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1. Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the AgBioData Consortium

Author

Clarke, Jennifer L., Cooper, Laurel D., Poelchau, Monica F., Berardini, Tanya Z., Elser, Justin, Farmer, Andrew D., Ficklin, Stephen, Kumari, Sunita, Laporte, Marie-Angélique, Nelson, Rex T., Sadohara, Rie, Selby, Peter, Thessen, Anne E., Whitehead, Brandon, and Sen, Taner Z.

Subjects
Computer Science - Databases
Abstract

Over the last several decades, there has been rapid growth in the number and scope of agricultural genetics, genomics and breeding (GGB) databases and resources. The AgBioData Consortium (https://www.agbiodata.org/) currently represents 44 databases and resources covering model or crop plant and animal GGB data, ontologies, pathways, genetic variation and breeding platforms (referred to as 'databases' throughout). One of the goals of the Consortium is to facilitate FAIR (Findable, Accessible, Interoperable, and Reusable) data management and the integration of datasets which requires data sharing, along with structured vocabularies and/or ontologies. Two AgBioData working groups, focused on Data Sharing and Ontologies, conducted a survey to assess the status and future needs of the members in those areas. A total of 33 researchers responded to the survey, representing 37 databases. Results suggest that data sharing practices by AgBioData databases are in a healthy state, but it is not clear whether this is true for all metadata and data types across all databases; and that ontology use has not substantially changed since a similar survey was conducted in 2017. We recommend 1) providing training for database personnel in specific data sharing techniques, as well as in ontology use; 2) further study on what metadata is shared, and how well it is shared among databases; 3) promoting an understanding of data sharing and ontologies in the stakeholder community; 4) improving data sharing and ontologies for specific phenotypic data types and formats; and 5) lowering specific barriers to data sharing and ontology use, by identifying sustainability solutions, and the identification, promotion, or development of data standards. Combined, these improvements are likely to help AgBioData databases increase development efforts towards improved ontology use, and data sharing via programmatic means., Comment: 17 pages, 8 figures

Published
2023

2. Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium

Author

Clarke, Jennifer L, Cooper, Laurel D, Poelchau, Monica F, Berardini, Tanya Z, Elser, Justin, Farmer, Andrew D, Ficklin, Stephen, Kumari, Sunita, Laporte, Marie-Angélique, Nelson, Rex T, Sadohara, Rie, Selby, Peter, Thessen, Anne E, Whitehead, Brandon, and Sen, Taner Z

Subjects
Biological Sciences, Genetics, Networking and Information Technology R&D (NITRD), Data Format, Library and Information Studies, Bioinformatics and computational biology, Data management and data science
Abstract

Over the last couple of decades, there has been a rapid growth in the number and scope of agricultural genetics, genomics and breeding databases and resources. The AgBioData Consortium (https://www.agbiodata.org/) currently represents 44 databases and resources (https://www.agbiodata.org/databases) covering model or crop plant and animal GGB data, ontologies, pathways, genetic variation and breeding platforms (referred to as 'databases' throughout). One of the goals of the Consortium is to facilitate FAIR (Findable, Accessible, Interoperable, and Reusable) data management and the integration of datasets which requires data sharing, along with structured vocabularies and/or ontologies. Two AgBioData working groups, focused on Data Sharing and Ontologies, respectively, conducted a Consortium-wide survey to assess the current status and future needs of the members in those areas. A total of 33 researchers responded to the survey, representing 37 databases. Results suggest that data-sharing practices by AgBioData databases are in a fairly healthy state, but it is not clear whether this is true for all metadata and data types across all databases; and that, ontology use has not substantially changed since a similar survey was conducted in 2017. Based on our evaluation of the survey results, we recommend (i) providing training for database personnel in a specific data-sharing techniques, as well as in ontology use; (ii) further study on what metadata is shared, and how well it is shared among databases; (iii) promoting an understanding of data sharing and ontologies in the stakeholder community; (iv) improving data sharing and ontologies for specific phenotypic data types and formats; and (v) lowering specific barriers to data sharing and ontology use, by identifying sustainability solutions, and the identification, promotion, or development of data standards. Combined, these improvements are likely to help AgBioData databases increase development efforts towards improved ontology use, and data sharing via programmatic means. Database URL  https://www.agbiodata.org/databases.

Published
2023

3. Recommendations for extending the GFF3 specification for improved interoperability of genomic data

Author

Saha, Surya, Cain, Scott, Cannon, Ethalinda K. S., Dunn, Nathan, Farmer, Andrew, Hu, Zhi-Liang, Maslen, Gareth, Moxon, Sierra, Mungall, Christopher J, Nelson, Rex, and Poelchau, Monica F.

Subjects
Quantitative Biology - Other Quantitative Biology
Abstract

The GFF3 format is a common, flexible tab-delimited format representing the structure and function of genes or other mapped features (https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md). However, with increasing re-use of annotation data, this flexibility has become an obstacle for standardized downstream processing. Common software packages that export annotations in GFF3 format model the same data and metadata in different notations, which puts the burden on end-users to interpret the data model. The AgBioData consortium is a group of genomics, genetics and breeding databases and partners working towards shared practices and standards. Providing concrete guidelines for generating GFF3, and creating a standard representation of the most common biological data types would provide a major increase in efficiency for AgBioData databases and the genomics research community that use the GFF3 format in their daily operations. The AgBioData GFF3 working group has developed recommendations to solve common problems in the GFF3 format. We suggest improvements for each of the GFF3 fields, as well as the special cases of modeling functional annotations, and standard protein-coding genes. We welcome further discussion of these recommendations. We request the genomics and bioinformatics community to utilize the github repository (https://github.com/NAL-i5K/AgBioData_GFF3_recommendation) to provide feedback via issues or pull requests., Comment: 23 pages

