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1. High-quality, chromosome-scale genome assemblies: comparisons of three Diaphorina citri (Asian citrus psyllid) geographic populations

Author

Carlson, Curtis R, Horst, Anneliek M ter, Johnston, J Spencer, Henry, Elizabeth, Falk, Bryce W, and Kuo, Yen-Wen

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Animals, Chromosomes, Citrus, Hemiptera, Sequence Analysis, DNA, citrus greening disease, huanglongbing, California, Taiwan, Uruguay, Plant Biology & Botany
Abstract

The Asian citrus psyllid, Diaphorina citri, is the insect vector of the causal agent of huanglongbing (HLB), a devastating bacterial disease of commercial citrus. Presently, few genomic resources exist for D. citri. In this study, we utilized PacBio HiFi and chromatin confirmation contact (Hi-C) sequencing to sequence, assemble, and compare three high-quality, chromosome-scale genome assemblies of D. citri collected from California, Taiwan, and Uruguay. Our assemblies had final sizes of 282.67 Mb (California), 282.89 Mb (Taiwan), and 266.67 Mb (Uruguay) assembled into 13 pseudomolecules-a reduction in assembly size of 41-45% compared with previous assemblies which we validated using flow cytometry. We identified the X chromosome in D. citri and annotated each assembly for repetitive elements, protein-coding genes, transfer RNAs, ribosomal RNAs, piwi-interacting RNA clusters, and endogenous viral elements. Between 19,083 and 20,357 protein-coding genes were predicted. Repetitive DNA accounts for 36.87-38.26% of each assembly. Comparative analyses and mitochondrial haplotype networks suggest that Taiwan and Uruguay D. citri are more closely related, while California D. citri are closely related to Florida D. citri. These high-quality, chromosome-scale assemblies provide new genomic resources to researchers to further D. citri and HLB research.

Published
2022

3. Whole-genome assembly of Culex tarsalis

Author

Main, Bradley J, Marcantonio, Matteo, Johnston, J Spencer, Rasgon, Jason L, Brown, C Titus, and Barker, Christopher M

Subjects
Biological Sciences, Genetics, Human Genome, Infectious Diseases, 2.2 Factors relating to the physical environment, Infection, Animals, Bayes Theorem, Culex, Culicidae, Humans, Male, Mosquito Vectors, Phylogeny, Genome, mosquito, Vector, PacBio, Biochemistry and cell biology, Statistics
Abstract

The mosquito, Culex tarsalis, is a key vector in the western United States due to its role in transmission of zoonotic arboviruses that affect human health. Extensive research has been conducted on Cx. tarsalis ecology, feeding behavior, vector competence, autogeny, diapause, genetics, and insecticide resistance. Population genetic analyses in the western U.S. have identified at least three genetic clusters that are geographically distinct. However, in-depth genetic studies have been hindered by the lack of a reference genome. In this study, we present the first whole-genome assembly of this mosquito species (CtarK1) based on PacBio HiFi reads from high-molecular-weight DNA extracted from a single male. The CtarK1 assembly is 790 Mb with an N50 of 58 kb, which is 27% larger than Culex quinquefasciatus (578 Mb). This difference appears to be mostly composed of transposable elements. To annotate CtarK1, we used a previously assembled Cx. tarsalis transcriptome and approximately 17,456 protein genes from Cx. quinquefasciatus (N = 17,456). Genome completeness was assessed using the Benchmarking Universal Single-Copy Orthologs (BUSCO) tool, which identified 84.8% of the 2799 Dipteran BUSCO genes. Using a Bayesian phylogeny based on mitochondrial genomes, we place Cx. tarsalis in the context of other mosquito species and estimate the divergence between Cx. tarsalis and Cx. quinquefasciatus to be between 15.8 and 22.2 million years ago (MYA). Important next steps from this work include characterizing the genetic basis of diapause and sex determination in Culex mosquitoes.

