%0 Journal Article %J PLoS Negl Trop Dis %D 2023 %T Genomic analysis of two phlebotomine sand fly vectors of Leishmania from the New and Old World. %A Labbé, Frédéric %A Abdeladhim, Maha %A Abrudan, Jenica %A Araki, Alejandra Saori %A Araujo, Ricardo N %A Arensburger, Peter %A Benoit, Joshua B %A Brazil, Reginaldo Pecanha %A Bruno, Rafaela V %A Bueno da Silva Rivas, Gustavo %A Carvalho de Abreu, Vinicius %A Charamis, Jason %A Coutinho-Abreu, Iliano V %A da Costa-Latgé, Samara G %A Darby, Alistair %A Dillon, Viv M %A Emrich, Scott J %A Fernandez-Medina, Daniela %A Figueiredo Gontijo, Nelder %A Flanley, Catherine M %A Gatherer, Derek %A Genta, Fernando A %A Gesing, Sandra %A Giraldo-Calderón, Gloria I %A Gomes, Bruno %A Aguiar, Eric Roberto Guimaraes Rocha %A Hamilton, James G C %A Hamarsheh, Omar %A Hawksworth, Mallory %A Hendershot, Jacob M %A Hickner, Paul V %A Imler, Jean-Luc %A Ioannidis, Panagiotis %A Jennings, Emily C %A Kamhawi, Shaden %A Karageorgiou, Charikleia %A Kennedy, Ryan C %A Krueger, Andreas %A Latorre-Estivalis, José M %A Ligoxygakis, Petros %A Meireles-Filho, Antonio Carlos A %A Minx, Patrick %A Miranda, Jose Carlos %A Montague, Michael J %A Nowling, Ronald J %A Oliveira, Fabiano %A Ortigão-Farias, João %A Pavan, Marcio G %A Horacio Pereira, Marcos %A Nobrega Pitaluga, Andre %A Proveti Olmo, Roenick %A Ramalho-Ortigao, Marcelo %A Ribeiro, Jose M C %A Rosendale, Andrew J %A Sant'Anna, Mauricio R V %A Steven E Scherer %A Secundino, Nágila F C %A Shoue, Douglas A %A da Silva Moraes, Caroline %A Gesto, João Silveira Moledo %A Souza, Nataly Araujo %A Syed, Zainulabueddin %A Tadros, Samuel %A Teles-de-Freitas, Rayane %A Telleria, Erich L %A Tomlinson, Chad %A Traub-Csekö, Yara M %A Marques, João Trindade %A Tu, Zhijian %A Unger, Maria F %A Valenzuela, Jesus %A Ferreira, Flávia V %A de Oliveira, Karla P V %A Vigoder, Felipe M %A Vontas, John %A Wang, Lihui %A Weedall, Gareth D %A Zhioua, Elyes %A Stephen Richards %A Warren, Wesley C %A Waterhouse, Robert M %A Dillon, Rod J %A McDowell, Mary Ann %K Animals %K Genomics %K Humans %K Leishmania %K Leishmaniasis, Cutaneous %K Phlebotomus %K Psychodidae %X
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.
%B PLoS Negl Trop Dis %V 17 %P e0010862 %8 2023 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/37043542?dopt=Abstract %R 10.1371/journal.pntd.0010862 %0 Journal Article %J BMC Genomics %D 2020 %T Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest. %A Sparks, Michael E %A Bansal, Raman %A Benoit, Joshua B %A Blackburn, Michael B %A Chao, Hsu %A Chen, Mengyao %A Cheng, Sammy %A Childers, Christopher %A Dinh, Huyen %A Harshavardhan Doddapaneni %A Dugan, Shannon %A Elpidina, Elena N %A Farrow, David W %A Friedrich, Markus %A Richard A Gibbs %A Hall, Brantley %A Yi Han %A Hardy, Richard W %A Holmes, Christopher J %A Hughes, Daniel S T %A Ioannidis, Panagiotis %A Cheatle Jarvela, Alys M %A Johnston, J Spencer %A Jones, Jeffery W %A Kronmiller, Brent A %A Kung, Faith %A Lee, Sandra L %A Martynov, Alexander G %A Masterson, Patrick %A Maumus, Florian %A Munoz-Torres, Monica %A Murali, Shwetha C %A Murphy, Terence D %A Donna M Muzny %A Nelson, David R %A Oppert, Brenda %A Panfilio, Kristen A %A Paula, Débora Pires %A Pick, Leslie %A Poelchau, Monica F %A Qu, Jiaxin %A Reding, Katie %A Rhoades, Joshua H %A Rhodes, Adelaide %A Stephen Richards %A Richter, Rose %A Robertson, Hugh M %A Rosendale, Andrew J %A Tu, Zhijian Jake %A Velamuri, Arun S %A Waterhouse, Robert M %A Weirauch, Matthew T %A Wells, Jackson T %A Werren, John H %A Kim C Worley %A Zdobnov, Evgeny M %A Gundersen-Rindal, Dawn E %K Animals %K Ecosystem %K Gene Transfer, Horizontal %K Genome Size %K Heteroptera %K Insect Proteins %K Insecticide Resistance %K Introduced Species %K Phylogeny %K Whole Genome Sequencing %XBACKGROUND: 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.
