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2. Deep Learning for Reference-Free Geolocation for Poplar Trees

Author

John, Cai W., Queen, Owen, Muchero, Wellington, and Emrich, Scott J.

Subjects
Quantitative Biology - Genomics, Computer Science - Machine Learning
Abstract

A core task in precision agriculture is the identification of climatic and ecological conditions that are advantageous for a given crop. The most succinct approach is geolocation, which is concerned with locating the native region of a given sample based on its genetic makeup. Here, we investigate genomic geolocation of Populus trichocarpa, or poplar, which has been identified by the US Department of Energy as a fast-rotation biofuel crop to be harvested nationwide. In particular, we approach geolocation from a reference-free perspective, circumventing the need for compute-intensive processes such as variant calling and alignment. Our model, MashNet, predicts latitude and longitude for poplar trees from randomly-sampled, unaligned sequence fragments. We show that our model performs comparably to Locator, a state-of-the-art method based on aligned whole-genome sequence data. MashNet achieves an error of 34.0 km^2 compared to Locator's 22.1 km^2. MashNet allows growers to quickly and efficiently identify natural varieties that will be most productive in their growth environment based on genotype. This paper explores geolocation for precision agriculture while providing a framework and data source for further development by the machine learning community., Comment: Accepted at NeurIPS 2022 AI for Science Workshop

Published
2023

3. Dynamic network analysis improves protein 3D structural classification

Author

Newaz, Khalique, Piland, Jacob, Clark, Patricia L., Emrich, Scott J., Li, Jun, and Milenkovic, Tijana

Subjects
Quantitative Biology - Molecular Networks
Abstract

Protein structural classification (PSC) is a supervised problem of assigning proteins into pre-defined structural (e.g., CATH or SCOPe) classes based on the proteins' sequence or 3D structural features. We recently proposed PSC approaches that model protein 3D structures as protein structure networks (PSNs) and analyze PSN-based protein features, which performed better than or comparable to state-of-the-art sequence or other 3D structure-based approaches in the task of PSC. However, existing PSN-based PSC approaches model the whole 3D structure of a protein as a static PSN. Because folding of a protein is a dynamic process, where some parts of a protein fold before others, modeling the 3D structure of a protein as a dynamic PSN might further help improve the existing PSC performance. Here, we propose for the first time a way to model 3D structures of proteins as dynamic PSNs, with the hypothesis that this will improve upon the current state-of-the-art PSC approaches that are based on static PSNs (and thus upon the existing state-of-the-art sequence and other 3D structural approaches). Indeed, we confirm this on 71 datasets spanning ~44,000 protein domains from CATH and SCOPe

Published
2021

4. Publisher Correction: The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control

Author

Olafson, Pia U, Aksoy, Serap, Attardo, Geoffrey M, Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J, Davis, Megan, Dykema, Justin, Emrich, Scott J, Friedrich, Markus, Holmes, Christopher J, Ioannidis, Panagiotis, Jansen, Evan N, Jennings, Emily C, Lawson, Daniel, Martinson, Ellen O, Maslen, Gareth L, Meisel, Richard P, Murphy, Terence D, Nayduch, Dana, Nelson, David R, Oyen, Kennan J, Raszick, Tyler J, Ribeiro, José MC, Robertson, Hugh M, Rosendale, Andrew J, Sackton, Timothy B, Saelao, Perot, Swiger, Sonja L, Sze, Sing-Hoi, Tarone, Aaron M, Taylor, David B, Warren, Wesley C, Waterhouse, Robert M, Weirauch, Matthew T, Werren, John H, Wilson, Richard K, Zdobnov, Evgeny M, and Benoit, Joshua B

Subjects
Microbiology, Biological Sciences, Developmental Biology, Biological sciences
Abstract

Following publication of the original article [1], it was reported that the article copyright was incorrect. The correct copyright statement is: © This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2021. The original article [1] has been corrected.

Published
2021

5. The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control.

Author

Olafson, Pia U, Aksoy, Serap, Attardo, Geoffrey M, Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J, Davis, Megan, Dykema, Justin, Emrich, Scott J, Friedrich, Markus, Holmes, Christopher J, Ioannidis, Panagiotis, Jansen, Evan N, Jennings, Emily C, Lawson, Daniel, Martinson, Ellen O, Maslen, Gareth L, Meisel, Richard P, Murphy, Terence D, Nayduch, Dana, Nelson, David R, Oyen, Kennan J, Raszick, Tyler J, Ribeiro, José MC, Robertson, Hugh M, Rosendale, Andrew J, Sackton, Timothy B, Saelao, Perot, Swiger, Sonja L, Sze, Sing-Hoi, Tarone, Aaron M, Taylor, David B, Warren, Wesley C, Waterhouse, Robert M, Weirauch, Matthew T, Werren, John H, Wilson, Richard K, Zdobnov, Evgeny M, and Benoit, Joshua B

Subjects
Chemoreceptor genes, Gene regulation, Insect adaptation, Insect immunity, Insect orthology, Metabolic detoxification genes, Muscid genomics, Opsin gene duplication, Stable fly genome, Biological Sciences, Developmental Biology
Abstract

