Rho 0.988 vs 0.945, p=0.051). Accuracy (Bias) was comparable between protocols. Two samples carried a PIK3CA mutation, and measurements of transcribed mutant allele fraction was similar in FF and FFPE samples and appeared more precise with the modified SET4 assay. Amplification efficiency (reads per UMI) was consistent in FF and FFPE samples, and close to the theoretically expected value, when the library size exceeded 400,000 aligned reads. Conclusions Modifications to the targeted RNAseq protocol for SET4 assay significantly increased the precision of UMI-based and reads-based measurements of individual transcripts, multi-gene signatures, and mutant transcript fraction, particularly with FFPE samples.
Published: 2021

18. Full Hardware Image Encryption for Oscillating Memristor Circuits

Author: Lu Wang, Jiaxin Qu, Jiazhuang Li, and Dianzhong Wen
Subjects: Mechanics of Materials, General Materials Science, Industrial and Manufacturing Engineering
Published: 2022

19. The investigation of the role of nitrogen in the improvement of catalytic activity and stability of Zr/Ti-based material for carbon disulfide hydrolysis

Author: Jiaxin Qu, Xueqian Wang, Langlang Wang, Bowen Xu, Ping Ning, Yixing Ma, Yibing Xie, Rui Cao, and Qiang Ma
Subjects: Filtration and Separation, Analytical Chemistry
Published: 2022

20. DNA methylation variation and growth in the clonal Duchesnea indica is regulated by both past and present lead environments

Author: Jiaxin Quan, Shanshan Song, Linya Xing, Xiao Liu, and Ming Yue
Subjects: Heterogeneous environment, morphological plasticity, stress legacy, epigenetic, DNA methylation, lead contaminated, Genetics, QH426-470
Abstract: ABSTRACTStudies suggest that clonal plants’ ability to select habitats and forage in a heterogeneous environment is influenced by their past environment, with stress legacy potentially playing a crucial role. In this study, we examined parental ramets of Duchesnea indica Focke that were subject to either a control or lead-contaminated environment (past environment), and their newborn offspring were then transplanted into control, homogeneous lead or heterogeneous lead environment (present environment). We analysed how past and present environments affect plant growth and DNA methylation in offspring. The result shown that the DNA methylation loci composition of offspring was affected by the interaction of parental environment and offspring environment, and DNA methylation levels were higher in heterogeneous environments. Moreover, our findings indicate that offspring would thrive in the heterogeneous lead environment if they did not experience lead pollution in the past, their progeny will avoid lead toxicity by reducing underground biomass allocation. However, when the parents experienced lead stress environment, their biomass allocation strategies disappeared, and they prefer to grow in favourable patches to avoid lead-contaminated patches. We concluded that the integration of historical parental exposure to lead-contaminated and current information about their offspring’s environment are impacting plant phenotypes. It is possible that the stress legacy from the parents has been transmitted to their offspring ramets, and the stress legacy is at least partly based on heritable epigenetic variation. The phenotypic variation regulated by the stress legacy affects the growth performance, biomass allocation strategy, and even the behaviour of D. indica.
Published: 2024
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21. Additional file 4 of Targeted RNAseq assay incorporating unique molecular identifiers for improved quantification of gene expression signatures and transcribed mutation fraction in fixed tumor samples

Author: Chunxiao Fu, Marczyk, Michal, Samuels, Michael, Trevarton, Alexander J., Jiaxin Qu, Lau, Rosanna, Du, Lili, Pappas, Todd, Sinn, Bruno V., Gould, Rebekah E., Pusztai, Lajos, Hatzis, Christos, and Symmans, W. Fraser
Abstract: Additional File 4: Fig. S4. Concordance between wtRNAseq and targeted RNAseq of gene expression levels and transcriptional signature scores. Distribution of Pearson correlation (Rho), bias, scale and location coefficient (components of concordance correlation coefficient (CCC)) for all 28 targeted genes within each protocol. The green points represent the two transcriptional signatures.
Published: 2021
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22. Additional file 1 of Targeted RNAseq assay incorporating unique molecular identifiers for improved quantification of gene expression signatures and transcribed mutation fraction in fixed tumor samples

Author: Chunxiao Fu, Marczyk, Michal, Samuels, Michael, Trevarton, Alexander J., Jiaxin Qu, Lau, Rosanna, Du, Lili, Pappas, Todd, Sinn, Bruno V., Gould, Rebekah E., Pusztai, Lajos, Hatzis, Christos, and Symmans, W. Fraser
Abstract: Additional file 1: Fig. S1. Technical variance of expression measurements in targeted RNAseq data using FF samples. (A) Distribution of absolute difference in expression between replicates for 28 targeted genes within each protocol. (B) Distribution of absolute difference in molecular signature score between replicates for 2 signatures within each protocol.
Published: 2021
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23. Additional file 3 of Targeted RNAseq assay incorporating unique molecular identifiers for improved quantification of gene expression signatures and transcribed mutation fraction in fixed tumor samples

Author: Chunxiao Fu, Marczyk, Michal, Samuels, Michael, Trevarton, Alexander J., Jiaxin Qu, Lau, Rosanna, Du, Lili, Pappas, Todd, Sinn, Bruno V., Gould, Rebekah E., Pusztai, Lajos, Hatzis, Christos, and Symmans, W. Fraser
Abstract: Additional File 3: Fig. S3. Distribution of raw read depth across all gene targets in FFPE samples. Line type (solid or dashed) distinguishes two technical replicates, while color represents different protocol. Genes are sorted by average read depth in all samples.
Published: 2021
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24. Additional file 2 of Targeted RNAseq assay incorporating unique molecular identifiers for improved quantification of gene expression signatures and transcribed mutation fraction in fixed tumor samples

Author: Chunxiao Fu, Marczyk, Michal, Samuels, Michael, Trevarton, Alexander J., Jiaxin Qu, Lau, Rosanna, Du, Lili, Pappas, Todd, Sinn, Bruno V., Gould, Rebekah E., Pusztai, Lajos, Hatzis, Christos, and Symmans, W. Fraser
Abstract: Additional File 2: Fig. S2. Distribution of raw read depth across all gene targets in FF samples. Line type (solid or dashed) distinguishes two technical replicates (6 samples have only 1 replicate in FF), while color represents different protocol. Genes are sorted by average read depth in all samples.
Published: 2021
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25. Changes induced by parental neighboring touch in the clonal plant Glechoma longituba depend on the light environment

Author: Linya Xing, Jiaxin Quan, Shuqi Zhang, Xiao Liu, Hua Bai, and Ming Yue
Subjects: clonal plant, parental neighboring touch, thigmomorphogenetic, shade response, maternal effect, light adaptability, Plant culture, SB1-1110
Abstract: IntroductionTouch by neighboring plants is a common but overlooked environmental variable for plants, especially in dense vegetation. In addition, shade is inevitable for understory plants. The growth performance of clonal plant to the interaction between thigmomorphogenesis and shade response, and their impact on light adaptability is still unknown.MethodsAt the present study, parental ramets of Glechoma longituba were exposed to two conditions (neighboring touch and shade), and their offspring ramets were in ambient or shaded environment. The phenotype and growth of parental and offspring ramets were analyzed. ResultsThe results showed that neighboring touch of parental ramets regulated the performance of offspring ramets, while the effect depended on the light environment. The parental neighboring touch occurring in ambient environment suppressed the expansion of leaf organ, showed as a shorter petiole and smaller leaf area. Moreover, G. longituba exhibited both shade avoidance and shade tolerance characters to shaded environment, such as increased leaf area ratio and leaf mass ratio, longer specific petiole length and specific stolon length. It was notable that these characters of shade response could be promoted by parental neighboring touch to some extent. Additionally, parental light environment plays an important role in offspring growth, parent with ambient light always had well-grown offspring whatever the light condition of offspring, but the growth of offspring whose parent in shaded environment was inhibited. Finally, for the offspring with shaded environment, the touch between parental ramets in shade environment showed a disadvantage on their growth, but the influence of the touch between parental ramets in ambient environment was slight. DiscussionOverall, the interaction of parental neighboring touch and shade environment complicate the growth of understory plants, the performance of plants is the integrated effect of both. These findings are conducive to an in-depth understanding of the environmental adaptation of plants.
Published: 2024
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26. Low-temperature hydrolysis of carbonyl sulfide in blast furnace gas using Al2O3-based catalysts with high oxidation resistance

Author: Yixing Ma, Xueqian Wang, Jiaxin Qu, Yibing Xie, Hui Zhang, Cao Rui, Ping Ning, and Langlang Wang
Subjects: inorganic chemicals, Chemistry, General Chemical Engineering, Organic Chemistry, Energy Engineering and Power Technology, Nanoparticle, Potassium oxide, Catalysis, chemistry.chemical_compound, Hydrolysis, Fuel Technology, Adsorption, Chemical engineering, Sulfate, Carbonyl sulfide, Blast furnace gas
Abstract: Water vapor, O2 and various sulfides in blast furnace gases affect the carbonyl sulfide (COS) hydrolysis reaction. In this study, we investigated the hydrolysis and deactivation mechanisms of a series of catalysts that were synthesized by depositing K2O and MoO3 on industrial alumina-based catalysts. Alumina nanosheets were deposited with potassium oxide, in which MoO3 nanoparticles were incorporated resulting in needle-like structures. The modified catalysts had substantially enhanced COS hydrolysis activity at low temperatures. The introduction of K2O and MoO3 significantly increased the number of weakly basic sites on the catalysts and reduced the lattice oxygen content. The catalysts exhibited high oxidation resistance and hydrolysis properties. According to the poisoning mechanism, the deposition of sulfate species tended to reduce weakly basic sites. High-valent Mo easily excited the adsorbed H2O on the catalysts, producing –OH groups that facilitated the COS hydrolysis reaction. This modification facilitates the further investigation of catalysts capable of promoting COS hydrolysis and their application in the manufacturing industry.
Published: 2022

27. Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera

Author: Sebastian Martin, Huyen Dinh, Kim C. Worley, Björn M. von Reumont, Tanja Ziesmann, Elena N. Elpidina, Cameron Gudobba, Alexander G. Martynov, Patrice Baa-Puyoulet, Cornelis J. P. Grimmelikhuijzen, Elizabeth Cash, Olivia R.A. Tidswell, Federica Calevro, Aaron Stahl, Markus Friedrich, Jiaxin Qu, Andrew J. Rosendale, Joshua B. Benoit, Leo W. Beukeboom, Shwetha C. Murali, Mackenzie Lovegrove, Panagiotis Ioannidis, Brenda Oppert, Daniel Dowling, Mei-Ju May Chen, Peter Lesný, Elzemiek Geuverink, Jan Philip Oeyen, Bernhard Misof, Maarten J.M.F. Reijnders, Masatsugu Hatakeyama, Emily C. Jennings, Christoph Mayer, Lucia Vedder, Daisuke S. Yamamoto, Anja Buttstedt, Hsu Chao, Elizabeth J. Duncan, Louis van de Zande, Daniel S.T. Hughes, Monica Munoz-Torres, Erich Bornberg-Bauer, Richard A. Gibbs, Lars Podsiadlowski, Peter K. Dearden, Alexandros G Sotiropoulos, Ralph S. Peters, Nicolas Montagné, Jeanne Wilbrandt, Andrew G. Cridge, Stephen Richards, John H. Werren, Yi Han, Sandra L. Lee, Megumi Sumitani, Victoria C. Moris, Oliver Niehuis, Ewald Große-Wilde, Amanda Dolan, Elise M. Szuter, Nicolas Parisot, Christopher P. Childers, Emmanuelle Jacquin-Joly, Sonja Grath, Panagiotis Provataris, Donna M. Muzny, Thomas Pauli, Joshua D. Gibson, Steffen Klasberg, Frank Hauser, John Skelly, Robert M. Waterhouse, Alexander Donath, Monica F. Poelchau, Shannon Dugan, Bill S. Hansson, Hubert Charles, Harshavardhan Doddapaneni, Malte Petersen, Evgeny M. Zdobnov, Evangelos Tsitlakidis, Christian Pick, Felipe A. Simão, Emma Persyn, Jeffery W. Jones, Lavrov, Dennis, Beukeboom lab, Evolutionary Genetics, Development & Behaviour, Van de Zande lab, Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Groningen Institute for Evolutionary Life Sciences [Groningen] (GELIFES), University of Groningen [Groningen], Westfälische Wilhelms-Universität Münster (WWU), Biochemistry Department, University of Otago [Dunedin, Nouvelle-Zélande], Max-Planck-Institut für Kernphysik (MPIK), Max-Planck-Gesellschaft, Max Planck Institute for Chemical Ecology, Physiologie de l'Insecte : Signalisation et Communication (PISC), Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech, Institute for Evolution and Biodiversity (IEB), Department of Chemistry [Vancouver] (UBC Chemistry), University of British Columbia (UBC), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Human Genome Sequencing Center, Baylor College of Medicine, Baylor College of Medicine (BCM), Baylor University-Baylor University, Center for Molecular Biodiversity Research (ZMB), Zoological Research Museum Alexander Koenig (ZFMK), Department of Biology, Georgetown University, Université de Lausanne (UNIL), Human Genome Sequencing Center [Houston] (HGSC), Grad Sch Life Sci, Div Neurogenet, Tohoku University [Sendai], Department of Genetic Medicine and Development [Geneva], Université de Genève (UNIGE), Zoologisches Forschungsmuseum Alexander Koenig, Center for Molecular Biodiversity Research, Lavrov, Dennis (ed.), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Zdobnov, Evgeny
Subjects: AcademicSubjects/SCI01140, 0106 biological sciences, Most recent common ancestor, Male, Vision, Genome, Insect, Gene Dosage, Hymenoptera, JEWEL WASP NASONIA, Receptors, Odorant, 01 natural sciences, Genome, Parasitoid, MULTIPLE SEQUENCE ALIGNMENT, opsin, Receptors, phytophagy, ddc:576.5, Apocrita, Conserved Sequence, 0303 health sciences, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], HOST LOCATION, Eusociality, ROYAL JELLY PROTEIN, ATHALIA-ROSAE, Sawfly, Odorant, APIS-MELLIFERA, Multigene Family, Insect Proteins, Female, Research Article, Genetics, Ecology, Evolution, Behavior and Systematics, hexamerin, major royal jelly protein, microsynteny, odorant receptor, CHEMORECEPTOR SUPERFAMILY, Genetic Speciation, Biology, 010603 evolutionary biology, Host-Parasite Interactions, 03 medical and health sciences, Ocular, Animals, Amino Acid Sequence, Herbivory, Social Behavior, DRAFT GENOME, Life Below Water, Vision, Ocular, 030304 developmental biology, MODEL SELECTION, Glycoproteins, Orussidae, Evolutionary Biology, fungi, Human Genome, AcademicSubjects/SCI01130, Immunity, biology.organism_classification, MOLECULAR EVOLUTION, Evolutionary biology, DNA Transposable Elements, Biochemistry and Cell Biology, Insect, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis, Developmental Biology
Abstract: The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (Orussidae) and wasp-waisted Hymenoptera (Apocrita). However, Apocrita and Orussidae differ dramatically in their species richness, indicating that the diversification of Apocrita was promoted by additional traits. These traits have remained elusive due to a paucity of sawfly genome sequences, in particular those of parasitoid sawflies. Here, we present comparative analyses of draft genomes of the primarily phytophagous sawfly Athalia rosae and the parasitoid sawfly Orussus abietinus. Our analyses revealed that the ancestral hymenopteran genome exhibited traits that were previously considered unique to eusocial Apocrita (e.g., low transposable element content and activity) and a wider gene repertoire than previously thought (e.g., genes for CO2 detection). Moreover, we discovered that Apocrita evolved a significantly larger array of odorant receptors than sawflies, which could be relevant to the remarkable diversification of Apocrita by enabling efficient detection and reliable identification of hosts.
Published: 2020

28. Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest

Author: J. Spencer Johnston, John H. Werren, Hugh M. Robertson, Joshua B. Benoit, Shannon Dugan, Monica Munoz-Torres, Richard A. Gibbs, Kim C. Worley, Raman Bansal, Patrick Masterson, Joshua H. Rhoades, Panagiotis Ioannidis, Christopher P. Childers, Dawn E. Gundersen-Rindal, Yi Han, Brent A. Kronmiller, Alexander G. Martynov, Brenda Oppert, Harshavardhan Doddapaneni, Stephen Richards, Zhijian Jake Tu, Richard W. Hardy, Christopher J. Holmes, Florian Maumus, Shwetha C. Murali, Markus Friedrich, Evgeny M. Zdobnov, Alys M. Cheatle Jarvela, Arun S. Velamuri, Mengyao Chen, Monica F. Poelchau, Matthew T. Weirauch, Michael E. Sparks, Robert M. Waterhouse, Katie Reding, Brantley Hall, Sandra L. Lee, Jiaxin Qu, Jeffery W. Jones, David W. Farrow, Kristen A. Panfilio, Adelaide C. Rhodes, Jackson Wells, Hsu Chao, Donna M. Muzny, Sammy Cheng, Huyen Dinh, David R. Nelson, Leslie Pick, Elena N. Elpidina, Michael B. Blackburn, Rose Richter, Daniel S.T. Hughes, Terence Murphy, Faith Kung, Andrew J. Rosendale, Débora P. Paula, Biochemistry, Ioannidis, Panagiotis, Zdobnov, Evgeny, Department of Biochemistry and Molecular Biology [Houston, TX, USA], The University of Texas Medical School at Houston, Human Genome Sequencing Center [Houston] (HGSC), Baylor College of Medicine (BCM), Baylor University-Baylor University, Human Genome Sequencing Center, Baylor College of Medicine, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Recherche Génomique Info (URGI), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), National Center for Biotechnology Information (NCBI), University of Tennessee, Department of Biology, Georgetown University, University of Illinois [Chicago] (UIC), University of Illinois System, Université de Lausanne (UNIL), Cincinnati Children's Hospital Medical Center, Department of Genetic Medicine and Development [Geneva], Université de Genève (UNIGE), Invasive Insect Biocontrol and Behavior Laboratory [Beltsville, USA], USDA Agricultural Research Service [Beltsville, Maryland], and USDA-ARS : Agricultural Research Service-USDA-ARS : Agricultural Research Service
Subjects: 0106 biological sciences, Integrated pest management, Gene Transfer, Insect, 01 natural sciences, Genome, Medical and Health Sciences, chemoreceptors, Invasive species, invasive species, Insecticide Resistance, Genome Size, ddc:576.5, ComputingMilieux_MISCELLANEOUS, Phylogeny, media_common, 0303 health sciences, biology, Ecology, Biological Sciences, Habitat, Insect Proteins, Brown marmorated stink bug genome, odorant binding proteins, Biotechnology, Research Article, lcsh:QH426-470, Gene Transfer, Horizontal, Bioinformatics, media_common.quotation_subject, lcsh:Biotechnology, 010603 evolutionary biology, Horizontal, Heteroptera, 03 medical and health sciences, lcsh:TP248.13-248.65, Information and Computing Sciences, Genetics, Animals, polyphagy, Brown marmorated stink bug, Ecosystem, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, QL, Whole Genome Sequencing, opsins, Human Genome, fungi, 15. Life on land, Pesticide, biology.organism_classification, Pentatomid genomics, lcsh:Genetics, PEST analysis, cathepsins, Introduced Species, xenobiotic detoxification
Abstract: BackgroundHalyomorpha halys(Stål), the brown marmorated stink bug, is a highly invasive insect species due in part to its exceptionally high levels of polyphagy. This species is also a nuisance due to overwintering in human-made structures. It has caused significant agricultural losses in recent years along the Atlantic seaboard of North America and in continental Europe. Genomic resources will assist with determining the molecular basis for this species’ feeding and habitat traits, defining potential targets for pest management strategies.ResultsAnalysis of the 1.15-Gb draft genome assembly has identified a wide variety of genetic elements underpinning the biological characteristics of this formidable pest species, encompassing the roles of sensory functions, digestion, immunity, detoxification and development, all of which likely supportH. halys’ capacity for invasiveness. Many of the genes identified herein have potential for biomolecular pesticide applications.ConclusionsAvailability of theH. halysgenome sequence will be useful for the development of environmentally friendly biomolecular pesticides to be applied in concert with more traditional, synthetic chemical-based controls.
Published: 2020