Published
2021

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. Improved reference genome of the arboviral vector Aedes albopictus

Author

Palatini, Umberto, Masri, Reem A, Cosme, Luciano V, Koren, Sergey, Thibaud-Nissen, Françoise, Biedler, James K, Krsticevic, Flavia, Johnston, J Spencer, Halbach, Rebecca, Crawford, Jacob E, Antoshechkin, Igor, Failloux, Anna-Bella, Pischedda, Elisa, Marconcini, Michele, Ghurye, Jay, Rhie, Arang, Sharma, Atashi, Karagodin, Dmitry A, Jenrette, Jeremy, Gamez, Stephanie, Miesen, Pascal, Masterson, Patrick, Caccone, Adalgisa, Sharakhova, Maria V, Tu, Zhijian, Papathanos, Philippos A, Van Rij, Ronald P, Akbari, Omar S, Powell, Jeffrey, Phillippy, Adam M, and Bonizzoni, Mariangela

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Prevention, Infectious Diseases, Emerging Infectious Diseases, Rare Diseases, Human Genome, Vector-Borne Diseases, Biotechnology, Biodefense, 1.1 Normal biological development and functioning, 2.2 Factors relating to the physical environment, 3.2 Interventions to alter physical and biological environmental risks, Infection, Generic health relevance, Good Health and Well Being, Aedes, Animals, Arboviruses, Chromosome Mapping, Chromosomes, Genome, Genome Size, Immunity, Insect Vectors, Mosquito Vectors, RNA, Small Interfering, Transcriptome, Ae, albopictus, miRNAs, piRNA clusters, Viral integrations, Sex locus, Population differentiation, Developmental transcriptome, Ae. albopictus, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundThe Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albopictus genome is essential to develop new approaches that involve genetic manipulation of mosquitoes.ResultsWe use long-read sequencing methods and modern scaffolding techniques (PacBio, 10X, and Hi-C) to produce AalbF2, a dramatically improved assembly of the Ae. albopictus genome. AalbF2 reveals widespread viral insertions, novel microRNAs and piRNA clusters, the sex-determining locus, and new immunity genes, and enables genome-wide studies of geographically diverse Ae. albopictus populations and analyses of the developmental and stage-dependent network of expression data. Additionally, we build the first physical map for this species with 75% of the assembled genome anchored to the chromosomes.ConclusionThe AalbF2 genome assembly represents the most up-to-date collective knowledge of the Ae. albopictus genome. These resources represent a foundation to improve understanding of the adaptation potential and the epidemiological relevance of this species and foster the development of innovative control measures.

Published
2020

7. 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, Human Genome, Biotechnology, 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

8. Improved reference genome of Aedes aegypti informs arbovirus vector control

Author

Matthews, Benjamin J, Dudchenko, Olga, Kingan, Sarah B, Koren, Sergey, Antoshechkin, Igor, Crawford, Jacob E, Glassford, William J, Herre, Margaret, Redmond, Seth N, Rose, Noah H, Weedall, Gareth D, Wu, Yang, Batra, Sanjit S, Brito-Sierra, Carlos A, Buckingham, Steven D, Campbell, Corey L, Chan, Saki, Cox, Eric, Evans, Benjamin R, Fansiri, Thanyalak, Filipović, Igor, Fontaine, Albin, Gloria-Soria, Andrea, Hall, Richard, Joardar, Vinita S, Jones, Andrew K, Kay, Raissa GG, Kodali, Vamsi K, Lee, Joyce, Lycett, Gareth J, Mitchell, Sara N, Muehling, Jill, Murphy, Michael R, Omer, Arina D, Partridge, Frederick A, Peluso, Paul, Aiden, Aviva Presser, Ramasamy, Vidya, Rašić, Gordana, Roy, Sourav, Saavedra-Rodriguez, Karla, Sharan, Shruti, Sharma, Atashi, Smith, Melissa Laird, Turner, Joe, Weakley, Allison M, Zhao, Zhilei, Akbari, Omar S, Black, William C, Cao, Han, Darby, Alistair C, Hill, Catherine A, Johnston, J Spencer, Murphy, Terence D, Raikhel, Alexander S, Sattelle, David B, Sharakhov, Igor V, White, Bradley J, Zhao, Li, Aiden, Erez Lieberman, Mann, Richard S, Lambrechts, Louis, Powell, Jeffrey R, Sharakhova, Maria V, Tu, Zhijian, Robertson, Hugh M, McBride, Carolyn S, Hastie, Alex R, Korlach, Jonas, Neafsey, Daniel E, Phillippy, Adam M, and Vosshall, Leslie B