BackgroundThe stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies.ResultsThis study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were manually curated to characterize genetic features related to stable fly reproduction, vector host interactions, host-microbe dynamics, and putative targets for control. Most notable was characterization of genes associated with reproduction and identification of expanded gene families with functional associations to vision, chemosensation, immunity, and metabolic detoxification pathways.ConclusionsThe combined sequencing, assembly, and curation of the male stable fly genome followed by RNA-Seq and downstream analyses provide insights necessary to understand the biology of this important pest. These resources and new data will provide the groundwork for expanding the tools available to control stable fly infestations. The close relationship of Stomoxys to other blood-feeding (horn flies and Glossina) and non-blood-feeding flies (house flies, medflies, Drosophila) will facilitate understanding of the evolutionary processes associated with development of blood feeding among the Cyclorrhapha.

Published
2021

6. Network approach integrates 3D structural and sequence data to improve protein structural comparison

Author

Faisal, Fazle E., Chaney, Julie L., Newaz, Khalique, Li, Jun, Emrich, Scott J., Clark, Patricia L., and Milenkovic, Tijana

Subjects
Quantitative Biology - Molecular Networks
Abstract

Initial protein structural comparisons were sequence-based. Since amino acids that are distant in the sequence can be close in the 3-dimensional (3D) structure, 3D contact approaches can complement sequence approaches. Traditional 3D contact approaches study 3D structures directly. Instead, 3D structures can be modeled as protein structure networks (PSNs). Then, network approaches can compare proteins by comparing their PSNs. Network approaches may improve upon traditional 3D contact approaches. We cannot use existing PSN approaches to test this, because: 1) They rely on naive measures of network topology. 2) They are not robust to PSN size. They cannot integrate 3) multiple PSN measures or 4) PSN data with sequence data, although this could help because the different data types capture complementary biological knowledge. We address these limitations by: 1) exploiting well-established graphlet measures via a new network approach, 2) introducing normalized graphlet measures to remove the bias of PSN size, 3) allowing for integrating multiple PSN measures, and 4) using ordered graphlets to combine the complementary PSN data and sequence data. We compare both synthetic networks and real-world PSNs more accurately and faster than existing network, 3D contact, or sequence approaches. Our approach finds PSN patterns that may be biochemically interesting.

Published
2016

7. Hot RAD: A Tool for Analysis of Next-Gen RAD Tag Data

Author

Assour, Lauren A., LaRosa, Nicholas, and Emrich, Scott J.

Subjects
Quantitative Biology - Genomics, Quantitative Biology - Quantitative Methods
Abstract

Restriction site Associated DNA (RAD) tagging (also known as RAD-seq, etc.) is an emerging method for analyzing an organism's genome without completely sequencing it. This can be applied to a non-model organism without a reference genome, though this creates the problem of how to begin data analysis on unmapped and unannotated reads. Our program, Hot RAD, presents a straightforward and easy-to-use method to take raw Illumina data that has been RAD tagged and produce consensus contigs or sequence stacks using a distributed framework, creating a basis on which to begin analyzing an organism's DNA. The GUI (graphical user interface) element of our tool makes it easy for those not familiar with the command line to take raw sequence files and produce usable data in a timely manner.

Published
2015

8. Synonymous codon substitutions modulate transcription and translation of a divergent upstream gene by modulating antisense RNA production.

Author

Rodriguez, Anabel, Diehl, Jacob D., Wright, Gabriel S., Bonar, Christopher D., Lundgren, Taylor J., Moss, McKenze J., Jun Li, Milenkovic, Tijana, Huber, Paul W., Champion, Matthew M., Emrich, Scott J., and Clark, Patricia L.

Subjects
GENE expression, ANTISENSE RNA, GENETIC transcription, NUCLEOTIDE sequence, AMINO acid sequence
Abstract

Synonymous codons were originally viewed as interchangeable, with no phenotypic consequences. However, substantial evidence has now demonstrated that synonymous substitutions can perturb a variety of gene expression and protein homeostasis mechanisms, including translational efficiency, translational fidelity, and cotranslational folding of the encoded protein. To date, most studies of synonymous codon-derived perturbations have focused on effects within a single gene. Here, we show that synonymous codon substitutions made far within the coding sequence of Escherichia coli plasmid-encoded chloramphenicol acetyltransferase (cat) can significantly increase expression of the divergent upstream tetracycline resistance gene, tetR. In four out of nine synonymously recoded cat sequences tested, expression of the upstream tetR gene was significantly elevated due to transcription of a long antisense RNA (asRNA) originating from a transcription start site within cat. Surprisingly, transcription of this asRNA readily bypassed the native tet transcriptional repression mechanism. Even more surprisingly, accumulation of the TetR protein correlated with the level of asRNA, rather than total tetR RNA. These effects of synonymous codon substitutions on transcription and translation of a neighboring gene suggest that synonymous codon usage in bacteria may be under selection to both preserve the amino acid sequence of the encoded gene and avoid DNA sequence elements that can significantly perturb expression of neighboring genes. Avoiding such sequences may be especially important in plasmids and prokaryotic genomes, where genes and regulatory elements are often densely packed. Similar considerations may apply to the design of genetic circuits for synthetic biology applications. [ABSTRACT FROM AUTHOR]