Published
2022

4. Standards recommendations for the Earth BioGenome Project

Author

Lawniczak, Mara KN, Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M, Baker, William J, Belov, Katherine, Blaxter, Mark L, Bonet, Tomas Marques, Childers, Anna K, Coddington, Jonathan A, Crandall, Keith A, Crawford, Andrew J, Davey, Robert P, Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J, Howe, Kerstin, Jarvis, Erich D, Johnson, Warren E, Johnson, Rebecca N, Kersey, Paul J, Liu, Xin, Lopez, Jose Victor, Myers, Eugene W, Pettersson, Olga Vinnere, Phillippy, Adam M, Poelchau, Monica F, Pruitt, Kim D, Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A, Soltis, Pamela S, Swarbreck, David, Thibaud-Nissen, Françoise, Wang, Sibo, Wegrzyn, Jill L, Zhang, Guojie, Zhang, He, Lewin, Harris A, and Richards, Stephen

Subjects
Human Genome, Genetics, Animals, Base Sequence, Biodiversity, Eukaryota, Genomics, Humans, Reference Standards, Reference Values, Sequence Analysis, DNA, Earth BioGenome Project, genomics, ethics, genome assembly
Abstract

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

Published
2022

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

Author

Sparks, Michael E, Bansal, Raman, Benoit, Joshua B, Blackburn, Michael B, Chao, Hsu, Chen, Mengyao, Cheng, Sammy, Childers, Christopher, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dugan, Shannon, Elpidina, Elena N, Farrow, David W, Friedrich, Markus, Gibbs, Richard A, Hall, Brantley, Han, Yi, Hardy, Richard W, Holmes, Christopher J, Hughes, Daniel ST, Ioannidis, Panagiotis, Cheatle Jarvela, Alys M, Johnston, J Spencer, Jones, Jeffery W, Kronmiller, Brent A, Kung, Faith, Lee, Sandra L, Martynov, Alexander G, Masterson, Patrick, Maumus, Florian, Munoz-Torres, Monica, Murali, Shwetha C, Murphy, Terence D, Muzny, Donna M, Nelson, David R, Oppert, Brenda, Panfilio, Kristen A, Paula, Débora Pires, Pick, Leslie, Poelchau, Monica F, Qu, Jiaxin, Reding, Katie, Rhoades, Joshua H, Rhodes, Adelaide, Richards, Stephen, Richter, Rose, Robertson, Hugh M, Rosendale, Andrew J, Tu, Zhijian Jake, Velamuri, Arun S, Waterhouse, Robert M, Weirauch, Matthew T, Wells, Jackson T, Werren, John H, Worley, Kim C, Zdobnov, Evgeny M, and Gundersen-Rindal, Dawn E

Subjects
Genetics, Biotechnology, Human Genome, Animals, Ecosystem, Gene Transfer, Horizontal, Genome Size, Heteroptera, Insect Proteins, Insecticide Resistance, Introduced Species, Phylogeny, Whole Genome Sequencing, Brown marmorated stink bug genome, Pentatomid genomics, polyphagy, chemoreceptors, odorant binding proteins, opsins, cathepsins, xenobiotic detoxification, invasive species, Biological Sciences, Information and Computing Sciences, Medical and Health Sciences, Bioinformatics
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 support H. halys' capacity for invasiveness. Many of the genes identified herein have potential for biomolecular pesticide applications.ConclusionsAvailability 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

6. Gene content evolution in the arthropods

Author

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

Subjects
Human Genome, Genetics, Biotechnology, Generic health relevance, Animals, Arthropods, DNA Methylation, Evolution, Molecular, Genetic Speciation, Genetic Variation, Phylogeny, Genome assembly, Genomics, Protein domains, Gene content, Evolution, DNA methylation, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundArthropods 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.ResultsUsing 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.ConclusionsThese 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

7. Correction to: Genome-enabled insights into the biology of thrips as crop pests

Author

Rotenberg, Dorith, Baumann, Aaron A, Ben-Mahmoud, Sulley, Christiaens, Olivier, Dermauw, Wannes, Ioannidis, Panagiotis, Jacobs, Chris GC, Vargas Jentzsch, Iris M, Oliver, Jonathan E, Poelchau, Monica F, Rajarapu, Swapna Priya, Schneweis, Derek J, Snoeck, Simon, Taning, Clauvis NT, Wei, Dong, Widana Gamage, Shirani MK, Hughes, Daniel ST, Murali, Shwetha C, 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, Chao, Hsu, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dugan, Shannon, Han, Yi, Lee, Sandra L, Muzny, Donna M, Qu, Jiaxin, Worley, Kim C, Benoit, Joshua B, Friedrich, Markus, Jones, Jeffery W, Panfilio, Kristen A, Park, Yoonseong, Robertson, Hugh M, Smagghe, Guy, Ullman, Diane E, van der Zee, Maurijn, Van Leeuwen, Thomas, 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
Biological Sciences, Developmental Biology, Biological sciences
Abstract

An amendment to this paper has been published and can be accessed via the original article.