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Rare Diseases, Emerging Infectious Diseases, Biodefense, Infectious Diseases, Vector-Borne Diseases, 2.2 Factors relating to the physical environment, 3.2 Interventions to alter physical and biological environmental risks, Infection, Good Health and Well Being, Aedes, Animals, Arbovirus Infections, Arboviruses, DNA Copy Number Variations, Dengue Virus, Female, Genetic Variation, Genetics, Population, Genome, Insect, Genomics, Glutathione Transferase, Insect Control, Insecticide Resistance, Male, Molecular Sequence Annotation, Mosquito Vectors, Multigene Family, Pyrethrins, Reference Standards, Sex Determination Processes, General Science & Technology
Abstract

Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of mosquitoes and developing the tools to fight them has been slowed by the lack of a high-quality genome assembly. Here we combine diverse technologies to produce the markedly improved, fully re-annotated AaegL5 genome assembly, and demonstrate how it accelerates mosquito science. We anchored physical and cytogenetic maps, doubled the number of known chemosensory ionotropic receptors that guide mosquitoes to human hosts and egg-laying sites, provided further insight into the size and composition of the sex-determining M locus, and revealed copy-number variation among glutathione S-transferase genes that are important for insecticide resistance. Using high-resolution quantitative trait locus and population genomic analyses, we mapped new candidates for dengue vector competence and insecticide resistance. AaegL5 will catalyse new biological insights and intervention strategies to fight this deadly disease vector.

Published
2018

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

Author

Poynton, Helen C, Hasenbein, Simone, Benoit, Joshua B, Sepulveda, Maria S, Poelchau, Monica F, Hughes, Daniel ST, Murali, Shwetha C, Chen, Shuai, Glastad, Karl M, Goodisman, Michael AD, Werren, John H, Vineis, Joseph H, Bowen, Jennifer L, Friedrich, Markus, Jones, Jeffery, Robertson, Hugh M, Feyereisen, René, Mechler-Hickson, Alexandra, Mathers, Nicholas, Lee, Carol Eunmi, Colbourne, John K, Biales, Adam, Johnston, J Spencer, Wellborn, Gary A, Rosendale, Andrew J, Cridge, Andrew G, Munoz-Torres, Monica C, Bain, Peter A, Manny, Austin R, Major, Kaley M, Lambert, Faith N, Vulpe, Chris D, Tuck, Padrig, Blalock, Bonnie J, Lin, Yu-Yu, Smith, Mark E, Ochoa-Acuña, Hugo, Chen, Mei-Ju May, Childers, Christopher P, Qu, Jiaxin, Dugan, Shannon, Lee, Sandra L, Chao, Hsu, Dinh, Huyen, Han, Yi, Doddapaneni, HarshaVardhan, Worley, Kim C, Muzny, Donna M, Gibbs, Richard A, and Richards, Stephen

Subjects
Ecological Applications, Environmental Sciences, Genetics, Biological Sciences, Biotechnology, Generic health relevance, Life on Land, Amphipoda, Animals, Ecotoxicology, Geologic Sediments, North America, Toxicity Tests, Water Pollutants, Chemical
Abstract