Published
2024
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9. Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes

Author

Hall, Andrew Brantley, Papathanos, Philippos-Aris, Sharma, Atashi, Cheng, Changde, Akbari, Omar S, Assour, Lauren, Bergman, Nicholas H, Cagnetti, Alessia, Crisanti, Andrea, Dottorini, Tania, Fiorentini, Elisa, Galizi, Roberto, Hnath, Jonathan, Jiang, Xiaofang, Koren, Sergey, Nolan, Tony, Radune, Diane, Sharakhova, Maria V, Steele, Aaron, Timoshevskiy, Vladimir A, Windbichler, Nikolai, Zhang, Simo, Hahn, Matthew W, Phillippy, Adam M, Emrich, Scott J, Sharakhov, Igor V, Tu, Zhijian Jake, and Besansky, Nora J

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Clinical Sciences, Medical Microbiology, Human Genome, Infectious Diseases, Vector-Borne Diseases, Rare Diseases, Biotechnology, Malaria, 2.2 Factors relating to the physical environment, 1.1 Normal biological development and functioning, Aetiology, Underpinning research, Infection, Good Health and Well Being, Animals, Anopheles, Chromosomes, Insect, Female, Insect Vectors, Male, Phylogeny, Sequence Analysis, DNA, X Chromosome, Y Chromosome, Anopheles gambiae, PacBio, RNA-Seq, tandem repetitive DNA, Y-chromosome
Abstract

Y chromosomes control essential male functions in many species, including sex determination and fertility. However, because of obstacles posed by repeat-rich heterochromatin, knowledge of Y chromosome sequences is limited to a handful of model organisms, constraining our understanding of Y biology across the tree of life. Here, we leverage long single-molecule sequencing to determine the content and structure of the nonrecombining Y chromosome of the primary African malaria mosquito, Anopheles gambiae We find that the An. gambiae Y consists almost entirely of a few massively amplified, tandemly arrayed repeats, some of which can recombine with similar repeats on the X chromosome. Sex-specific genome resequencing in a recent species radiation, the An. gambiae complex, revealed rapid sequence turnover within An. gambiae and among species. Exploiting 52 sex-specific An. gambiae RNA-Seq datasets representing all developmental stages, we identified a small repertoire of Y-linked genes that lack X gametologs and are not Y-linked in any other species except An. gambiae, with the notable exception of YG2, a candidate male-determining gene. YG2 is the only gene conserved and exclusive to the Y in all species examined, yet sequence similarity to YG2 is not detectable in the genome of a more distant mosquito relative, suggesting rapid evolution of Y chromosome genes in this highly dynamic genus of malaria vectors. The extensive characterization of the An. gambiae Y provides a long-awaited foundation for studying male mosquito biology, and will inform novel mosquito control strategies based on the manipulation of Y chromosomes.

Published
2016

11. Whole genome comparisons reveal panmixia among fall armyworm (Spodoptera frugiperda) from diverse locations

Author

Schlum, Katrina A., Lamour, Kurt, de Bortoli, Caroline Placidi, Banerjee, Rahul, Meagher, Robert, Pereira, Eliseu, Murua, Maria Gabriela, Sword, Gregory A., Tessnow, Ashley E., Viteri Dillon, Diego, Linares Ramirez, Angela M., Akutse, Komivi S., Schmidt-Jeffris, Rebecca, Huang, Fangneng, Reisig, Dominic, Emrich, Scott J., and Jurat-Fuentes, Juan Luis

Published
2021
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12. The power and promise of genetic mapping from Plasmodium falciparum crosses utilizing human liver-chimeric mice

Author

Button-Simons, Katrina A., Kumar, Sudhir, Carmago, Nelly, Haile, Meseret T., Jett, Catherine, Checkley, Lisa A., Kennedy, Spencer Y., Pinapati, Richard S., Shoue, Douglas A., McDew-White, Marina, Li, Xue, Nosten, François H., Kappe, Stefan H., Anderson, Timothy J. C., Romero-Severson, Jeanne, Ferdig, Michael T., Emrich, Scott J., Vaughan, Ashley M., and Cheeseman, Ian H.

Published
2021
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15. VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics.

Author

Megy, Karine, Emrich, Scott J, Lawson, Daniel, Campbell, David, Dialynas, Emmanuel, Hughes, Daniel ST, Koscielny, Gautier, Louis, Christos, Maccallum, Robert M, Redmond, Seth N, Sheehan, Andrew, Topalis, Pantelis, Wilson, Derek, and VectorBase Consortium

Subjects
VectorBase Consortium, Animals, Ixodes, Culicidae, Tsetse Flies, Rhodnius, Pediculus, Genomics, Insect Vectors, Insecticide Resistance, Databases, Genetic, Genome, Insect, Genetic Variation, Databases, Genetic, Genome, Insect, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Developmental Biology
Abstract