29. Additional file 4 of Genome-enabled insights into the biology of thrips as crop pests

Author: Rotenberg, Dorith, Baumann, Aaron A., Sulley Ben-Mahmoud, Christiaens, Olivier, Wannes Dermauw, Ioannidis, Panagiotis, Jacobs, Chris G. C., Jentzsch, Iris M. Vargas, Oliver, Jonathan E., Poelchau, Monica F., Rajarapu, Swapna Priya, Schneweis, Derek J., Snoeck, Simon, Clauvis N. T. Taning, Wei, Dong, Shirani M. K. Widana Gamage, Hughes, Daniel S. T., Shwetha C. Murali, Bailey, Samuel T., Bejerman, Nicolas E., Holmes, Christopher J., Jennings, Emily C., Rosendale, Andrew J., Rosselot, Andrew, Hervey, Kaylee, Schneweis, Brandi A., Cheng, Sammy, Childers, Christopher, Simão, Felipe A., Dietzgen, Ralf G., Hsu Chao, Dinh, Huyen, Harsha Vardhan Doddapaneni, Dugan, Shannon, Han, Yi, Lee, Sandra L., Muzny, Donna M., Jiaxin Qu, Worley, Kim C., Benoit, Joshua B., Friedrich, Markus, Jones, Jeffery W., Panfilio, Kristen A., Yoonseong Park, Robertson, Hugh M., Smagghe, Guy, Ullman, Diane E., Maurijn Van Der Zee, Leeuwen, Thomas Van, Veenstra, Jan A., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Whitfield, Anna E., Zdobnov, Evgeny M., Gibbs, Richard A., and Richards, Stephen
Abstract: Additional file 4. Chemosensory receptor sequences.
Published: 2020
Full Text: View/download PDF

30. Additional file 7 of Genome-enabled insights into the biology of thrips as crop pests

Author: Rotenberg, Dorith, Baumann, Aaron A., Sulley Ben-Mahmoud, Christiaens, Olivier, Wannes Dermauw, Ioannidis, Panagiotis, Jacobs, Chris G. C., Jentzsch, Iris M. Vargas, Oliver, Jonathan E., Poelchau, Monica F., Rajarapu, Swapna Priya, Schneweis, Derek J., Snoeck, Simon, Clauvis N. T. Taning, Wei, Dong, Shirani M. K. Widana Gamage, Hughes, Daniel S. T., Shwetha C. Murali, Bailey, Samuel T., Bejerman, Nicolas E., Holmes, Christopher J., Jennings, Emily C., Rosendale, Andrew J., Rosselot, Andrew, Hervey, Kaylee, Schneweis, Brandi A., Cheng, Sammy, Childers, Christopher, Simão, Felipe A., Dietzgen, Ralf G., Hsu Chao, Dinh, Huyen, Harsha Vardhan Doddapaneni, Dugan, Shannon, Han, Yi, Lee, Sandra L., Muzny, Donna M., Jiaxin Qu, Worley, Kim C., Benoit, Joshua B., Friedrich, Markus, Jones, Jeffery W., Panfilio, Kristen A., Yoonseong Park, Robertson, Hugh M., Smagghe, Guy, Ullman, Diane E., Maurijn Van Der Zee, Leeuwen, Thomas Van, Veenstra, Jan A., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Whitfield, Anna E., Zdobnov, Evgeny M., Gibbs, Richard A., and Richards, Stephen
Abstract: Additional file 7. Complete ATP-binding cassette transporter (ABC) and carboxylesterase sequences.
Published: 2020
Full Text: View/download PDF

31. Additional file 1 of Genome-enabled insights into the biology of thrips as crop pests

Author: Rotenberg, Dorith, Baumann, Aaron A., Sulley Ben-Mahmoud, Christiaens, Olivier, Wannes Dermauw, Ioannidis, Panagiotis, Jacobs, Chris G. C., Jentzsch, Iris M. Vargas, Oliver, Jonathan E., Poelchau, Monica F., Rajarapu, Swapna Priya, Schneweis, Derek J., Snoeck, Simon, Clauvis N. T. Taning, Wei, Dong, Shirani M. K. Widana Gamage, Hughes, Daniel S. T., Shwetha C. Murali, Bailey, Samuel T., Bejerman, Nicolas E., Holmes, Christopher J., Jennings, Emily C., Rosendale, Andrew J., Rosselot, Andrew, Hervey, Kaylee, Schneweis, Brandi A., Cheng, Sammy, Childers, Christopher, Simão, Felipe A., Dietzgen, Ralf G., Hsu Chao, Dinh, Huyen, Harsha Vardhan Doddapaneni, Dugan, Shannon, Han, Yi, Lee, Sandra L., Muzny, Donna M., Jiaxin Qu, Worley, Kim C., Benoit, Joshua B., Friedrich, Markus, Jones, Jeffery W., Panfilio, Kristen A., Yoonseong Park, Robertson, Hugh M., Smagghe, Guy, Ullman, Diane E., Maurijn Van Der Zee, Leeuwen, Thomas Van, Veenstra, Jan A., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Whitfield, Anna E., Zdobnov, Evgeny M., Gibbs, Richard A., and Richards, Stephen
Abstract: Additional file 1. Supplementary notes, figures and small tables.
Published: 2020
Full Text: View/download PDF

32. Additional file 3. of Gene content evolution in the arthropods

Author: Thomas, Gregg, Dohmen, Elias, Hughes, Daniel, Shwetha Murali, Poelchau, Monica, Glastad, Karl, Anstead, Clare, Ayoub, Nadia, Batterham, Phillip, Bellair, Michelle, Binford, Greta, Hsu Chao, Chen, Yolanda, Childers, Christopher, Dinh, Huyen, Harsha Doddapaneni, Duan, Jian, Dugan, Shannon, Esposito, Lauren, Friedrich, Markus, Garb, Jessica, Gasser, Robin, Goodisman, Michael, Gundersen-Rindal, Dawn, Han, Yi, Handler, Alfred, Masatsugu Hatakeyama, Hering, Lars, Hunter, Wayne, Ioannidis, Panagiotis, Jayaseelan, Joy, Kalra, Divya, Abderrahman Khila, Korhonen, Pasi, Lee, Carol, Lee, Sandra, Yiyuan Li, Lindsey, Amelia, Mayer, Georg, McGregor, Alistair, McKenna, Duane, Misof, Bernhard, Munidasa, Mala, Munoz-Torres, Monica, Muzny, Donna, Niehuis, Oliver, Nkechinyere Osuji-Lacy, Subba Palli, Panfilio, Kristen, Pechmann, Matthias, Perry, Trent, Peters, Ralph, Poynton, Helen, Nikola-Michael Prpic, Jiaxin Qu, Rotenberg, Dorith, Schal, Coby, Schoville, Sean, Scully, Erin, Skinner, Evette, Sloan, Daniel, Stouthamer, Richard, Strand, Michael, Szucsich, Nikolaus, Asela Wijeratne, Young, Neil, Zattara, Eduardo, Benoit, Joshua, Zdobnov, Evgeny, Pfrender, Michael, Hackett, Kevin, Werren, John, Worley, Kim, Gibbs, Richard, Chipman, Ariel, Waterhouse, Robert, Bornberg-Bauer, Erich, Hahn, Matthew, and Richards, Stephen
Abstract: Review history.
Published: 2020
Full Text: View/download PDF

33. Additional file 2. of Gene content evolution in the arthropods

Author: Thomas, Gregg, Dohmen, Elias, Hughes, Daniel, Shwetha Murali, Poelchau, Monica, Glastad, Karl, Anstead, Clare, Ayoub, Nadia, Batterham, Phillip, Bellair, Michelle, Binford, Greta, Hsu Chao, Chen, Yolanda, Childers, Christopher, Dinh, Huyen, Harsha Doddapaneni, Duan, Jian, Dugan, Shannon, Esposito, Lauren, Friedrich, Markus, Garb, Jessica, Gasser, Robin, Goodisman, Michael, Gundersen-Rindal, Dawn, Han, Yi, Handler, Alfred, Masatsugu Hatakeyama, Hering, Lars, Hunter, Wayne, Ioannidis, Panagiotis, Jayaseelan, Joy, Kalra, Divya, Abderrahman Khila, Korhonen, Pasi, Lee, Carol, Lee, Sandra, Yiyuan Li, Lindsey, Amelia, Mayer, Georg, McGregor, Alistair, McKenna, Duane, Misof, Bernhard, Munidasa, Mala, Munoz-Torres, Monica, Muzny, Donna, Niehuis, Oliver, Nkechinyere Osuji-Lacy, Subba Palli, Panfilio, Kristen, Pechmann, Matthias, Perry, Trent, Peters, Ralph, Poynton, Helen, Nikola-Michael Prpic, Jiaxin Qu, Rotenberg, Dorith, Schal, Coby, Schoville, Sean, Scully, Erin, Skinner, Evette, Sloan, Daniel, Stouthamer, Richard, Strand, Michael, Szucsich, Nikolaus, Asela Wijeratne, Young, Neil, Zattara, Eduardo, Benoit, Joshua, Zdobnov, Evgeny, Pfrender, Michael, Hackett, Kevin, Werren, John, Worley, Kim, Gibbs, Richard, Chipman, Ariel, Waterhouse, Robert, Bornberg-Bauer, Erich, Hahn, Matthew, and Richards, Stephen
Abstract: Supplementary Text and Supplementary Figures: Figures S1 â€“ S34.
Published: 2020
Full Text: View/download PDF