Hyalella azteca is a cryptic species complex of epibenthic amphipods of interest to ecotoxicology and evolutionary biology. It is the primary crustacean used in North America for sediment toxicity testing and an emerging model for molecular ecotoxicology. To provide molecular resources for sediment quality assessments and evolutionary studies, we sequenced, assembled, and annotated the genome of the H. azteca U.S. Lab Strain. The genome quality and completeness is comparable with other ecotoxicological model species. Through targeted investigation and use of gene expression data sets of H. azteca exposed to pesticides, metals, and other emerging contaminants, we annotated and characterized the major gene families involved in sequestration, detoxification, oxidative stress, and toxicant response. Our results revealed gene loss related to light sensing, but a large expansion in chemoreceptors, likely underlying sensory shifts necessary in their low light habitats. Gene family expansions were also noted for cytochrome P450 genes, cuticle proteins, ion transporters, and include recent gene duplications in the metal sequestration protein, metallothionein. Mapping of differentially expressed transcripts to the genome significantly increased the ability to functionally annotate toxicant responsive genes. The H. azteca genome will greatly facilitate development of genomic tools for environmental assessments and promote an understanding of how evolution shapes toxicological pathways with implications for environmental and human health.

Published
2018

12. Genome assembly of the southern pine beetle (Dendroctonus frontalis Zimmerman) reveal the origins of gene content reduction in Dendroctonus

Author

Copeland, Megan, primary, Landa, Shelby, additional, Owoyemi, Adekola, additional, Jonika, Michelle M, additional, Alfieri, Jamie, additional, Sylvester, Terrence, additional, Hoover, Zachary, additional, Hjelmen, Carl E, additional, Johnston, J Spencer, additional, Kyre, Bethany R, additional, Rieske, Lynne K, additional, Blackmon, Heath, additional, and Casola, Claudio, additional

Published
2024
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14. 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

16. A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography

Author

Bukhman, Yury V, primary, Morin, Phillip A, additional, Meyer, Susanne, additional, Chu, Li-Fang, additional, Jacobsen, Jeff K, additional, Antosiewicz-Bourget, Jessica, additional, Mamott, Daniel, additional, Gonzales, Maylie, additional, Argus, Cara, additional, Bolin, Jennifer, additional, Berres, Mark E, additional, Fedrigo, Olivier, additional, Steill, John, additional, Swanson, Scott A, additional, Jiang, Peng, additional, Rhie, Arang, additional, Formenti, Giulio, additional, Phillippy, Adam M, additional, Harris, Robert S, additional, Wood, Jonathan M D, additional, Howe, Kerstin, additional, Kirilenko, Bogdan M, additional, Munegowda, Chetan, additional, Hiller, Michael, additional, Jain, Aashish, additional, Kihara, Daisuke, additional, Johnston, J Spencer, additional, Ionkov, Alexander, additional, Raja, Kalpana, additional, Toh, Huishi, additional, Lang, Aimee, additional, Wolf, Magnus, additional, Jarvis, Erich D, additional, Thomson, James A, additional, Chaisson, Mark J P, additional, and Stewart, Ron, additional

Published
2024
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17. Author Correction: Improved reference genome of the arboviral vector Aedes albopictus

Author

Palatini, Umberto, Masri, Reem A., Cosme, Luciano V., Koren, Sergey, Thibaud-Nissen, Françoise, Biedler, James K., Krsticevic, Flavia, Johnston, J. Spencer, Halbach, Rebecca, Crawford, Jacob E., Antoshechkin, Igor, Failloux, Anna-Bella, Pischedda, Elisa, Marconcini, Michele, Ghurye, Jay, Rhie, Arang, Sharma, Atashi, Karagodin, Dmitry A., Jenrette, Jeremy, Gamez, Stephanie, Miesen, Pascal, Masterson, Patrick, Caccone, Adalgisa, Sharakhova, Maria V., Tu, Zhijian, Papathanos, Philippos A., Van Rij, Ronald P., Akbari, Omar S., Powell, Jeffrey, Phillippy, Adam M., and Bonizzoni, Mariangela

Published
2021
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18. Compact genome of the Antarctic midge is likely an adaptation to an extreme environment

Author

Kelley, Joanna L, Peyton, Justin T, Fiston-Lavier, Anna-Sophie, Teets, Nicholas M, Yee, Muh-Ching, Johnston, J Spencer, Bustamante, Carlos D, Lee, Richard E, and Denlinger, David L

Subjects
Biological Sciences, Genetics, Biotechnology, Human Genome, Acclimatization, Adaptation, Physiological, Animals, Antarctic Regions, Chironomidae, Cold Temperature, DNA, Environment, Genes, Insect, Genome, Insect, Introns, Multigene Family
Abstract