VectorBase (http://www.vectorbase.org) is a NIAID-supported bioinformatics resource for invertebrate vectors of human pathogens. It hosts data for nine genomes: mosquitoes (three Anopheles gambiae genomes, Aedes aegypti and Culex quinquefasciatus), tick (Ixodes scapularis), body louse (Pediculus humanus), kissing bug (Rhodnius prolixus) and tsetse fly (Glossina morsitans). Hosted data range from genomic features and expression data to population genetics and ontologies. We describe improvements and integration of new data that expand our taxonomic coverage. Releases are bi-monthly and include the delivery of preliminary data for emerging genomes. Frequent updates of the genome browser provide VectorBase users with increasing options for visualizing their own high-throughput data. One major development is a new population biology resource for storing genomic variations, insecticide resistance data and their associated metadata. It takes advantage of improved ontologies and controlled vocabularies. Combined, these new features ensure timely release of multiple types of data in the public domain while helping overcome the bottlenecks of bioinformatics and annotation by engaging with our user community.

Published
2012

18. Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

Author

Waterhouse, Robert M., Aganezov, Sergey, Anselmetti, Yoann, Lee, Jiyoung, Ruzzante, Livio, Reijnders, Maarten J. M. F., Feron, Romain, Bérard, Sèverine, George, Phillip, Hahn, Matthew W., Howell, Paul I., Kamali, Maryam, Koren, Sergey, Lawson, Daniel, Maslen, Gareth, Peery, Ashley, Phillippy, Adam M., Sharakhova, Maria V., Tannier, Eric, Unger, Maria F., Zhang, Simo V., Alekseyev, Max A., Besansky, Nora J., Chauve, Cedric, Emrich, Scott J., and Sharakhov, Igor V.

Published
2020
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19. MIReAD, a minimum information standard for reporting arthropod abundance data

Author

Rund, Samuel S. C., Braak, Kyle, Cator, Lauren, Copas, Kyle, Emrich, Scott J., Giraldo-Calderón, Gloria I., Johansson, Michael A., Heydari, Naveed, Hobern, Donald, Kelly, Sarah A., Lawson, Daniel, Lord, Cynthia, MacCallum, Robert M., Roche, Dominique G., Ryan, Sadie J., Schigel, Dmitry, Vandegrift, Kurt, Watts, Matthew, Zaspel, Jennifer M., and Pawar, Samraat

Published
2019
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20. Genomic analysis of two phlebotomine sand fly vectors of Leishmania from the New and Old World

Author

Labbe, Frédéric, Abdeladhim, Maha, Abrudan, Jenica, Araki, Alejandra Saori, Araujo, Ricardo N., Arensburger, Peter, Benoit, Joshua B., Brazil, Reginaldo Pecanha, Bruno, Rafaela V., Bueno da Silva Rivas, Gustavo, Carvalho de Abreu, Vinicius, Charamis, Jason, Coutinho-Abreu, Iliano V., da Costa-Latgé, Samara G., Darby, Alistair, Dillon, Viv M., Emrich, Scott J., Fernandez-Medina, Daniela, Figueiredo Gontijo, Nelder, Flanley, Catherine M., Gatherer, Derek, Genta, Fernando A., Gesing, Sandra, Giraldo-Calderón, Gloria I., Gomes, Bruno, Aguiar, Eric Roberto Guimaraes Rocha, Hamilton, James G. C., Hamarsheh, Omar, Hawksworth, Mallory, et al., Labbe, Frédéric, Abdeladhim, Maha, Abrudan, Jenica, Araki, Alejandra Saori, Araujo, Ricardo N., Arensburger, Peter, Benoit, Joshua B., Brazil, Reginaldo Pecanha, Bruno, Rafaela V., Bueno da Silva Rivas, Gustavo, Carvalho de Abreu, Vinicius, Charamis, Jason, Coutinho-Abreu, Iliano V., da Costa-Latgé, Samara G., Darby, Alistair, Dillon, Viv M., Emrich, Scott J., Fernandez-Medina, Daniela, Figueiredo Gontijo, Nelder, Flanley, Catherine M., Gatherer, Derek, Genta, Fernando A., Gesing, Sandra, Giraldo-Calderón, Gloria I., Gomes, Bruno, Aguiar, Eric Roberto Guimaraes Rocha, Hamilton, James G. C., Hamarsheh, Omar, Hawksworth, Mallory, and et al.

Abstract

Phlebotomine sand flies are of global significance as important vectors of human disease, transmitting bacterial, viral, and protozoan pathogens, including the kinetoplastid parasites of the genus Leishmania, the causative agents of devastating diseases collectively termed leishmaniasis. More than 40 pathogenic Leishmania species are transmitted to humans by approximately 35 sand fly species in 98 countries with hundreds of millions of people at risk around the world. No approved efficacious vaccine exists for leishmaniasis and available therapeutic drugs are either toxic and/or expensive, or the parasites are becoming resistant to the more recently developed drugs. Therefore, sand fly and/or reservoir control are currently the most effective strategies to break transmission. To better understand the biology of sand flies, including the mechanisms involved in their vectorial capacity, insecticide resistance, and population structures we sequenced the genomes of two geographically widespread and important sand fly vector species: Phlebotomus papatasi, a vector of Leishmania parasites that cause cutaneous leishmaniasis, (distributed in Europe, the Middle East and North Africa) and Lutzomyia longipalpis, a vector of Leishmania parasites that cause visceral leishmaniasis (distributed across Central and South America). We categorized and curated genes involved in processes important to their roles as disease vectors, including chemosensation, blood feeding, circadian rhythm, immunity, and detoxification, as well as mobile genetic elements. We also defined gene orthology and observed micro-synteny among the genomes. Finally, we present the genetic diversity and population structure of these species in their respective geographical areas. These genomes will be a foundation on which to base future efforts to prevent vector-borne transmission of Leishmania parasites.