34. Additional file 6 of Genome-enabled insights into the biology of thrips as crop pests

Author: Rotenberg, Dorith, Baumann, Aaron A., Sulley Ben-Mahmoud, Christiaens, Olivier, Wannes Dermauw, Ioannidis, Panagiotis, Jacobs, Chris G. C., Jentzsch, Iris M. Vargas, Oliver, Jonathan E., Poelchau, Monica F., Rajarapu, Swapna Priya, Schneweis, Derek J., Snoeck, Simon, Clauvis N. T. Taning, Wei, Dong, Shirani M. K. Widana Gamage, Hughes, Daniel S. T., Shwetha C. Murali, Bailey, Samuel T., Bejerman, Nicolas E., Holmes, Christopher J., Jennings, Emily C., Rosendale, Andrew J., Rosselot, Andrew, Hervey, Kaylee, Schneweis, Brandi A., Cheng, Sammy, Childers, Christopher, Simão, Felipe A., Dietzgen, Ralf G., Hsu Chao, Dinh, Huyen, Harsha Vardhan Doddapaneni, Dugan, Shannon, Han, Yi, Lee, Sandra L., Muzny, Donna M., Jiaxin Qu, Worley, Kim C., Benoit, Joshua B., Friedrich, Markus, Jones, Jeffery W., Panfilio, Kristen A., Yoonseong Park, Robertson, Hugh M., Smagghe, Guy, Ullman, Diane E., Maurijn Van Der Zee, Leeuwen, Thomas Van, Veenstra, Jan A., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Whitfield, Anna E., Zdobnov, Evgeny M., Gibbs, Richard A., and Richards, Stephen
Subjects: enzymes and coenzymes (carbohydrates), organic chemicals, heterocyclic compounds, respiratory system, urologic and male genital diseases
Abstract: Additional file 6. Complete and partial cytochrome p450 (CYP) sequences.
Published: 2020
Full Text: View/download PDF

35. Additional file 5 of Genome-enabled insights into the biology of thrips as crop pests

Author: Rotenberg, Dorith, Baumann, Aaron A., Sulley Ben-Mahmoud, Christiaens, Olivier, Wannes Dermauw, Ioannidis, Panagiotis, Jacobs, Chris G. C., Jentzsch, Iris M. Vargas, Oliver, Jonathan E., Poelchau, Monica F., Rajarapu, Swapna Priya, Schneweis, Derek J., Snoeck, Simon, Clauvis N. T. Taning, Wei, Dong, Shirani M. K. Widana Gamage, Hughes, Daniel S. T., Shwetha C. Murali, Bailey, Samuel T., Bejerman, Nicolas E., Holmes, Christopher J., Jennings, Emily C., Rosendale, Andrew J., Rosselot, Andrew, Hervey, Kaylee, Schneweis, Brandi A., Cheng, Sammy, Childers, Christopher, Simão, Felipe A., Dietzgen, Ralf G., Hsu Chao, Dinh, Huyen, Harsha Vardhan Doddapaneni, Dugan, Shannon, Han, Yi, Lee, Sandra L., Muzny, Donna M., Jiaxin Qu, Worley, Kim C., Benoit, Joshua B., Friedrich, Markus, Jones, Jeffery W., Panfilio, Kristen A., Yoonseong Park, Robertson, Hugh M., Smagghe, Guy, Ullman, Diane E., Maurijn Van Der Zee, Leeuwen, Thomas Van, Veenstra, Jan A., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Whitfield, Anna E., Zdobnov, Evgeny M., Gibbs, Richard A., and Richards, Stephen
Abstract: Additional file 5. Neuropeptide and protein hormone peptide sequences with highlighted features.
Published: 2020
Full Text: View/download PDF

36. Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum

Author: Harshavardhan Doddapaneni, Soojin V. Yi, Shannon Dugan, Shwetha C. Murali, John H. Werren, Gongyin Ye, Richard A. Gibbs, Xin Wu, Amelia R.I. Lindsey, Yi Han, Huyen Dinh, Sandra L. Lee, Jiaxin Qu, Zhichao Yan, Richard Stouthamer, Paul F. Rugman-Jones, Kim C. Worley, Yogeshwar D. Kelkar, Hsu Chao, Dan Sun, Daniel S.T. Hughes, Donna M. Muzny, Ellen O. Martinson, and Stephen Richards
Subjects: 0301 basic medicine, Genome evolution, Chalcidoidea, Physiology, media_common.quotation_subject, Wasps, Parthenogenesis, Asexual reproduction, Plant Science, Insect, Moths, Methylation, General Biochemistry, Genetics and Molecular Biology, Parasitoid, Evolution, Molecular, 03 medical and health sciences, Structural Biology, Animals, Pest Control, Biological, Symbiosis, lcsh:QH301-705.5, Phylogeny, Ecology, Evolution, Behavior and Systematics, media_common, Comparative genomics, Miniaturization, Whole Genome Sequencing, biology, fungi, Genomics, Cell Biology, biology.organism_classification, 030104 developmental biology, Trichogrammatidae, lcsh:Biology (General), Evolutionary biology, Biological control, Wolbachia, General Agricultural and Biological Sciences, Trichogramma, Research Article, Developmental Biology, Biotechnology
Abstract: Background Trichogrammatids are minute parasitoid wasps that develop within other insect eggs. They are less than half a millimeter long, smaller than some protozoans. The Trichogrammatidae are one of the earliest branching families of Chalcidoidea: a diverse superfamily of approximately half a million species of parasitoid wasps, proposed to have evolved from a miniaturized ancestor. Trichogramma are frequently used in agriculture, released as biological control agents against major moth and butterfly pests. Additionally, Trichogramma are well known for their symbiotic bacteria that induce asexual reproduction in infected females. Knowledge of the genome sequence of Trichogramma is a major step towards further understanding its biology and potential applications in pest control. Results We report the 195-Mb genome sequence of Trichogramma pretiosum and uncover signatures of miniaturization and adaptation in Trichogramma and related parasitoids. Comparative analyses reveal relatively rapid evolution of proteins involved in ribosome biogenesis and function, transcriptional regulation, and ploidy regulation. Chalcids also show loss or especially rapid evolution of 285 gene clusters conserved in other Hymenoptera, including many that are involved in signal transduction and embryonic development. Comparisons between sexual and asexual lineages of Trichogramma pretiosum reveal that there is no strong evidence for genome degradation (e.g., gene loss) in the asexual lineage, although it does contain a lower repeat content than the sexual lineage. Trichogramma shows particularly rapid genome evolution compared to other hymenopterans. We speculate these changes reflect adaptations to miniaturization, and to life as a specialized egg parasitoid. Conclusions The genomes of Trichogramma and related parasitoids are a valuable resource for future studies of these diverse and economically important insects, including explorations of parasitoid biology, symbiosis, asexuality, biological control, and the evolution of miniaturization. Understanding the molecular determinants of parasitism can also inform mass rearing of Trichogramma and other parasitoids for biological control. Electronic supplementary material The online version of this article (10.1186/s12915-018-0520-9) contains supplementary material, which is available to authorized users.
Published: 2018

37. Hemimetabolous genomes reveal molecular basis of termite eusociality

Author: Maria-Dolors Piulachs, Donna M. Muzny, Qiaolin Xie, Shwetha C. Murali, Monica F. Poelchau, Christopher P. Childers, Ludovic Mallet, Kim C. Worley, Yi Han, Michael Poulsen, Stephen Richards, Haofu Hu, Xavier Bellés, Coby Schal, Judith Korb, Lukas P.M. Kremer, Johannes Gowin, Shannon Dugan, Huyen Dinh, Harshavardhan Doddapaneni, Erich Bornberg-Bauer, Sandra L. Lee, Guillem Ylla, Nicolas Arning, Hugh M. Robertson, Carolin Greiner, Richard A. Gibbs, Mark C Harrison, Jiaxin Qu, Ayako Wada-Katsumata, Hsu Chao, Annabell Moser, Carsten Kemena, Saria Otani, Jose M. Monroy-Kuhn, Florentine Schaub, Tristan Bitard-Feildel, Evelien Jongepier, Alberto Lopez-Ezquerra, Ann Kathrin Huylmans, and Daniel S.T. Hughes
Subjects: 0301 basic medicine, Evolution of eusociality, Isoptera, Hymenoptera, Genome, Article, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Molecular evolution, biology.animal, Animals, Social Behavior, Phylogeny, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Comparative genomics, 0303 health sciences, German cockroach, Cockroach, 576 Genetics and evolution, Ecology, biology, Blattellidae, biology.organism_classification, Biological Evolution, Eusociality, 030104 developmental biology, Evolutionary biology, Sex pheromone, Social evolution, Caste determination, 030217 neurology & neurosurgery
Abstract: Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity.
Published: 2018