The midge, Belgica antarctica, is the only insect endemic to Antarctica, and thus it offers a powerful model for probing responses to extreme temperatures, freeze tolerance, dehydration, osmotic stress, ultraviolet radiation and other forms of environmental stress. Here we present the first genome assembly of an extremophile, the first dipteran in the family Chironomidae, and the first Antarctic eukaryote to be sequenced. At 99 megabases, B. antarctica has the smallest insect genome sequenced thus far. Although it has a similar number of genes as other Diptera, the midge genome has very low repeat density and a reduction in intron length. Environmental extremes appear to constrain genome architecture, not gene content. The few transposable elements present are mainly ancient, inactive retroelements. An abundance of genes associated with development, regulation of metabolism and responses to external stimuli may reflect adaptations for surviving in this harsh environment.

Published
2014

25. The evolution of genome size in ants

Author

Tsutsui, Neil D, Suarez, Andrew V, Spagna, Joseph C, and Johnston, J Spencer

Abstract

Background: Despite the economic and ecological importance of ants, genomic tools for this family (Formicidae) remain woefully scarce. Knowledge of genome size, for example, is a useful and necessary prerequisite for the development of many genomic resources, yet it has been reported for only one ant species (Solenopsis invicta), and the two published estimates for this species differ by 146.7 Mb (0.15 pg).Results: Here, we report the genome size for 40 species of ants distributed across 10 of the 20 currently recognized subfamilies, thus making Formicidae the 4(th) most surveyed insect family and elevating the Hymenoptera to the 5(th) most surveyed insect order. Our analysis spans much of the ant phylogeny, from the less derived Amblyoponinae and Ponerinae to the more derived Myrmicinae, Formicinae and Dolichoderinae. We include a number of interesting and important taxa, including the invasive Argentine ant (Linepithema humile), Neotropical army ants (genera Eciton and Labidus), trapjaw ants (Odontomachus), fungus-growing ants (Apterostigma, Atta and Sericomyrmex), harvester ants (Messor, Pheidole and Pogonomyrmex), carpenter ants (Camponotus), a fire ant (Solenopsis), and a bulldog ant (Myrmecia). Our results show that ants possess small genomes relative to most other insects, yet genome size varies three-fold across this insect family. Moreover, our data suggest that two whole-genome duplications may have occurred in the ancestors of the modern Ectatomma and Apterostigma. Although some previous studies of other taxa have revealed a relationship between genome size and body size, our phylogenetically-controlled analysis of this correlation did not reveal a significant relationship.Conclusion: This is the first analysis of genome size in ants (Formicidae) and the first across multiple species of social insects. We show that genome size is a variable trait that can evolve gradually over long time spans, as well as rapidly, through processes that may include occasional whole-genome duplication. The small genome sizes of ants, combined with their ecological, evolutionary and agricultural importance, suggest that some of these species may be good candidates for future whole-genome sequencing projects.

Published
2008

34. Genomic signatures of evolutionary transitions from solitary to group living

Author

Kapheim, Karen M., Pan, Hailin, Li, Cai, Salzberg, Steven L., Puiu, Daniela, Magoc, Tanja, Robertson, Hugh M., Hudson, Matthew E., Venkat, Aarti, Fischman, Brielle J., Hernandez, Alvaro, Yandell, Mark, Ence, Daniel, Holt, Carson, Yocum, George D., Kemp, William P., Bosch, Jordi, Waterhouse, Robert M., Zdobnov, Evgeny M., Stolle, Eckart, Kraus, F. Bernhard, Helbing, Sophie, Moritz, Robin F. A., Glastad, Karl M., Hunt, Brendan G., Goodisman, Michael A. D., Hauser, Frank, Grimmelikhuijzen, Cornelis J. P., Pinheiro, Daniel Guariz, Nunes, Francis Morais Franco, Soares, Michelle Prioli Miranda, Tanaka, Érica Donato, Simões, Zilá Luz Paulino, Hartfelder, Klaus, Evans, Jay D., Barribeau, Seth M., Johnson, Reed M., Massey, Jonathan H., Southey, Bruce R., Hasselmann, Martin, Hamacher, Daniel, Biewer, Matthias, Kent, Clement F., Zayed, Amro, Blatti, Charles, Sinha, Saurabh, Johnston, J. Spencer, Hanrahan, Shawn J., Kocher, Sarah D., Wang, Jun, Robinson, Gene E., and Zhang, Guojie