Published
2023

21. Genomic analysis of two phlebotomine sand fly vectors of Leishmania from the New and Old World

Author

Labbé, Frédéric, primary, Abdeladhim, Maha, additional, Abrudan, Jenica, additional, Araki, Alejandra Saori, additional, Araujo, Ricardo N., additional, Arensburger, Peter, additional, Benoit, Joshua B., additional, Brazil, Reginaldo Pecanha, additional, Bruno, Rafaela V., additional, Bueno da Silva Rivas, Gustavo, additional, Carvalho de Abreu, Vinicius, additional, Charamis, Jason, additional, Coutinho-Abreu, Iliano V., additional, da Costa-Latgé, Samara G., additional, Darby, Alistair, additional, Dillon, Viv M., additional, Emrich, Scott J., additional, Fernandez-Medina, Daniela, additional, Figueiredo Gontijo, Nelder, additional, Flanley, Catherine M., additional, Gatherer, Derek, additional, Genta, Fernando A., additional, Gesing, Sandra, additional, Giraldo-Calderón, Gloria I., additional, Gomes, Bruno, additional, Aguiar, Eric Roberto Guimaraes Rocha, additional, Hamilton, James G. C., additional, Hamarsheh, Omar, additional, Hawksworth, Mallory, additional, Hendershot, Jacob M., additional, Hickner, Paul V., additional, Imler, Jean-Luc, additional, Ioannidis, Panagiotis, additional, Jennings, Emily C., additional, Kamhawi, Shaden, additional, Karageorgiou, Charikleia, additional, Kennedy, Ryan C., additional, Krueger, Andreas, additional, Latorre-Estivalis, José M., additional, Ligoxygakis, Petros, additional, Meireles-Filho, Antonio Carlos A., additional, Minx, Patrick, additional, Miranda, Jose Carlos, additional, Montague, Michael J., additional, Nowling, Ronald J., additional, Oliveira, Fabiano, additional, Ortigão-Farias, João, additional, Pavan, Marcio G., additional, Horacio Pereira, Marcos, additional, Nobrega Pitaluga, Andre, additional, Proveti Olmo, Roenick, additional, Ramalho-Ortigao, Marcelo, additional, Ribeiro, José M. C., additional, Rosendale, Andrew J., additional, Sant’Anna, Mauricio R. V., additional, Scherer, Steven E., additional, Secundino, Nágila F. C., additional, Shoue, Douglas A., additional, da Silva Moraes, Caroline, additional, Gesto, João Silveira Moledo, additional, Souza, Nataly Araujo, additional, Syed, Zainulabueddin, additional, Tadros, Samuel, additional, Teles-de-Freitas, Rayane, additional, Telleria, Erich L., additional, Tomlinson, Chad, additional, Traub-Csekö, Yara M., additional, Marques, João Trindade, additional, Tu, Zhijian, additional, Unger, Maria F., additional, Valenzuela, Jesus, additional, Ferreira, Flávia V., additional, de Oliveira, Karla P. V., additional, Vigoder, Felipe M., additional, Vontas, John, additional, Wang, Lihui, additional, Weedall, Gareth D., additional, Zhioua, Elyes, additional, Richards, Stephen, additional, Warren, Wesley C., additional, Waterhouse, Robert M., additional, Dillon, Rod J., additional, and McDowell, Mary Ann, additional

Published
2023
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23. Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection

Author

Mesquita, Rafael D., Vionette-Amaral, Raquel J., Lowenberger, Carl, Rivera-Pomar, Rolando, Monteiro, Fernando A., Minx, Patrick, Spieth, John, Carvalho, A. Bernardo, Panzera, Francisco, Lawson, Daniel, Torres, André Q., Ribeiro, Jose M. C., Sorgine, Marcos H. F., Waterhouse, Robert M., Montague, Michael J., Abad-Franch, Fernando, Alves-Bezerra, Michele, Amaral, Laurence R., Araujo, Helena M., Araujo, Ricardo N., Aravind, L., Atella, Georgia C., Azambuja, Patricia, Berni, Mateus, Bittencourt-Cunha, Paula R., Braz, Gloria R. C., Calderón-Fernández, Gustavo, Carareto, Claudia M. A., Christensen, Mikkel B., Costa, Igor R., Costa, Samara G., Dansa, Marilvia, Daumas-Filho, Carlos R. O., De-Paula, Iron F., Dias, Felipe A., Dimopoulos, George, Emrich, Scott J., Esponda-Behrens, Natalia, Fampa, Patricia, Fernandez-Medina, Rita D., da Fonseca, Rodrigo N., Fontenele, Marcio, Fronick, Catrina, Fulton, Lucinda A., Gandara, Ana Caroline, Garcia, Eloi S., Genta, Fernando A., Giraldo-Calderón, Gloria I., Gomes, Bruno, Gondim, Katia C., Granzotto, Adriana, Guarneri, Alessandra A., Guigó, Roderic, Harry, Myriam, Hughes, Daniel S. T., Jablonka, Willy, Jacquin-Joly, Emmanuelle, Juárez, M. Patricia, Koerich, Leonardo B., Lange, Angela B., Latorre-Estivalis, José Manuel, Lavore, Andrés, Lawrence, Gena G., Lazoski, Cristiano, Lazzari, Claudio R., Lopes, Raphael R., Lorenzo, Marcelo G., Lugon, Magda D., Majerowicz, David, Marcet, Paula L., Mariotti, Marco, Masuda, Hatisaburo, Megy, Karine, Melo, Ana C. A., Missirlis, Fanis, Mota, Theo, Noriega, Fernando G., Nouzova, Marcela, Nunes, Rodrigo D., Oliveira, Raquel L. L., Oliveira-Silveira, Gilbert, Ons, Sheila, Orchard, Ian, Pagola, Lucia, Paiva-Silva, Gabriela O., Pascual, Agustina, Pavan, Marcio G., Pedrini, Nicolás, Peixoto, Alexandre A., Pereira, Marcos H., Pike, Andrew, Polycarpo, Carla, Prosdocimi, Francisco, Ribeiro-Rodrigues, Rodrigo, Robertson, Hugh M., Salerno, Ana Paula, Salmon, Didier, Santesmasses, Didac, Schama, Renata, Seabra-Junior, Eloy S., Silva-Cardoso, Livia, Silva-Neto, Mario A. C., Souza-Gomes, Matheus, Sterkel, Marcos, Taracena, Mabel L., Tojo, Marta, Tu, Zhijian Jake, Tubio, Jose M. C., Ursic-Bedoya, Raul, Venancio, Thiago M., Walter-Nuno, Ana Beatriz, Wilson, Derek, Warren, Wesley C., Wilson, Richard K., Huebner, Erwin, Dotson, Ellen M., and Oliveira, Pedro L.

Published
2015

26. Extensive introgression in a malaria vector species complex revealed by phylogenomics

Author

Fontaine, Michael C., Pease, James B., Steele, Aaron, Waterhouse, Robert M., Neafsey, Daniel E., Sharakhov, Igor V., Jiang, Xiaofang, Hall, Andrew B., Catteruccia, Flaminia, Kakani, Evdoxia, Mitchell, Sara N., Wu, Yi-Chieh, Smith, Hilary A., Love, R. Rebecca, Lawniczak, Mara K., Slotman, Michel A., Emrich, Scott J., Hahn, Matthew W., and Besansky, Nora J.

Published
2015

27. Alignment and Analysis of Closely Related Genomes

Author

Regier, Allison, Olson, Michael, Emrich, Scott J., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, and Rajasekaran, Sanguthevar, editor

Published
2009
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31. Screening for resistance alleles to Cry1 proteins through targeted sequencing in the native and invasive range of Spodoptera frugiperda (Lepidoptera: Noctuidae).

Author

Tandy, Peter, Lamour, Kurt, Bortoli, Caroline Placidi de, Nagoshi, Rodney, Emrich, Scott J, and Jurat-Fuentes, Juan Luis

Subjects
FALL armyworm, NOCTUIDAE, ALLELES, LEPIDOPTERA, TRANSGENIC plants
Abstract

The fall armyworm, Spodoptera frugiperda (J. E. Smith), is a highly polyphagous pest native to the tropical Americas that has recently spread to become a global super-pest threatening food and fiber production. Transgenic crops producing insecticidal Cry and Vip3Aa proteins from Bacillus thuringiensis (Bt) are used for control of this pest in its native range. The evolution of practical resistance represents the greatest threat to sustainability of this technology and its potential efficacy in the S. frugiperda invasive range. Monitoring for resistance is vital to management approaches delaying S. frugiperda resistance to Bt crops. DNA-based resistance screening provides higher sensitivity and cost-effectiveness than currently used bioassay-based monitoring. So far, practical S. frugiperda resistance to Bt corn-producing Cry1F has been genetically linked to mutations in the SfABCC2 gene, providing a model to develop and test monitoring tools. In this study, we performed targeted SfABCC2 sequencing followed by Sanger sequencing to confirm the detection of known and candidate resistance alleles to Cry1F corn in field-collected S. frugiperda from continental USA, Puerto Rico, Africa (Ghana, Togo, and South Africa), and Southeast Asia (Myanmar). Results confirm that the distribution of a previously characterized resistance allele (SfABCC2mut) is limited to Puerto Rico and identify 2 new candidate SfABCC2 alleles for resistance to Cry1F, one of them potentially spreading along the S. frugiperda migratory route in North America. No candidate resistance alleles were found in samples from the invasive S. frugiperda range. These results provide support for the potential use of targeted sequencing in Bt resistance monitoring programs. [ABSTRACT FROM AUTHOR]