Published
2020

8. Genome-enabled insights into the biology of thrips as crop pests

Author

Rotenberg, Dorith, Baumann, Aaron A, Ben-Mahmoud, Sulley, Christiaens, Olivier, Dermauw, Wannes, Ioannidis, Panagiotis, Jacobs, Chris GC, Vargas Jentzsch, Iris M, Oliver, Jonathan E, Poelchau, Monica F, Rajarapu, Swapna Priya, Schneweis, Derek J, Snoeck, Simon, Taning, Clauvis NT, Wei, Dong, Widana Gamage, Shirani MK, Hughes, Daniel ST, Murali, Shwetha C, 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, Chao, Hsu, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dugan, Shannon, Han, Yi, Lee, Sandra L, Muzny, Donna M, Qu, Jiaxin, Worley, Kim C, Benoit, Joshua B, Friedrich, Markus, Jones, Jeffery W, Panfilio, Kristen A, Park, Yoonseong, Robertson, Hugh M, Smagghe, Guy, Ullman, Diane E, van der Zee, Maurijn, Van Leeuwen, Thomas, 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
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Animals, Crops, Agricultural, Feeding Behavior, Food Chain, Genome, Insect, Immunity, Innate, Life History Traits, Perception, Phylogeny, Reproduction, Thysanoptera, Transcriptome, Western flower thrips, Hemipteroid assemblage, Insect genomics, Tospovirus, Salivary glands, Chemosensory receptors, Opsins, Detoxification, Innate immunity, Developmental Biology, Biological sciences
Abstract

BackgroundThe 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.ResultsWe 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.ConclusionsAnalysis 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

9. Sawfly genomes reveal evolutionary acquisitions that fostered the mega-radiation of parasitoid and eusocial Hymenoptera

Author

Oeyen, Jan Philip, Baa-Puyoulet, Patrice, Benoit, Joshua B, Beukeboom, Leo W, Bornberg-Bauer, Erich, Buttstedt, Anja, Calevro, Federica, Cash, Elizabeth I, Chao, Hsu, Charles, Hubert, Chen, Mei-Ju May, Childers, Christopher, Cridge, Andrew G, Dearden, Peter, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dolan, Amanda, Donath, Alexander, Dowling, Daniel, Dugan, Shannon, Duncan, Elizabeth, Elpidina, Elena N, Friedrich, Markus, Geuverink, Elzemiek, Gibson, Joshua D, Grath, Sonja, Grimmelikhuijzen, Cornelis JP, Große-Wilde, Ewald, Gudobba, Cameron, Han, Yi, Hansson, Bill S, Hauser, Frank, Hughes, Daniel ST, Ioannidis, Panagiotis, Jacquin-Joly, Emmanuelle, Jennings, Emily C, Jones, Jeffery W, Klasberg, Steffen, Lee, Sandra L, Lesný, Peter, Lovegrove, Mackenzie, Martin, Sebastian, Martynov, Alexander G, Mayer, Christoph, Montagné, Nicolas, Moris, Victoria C, Munoz-Torres, Monica, Murali, Shwetha Canchi, Muzny, Donna M, Oppert, Brenda, Parisot, Nicolas, Pauli, Thomas, Peters, Ralph S, Petersen, Malte, Pick, Christian, Persyn, Emma, Podsiadlowski, Lars, Poelchau, Monica F, Provataris, Panagiotis, Qu, Jiaxin, Reijnders, Maarten JMF, von Reumont, Björn Marcus, Rosendale, Andrew J, Simao, Felipe A, Skelly, John, Sotiropoulos, Alexandros G, Stahl, Aaron L, Sumitani, Megumi, Szuter, Elise M, Tidswell, Olivia, Tsitlakidis, Evangelos, Vedder, Lucia, Waterhouse, Robert M, Werren, John H, Wilbrandt, Jeanne, Worley, Kim C, Yamamoto, Daisuke S, van de Zande, Louis, Zdobnov, Evgeny M, Ziesmann, Tanja, Gibbs, Richard A, Richards, Stephen, Hatakeyama, Masatsugu, Misof, Bernhard, and Niehuis, Oliver

Subjects
Human Genome, Genetics, Life Below Water, Amino Acid Sequence, Animals, Conserved Sequence, DNA Transposable Elements, Female, Gene Dosage, Genetic Speciation, Genome, Insect, Glycoproteins, Herbivory, Host-Parasite Interactions, Hymenoptera, Immunity, Insect Proteins, Male, Multigene Family, Receptors, Odorant, Social Behavior, Vision, Ocular, hexamerin, major royal jelly protein, microsynteny, odorant receptor, opsin, phytophagy, Biochemistry and Cell Biology, Evolutionary Biology, 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

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

Author

Panfilio, Kristen A, Vargas Jentzsch, Iris M, Benoit, Joshua B, Erezyilmaz, Deniz, Suzuki, Yuichiro, Colella, Stefano, Robertson, Hugh M, Poelchau, Monica F, Waterhouse, Robert M, Ioannidis, Panagiotis, Weirauch, Matthew T, Hughes, Daniel ST, Murali, Shwetha C, Werren, John H, Jacobs, Chris GC, Duncan, Elizabeth J, Armisén, David, Vreede, Barbara MI, Baa-Puyoulet, Patrice, Berger, Chloé S, Chang, Chun-che, Chao, Hsu, Chen, Mei-Ju M, Chen, Yen-Ta, Childers, Christopher P, Chipman, Ariel D, Cridge, Andrew G, Crumière, Antonin JJ, Dearden, Peter K, Didion, Elise M, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dolan, Amanda, Dugan, Shannon, Extavour, Cassandra G, Febvay, Gérard, Friedrich, Markus, Ginzburg, Neta, Han, Yi, Heger, Peter, Holmes, Christopher J, Horn, Thorsten, Hsiao, Yi-min, Jennings, Emily C, Johnston, J Spencer, Jones, Tamsin E, Jones, Jeffery W, Khila, Abderrahman, Koelzer, Stefan, Kovacova, Viera, Leask, Megan, Lee, Sandra L, Lee, Chien-Yueh, Lovegrove, Mackenzie R, Lu, Hsiao-ling, Lu, Yong, Moore, Patricia J, Munoz-Torres, Monica C, Muzny, Donna M, Palli, Subba R, Parisot, Nicolas, Pick, Leslie, Porter, Megan L, Qu, Jiaxin, Refki, Peter N, Richter, Rose, Rivera-Pomar, Rolando, Rosendale, Andrew J, Roth, Siegfried, Sachs, Lena, Santos, M Emília, Seibert, Jan, Sghaier, Essia, Shukla, Jayendra N, Stancliffe, Richard J, Tidswell, Olivia, Traverso, Lucila, van der Zee, Maurijn, Viala, Séverine, Worley, Kim C, Zdobnov, Evgeny M, Gibbs, Richard A, and Richards, Stephen