38. Preparation of artificial red cell and its application on alleviation of tumor hypoxia

Author: Xiaoyi Yin, Jian You, Lihua Luo, Wanqing Hou, Yan Lou, Jiaxin Qu, Yong-Zhong Du, Xiaomeng Guo, Hanbo Zhang, Jie Yang, Dawei Chen, Chunqi Zhu, Yuan Tao, and Wei Li
Subjects: Male, Vascular Endothelial Growth Factor A, 0301 basic medicine, Programmed cell death, Cell Survival, Pharmacology, Metastasis, Hemoglobins, Mice, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Colloid and Surface Chemistry, Microscopy, Electron, Transmission, Cell Line, Tumor, medicine, Animals, Tissue Distribution, Physical and Theoretical Chemistry, Cytotoxicity, Mice, Inbred BALB C, Mice, Inbred ICR, Red Cell, Tumor hypoxia, Neoplasms, Experimental, Surfaces and Interfaces, General Medicine, Hypoxia (medical), Hypoxia-Inducible Factor 1, alpha Subunit, medicine.disease, Vascular endothelial growth factor, 030104 developmental biology, chemistry, 030220 oncology & carcinogenesis, Liposomes, Immunology, Nanoparticles, Tumor Hypoxia, Hemoglobin, medicine.symptom, Biotechnology
Abstract: Hemoglobin-based oxygen carriers were developed as an alternative for blood transfusion. However, the research progress for their further clinic applications was slow in recent several years. Hypoxia is found in most solid tumors, which is responsible for the tumor formation, increased metastasis, drug resistance during therapeutic process as well as poor patient survival. In this work, novel hemoglobin (Hb) loaded nanoliposomes, as artificial red cells for oxygen delivery, were optimized by screening various types of phospholipids and analyzing different mole ratio of phospholipid to cholesterol. The nanoliposomes presented a high encapsulating efficiency to hemoglobin and also significantly enhanced its stability. The obtained hemoglobin loaded nanoliposome (HLL) could be lyophilized for long term storage. HLL did not cause significant cell death in the concentration range of 0-100μg equivalent Hb/mL under normoxia and hypoxia incubation conditions, suggesting the low cytotoxicity and high biocompatibility of HLL. Importantly, HLL could efficiently accumulate into subcutaneous and deep orthotopic tumors, inducing a significant decrease of hypoxia-inducible factors 1α subunits (HIF-1α) in the tumors and remarkably reduced expression of vascular endothelial growth factor (VEGF). The study of acute and chronic toxicity indicated that HLL did not induce obvious damage to main organs of mice after intravenous injections with total Hb dose of 120mg/kg. We presented a promising method for relieving the hypoxia degree in solid tumors and down-regulating HIF-1α protein by directly delivering oxygen into tumors, which will be very helpful for subsequent cancer therapy.
Published: 2017

39. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome

Author: Shwetha C. Murali, Hsiao-ling Lu, Siegfried Roth, Huyen Dinh, Peter K. Dearden, Barbara M. I. Vreede, M. Emília Santos, Evgeny M. Zdobnov, Viera Kovacova, Christopher J. Holmes, Stefano Colella, Yuichiro Suzuki, Tamsin E. M. Jones, Chun-che Chang, Stefan Koelzer, Jeffery W. Jones, Essia Sghaier, Thorsten Horn, Richard A. Gibbs, Mackenzie Lovegrove, Panagiotis Ioannidis, Lucila Traverso, Subba Reddy Palli, Megan L. Porter, Olivia Tidswell, Peter Nagui Refki, Neta Ginzburg, Rolando Rivera-Pomar, Sandra L. Lee, Chris Jacobs, Cassandra G. Extavour, Jan Seibert, Amanda Dolan, David Armisén, Jayendra Nath Shukla, Kristen A. Panfilio, Christopher P. Childers, Matthew T. Weirauch, Daniel S.T. Hughes, Jiaxin Qu, Kim C. Worley, Hugh M. Robertson, Monica Munoz-Torres, Markus Friedrich, Emily C. Jennings, Elizabeth J. Duncan, Andrew G. Cridge, Hsu Chao, J. Spencer Johnston, Maurijn van der Zee, Mei-Ju May Chen, John H. Werren, Abderrahman Khila, Shannon Dugan, Stephen Richards, Lena Sachs, Joshua B. Benoit, Antonin J.J. Crumière, Nicolas Parisot, Megan Leask, Yen-Ta Chen, Harshavardhan Doddapaneni, Gérard Febvay, Donna M. Muzny, Ariel D. Chipman, Rose Richter, Robert M. Waterhouse, Leslie Pick, Monica F. Poelchau, Patricia J. Moore, Chloé Suzanne Berger, Richard J. Stancliffe, Yi Min Hsiao, Séverine Viala, Chien-Yueh Lee, Yi Han, Iris M. Vargas Jentzsch, Elise M. Didion, Deniz F. Erezyilmaz, Yong Lu, Andrew J. Rosendale, Peter Heger, Patrice Baa-Puyoulet, Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), University of Illinois [Chicago] (UIC), University of Illinois System, Department of Biology, Georgetown University, Université de Lausanne (UNIL), Cincinnati Children's Hospital Medical Center, Biochemistry Department, University of Otago [Dunedin, Nouvelle-Zélande], Human Genome Sequencing Center, Baylor College of Medicine, Baylor College of Medicine (BCM), Baylor University-Baylor University, University of Edinburgh, Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Department of Entomology [Lexington], University of Kentucky, Cologne Biocenter, Institute of Developmental Biology, Institute of Developmental Biology, University of Basel (Unibas), Institut de Génomique Fonctionnelle de Lyon (IGFL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Human Genome Sequencing Center [Houston] (HGSC), Department of Genetic Medicine and Development [Geneva], Université de Genève (UNIGE), United States Department of Health & Human Services National Institutes of Health (NIH) - USA [U54 HG003273], German Research Foundation (DFG) [PA 2044/1 1 SFB 680], Swiss National Science Foundation (SNSF) [31003A_143936, PP00P3_170664], European Research Council grant ERC-CoG [616346], German Research Foundation (DFG) [SFB 680], National Science Foundation (NSF) [US NSF DEB1257053], United States Department of Health & Human Services National Institutes of Health (NIH) - USA [5R01GM080203, 5R01HG004483, R01GM113230], United States Department of Energy (DOE) [DE-AC02-05CH11231], École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Georgetown University [Washington] (GU), Université de Lausanne = University of Lausanne (UNIL), University of Kentucky (UK), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Genève = University of Geneva (UNIGE), Panfilio, Kristen A [0000-0002-6417-251X], Vargas Jentzsch, Iris M [0000-0003-4527-1560], Benoit, Joshua B [0000-0002-4018-3513], Erezyilmaz, Deniz [0000-0001-8416-8561], Suzuki, Yuichiro [0000-0002-0957-3564], Colella, Stefano [0000-0003-3139-6055], Poelchau, Monica F [0000-0002-4584-6056], Waterhouse, Robert M [0000-0003-4199-9052], Ioannidis, Panagiotis [0000-0003-0939-6745], Weirauch, Matthew T [0000-0001-7977-9122], Werren, John H [0000-0001-9353-2070], Jacobs, Chris GC [0000-0002-3128-2288], Duncan, Elizabeth J [0000-0002-1841-504X], Vreede, Barbara MI [0000-0002-5023-4601], Chang, Chun-Che [0000-0002-3586-1607], Chen, Mei-Ju M [0000-0001-7768-8905], Chen, Yen-Ta [0000-0002-4570-6061], Childers, Christopher P [0000-0002-1253-5550], Chipman, Ariel D [0000-0001-6696-840X], Cridge, Andrew G [0000-0002-1399-5188], Crumière, Antonin JJ [0000-0003-2214-2993], Dearden, Peter K [0000-0001-7790-9675], Didion, Elise M [0000-0002-4987-8901], Dinh, Huyen [0000-0003-0336-0362], Doddapaneni, Harsha Vardhan [0000-0002-2433-633X], Dugan, Shannon [0000-0003-1482-816X], Extavour, Cassandra G [0000-0003-2922-5855], Febvay, Gérard [0000-0002-0654-2340], Friedrich, Markus [0000-0002-5622-7920], Han, Yi [0000-0001-7605-8979], Holmes, Christopher J [0000-0001-9612-366X], Horn, Thorsten [0000-0001-8181-939X], Hsiao, Yi-Min [0000-0002-1817-0302], Jennings, Emily C [0000-0002-7687-5319], Johnston, J Spencer [0000-0003-4792-2945], Jones, Tamsin E [0000-0002-0027-0858], Khila, Abderrahman [0000-0003-0908-483X], Kovacova, Viera [0000-0003-4581-4254], Lee, Chien-Yueh [0000-0002-4304-974X], Lu, Hsiao-Ling [0000-0002-4029-6470], Moore, Patricia J [0000-0001-9802-7217], Munoz-Torres, Monica C [0000-0001-8430-6039], Muzny, Donna M [0000-0002-3055-0359], Palli, Subba R [0000-0002-0873-3247], Parisot, Nicolas [0000-0001-5217-8415], Pick, Leslie [0000-0002-4505-5107], Porter, Megan L [0000-0001-7985-2887], Qu, Jiaxin [0000-0002-1122-9391], Rivera-Pomar, Rolando [0000-0002-7720-7064], Rosendale, Andrew J [0000-0002-2463-8856], Roth, Siegfried [0000-0001-5772-3558], Shukla, Jayendra N [0000-0003-1589-1929], Stancliffe, Richard J [0000-0002-6972-9655], van der Zee, Maurijn [0000-0002-8728-8646], Worley, Kim C [0000-0002-0282-1000], Richards, Stephen [0000-0001-8959-5466], and Apollo - University of Cambridge Repository
Subjects: gene family evolution, Lineage (evolution), [SDV]Life Sciences [q-bio], Genome, Insect, Gene Transfer, Gene Dosage, Insect, Genome, purl.org/becyt/ford/1 [https], 0302 clinical medicine, CYS2-HIS2 Zinc Fingers, phytophagy, ddc:576.5, lcsh:QH301-705.5, media_common, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, biology, Large milkweed bug, Ecology, Pigmentation, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Genes, Homeobox, Biological Sciences, Lygaeidae, Hemiptera, séquence du génome, Smell, evolution of development, TRANSCRIPTION FACTORS, puceron, Biotechnology, lcsh:QH426-470, Gene Transfer, Horizontal, ddc:025.063/570, Evolution, Bioinformatics, media_common.quotation_subject, 1.1 Normal biological development and functioning, Transcription Factors/genetics, Zoology, Amino Acid Sequence, Animals, Evolution, Molecular, Feeding Behavior, Gene Expression Profiling, Hemiptera/genetics, Hemiptera/growth & development, Hemiptera/metabolism, Pigmentation/genetics, Evolution of development, Gene family evolution, Gene structure, Lateral gene transfer, Phytophagy, RNAi, Transcription factors, GENE FAMILY EVOLUTION, Genomics, Biotechnologies, LATERAL GENE TRANSFER, Horizontal, 03 medical and health sciences, Molecular evolution, Underpinning research, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Information and Computing Sciences, transcription factors, RNAI, Genetics, Homeobox, GENE STRUCTURE, purl.org/becyt/ford/1.6 [https], SB, Genome size, Ciencias Exactas, 030304 developmental biology, Whole genome sequencing, QL, QH, Research, gene structure, lateral gene transfer, Human Genome, fungi, Molecular, biology.organism_classification, Hemiptera/genetics/growth & development/metabolism, diversité des populations, lcsh:Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, PHYTOPHAGY, lcsh:Biology (General), Genes, Animal ecology, Evolutionary biology, EVOLUTION OF DEVELOPMENT, Evolutionary developmental biology, 030217 neurology & neurosurgery, Environmental Sciences
Abstract: Background: The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. Results: The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. Conclusions: With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus’s strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes., La lista completa de autores puede verse en el archivo asociado., Facultad de Ciencias Exactas, Centro Regional de Estudios Genómicos
Published: 2019