Published
2015

42. A high-quality blue whale genome, segmental duplications, and historical demography

Author

Bukhman, Yury V, primary, Morin, Phillip A., additional, Meyer, Susanne, additional, Chu, Li-Fang (Jack), additional, Jacobsen, Jeff K., additional, Antosiewicz-Bourget, Jessica, additional, Mamott, Daniel, additional, Gonzales, Maylie, additional, Argus, Cara, additional, Bolin, Jennifer, additional, Berres, Mark E., additional, Fedrigo, Olivier, additional, Steill, John, additional, Swanson, Scott Allen, additional, Jiang, Peng, additional, Rhie, Arang, additional, Formenti, Giulio, additional, Phillippy, Adam M., additional, Harris, Robert S., additional, Wood, Jonathan M. D., additional, Howe, Kerstin, additional, Kirilenko, Bogdan, additional, Munegowda, Chetan, additional, Hiller, Michael, additional, Jain, Aashish, additional, Kihara, Daisuke, additional, Johnston, J. Spencer, additional, Ionkov, Alexander, additional, Raja, Kalpana, additional, Toh, Huishi, additional, Lang, Aimee, additional, Wolf, Magnus, additional, Jarvis, Erich, additional, Thomson, James A., additional, Chaisson, Mark J.P., additional, and Stewart, Ron, additional

Published
2022
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43. The genome of pest Rhynchophorus ferrugineus reveals gene families important at the plant-beetle interface

Author

Claude Desplan, Biduth Kundu, Naganeeswaran Sudalaimuthuasari, Khaled M. A. Amiri, Khaled M. Hazzouri, David R. Nelson, Johnston J. Spencer, Mohammad Ali Al-Deeb, and Alain Le Mansour

Subjects
0106 biological sciences, 0301 basic medicine, Male, Gene Transfer, Horizontal, Genome, Insect, Medicine (miscellaneous), Sequence assembly, Genomics, Evolutionary ecology, Receptors, Odorant, 010603 evolutionary biology, 01 natural sciences, Genome, Synteny, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Cytochrome P-450 Enzyme System, Genetics, Gene family, Animals, Gene, lcsh:QH301-705.5, Population Density, Genetic diversity, Sex Chromosomes, biology, Ecology, fungi, food and beverages, Molecular Sequence Annotation, Plants, biology.organism_classification, Biological Evolution, Computational biology and bioinformatics, Rhynchophorus, 030104 developmental biology, lcsh:Biology (General), Multigene Family, DNA Transposable Elements, Insect Proteins, Weevils, Female, General Agricultural and Biological Sciences
Abstract

The red palm weevil, Rhynchophorus ferrugineus, infests palm plantations, leading to large financial losses and soil erosion. Pest-host interactions are poorly understood in R. ferrugineus, but the analysis of genetic diversity and pest origins will help advance efforts to eradicate this pest. We sequenced the genome of R. ferrugineus using a combination of paired-end Illumina sequencing (150 bp), Oxford Nanopore long reads, 10X Genomics and synteny analysis to produce an assembly with a scaffold N50 of ~60 Mb. Structural variations showed duplication of detoxifying and insecticide resistance genes (e.g., glutathione S-transferase, P450, Rdl). Furthermore, the evolution of gene families identified those under positive selection including one glycosyl hydrolase (GH16) gene family, which appears to result from horizontal gene transfer. This genome will be a valuable resource to understand insect evolution and behavior and to allow the genetic modification of key genes that will help control this pest., Khaled Michel Hazzouri et al. study the red palm weevil, Rhynchophorus ferrugineus, which causes agricultural damage. They provide a genome assembly and report duplications of detoxifying and insecticide resistance genes as well as genes under positive selection like the glycosyl hydrolyase gene family. Their work provides genetic insights that can help control this pest.