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Underpinning research, 1.1 Normal biological development and functioning, Amino Acid Sequence, Animals, CYS2-HIS2 Zinc Fingers, Evolution, Molecular, Feeding Behavior, Gene Dosage, Gene Expression Profiling, Gene Transfer, Horizontal, Genes, Homeobox, Genome, Insect, Hemiptera, Pigmentation, Smell, Transcription Factors, Evolution of development, Gene family evolution, Gene structure, Lateral gene transfer, Phytophagy, RNAi, Transcription factors, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundThe 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.ResultsThe 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.ConclusionsWith 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

11. A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae).

Author

Schoville, Sean D, Chen, Yolanda H, Andersson, Martin N, Benoit, Joshua B, Bhandari, Anita, Bowsher, Julia H, Brevik, Kristian, Cappelle, Kaat, Chen, Mei-Ju M, Childers, Anna K, Childers, Christopher, Christiaens, Olivier, Clements, Justin, Didion, Elise M, Elpidina, Elena N, Engsontia, Patamarerk, Friedrich, Markus, García-Robles, Inmaculada, Gibbs, Richard A, Goswami, Chandan, Grapputo, Alessandro, Gruden, Kristina, Grynberg, Marcin, Henrissat, Bernard, Jennings, Emily C, Jones, Jeffery W, Kalsi, Megha, Khan, Sher A, Kumar, Abhishek, Li, Fei, Lombard, Vincent, Ma, Xingzhou, Martynov, Alexander, Miller, Nicholas J, Mitchell, Robert F, Munoz-Torres, Monica, Muszewska, Anna, Oppert, Brenda, Palli, Subba Reddy, Panfilio, Kristen A, Pauchet, Yannick, Perkin, Lindsey C, Petek, Marko, Poelchau, Monica F, Record, Éric, Rinehart, Joseph P, Robertson, Hugh M, Rosendale, Andrew J, Ruiz-Arroyo, Victor M, Smagghe, Guy, Szendrei, Zsofia, Thomas, Gregg WC, Torson, Alex S, Vargas Jentzsch, Iris M, Weirauch, Matthew T, Yates, Ashley D, Yocum, George D, Yoon, June-Sun, and Richards, Stephen

Subjects
Animals, Insect Proteins, Transcription Factors, DNA Transposable Elements, Genetics, Population, Genomics, Pest Control, Biological, Evolution, Molecular, Phylogeny, Gene Expression Regulation, RNA Interference, Insecticide Resistance, Multigene Family, Agriculture, Female, Male, Solanum tuberosum, Genome, Insect, Host-Parasite Interactions, Genetic Variation, Molecular Sequence Annotation, Coleoptera, Genetics, Population, Pest Control, Biological, Evolution, Molecular, Genome, Insect, Biochemistry and Cell Biology, Other Physical Sciences
Abstract

The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain why Leptinotarsa decemlineata has high sensitivity to dsRNA. The L. decemlineata genome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest.

Published
2018

12. AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

Author

Harper, Lisa, Campbell, Jacqueline, Cannon, Ethalinda KS, Jung, Sook, Poelchau, Monica, Walls, Ramona, Andorf, Carson, Arnaud, Elizabeth, Berardini, Tanya Z, Birkett, Clayton, Cannon, Steve, Carson, James, Condon, Bradford, Cooper, Laurel, Dunn, Nathan, Elsik, Christine G, Farmer, Andrew, Ficklin, Stephen P, Grant, David, Grau, Emily, Herndon, Nic, Hu, Zhi-Liang, Humann, Jodi, Jaiswal, Pankaj, Jonquet, Clement, Laporte, Marie-Angélique, Larmande, Pierre, Lazo, Gerard, McCarthy, Fiona, Menda, Naama, Mungall, Christopher J, Munoz-Torres, Monica C, Naithani, Sushma, Nelson, Rex, Nesdill, Daureen, Park, Carissa, Reecy, James, Reiser, Leonore, Sanderson, Lacey-Anne, Sen, Taner Z, Staton, Margaret, Subramaniam, Sabarinath, Tello-Ruiz, Marcela Karey, Unda, Victor, Unni, Deepak, Wang, Liya, Ware, Doreen, Wegrzyn, Jill, Williams, Jason, Woodhouse, Margaret, Yu, Jing, and Main, Doreen

Subjects
Information and Computing Sciences, Biological Sciences, Library and Information Studies, Zero Hunger, Agriculture, Breeding, Databases, Genetic, Gene Ontology, Genomics, Metadata, Surveys and Questionnaires, Data Format, Bioinformatics and computational biology, Data management and data science
Abstract

The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require data management plans for publicly funded research. Furthermore, the value of data increases exponentially when they are properly stored, described, integrated and shared, so that they can be easily utilized in future analyses. AgBioData (https://www.agbiodata.org) is a consortium of people working at agricultural biological databases, data archives and knowledgbases who strive to identify common issues in database development, curation and management, with the goal of creating database products that are more Findable, Accessible, Interoperable and Reusable. We strive to promote authentic, detailed, accurate and explicit communication between all parties involved in scientific data. As a step toward this goal, we present the current state of biocuration, ontologies, metadata and persistence, database platforms, programmatic (machine) access to data, communication and sustainability with regard to data curation. Each section describes challenges and opportunities for these topics, along with recommendations and best practices.