40. Additional file 1: of Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome

Author: Panfilio, Kristen, Jentzsch, Iris Vargas, Benoit, Joshua, Erezyilmaz, Deniz, Suzuki, Yuichiro, Colella, Stefano, Robertson, Hugh, Poelchau, Monica, Waterhouse, Robert, Ioannidis, Panagiotis, Weirauch, Matthew, Hughes, Daniel, Shwetha Murali, Werren, John, Jacobs, Chris, Duncan, Elizabeth, ArmisĂŠn, David, Vreede, Barbara, Baa-Puyoulet, Patrice, ChloĂŠ Berger, Chun-Che Chang, Hsu Chao, Chen, Mei-Ju, Yen-Ta Chen, Childers, Christopher, Chipman, Ariel, Cridge, Andrew, CrumiĂ¨Re, Antonin, Dearden, Peter, Didion, Elise, Dinh, Huyen, Harsha Doddapaneni, Dolan, Amanda, Dugan, Shannon, Extavour, Cassandra, GĂŠrard Febvay, Friedrich, Markus, Ginzburg, Neta, Han, Yi, Heger, Peter, Holmes, Christopher, Horn, Thorsten, Hsiao, Yi-Min, Jennings, Emily, J. Johnston, Jones, Tamsin, Jones, Jeffery, Abderrahman Khila, Koelzer, Stefan, Kovacova, Viera, Leask, Megan, Lee, Sandra, Chien-Yueh Lee, Lovegrove, Mackenzie, Hsiao-Ling Lu, Lu, Yong, Moore, Patricia, Munoz-Torres, Monica, Muzny, Donna, Subba Palli, Parisot, Nicolas, Pick, Leslie, Porter, Megan, Jiaxin Qu, Refki, Peter, Richter, Rose, Rivera-Pomar, Rolando, Rosendale, Andrew, Roth, Siegfried, Sachs, Lena, M. Santos, Seibert, Jan, Essia Sghaier, Jayendra Shukla, Stancliffe, Richard, Tidswell, Olivia, Traverso, Lucila, Maurijn Zee, SĂŠverine Viala, Worley, Kim, Zdobnov, Evgeny, Gibbs, Richard, and Richards, Stephen
Abstract: Supplementary notes, figures, and small tables. (PDF 6142 kb)
Published: 2019
Full Text: View/download PDF

41. The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water

Author: Andrew G. Cridge, Arjuna Rajakumar, Emily C. Jennings, Yi Han, Cédric Finet, Elizabeth J. Duncan, Hsu Chao, Richard A. Gibbs, Li Mei Chiang, Seung-Joon Ahn, Abderrahman Khila, Joshua B. Benoit, Chris Jacobs, Sandra L. Lee, Kim C. Worley, Antonin J.J. Crumière, Markus Friedrich, Séverine Viala, Rajendhran Rajakumar, Andrew J. Rosendale, Harshavardhan Doddapaneni, Maryna P. Lesoway, Travis Chen, Aidamalia Vargas Lowman, Alys M. Cheatle Jarvela, Mackenzie Lovegrove, Daniel S.T. Hughes, Jeffery W. Jones, Shwetha C. Murali, Christopher P. Childers, Donna M. Muzny, Monica Munoz-Torres, Iris M. Vargas Jentzsch, Brenda Oppert, Huyen Dinh, David Armisén, Marie-Julie Favé, Elise M. Didion, Stephen Richards, François Bonneton, William Toubiana, Elena N. Elpidina, Amélie Decaras, Peter N Refki, Monica F. Poelchau, Shannon Dugan, Angelica Lillico-Ouachour, Maria Emilia Santos, Kristen A. Panfilio, Ehab Abouheif, Hugh M. Robertson, Maurijn van der Zee, Alexander G. Martynov, Jiaxin Qu, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Max Planck Institute for Chemical Ecology, Max-Planck-Gesellschaft, Georgetown University [Washington] (GU), Human Genome Sequencing Center, Baylor College of Medicine, Baylor College of Medicine (BCM), Baylor University-Baylor University, Human Genome Sequencing Center [Houston] (HGSC), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL), Reproduction et développement des plantes (RDP), Clinical Genetics, Guy's and St. Thomas' NHS Foundation Trust, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), École pratique des hautes études (EPHE), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Apollo - University of Cambridge Repository
Subjects: 0106 biological sciences, Genome evolution, lcsh:QH426-470, Evolution, lcsh:Biotechnology, [SDV]Life Sciences [q-bio], Genomics, Biology, 010603 evolutionary biology, 01 natural sciences, Genome, Evolution, Molecular, Heteroptera, 03 medical and health sciences, lcsh:TP248.13-248.65, Gene family, Animals, 14. Life underwater, Epigenetics, Adaptation, Gene, QH426, Phylogeny, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, QL, [SDV.GEN]Life Sciences [q-bio]/Genetics, Water striders, Adaptation, Physiological, lcsh:Genetics, Phenotype, Evolutionary biology, Genome sequence, Insect Proteins, Evolutionary ecology, Water surface locomotion, Research Article
Abstract: Background Having conquered water surfaces worldwide, the semi-aquatic bugs occupy ponds, streams, lakes, mangroves, and even open oceans. The diversity of this group has inspired a range of scientific studies from ecology and evolution to developmental genetics and hydrodynamics of fluid locomotion. However, the lack of a representative water strider genome hinders our ability to more thoroughly investigate the molecular mechanisms underlying the processes of adaptation and diversification within this group. Results Here we report the sequencing and manual annotation of the Gerris buenoi (G. buenoi) genome; the first water strider genome to be sequenced thus far. The size of the G. buenoi genome is approximately 1,000 Mb, and this sequencing effort has recovered 20,949 predicted protein-coding genes. Manual annotation uncovered a number of local (tandem and proximal) gene duplications and expansions of gene families known for their importance in a variety of processes associated with morphological and physiological adaptations to a water surface lifestyle. These expansions may affect key processes associated with growth, vision, desiccation resistance, detoxification, olfaction and epigenetic regulation. Strikingly, the G. buenoi genome contains three insulin receptors, suggesting key changes in the rewiring and function of the insulin pathway. Other genomic changes affecting with opsin genes may be associated with wavelength sensitivity shifts in opsins, which is likely to be key in facilitating specific adaptations in vision for diverse water habitats. Conclusions Our findings suggest that local gene duplications might have played an important role during the evolution of water striders. Along with these findings, the sequencing of the G. buenoi genome now provides us the opportunity to pursue exciting research opportunities to further understand the genomic underpinnings of traits associated with the extreme body plan and life history of water striders. Electronic supplementary material The online version of this article (10.1186/s12864-018-5163-2) contains supplementary material, which is available to authorized users.
Published: 2018

42. Comparative Genomics of Two Closely RelatedWolbachiawith Different Reproductive Effects on Hosts

Author: Irene L. G. Newton, Bethany N. Kent, Seth R. Bordenstein, John H. Werren, Yogeshwar D. Kelkar, Michael E. Clark, Stephen Richards, and Jiaxin Qu
Subjects: Male, 0301 basic medicine, Cytoplasm, Mutation rate, Lineage (genetic), 030106 microbiology, Biology, Host Specificity, Nasonia vitripennis, 03 medical and health sciences, mutational bias, Genetics, Animals, Selection, Genetic, Arthropods, Phylogeny, reproductive manipulation, Ecology, Evolution, Behavior and Systematics, Comparative genomics, Reproduction, Genomics, biology.organism_classification, 030104 developmental biology, Muscidifurax uniraptor, Mutation, Drosophila, Wolbachia, Synonymous substitution, endosymbiont, Genome, Bacterial, Cytoplasmic incompatibility, Research Article
Abstract: Wolbachia pipientis are obligate intracellular bacteria commonly found in many arthropods. They can induce various reproductive alterations in hosts, including cytoplasmic incompatibility, male-killing, feminization, and parthenogenetic development, and can provide host protection against some viruses and other pathogens. Wolbachia differ from many other primary endosymbionts in arthropods because they undergo frequent horizontal transmission between hosts and are well known for an abundance of mobile elements and relatively high recombination rates. Here, we compare the genomes of two closely related Wolbachia (with 0.57% genome-wide synonymous divergence) that differ in their reproductive effects on hosts. wVitA induces a sperm–egg incompatibility (also known as cytoplasmic incompatibility) in the parasitoid insect Nasonia vitripennis, whereas wUni causes parthenogenetic development in a different parasitoid, Muscidifurax uniraptor. Although these bacteria are closely related, the genomic comparison reveals rampant rearrangements, protein truncations (particularly in proteins predicted to be secreted), and elevated substitution rates. These changes occur predominantly in the wUni lineage, and may be due in part to adaptations by wUni to a new host environment, or its phenotypic shift to parthenogenesis induction. However, we conclude that the approximately 8-fold elevated synonymous substitution rate in wUni is due to a either an elevated mutation rate or a greater number of generations per year in wUni, which occurs in semitropical host species. We identify a set of genes whose loss or pseudogenization in the wUni lineage implicates them in the phenotypic shift from cytoplasmic incompatibility to parthenogenesis induction. Finally, comparison of these closely related strains allows us to determine the fine-scale mutation patterns in Wolbachia. Although Wolbachia are AT rich, mutation probabilities estimated from 4-fold degenerate sites are not AT biased, and predict an equilibrium AT content much less biased than observed (57–50% AT predicted vs. 76% current content at degenerate sites genome wide). The contrast suggests selection for increased AT content within Wolbachia genomes.
Published: 2016