Published
2023
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35. The B73 Maize Genome: Complexity, Diversity, and Dynamics

Author

Schnable, Patrick S., Ware, Doreen, Fulton, Robert S., Stein, Joshua C., Wei, Fusheng, Pasternak, Shiran, Liang, Chengzhi, Zhang, Jianwei, Fulton, Lucinda, Graves, Tina A., Minx, Patrick, Reily, Amy Denise, Courtney, Laura, Kruchowski, Scott S., Tomlinson, Chad, Strong, Cindy, Delehaunty, Kim, Fronick, Catrina, Courtney, Bill, Rock, Susan M., Belter, Eddie, Du, Feiyu, Kim, Kyung, Abbott, Rachel M., Cotton, Marc, Levy, Andy, Marchetto, Pamela, Ochoa, Kerri, Jackson, Stephanie M., Gillam, Barbara, Chen, Weizu, Yan, Le, Higginbotham, Jamey, Cardenas, Marco, Waligorski, Jason, Applebaum, Elizabeth, Phelps, Lindsey, Falcone, Jason, Kanchi, Krishna, Thane, Thynn, Scimone, Adam, Thane, Nay, Henke, Jessica, Wang, Tom, Ruppert, Jessica, Shah, Neha, Rotter, Kelsi, Hodges, Jennifer, Ingenthron, Elizabeth, Cordes, Matt, Kohlberg, Sara, Sgro, Jennifer, Delgado, Brandon, Mead, Kelly, Chinwalla, Asif, Leonard, Shawn, Crouse, Kevin, Collura, Kristi, Kudrna, Dave, Currie, Jennifer, He, Ruifeng, Angelova, Angelina, Rajasekar, Shanmugam, Mueller, Teri, Lomeli, Rene, Scara, Gabriel, Ko, Ara, Delaney, Krista, Wissotski, Marina, Lopez, Georgina, Campos, David, Braidotti, Michele, Ashley, Elizabeth, Golser, Wolfgang, Kim, HyeRan, Lee, Seunghee, Lin, Jinke, Dujmic, Zeljko, Kim, Woojin, Talag, Jayson, Zuccolo, Andrea, Fan, Chuanzhu, Sebastian, Aswathy, Kramer, Melissa, Spiegel, Lori, Nascimento, Lidia, Zutavern, Theresa, Miller, Beth, Ambroise, Claude, Muller, Stephanie, Spooner, Will, Narechania, Apurva, Ren, Liya, Wei, Sharon, Kumari, Sunita, Faga, Ben, Levy, Michael J., McMahan, Linda, Van Buren, Peter, Vaughn, Matthew W., Ying, Kai, Yeh, Cheng-Ting, Emrich, Scott J., Jia, Yi, Kalyanaraman, Ananth, Hsia, An-Ping, Barbazuk, W. Brad, Baucom, Regina S., Brutnell, Thomas P., Carpita, Nicholas C., Chaparro, Cristian, Chia, Jer-Ming, Deragon, Jean-Marc, Estill, James C., Fu, Yan, Jeddeloh, Jeffrey A., Han, Yujun, Lee, Hyeran, Li, Pinghua, Lisch, Damon R., Liu, Sanzhen, Liu, Zhijie, Nagel, Dawn Holligan, McCann, Maureen C., SanMiguel, Phillip, Myers, Alan M., Nettleton, Dan, Nguyen, John, Penning, Bryan W., Ponnala, Lalit, Schneider, Kevin L., Schwartz, David C., Sharma, Anupma, Soderlund, Carol, Springer, Nathan M., Sun, Qi, Wang, Hao, Waterman, Michael, Westerman, Richard, Wolfgruber, Thomas K., Yang, Lixing, Yu, Yeisoo, Zhang, Lifang, Zhou, Shiguo, Zhu, Qihui, Bennetzen, Jeffrey L., Dawe, R. Kelly, Jiang, Jiming, Jiang, Ning, Presting, Gernot G., Wessler, Susan R., Aluru, Srinivas, Martienssen, Robert A., Clifton, Sandra W., McCombie, W. Richard, Wing, Rod A., and Wilson, Richard K.

Published
2009
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40. MOSQUITO GENOMICS: Extensive introgression in a malaria vector species complex revealed by phylogenomics

Author

Fontaine, Michael C., Pease, James B., Steele, Aaron, Waterhouse, Robert M., Neafsey, Daniel E., Sharakhov, Igor V., Jiang, Xiaofang, Hall, Andrew B., Catteruccia, Flaminia, Kakani, Evdoxia, Mitchell, Sara N., Wu, Yi-Chieh, Smith, Hilary A., Love, Rebecca R., Lawniczak, Mara K., Slotman, Michel A., Emrich, Scott J., Hahn, Matthew W., and Besansky, Nora J.

Published
2015
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41. High-throughput genetic mapping of mutants via quantitative Single nucleotide polymorphism typing

Author

Liu, Sanzhen, Chen, Hsin D., Makarevitch, Irina, Shirmer, Rebecca, Emrich, Scott J., Dietrich, Charles R., Barbazuk, W. Brad, Springer, Nathan M., and Schnable, Patrick S.