Published
2018

13. Unique features of a global human ectoparasite identified through sequencing of the bed bug genome.

Author

Benoit, Joshua B, Adelman, Zach N, Reinhardt, Klaus, Dolan, Amanda, Poelchau, Monica, Jennings, Emily C, Szuter, Elise M, Hagan, Richard W, Gujar, Hemant, Shukla, Jayendra Nath, Zhu, Fang, Mohan, M, Nelson, David R, Rosendale, Andrew J, Derst, Christian, Resnik, Valentina, Wernig, Sebastian, Menegazzi, Pamela, Wegener, Christian, Peschel, Nicolai, Hendershot, Jacob M, Blenau, Wolfgang, Predel, Reinhard, Johnston, Paul R, Ioannidis, Panagiotis, Waterhouse, Robert M, Nauen, Ralf, Schorn, Corinna, Ott, Mark-Christoph, Maiwald, Frank, Johnston, J Spencer, Gondhalekar, Ameya D, Scharf, Michael E, Peterson, Brittany F, Raje, Kapil R, Hottel, Benjamin A, Armisén, David, Crumière, Antonin Jean Johan, Refki, Peter Nagui, Santos, Maria Emilia, Sghaier, Essia, Viala, Sèverine, Khila, Abderrahman, Ahn, Seung-Joon, Childers, Christopher, Lee, Chien-Yueh, Lin, Han, Hughes, Daniel ST, Duncan, Elizabeth J, Murali, Shwetha C, Qu, Jiaxin, Dugan, Shannon, Lee, Sandra L, Chao, Hsu, Dinh, Huyen, Han, Yi, Doddapaneni, Harshavardhan, Worley, Kim C, Muzny, Donna M, Wheeler, David, Panfilio, Kristen A, Vargas Jentzsch, Iris M, Vargo, Edward L, Booth, Warren, Friedrich, Markus, Weirauch, Matthew T, Anderson, Michelle AE, Jones, Jeffery W, Mittapalli, Omprakash, Zhao, Chaoyang, Zhou, Jing-Jiang, Evans, Jay D, Attardo, Geoffrey M, Robertson, Hugh M, Zdobnov, Evgeny M, Ribeiro, Jose MC, Gibbs, Richard A, Werren, John H, Palli, Subba R, Schal, Coby, and Richards, Stephen

Subjects
Animals, Humans, Bedbugs, Ectoparasitic Infestations, Insecticides, Sequence Analysis, DNA, Feeding Behavior, Gene Transfer, Horizontal, Insecticide Resistance, Genome, Host-Parasite Interactions, Gene Transfer, Horizontal, Sequence Analysis, DNA
Abstract

The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host-symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human-bed bug and symbiont-bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite.

Published
2016

14. Hemimetabolous genomes reveal molecular basis of termite eusociality

Author

Harrison, Mark C., Jongepier, Evelien, Robertson, Hugh M., Arning, Nicolas, Bitard-Feildel, Tristan, Chao, Hsu, Childers, Christopher P., Dinh, Huyen, Doddapaneni, Harshavardhan, Dugan, Shannon, Gowin, Johannes, Greiner, Carolin, Han, Yi, Hu, Haofu, Hughes, Daniel S. T., Huylmans, Ann-Kathrin, Kemena, Carsten, Kremer, Lukas P. M., Lee, Sandra L., Lopez-Ezquerra, Alberto, Mallet, Ludovic, Monroy-Kuhn, Jose M., Moser, Annabell, Murali, Shwetha C., Muzny, Donna M., Otani, Saria, Piulachs, Maria-Dolors, Poelchau, Monica, Qu, Jiaxin, Schaub, Florentine, Wada-Katsumata, Ayako, Worley, Kim C., Xie, Qiaolin, Ylla, Guillem, Poulsen, Michael, Gibbs, Richard A., Schal, Coby, Richards, Stephen, Belles, Xavier, Korb, Judith, and Bornberg-Bauer, Erich

Published
2018
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18. NAPPN Annual Conference Abstract: Can we make phenomic, genetic, and genomic data FAIR? The AgBioData road trip towards best practices of data sharing and management in agricultural research and education

Author

Marrano, Annarita, primary, Campbell, Darwin, additional, Campbell, Jaqueline, additional, Cannon, Ethalinda, additional, Cooper, Laurel, additional, Harrison, Peter, additional, Harper6, Lisa, additional, Huala, Eva, additional, Jung, Sook, additional, Kumari, Sunita, additional, Mcnamara, John, additional, Naithani, Sushma, additional, Poelchau, Monica, additional, Reiser, Leonore, additional, Staton, Margaret, additional, and Tello-Ruiz, Marcela K, additional

Published
2023
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19. Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium

Author

Clarke, Jennifer L, primary, Cooper, Laurel D, additional, Poelchau, Monica F, additional, Berardini, Tanya Z, additional, Elser, Justin, additional, Farmer, Andrew D, additional, Ficklin, Stephen, additional, Kumari, Sunita, additional, Laporte, Marie-Angélique, additional, Nelson, Rex T, additional, Sadohara, Rie, additional, Selby, Peter, additional, Thessen, Anne E, additional, Whitehead, Brandon, additional, and Sen, Taner Z, additional

Published
2023
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22. The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water