43. Hemichordate genomes and deuterostome origins

Author: Shannon Dugan, Oleg Simakov, Ryo Koyanagi, Andrew Cree, Fuki Gyoja, Nicholas H. Putnam, Asao Fujiyama, Miyuki Kanda, Michael Holder, Geoffrey Okwuonu, Lynne V. Nazareth, Atsuko Sato, Christopher B. Cameron, Christopher J. Lowe, Jens H. Fritzenwanker, Yi Chih Chen, Therese Mitros, Paul Gonzalez, Daniel S. Rokhsar, Jireh Santibanez, Donna M. Muzny, Rui Chen, Kenneth W. Baughman, Jessen V. Bredeson, Shinichi Yamasaki, Hiroki Goto, Noriyuki Satoh, Nana Arakaki, Shalini N. Jhangiani, Richard A. Gibbs, Kanako Hisata, Takeshi Kawashima, Jia-Xing Yue, Jiaxin Qu, Donna Morton, Huyen Dinh, Christie Kovar, Jeremy Schmutz, Lora Lewis, Sandra L. Lee, Leonid Peshkin, Jerry Jenkins, Judith Levine, Stephen Richards, Kunifumi Tagawa, Kim C. Worley, John C. Gerhart, Robert Freeman, Manabu Fujie, Michael Wu, Yan Ding, Jr-Kai Yu, Marc W. Kirschner, Tom Humphreys, Ferdinand Marlétaz, Akane Sasaki, Andrew Gillis, Ariel M. Pani, Tomoe Hikosaka-Katayama, Eiichi Shoguchi, Yi-Hsien Su, Simakov, Oleg [0000-0002-3585-4511], Marlétaz, Ferdinand [0000-0001-8124-4266], Koyanagi, Ryo [0000-0002-9694-0288], Bredeson, Jessen [0000-0001-5489-8512], Yue, Jia-Xing [0000-0002-2122-9221], Fritzenwanker, Jens H [0000-0002-5201-4100], Richards, Stephen [0000-0001-8959-5466], Gillis, Andrew [0000-0003-2062-3777], Putnam, Nicholas H [0000-0002-1315-782X], Tagawa, Kunifumi [0000-0001-5634-9373], Worley, Kim C [0000-0002-0282-1000], Lowe, Christopher J [0000-0002-7789-8643], Rokhsar, Daniel S [0000-0002-8704-2224], and Apollo - University of Cambridge Repository
Subjects: 0106 biological sciences, Evolution, General Science & Technology, Hemichordate, Synteny, 010603 evolutionary biology, 01 natural sciences, Article, Conserved sequence, Evolution, Molecular, 03 medical and health sciences, Chordata, Nonvertebrate, Transforming Growth Factor beta, Phylogenetics, Genetics, Animals, 14. Life underwater, Chordata, Phylogeny, Conserved Sequence, 030304 developmental biology, Comparative genomics, 0303 health sciences, Genome, Multidisciplinary, Deuterostome, biology, Phylum, Human Genome, Molecular, biology.organism_classification, Nonvertebrate, Multigene Family, Evolutionary developmental biology, Generic health relevance, Echinodermata, Signal Transduction
Abstract: Acorn worms, also known as enteropneust (literally, 'gut-breathing') hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report the draft genome sequences of two acorn worms, Saccoglossus kowalevskii and Ptychodera flava. By comparing them with diverse bilaterian genomes, we identify shared traits that were probably inherited from the last common deuterostome ancestor, and then explore evolutionary trajectories leading from this ancestor to hemichordates, echinoderms and chordates. The hemichordate genomes exhibit extensive conserved synteny with amphioxus and other bilaterians, and deeply conserved non-coding sequences that are candidates for conserved gene-regulatory elements. Notably, hemichordates possess a deuterostome-specific genomic cluster of four ordered transcription factor genes, the expression of which is associated with the development of pharyngeal 'gill' slits, the foremost morphological innovation of early deuterostomes, and is probably central to their filter-feeding lifestyle. Comparative analysis reveals numerous deuterostome-specific gene novelties, including genes found in deuterostomes and marine microbes, but not other animals. The putative functions of these genes can be linked to physiological, metabolic and developmental specializations of the filter-feeding ancestor.
Published: 2015

44. Study on the Influence of the Thickness of Column on Axial Compression Behavior of Cold-Formed Steel Composite Wall

Author: Hong Liu, Jiaxin Qu, and Chungang Wang
Subjects: Materials science, Column (typography), law, Axial compression, Composite number, Composite material, Cold-formed steel, law.invention
Abstract: By changing the thickness of the column, the axial compression behavior of the one-side sheathed wall and the both-sides sheathed wall can be altered at different levels. Simulation and inspection of cold-formed thin-walled steel frame wall had been finished by using a finite element simulation software called ABAQUS, which was applied by test data from relevant literature. The axial carrying capacity of the sheathed wall was superior than the unsheathed wall, therefore, all models had been built and studied based on the one-side sheathed wall and both-sides similar sheathed wall. The analysis results proved that the axial compression behavior of the one-side sheathed wall and the both-sides sheathed wall could be increased substantially by adding the thickness of studs, and this change was more sensitive to the influence of the wall with one-side sheathed wall especially.
Published: 2020

45. Heterostructured WO3/RGO/protonated g-C3N4 three-layer nanosheets for enhanced visible-light photocatalytic activity

Author: Xuping Jia, Kezheng Chen, Lin Jiang, Yongchao Bao, Chenglin Zhang, Jiaxin Qu, Hao Guo, and Zhiyong Liu
Subjects: Photocurrent, Materials science, Photoluminescence, General Physics and Astronomy, Heterojunction, 02 engineering and technology, Surfaces and Interfaces, General Chemistry, 010402 general chemistry, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Photochemistry, 01 natural sciences, 0104 chemical sciences, Surfaces, Coatings and Films, Dielectric spectroscopy, Photocatalysis, Charge carrier, 0210 nano-technology, Photodegradation, Visible spectrum
Abstract: The novel WO3/RGO/protonated g-C3N4 (PCN) composites with a 2D/2D/2D architecture were successfully prepared through a microwave-assisted hydrothermal method. The 2D/2D/2D heterojunction exhibited a short charge migration path and a wide interface contact area, which could produce a large number of intimate high-speed charge transfer channels and enhance bulk-to-surface and interfacial charge transfer abilities. The WO3/RGO/PCN composites displayed dramatically improved photodegradation performance for tetracycline hydrochloride (TC-HCL) under illuminating of visible light as compared to PCN, WO3, as well as binary RGO/PCN and WO3/PCN heterojunctions. The photocatalytic mechanism was confirmed by photoluminescence spectra (PL), photocurrent response, electron spin resonance spectra (ESR) and electrochemical impedance spectroscopy (EIS). The synergistic effect of 2D/2D/2D architecture and Z-Scheme electron migration mechanism greatly boosts the migration and separation of photoexcited charge carriers that leads to the enhanced photodegradation activity.
Published: 2019

46. The Toxicogenome of Hyalella azteca: A Model for Sediment Ecotoxicology and Evolutionary Toxicology

Author: J. Spencer Johnston, John H. Werren, Mei-Ju May Chen, Shwetha C. Murali, Joshua B. Benoit, Kaley M. Major, Alexandra Mechler-Hickson, Jiaxin Qu, Hsu Chao, Shuai Chen, Michael A. D. Goodisman, René Feyereisen, Nicholas Mathers, Sandra L. Lee, Daniel S.T. Hughes, Andrew J. Rosendale, Karl M. Glastad, Christopher P. Childers, Joseph H. Vineis, Chris D. Vulpe, Huyen Dinh, Yi Han, Bonnie J. Blalock, Peter A. Bain, Jennifer L. Bowen, Carol Eunmi Lee, Simone Hasenbein, Padrig Tuck, Kim C. Worley, Shannon Dugan, Donna M. Muzny, Hugo Ochoa-Acuña, Gary A. Wellborn, Faith N. Lambert, Helen C. Poynton, Mark E. Smith, Adam D. Biales, Austin R. Manny, Monica Munoz-Torres, Jeffery W. Jones, Andrew G. Cridge, Richard A. Gibbs, Hugh M. Robertson, Stephen Richards, Monica F. Poelchau, Markus Friedrich, Harshavardhan Doddapaneni, John K. Colbourne, Yu-Yu Lin, and Maria S. Sepúlveda
Subjects: 0301 basic medicine, Species complex, Geologic Sediments, Amphipoda, Ecotoxicology, Genome, Article, 03 medical and health sciences, chemistry.chemical_compound, Toxicity Tests, Environmental Chemistry, Animals, biology, Ecology, Hyalella azteca, General Chemistry, biology.organism_classification, Major gene, Azteca, 030104 developmental biology, chemistry, North America, Water Pollutants, Chemical, Toxicant
Abstract: Hyalella azteca is a cryptic species complex of epibenthic amphipods of interest to ecotoxicology and evolutionary biology. It is the primary crustacean used in North America for sediment toxicity testing and an emerging model for molecular ecotoxicology. To provide molecular resources for sediment quality assessments and evolutionary studies, we sequenced, assembled, and annotated the genome of the H. azteca U.S. Lab Strain. The genome quality and completeness is comparable with other ecotoxicological model species. Through targeted investigation and use of gene expression data sets of H. azteca exposed to pesticides, metals, and other emerging contaminants, we annotated and characterized the major gene families involved in sequestration, detoxification, oxidative stress, and toxicant response. Our results revealed gene loss related to light sensing, but a large expansion in chemoreceptors, likely underlying sensory shifts necessary in their low light habitats. Gene family expansions were also noted for cytochrome P450 genes, cuticle proteins, ion transporters, and include recent gene duplications in the metal sequestration protein, metallothionein. Mapping of differentially expressed transcripts to the genome significantly increased the ability to functionally annotate toxicant responsive genes. The H. azteca genome will greatly facilitate development of genomic tools for environmental assessments and promote an understanding of how evolution shapes toxicological pathways with implications for environmental and human health.
Published: 2018