Published
2020
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44. Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle

Author

Kirkness, Ewen F., Haas, Brian J., Sun, Weilin, Braig, Henk R., Perotti, M. Alejandra, Clark, John M., Lee, Si Hyeock, Robertson, Hugh M., Kennedy, Ryan C., Elhaik, Eran, Gerlach, Daniel, Kriventseva, Evgenia V., Elsik, Christine G., Graur, Dan, Hill, Catherine A., Veenstra, Jan A., Walenz, Brian, Tubío, José Manuel C., Ribeiro, José M. C., Rozas, Julio, Johnston, J. Spencer, Reese, Justin T., Popadic, Aleksandar, Tojo, Marta, Raoult, Didier, Reed, David L., Tomoyasu, Yoshinori, Krause, Emily, Mittapalli, Omprakash, Margam, Venu M., Li, Hong-Mei, Meyer, Jason M., Johnson, Reed M., Romero-Severson, Jeanne, VanZee, Janice Pagel, Alvarez-Ponce, David, Vieira, Filipe G., Aguadé, Montserrat, Guirao-Rico, Sara, Anzola, Juan M., Yoon, Kyong S., Strycharz, Joseph P., Unger, Maria F., Christley, Scott, Lobo, Neil F., Seufferheld, Manfredo J., Wang, NaiKuan, Dasch, Gregory A., Struchiner, Claudio J., Madey, Greg, Hannick, Linda I., Bidwell, Shelby, Joardar, Vinita, Caler, Elisabet, Shao, Renfu, Barker, Stephen C., Cameron, Stephen, Bruggner, Robert V., Regier, Allison, Johnson, Justin, Viswanathan, Lakshmi, Utterback, Terry R., Sutton, Granger G., Lawson, Daniel, Waterhouse, Robert M., Venter, J. Craig, Strausberg, Robert L., Berenbaum, May R., Collins, Frank H., Zdobnov, Evgeny M., and Pittendrigh, Barry R.

Published
2010

45. Spodoptera littoralis genome mining brings insights on the dynamic of expansion of gustatory receptors in polyphagous noctuidae

Author

Meslin, Camille, Mainet, Pauline, Montagné, Nicolas, Robin, Stéphanie, Legeai, Fabrice, Bretaudeau, Anthony, Johnston, J Spencer, Koutroumpa, Fotini, Persyn, Emma, Monsempès, Christelle, François, Marie-Christine, Jacquin-Jolyb, Emmanuelle, Meslin, Camille, Mainet, Pauline, Montagné, Nicolas, Robin, Stéphanie, Legeai, Fabrice, Bretaudeau, Anthony, Johnston, J Spencer, Koutroumpa, Fotini, Persyn, Emma, Monsempès, Christelle, François, Marie-Christine, and Jacquin-Jolyb, Emmanuelle

Abstract

The bitter taste, triggered via gustatory receptors, serves as an important natural defense against the ingestion of poisonous foods in animals, and the increased host breadth is usually linked to an increase in the number of gustatory receptor genes. This has been especially observed in polyphagous insect species, such as noctuid species from the Spodoptera genus. However, the dynamic and physical mechanisms leading to these gene expansions and the evolutionary pressures behind them remain elusive. Among major drivers of genome dynamics are the transposable elements but, surprisingly, their potential role in insect gustatory receptor expansion has not been considered yet. In this work, we hypothesized that transposable elements and possibly positive selection would be involved in the highly dynamic evolution of gustatory receptor in Spodoptera spp. We first sequenced de novo the full 465 Mb genome of S. littoralis, and manually annotated the main chemosensory genes, including a large repertoire of 373 gustatory receptor genes (including 19 pseudogenes). We also improved the completeness of S. frugiperda and S. litura gustatory receptor gene repertoires. Then, we annotated transposable elements and revealed that a particular category of class I retrotransposons, the SINE transposons, was significantly enriched in the vicinity of gustatory receptor gene clusters, suggesting a transposon-mediated mechanism for the formation of these clusters. Selection pressure analyses indicated that positive selection within the gustatory receptor gene family is cryptic, only 7 receptors being identified as positively selected. Altogether, our data provide a new good quality Spodoptera genome, pinpoint interesting gustatory receptor candidates for further functional studies and bring valuable genomic information on the mechanisms of gustatory receptor expansions in polyphagous insect species.