Author

Armisén, David, Rajakumar, Rajendhran, Friedrich, Markus, Benoit, Joshua B., Robertson, Hugh M., Panfilio, Kristen A., Ahn, Seung-Joon, Poelchau, Monica F., Chao, Hsu, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dugan, Shannon, Gibbs, Richard A., Hughes, Daniel S. T., Han, Yi, Lee, Sandra L., Murali, Shwetha C., Muzny, Donna M., Qu, Jiaxin, Worley, Kim C., Munoz-Torres, Monica, Abouheif, Ehab, Bonneton, François, Chen, Travis, Chiang, Li-Mei, Childers, Christopher P., Cridge, Andrew G., Crumière, Antonin J. J., Decaras, Amelie, Didion, Elise M., Duncan, Elizabeth J., Elpidina, Elena N., Favé, Marie-Julie, Finet, Cédric, Jacobs, Chris G. C., Cheatle Jarvela, Alys M., Jennings, Emily C., Jones, Jeffery W., Lesoway, Maryna P., Lovegrove, Mackenzie R., Martynov, Alexander, Oppert, Brenda, Lillico-Ouachour, Angelica, Rajakumar, Arjuna, Refki, Peter Nagui, Rosendale, Andrew J., Santos, Maria Emilia, Toubiana, William, van der Zee, Maurijn, Vargas Jentzsch, Iris M., Lowman, Aidamalia Vargas, Viala, Severine, Richards, Stephen, and Khila, Abderrahman

Published
2018
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26. Standards recommendations for the Earth BioGenome Project

Author

Lawniczak, Mara K.N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J, Belov, Katherine, Blaxter, Mark, Marques-Bonet, Tomas, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina, Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca, Kersey, Paul J., Liu, Xin, Lopez, Jose V., Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica, Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela, Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill, Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen, Lawniczak, Mara K.N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J, Belov, Katherine, Blaxter, Mark, Marques-Bonet, Tomas, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina, Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca, Kersey, Paul J., Liu, Xin, Lopez, Jose V., Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica, Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela, Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill, Zhang, Guojie, Zhang, He, Lewin, Harris A., and Richards, Stephen

Abstract

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

Published
2022

27. Standards recommendations for the Earth BioGenome Project

Author

Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark L., Bonet, Tomas Marques, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, Lopez, Jose Victor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen, Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark L., Bonet, Tomas Marques, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, Lopez, Jose Victor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., and Richards, Stephen

Abstract

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

Published
2022
Full Text
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28. Standards recommendations for the Earth BioGenome Project

Author

National Library of Medicine (US), National Institutes of Health (US), Swedish Research Council, National Museum of Natural History Smithsonian Institution, Howard Hughes Medical Institute, Wellcome, European Molecular Biology Laboratory, National Science Foundation (US), Department of Agriculture (US), Agricultural Research Service (US), Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark, Marqués-Bonet, Tomàs, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, López, José Víctor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Kumar Sahu, Sunil, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen, National Library of Medicine (US), National Institutes of Health (US), Swedish Research Council, National Museum of Natural History Smithsonian Institution, Howard Hughes Medical Institute, Wellcome, European Molecular Biology Laboratory, National Science Foundation (US), Department of Agriculture (US), Agricultural Research Service (US), Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark, Marqués-Bonet, Tomàs, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, López, José Víctor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Kumar Sahu, Sunil, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., and Richards, Stephen

Abstract

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

Published
2022

31. The Genome of Rhyzopertha dominica (Fab.) (Coleoptera: Bostrichidae): Adaptation for Success

Author

Oppert, Brenda, primary, Muszewska, Anna, additional, Steczkiewicz, Kamil, additional, Šatović-Vukšić, Eva, additional, Plohl, Miroslav, additional, Fabrick, Jeffrey, additional, Vinokurov, Konstantin, additional, Koloniuk, Igor, additional, Johnston, J., additional, Smith, Timothy, additional, Guedes, Raul, additional, Terra, Walter, additional, Ferreira, Clélia, additional, Dias, Renata, additional, Chaply, Konstantin, additional, Elpidina, Elena, additional, Tereshchenkova, Valeriia, additional, Mitchell, Robert, additional, Jenson, Audra, additional, McKay, Rachel, additional, Shan, Tisheng, additional, Cao, Xiaolong, additional, Miao, Zelong, additional, Xiong, Chao, additional, Jiang, Haobo, additional, Morrison, William, additional, Koren, Sergey, additional, Schlipalius, David, additional, Lorenzen, Marcé, additional, Bansal, Raman, additional, Wang, Yu-Hui, additional, Perkin, Lindsey, additional, Poelchau, Monica, additional, Friesen, Kenlee, additional, Olmstead, Morgan, additional, Scully, Erin, additional, and Campbell, James, additional

Published
2022
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34. Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases

Author

Staton, Margaret, primary, Cannon, Ethalinda, additional, Sanderson, Lacey-Anne, additional, Wegrzyn, Jill, additional, Anderson, Tavis, additional, Buehler, Sean, additional, Cobo-Simón, Irene, additional, Faaberg, Kay, additional, Grau, Emily, additional, Guignon, Valentin, additional, Gunoskey, Jessica, additional, Inderski, Blake, additional, Jung, Sook, additional, Lager, Kelly, additional, Main, Dorrie, additional, Poelchau, Monica, additional, Ramnath, Risharde, additional, Richter, Peter, additional, West, Joe, additional, and Ficklin, Stephen, additional

Published
2021
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35. The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research

Author

Childers, Anna K., primary, Geib, Scott M., additional, Sim, Sheina B., additional, Poelchau, Monica F., additional, Coates, Brad S., additional, Simmonds, Tyler J., additional, Scully, Erin D., additional, Smith, Timothy P. L., additional, Childers, Christopher P., additional, Corpuz, Renee L., additional, Hackett, Kevin, additional, and Scheffler, Brian, additional

Published
2021
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36. Supplementary Tables and Legends Standards Recommendations for the Earth BioGenome Project

Author

Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark, Marqués-Bonet, Tomàs, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, López, José Víctor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Kumar Sahu, Sunil, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen, Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark, Marqués-Bonet, Tomàs, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, López, José Víctor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Kumar Sahu, Sunil, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., and Richards, Stephen

Published
2021

37. 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
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39. 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
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40. 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
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41. 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
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42. 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 – S34.