47. Additional file 4: of The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water

Author: Armisén, David, Rajendhran Rajakumar, Friedrich, Markus, Benoit, Joshua, Robertson, Hugh, Panfilio, Kristen, Seung-Joon Ahn, Poelchau, Monica, Hsu Chao, Dinh, Huyen, Harsha Doddapaneni, Dugan, Shannon, Gibbs, Richard, Hughes, Daniel, Han, Yi, Lee, Sandra, Shwetha Murali, Muzny, Donna, Jiaxin Qu, Worley, Kim, Munoz-Torres, Monica, Ehab Abouheif, Bonneton, François, Chen, Travis, Chiang, Li-Mei, Childers, Christopher, Cridge, Andrew, Crumière, Antonin, Decaras, Amelie, Didion, Elise, Duncan, Elizabeth, Elpidina, Elena, Marie-Julie Favé, Finet, Cédric, Jacobs, Chris, Jarvela, Alys Cheatle, Jennings, Emily, Jones, Jeffery, Lesoway, Maryna, Lovegrove, Mackenzie, Martynov, Alexander, Oppert, Brenda, Lillico-Ouachour, Angelica, Arjuna Rajakumar, Refki, Peter, Rosendale, Andrew, Santos, Maria, Toubiana, William, Maurijn Van Der Zee, Jentzsch, Iris Vargas, Aidamalia Lowman, Viala, Severine, Richards, Stephen, and Abderrahman Khila
Abstract: Nucleotide sequences of Insulin receptors genes annotated in Gerromorpha (Gerris buenoi, Aquarius paludum, Limnoporus dissortis, Rhagovelia antilleana, Microvelia longipes, Mesovelia furcata, Hydrometra cumata and Hebrus sp). (DOCX 40kb)
Published: 2018
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48. Additional file 8: of The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water

Author: ArmisĂŠn, David, Rajendhran Rajakumar, Friedrich, Markus, Benoit, Joshua, Robertson, Hugh, Panfilio, Kristen, Seung-Joon Ahn, Poelchau, Monica, Hsu Chao, Dinh, Huyen, Harsha Doddapaneni, Dugan, Shannon, Gibbs, Richard, Hughes, Daniel, Han, Yi, Lee, Sandra, Shwetha Murali, Muzny, Donna, Jiaxin Qu, Worley, Kim, Munoz-Torres, Monica, Ehab Abouheif, FranĂ§Ois Bonneton, Chen, Travis, Chiang, Li-Mei, Childers, Christopher, Cridge, Andrew, CrumiĂ¨Re, Antonin, Decaras, Amelie, Didion, Elise, Duncan, Elizabeth, Elpidina, Elena, Marie-Julie FavĂŠ, CĂŠdric Finet, Jacobs, Chris, Jarvela, Alys Cheatle, Jennings, Emily, Jones, Jeffery, Lesoway, Maryna, Lovegrove, Mackenzie, Martynov, Alexander, Oppert, Brenda, Lillico-Ouachour, Angelica, Arjuna Rajakumar, Refki, Peter, Rosendale, Andrew, Santos, Maria, Toubiana, William, Maurijn Van Der Zee, Jentzsch, Iris Vargas, Aidamalia Lowman, Viala, Severine, Richards, Stephen, and Abderrahman Khila
Abstract: Protein sequences of annotated chemoreceptors in Gerris buenoi : 155 Or, 135 Gr and 45 IR genes. (DOCX 83 kb)
Published: 2018
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49. Additional file 10: of The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water

Author: ArmisĂŠn, David, Rajendhran Rajakumar, Friedrich, Markus, Benoit, Joshua, Robertson, Hugh, Panfilio, Kristen, Seung-Joon Ahn, Poelchau, Monica, Hsu Chao, Dinh, Huyen, Harsha Doddapaneni, Dugan, Shannon, Gibbs, Richard, Hughes, Daniel, Han, Yi, Lee, Sandra, Shwetha Murali, Muzny, Donna, Jiaxin Qu, Worley, Kim, Munoz-Torres, Monica, Ehab Abouheif, FranĂ§Ois Bonneton, Chen, Travis, Chiang, Li-Mei, Childers, Christopher, Cridge, Andrew, CrumiĂ¨Re, Antonin, Decaras, Amelie, Didion, Elise, Duncan, Elizabeth, Elpidina, Elena, Marie-Julie FavĂŠ, CĂŠdric Finet, Jacobs, Chris, Jarvela, Alys Cheatle, Jennings, Emily, Jones, Jeffery, Lesoway, Maryna, Lovegrove, Mackenzie, Martynov, Alexander, Oppert, Brenda, Lillico-Ouachour, Angelica, Arjuna Rajakumar, Refki, Peter, Rosendale, Andrew, Santos, Maria, Toubiana, William, Maurijn Van Der Zee, Jentzsch, Iris Vargas, Aidamalia Lowman, Viala, Severine, Richards, Stephen, and Abderrahman Khila
Abstract: Gerris buenoi serosins nucleotide and protein sequences. (DOCX 12 kb)
Published: 2018
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50. A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor

Author: Brandon J. Schemerhorn, Mehwish Javaid, Kerstin P. Blankenburg, Marion O. Harris, Lora Perales, Lucio Navarro Escalante, Chaoyang Zhao, J. J. Stuart, Mustapha El-Bouhssini, Jacob Shreve, Doina Caragea, Marcus Coyle, Panagiotis Ioannidis, Subhashree Subramanyam, Martin Andersson, Kun Xue, David A. Wheeler, Ming-Shun Chen, DeNard Simmons, Christer Löfstedt, Swapnil Nagar, Geoffrey Okwuonu, Fiona Ongeri, Susan J. Brown, Nicolae Herndon, Xuming Liu, Dianhui Zhu, Richard H. Shukle, Sanjay Chellapilla, Tony Grace, George M. Weissenberger, Alisha J. Johnson, Shalini N. Jhangiani, Evgeny M. Zdobnov, Christopher B. Williams, Donna M. Muzny, Robert M. Waterhouse, Yiming Zhu, Lynne V. Nazareth, Rebecca Thornton, LaRonda Jackson, Steven E. Scherer, Cornelis J. P. Grimmelikhuijzen, Robert Mata, Liezl Francisco, Matthew Batterton, Riyue Bao, Divya Kalra, Sandra L. Lee, Markus Friedrich, Yi Han, Stephen Richards, Thiago R Benatti, Fremiet Lara, Viktoriya Korchina, John H. Werren, Navdeep Gill, Christie Kovar, Hang Chen, M. Holder, James C. Carolan, Kim C. Worley, Susanta K. Behura, Tittu Mathew, Ling Pu, Jiaxin Qu, Hugh M. Robertson, Frank Hauser, Brittany F. Peterson, Waterhouse, Robert, Ioannidis, Panagiotis, and Zdobnov, Evgeny
Subjects: 0106 biological sciences, Ubiquitin-Protein Ligases, Molecular Sequence Data, Adaptation, Biological, Plant Tumors, Sequence Homology, 01 natural sciences, Genome, Chromosomes, General Biochemistry, Genetics and Molecular Biology, Sexual Behavior, Animal, 03 medical and health sciences, Two-Hybrid System Techniques, Animals, Gene family, Gall, ddc:576.5, Amino Acid Sequence, Mayetiola destructor, Gene, Phylogeny, Triticum, 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, Base Sequence, Models, Genetic, Agricultural and Biological Sciences(all), biology, Biochemistry, Genetics and Molecular Biology(all), Effector, Diptera, fungi, food and beverages, Sequence Analysis, DNA, biology.organism_classification, Cecidomyiidae, Larva, Multigene Family, General Agricultural and Biological Sciences, 010606 plant biology & botany
Abstract: SummaryGall-forming arthropods are highly specialized herbivores that, in combination with their hosts, produce extended phenotypes with unique morphologies [1]. Many are economically important, and others have improved our understanding of ecology and adaptive radiation [2]. However, the mechanisms that these arthropods use to induce plant galls are poorly understood. We sequenced the genome of the Hessian fly (Mayetiola destructor; Diptera: Cecidomyiidae), a plant parasitic gall midge and a pest of wheat (Triticum spp.), with the aim of identifying genic modifications that contribute to its plant-parasitic lifestyle. Among several adaptive modifications, we discovered an expansive reservoir of potential effector proteins. Nearly 5% of the 20,163 predicted gene models matched putative effector gene transcripts present in the M. destructor larval salivary gland. Another 466 putative effectors were discovered among the genes that have no sequence similarities in other organisms. The largest known arthropod gene family (family SSGP-71) was also discovered within the effector reservoir. SSGP-71 proteins lack sequence homologies to other proteins, but their structures resemble both ubiquitin E3 ligases in plants and E3-ligase-mimicking effectors in plant pathogenic bacteria. SSGP-71 proteins and wheat Skp proteins interact in vivo. Mutations in different SSGP-71 genes avoid the effector-triggered immunity that is directed by the wheat resistance genes H6 and H9. Results point to effectors as the agents responsible for arthropod-induced plant gall formation.
Published: 2015

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