Subjects
DNA sequencing -- Research, Nucleotide sequencing -- Research, Gene mutations -- Research, Genetic polymorphisms -- Research, Population genetics -- Research, Biological sciences
Published
2010

43. Additional file 1 of Whole genome comparisons reveal panmixia among fall armyworm (Spodoptera frugiperda) from diverse locations

Author

Schlum, Katrina A., Lamour, Kurt, Bortoli, Caroline Placidi De, Banerjee, Rahul, Meagher, Robert, Pereira, Eliseu, Murua, Maria Gabriela, Sword, Gregory A., Tessnow, Ashley E., Dillon, Diego Viteri, Ramirez, Angela M. Linares, Komivi S. Akutse, Schmidt-Jeffris, Rebecca, Fangneng Huang, Reisig, Dominic, Emrich, Scott J., and Jurat-Fuentes, Juan Luis

Abstract

Additional file 1: Supplementary Table 1. Describing details of samples analyzed, and Table 2 showing Mash distances based on country. Supplementary Figure S1. Showing clustering based on Mash distances, Figure S2 showing amplification of Wolbachia in selected samples, Figure S3 showing the amplified sequences in Fig. S2, and Figure S4 showing the geographic locations sampled.

Published
2021
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44. Additional file 6 of High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum

Author

Upeka Samarakoon, Regier, Allison, Tan, Asako, Desany, Brian A, Collins, Brendan, Tan, John C, Emrich, Scott J, and Ferdig, Michael T

Abstract

Additional file 6:Distance between consecutive de novo SNPs. The distance between consecutive de novo SNPs were calculated to detect SNP clustering characteristic of sequencing errors or mis-mapping errors. 35% of the de novo SNPs were clustered in distances of less than 5 bps. (DOC 42 KB)

Published
2021
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45. Additional file 3 of High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum

Author

Upeka Samarakoon, Regier, Allison, Tan, Asako, Desany, Brian A, Collins, Brendan, Tan, John C, Emrich, Scott J, and Ferdig, Michael T

Abstract

Additional file 3:Refined views of previously unknown COs shown in Figure3. Previously unknown COs detected in the progeny lines (highlighted with black bars in Figure 3) are indicated by double arrows in the chromosomal view (top) and zoomed-in view (boxed, bottom). (A-D) previously unknown COs in 7C126, (E-H) previously unknown COs in SC05. SNP map by 454 sequencing is presented in comparison with the MS marker linkage map in P. falciparum[4]. Each line represents a single SNP marker. HB3 alleles are shown in green bars and Dd2 alleles are shown in red. (PDF 183 KB)

Published
2021
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46. Additional file 8 of High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum

Author

Upeka Samarakoon, Regier, Allison, Tan, Asako, Desany, Brian A, Collins, Brendan, Tan, John C, Emrich, Scott J, and Ferdig, Michael T

Subjects
mental disorders
Abstract

Additional file 8:Alternate SNP positions. The alternate SNP positions were assessed for their primary and secondary positions base call identity. Most primary base calls reflected the parental base call. The secondary base call position varied in the 2 progeny genomes in base call identity. Majority of the secondary base calls were parental in 7C126, whereas majority of the secondary base calls were non-parental in SC05 (A). Majority of the primary base calls were transitions in 7C126, while they were transversions in SC05 (B, C). (DOC 45 KB)

Published
2021
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47. Additional file 7 of High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum

Author

Upeka Samarakoon, Regier, Allison, Tan, Asako, Desany, Brian A, Collins, Brendan, Tan, John C, Emrich, Scott J, and Ferdig, Michael T

Abstract

Additional file 7:Base conversion trends in de novo SNPs. The type of base conversion was investigated for positions at which the parental base calls were identical. More transversions were detected for SC05 compared to 7C126 (A), but did not show a predominant base conversion bias from 7C126 (B). (DOC 36 KB)

Published
2021
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48. Additional file 4 of High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum

Author

Upeka Samarakoon, Regier, Allison, Tan, Asako, Desany, Brian A, Collins, Brendan, Tan, John C, Emrich, Scott J, and Ferdig, Michael T

Abstract

Additional file 4:Visual inspection of mapped WGS sequence at CO and NCO gene conversion breakpoints shown in Figure4. (A) simple CO breakpoint in 7C126, (B) NCO gene conversion in SC05 and (C) complex CO breakpoint accompanied by a conversion tract (defined by rapid allele changes at/near breakpoint) detected in 7C126. Chromosomal alignments at CO and NCO regions were visually inspected in comparison with the parental genomes, using Integrative Genomics Viewer [45]. (i) SNPs detected by 454 sequencing are ordered according to the chromosomal location (PlasmoDB v5.4 [27]). Each line represents a single SNP marker. HB3 alleles are shown in green bars and Dd2 alleles are shown in red. (ii) Comparison of SNPS and read alignments at selected SNP loci (arrow). SNPs are highlighted in blue [C], red [T], green [A] and brown [G]. (PDF 486 KB)

Published
2021
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