Published
2020
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43. 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
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44. 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
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45. Gene content evolution in the arthropods

Author

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

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

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

Author

Sparks, Michael E., Bansal, Raman, Benoit, Joshua B., Blackburn, Michael B., Chao, Hsu, Chen, Mengyao, Cheng, Sammy, Childers, Christopher, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dugan, Shannon, Elpidina, Elena N., Farrow, David W., Friedrich, Markus, Gibbs, Richard A., Hall, Brantley, Han, Yi, Hardy, Richard W., Holmes, Christopher J., Hughes, Daniel S. T., Ioannidis, Panagiotis, Jarvela, Alys M. Cheatle, Johnston, J. Spencer, Jones, Jeffery W., Kronmiller, Brent A., Kung, Faith, Lee, Sandra L., Martynov, Alexander G., Masterson, Patrick, Maumus, Florian, Munoz-Torres, Monica, Murali, Shwetha C., Murphy, Terence D., Muzny, Donna M., Nelson, David R., Oppert, Brenda, Panfilio, Kristen A., Paula, Debora Pires, Pick, Leslie, Poelchau, Monica F., Qu, Jiaxin, Reding, Katie, Rhoades, Joshua H., Rhodes, Adelaide, Richards, Stephen, Richter, Rose, Robertson, Hugh M., Rosendale, Andrew J., Tu, Zhijian Jake, Velamuri, Arun S., Waterhouse, Robert M., Weirauch, Matthew T., Wells, Jackson T., Werren, John H., Worley, Kim C., Zdobnov, Evgeny M., Gundersen-Rindal, Dawn E., Sparks, Michael E., Bansal, Raman, Benoit, Joshua B., Blackburn, Michael B., Chao, Hsu, Chen, Mengyao, Cheng, Sammy, Childers, Christopher, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dugan, Shannon, Elpidina, Elena N., Farrow, David W., Friedrich, Markus, Gibbs, Richard A., Hall, Brantley, Han, Yi, Hardy, Richard W., Holmes, Christopher J., Hughes, Daniel S. T., Ioannidis, Panagiotis, Jarvela, Alys M. Cheatle, Johnston, J. Spencer, Jones, Jeffery W., Kronmiller, Brent A., Kung, Faith, Lee, Sandra L., Martynov, Alexander G., Masterson, Patrick, Maumus, Florian, Munoz-Torres, Monica, Murali, Shwetha C., Murphy, Terence D., Muzny, Donna M., Nelson, David R., Oppert, Brenda, Panfilio, Kristen A., Paula, Debora Pires, Pick, Leslie, Poelchau, Monica F., Qu, Jiaxin, Reding, Katie, Rhoades, Joshua H., Rhodes, Adelaide, Richards, Stephen, Richter, Rose, Robertson, Hugh M., Rosendale, Andrew J., Tu, Zhijian Jake, Velamuri, Arun S., Waterhouse, Robert M., Weirauch, Matthew T., Wells, Jackson T., Werren, John H., Worley, Kim C., Zdobnov, Evgeny M., and Gundersen-Rindal, Dawn E.

Abstract

Background Halyomorpha halys (Stal), 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

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

Author

Biochemistry, Sparks, Michael E., Bansal, Raman, Benoit, Joshua B., Blackburn, Michael B., Chao, Hsu, Chen, Mengyao, Cheng, Sammy, Childers, Christopher, Dinh, Huyen, Doddapaneni, Harsha V., Dugan, Shannon, Elpidina, Elena N., Farrow, David W., Friedrich, Markus, Gibbs, Richard A., Hall, Brantley, Han, Yi, Hardy, Richard W., Holmes, Christopher J., Hughes, Daniel S. T., Ioannidis, Panagiotis, Cheatle Jarvela, Alys M., Johnston, J. Spencer, Jones, Jeffery W., Kronmiller, Brent A., Kung, Faith, Lee, Sandra L., Martynov, Alexander G., Masterson, Patrick, Maumus, Florian, Munoz-Torres, Monica, Murali, Shwetha C., Murphy, Terence D., Muzny, Donna M., Nelson, David R., Oppert, Brenda, Panfilio, Kristen A., Paula, Débora P., Pick, Leslie, Poelchau, Monica F., Qu, Jiaxin, Reding, Katie, Rhoades, Joshua H., Rhodes, Adelaide, Richards, Stephen, Richter, Rose, Robertson, Hugh M., Rosendale, Andrew J., Tu, Zhijian Jake, Velamuri, Arun S., Waterhouse, Robert M., Weirauch, Matthew T., Wells, Jackson T., Werren, John H., Worley, Kim C., Zdobnov, Evgeny M., Gundersen-Rindal, Dawn E., Biochemistry, Sparks, Michael E., Bansal, Raman, Benoit, Joshua B., Blackburn, Michael B., Chao, Hsu, Chen, Mengyao, Cheng, Sammy, Childers, Christopher, Dinh, Huyen, Doddapaneni, Harsha V., Dugan, Shannon, Elpidina, Elena N., Farrow, David W., Friedrich, Markus, Gibbs, Richard A., Hall, Brantley, Han, Yi, Hardy, Richard W., Holmes, Christopher J., Hughes, Daniel S. T., Ioannidis, Panagiotis, Cheatle Jarvela, Alys M., Johnston, J. Spencer, Jones, Jeffery W., Kronmiller, Brent A., Kung, Faith, Lee, Sandra L., Martynov, Alexander G., Masterson, Patrick, Maumus, Florian, Munoz-Torres, Monica, Murali, Shwetha C., Murphy, Terence D., Muzny, Donna M., Nelson, David R., Oppert, Brenda, Panfilio, Kristen A., Paula, Débora P., Pick, Leslie, Poelchau, Monica F., Qu, Jiaxin, Reding, Katie, Rhoades, Joshua H., Rhodes, Adelaide, Richards, Stephen, Richter, Rose, Robertson, Hugh M., Rosendale, Andrew J., Tu, Zhijian Jake, Velamuri, Arun S., Waterhouse, Robert M., Weirauch, Matthew T., Wells, Jackson T., Werren, John H., Worley, Kim C., Zdobnov, Evgeny M., and Gundersen-Rindal, Dawn E.