Published
2022

47. Genome Sequence of Aedes aegypti, a Major Arbovirus Vector

Author

Nene, Vishvanath, Wortman, Jennifer R., Lawson, Daniel, Haas, Brian, Kodira, Chinnappa, Tu, Zhijian (Jake), Loftus, Brendan, Xi, Zhiyong, Megy, Karyn, Grabherr, Manfred, Ren, Quinghu, Zdobnov, Evgeny M., Lobo, Neil F., Campbell, Kathryn S., Brown, Susan E., Bonaldo, Maria F., Zhu, Jingsong, Sinkins, Steven P., Hogenkamp, David G., Amedeo, Paolo, Arensburger, Peter, Atkinson, Peter W., Bidwell, Shelby, Biedler, Jim, Birney, Ewan, Bruggner, Robert V., Costas, Javier, Coy, Monique R., Crabtree, Jonathan, Crawford, Matt, deBruyn, Becky, DeCaprio, David, Eiglmeier, Karin, Eisenstadt, Eric, El-Dorry, Hamza, Gelbart, William M., Gomes, Suely L., Hammond, Martin, Hannick, Linda I., Hogan, James R., Holmes, Michael H., Jaffe, David, Johnston, J. Spencer, Kennedy, Ryan C., Koo, Hean, Kravitz, Saul, Kriventseva, Evgenia V., Kulp, David, LaButti, Kurt, Lee, Eduardo, Li, Song, Lovin, Diane D., Mao, Chunhong, Mauceli, Evan, Menck, Carlos F. M., Miller, Jason R., Montgomery, Philip, Mori, Akio, Nascimento, Ana L., Naveira, Horacio F., Nusbaum, Chad, O'Leary, Sinéad, Orvis, Joshua, Pertea, Mihaela, Quesneville, Hadi, Reidenbach, Kyanne R., Rogers, Yu-Hui, Roth, Charles W., Schneider, Jennifer R., Schatz, Michael, Shumway, Martin, Stanke, Mario, Stinson, Eric O., Tubio, Jose M. C., VanZee, Janice P., Verjovski-Almeida, Sergio, Werner, Doreen, White, Owen, Wyder, Stefan, Zeng, Qiandong, Zhao, Qi, Zhao, Yongmei, Hill, Catherine A., Raikhel, Alexander S., Soares, Marcelo B., Knudson, Dennis L., Lee, Norman H., Galagan, James, Salzberg, Steven L., Paulsen, Ian T., Dimopoulos, George, Collins, Frank H., Birren, Bruce, Fraser-Liggett, Claire M., and Severson, David W.

Published
2007
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48. Spodoptera littoralis genome mining brings insights on the dynamic of expansion of gustatory receptors in polyphagous noctuidae

Author

Meslin, Camille, primary, Mainet, Pauline, additional, Montagné, Nicolas, additional, Robin, Stéphanie, additional, Legeai, Fabrice, additional, Bretaudeau, Anthony, additional, Johnston, J Spencer, additional, Koutroumpa, Fotini, additional, Persyn, Emma, additional, Monsempès, Christelle, additional, François, Marie-Christine, additional, and Jacquin-Joly, Emmanuelle, additional

Published
2022
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50. Evolution of Genome Size in Brassicaceae

Author

JOHNSTON, J. SPENCER, PEPPER, ALAN E., HALL, ANNE E., CHEN, Z. JEFFREY, HODNETT, GEORGE, DRABEK, JANICE, LOPEZ, REBECCA, and PRICE, H. JAMES

Published
2005

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