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

48. Genome-enabled insights into the biology of thrips as crop pests

Author

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

Published
2020
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49. 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, ArmisÊn, David, Vreede, Barbara, Baa-Puyoulet, Patrice, ChloÊ Berger, Chun-Che Chang, Hsu Chao, Chen, Mei-Ju, Yen-Ta Chen, Childers, Christopher, Chipman, Ariel, Cridge, Andrew, CrumièRe, Antonin, Dearden, Peter, Didion, Elise, Dinh, Huyen, Harsha Doddapaneni, Dolan, Amanda, Dugan, Shannon, Extavour, Cassandra, GÊrard 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, SÊverine Viala, Worley, Kim, Zdobnov, Evgeny, Gibbs, Richard, and Richards, Stephen

Abstract

Supplementary notes, figures, and small tables. (PDF 6142 kb)

Published
2019
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50. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome

Author

Panfilio, Kristen A., Vargas Jentzsch, Iris M., Benoit, Joshua B., Erezyilmaz, Deniz, Suzuki, Yuichiro, Colella, Stefano, Robertson, Hugh M., Poelchau, Monica F., Waterhouse, Robert M., Ioannidis, Panagiotis, Weirauch, Matthew T., Hughes, Daniel S. T., Murali, Shwetha C., Werren, John H., Jacobs, Chris G. C., Duncan, Elizabeth J., Armisén, David, Vreede, Barbara M. I., Baa-Puyoulet, Patrice, Berger, Chloé S., Chang, Chun-che, Chao, Hsu, Chen, Mei-Ju M., Chen, Yen-Ta, Childers, Christopher P., Chipman, Ariel D., Cridge, Andrew G., Crumière, Antonin J. J., Dearden, Peter K., Didion, Elise M., Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dolan, Amanda, Dugan, Shannon, Extavour, Cassandra G., Febvay, Gérard, Friedrich, Markus, Ginzburg, Neta, Han, Yi, Heger, Peter, Holmes, Christopher J., Horn, Thorsten, Hsiao, Yi-min, Jennings, Emily C., Johnston, J. Spencer, Jones, Tamsin E., Jones, Jeffery W., Khila, Abderrahman, Koelzer, Stefan, Kovacova, Viera, Leask, Megan, Lee, Sandra L., Lee, Chien-Yueh, Lovegrove, Mackenzie R., Lu, Hsiao-ling, Lu, Yong, Moore, Patricia J., Munoz-Torres, Monica C., Muzny, Donna M., Palli, Subba R., Parisot, Nicolas, Pick, Leslie, Porter, Megan L., Qu, Jiaxin, Refki, Peter N., Richter, Rose, Rivera-Pomar, Rolando, Rosendale, Andrew J., Roth, Siegfried, Sachs, Lena, Santos, M. Emília, Seibert, Jan, Sghaier, Essia, Shukla, Jayendra N., Stancliffe, Richard J., Tidswell, Olivia, Traverso, Lucila, van der Zee, Maurijn, Viala, Séverine, Worley, Kim C., Zdobnov, Evgeny M., Gibbs, Richard A., Richards, Stephen, Panfilio, Kristen A., Vargas Jentzsch, Iris M., Benoit, Joshua B., Erezyilmaz, Deniz, Suzuki, Yuichiro, Colella, Stefano, Robertson, Hugh M., Poelchau, Monica F., Waterhouse, Robert M., Ioannidis, Panagiotis, Weirauch, Matthew T., Hughes, Daniel S. T., Murali, Shwetha C., Werren, John H., Jacobs, Chris G. C., Duncan, Elizabeth J., Armisén, David, Vreede, Barbara M. I., Baa-Puyoulet, Patrice, Berger, Chloé S., Chang, Chun-che, Chao, Hsu, Chen, Mei-Ju M., Chen, Yen-Ta, Childers, Christopher P., Chipman, Ariel D., Cridge, Andrew G., Crumière, Antonin J. J., Dearden, Peter K., Didion, Elise M., Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dolan, Amanda, Dugan, Shannon, Extavour, Cassandra G., Febvay, Gérard, Friedrich, Markus, Ginzburg, Neta, Han, Yi, Heger, Peter, Holmes, Christopher J., Horn, Thorsten, Hsiao, Yi-min, Jennings, Emily C., Johnston, J. Spencer, Jones, Tamsin E., Jones, Jeffery W., Khila, Abderrahman, Koelzer, Stefan, Kovacova, Viera, Leask, Megan, Lee, Sandra L., Lee, Chien-Yueh, Lovegrove, Mackenzie R., Lu, Hsiao-ling, Lu, Yong, Moore, Patricia J., Munoz-Torres, Monica C., Muzny, Donna M., Palli, Subba R., Parisot, Nicolas, Pick, Leslie, Porter, Megan L., Qu, Jiaxin, Refki, Peter N., Richter, Rose, Rivera-Pomar, Rolando, Rosendale, Andrew J., Roth, Siegfried, Sachs, Lena, Santos, M. Emília, Seibert, Jan, Sghaier, Essia, Shukla, Jayendra N., Stancliffe, Richard J., Tidswell, Olivia, Traverso, Lucila, van der Zee, Maurijn, Viala, Séverine, Worley, Kim C., Zdobnov, Evgeny M., Gibbs, Richard A., and Richards, Stephen

Published
2019

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