%B BMC Genomics %V 21 %P 227 %8 2020 Mar 14 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/32171258?dopt=Abstract %R 10.1186/s12864-020-6510-7 %0 Journal Article %J BMC Biol %D 2020 %T Correction to: Genome-enabled insights into the biology of thrips as crop pests. %A Rotenberg, Dorith %A Baumann, Aaron A %A Ben-Mahmoud, Sulley %A Christiaens, Olivier %A Dermauw, Wannes %A Ioannidis, Panagiotis %A Jacobs, Chris G C %A Vargas Jentzsch, Iris M %A Oliver, Jonathan E %A Poelchau, Monica F %A Rajarapu, Swapna Priya %A Schneweis, Derek J %A Snoeck, Simon %A Taning, Clauvis N T %A Wei, Dong %A Widana Gamage, Shirani M K %A Hughes, Daniel S T %A Murali, Shwetha C %A Bailey, Samuel T %A Bejerman, Nicolas E %A Holmes, Christopher J %A Jennings, Emily C %A Rosendale, Andrew J %A Rosselot, Andrew %A Hervey, Kaylee %A Schneweis, Brandi A %A Cheng, Sammy %A Childers, Christopher %A Simão, Felipe A %A Dietzgen, Ralf G %A Chao, Hsu %A Dinh, Huyen %A Harshavardhan Doddapaneni %A Dugan, Shannon %A Yi Han %A Lee, Sandra L %A Donna M Muzny %A Qu, Jiaxin %A Kim C Worley %A Benoit, Joshua B %A Friedrich, Markus %A Jones, Jeffery W %A Panfilio, Kristen A %A Park, Yoonseong %A Robertson, Hugh M %A Smagghe, Guy %A Ullman, Diane E %A Van der Zee, Maurijn %A Van Leeuwen, Thomas %A Veenstra, Jan A %A Waterhouse, Robert M %A Weirauch, Matthew T %A Werren, John H %A Whitfield, Anna E %A Zdobnov, Evgeny M %A Richard A Gibbs %A Stephen Richards %XAn amendment to this paper has been published and can be accessed via the original article.
%B BMC Biol %V 18 %P 169 %8 2020 Nov 16 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/33198778?dopt=Abstract %R 10.1186/s12915-020-00915-z %0 Journal Article %J Genome Biol %D 2020 %T Gene content evolution in the arthropods. %A Thomas, Gregg W C %A Dohmen, Elias %A Hughes, Daniel S T %A Murali, Shwetha C %A Poelchau, Monica %A Glastad, Karl %A Anstead, Clare A %A Ayoub, Nadia A %A Batterham, Phillip %A Bellair, Michelle %A Binford, Greta J %A Chao, Hsu %A Chen, Yolanda H %A Childers, Christopher %A Dinh, Huyen %A Harshavardhan Doddapaneni %A Duan, Jian J %A Dugan, Shannon %A Esposito, Lauren A %A Friedrich, Markus %A Garb, Jessica %A Gasser, Robin B %A Goodisman, Michael A D %A Gundersen-Rindal, Dawn E %A Yi Han %A Handler, Alfred M %A Hatakeyama, Masatsugu %A Hering, Lars %A Hunter, Wayne B %A Ioannidis, Panagiotis %A Jayaseelan, Joy C %A Kalra, Divya %A Khila, Abderrahman %A Korhonen, Pasi K %A Lee, Carol Eunmi %A Lee, Sandra L %A Li, Yiyuan %A Lindsey, Amelia R I %A Mayer, Georg %A McGregor, Alistair P %A McKenna, Duane D %A Misof, Bernhard %A Munidasa, Mala %A Munoz-Torres, Monica %A Donna M Muzny %A Niehuis, Oliver %A Osuji-Lacy, Nkechinyere %A Palli, Subba R %A Panfilio, Kristen A %A Pechmann, Matthias %A Perry, Trent %A Peters, Ralph S %A Poynton, Helen C %A Prpic, Nikola-Michael %A Qu, Jiaxin %A Rotenberg, Dorith %A Schal, Coby %A Schoville, Sean D %A Scully, Erin D %A Skinner, Evette %A Sloan, Daniel B %A Stouthamer, Richard %A Strand, Michael R %A Szucsich, Nikolaus U %A Wijeratne, Asela %A Young, Neil D %A Zattara, Eduardo E %A Benoit, Joshua B %A Zdobnov, Evgeny M %A Pfrender, Michael E %A Hackett, Kevin J %A Werren, John H %A Kim C Worley %A Richard A Gibbs %A Chipman, Ariel D %A Waterhouse, Robert M %A Bornberg-Bauer, Erich %A Hahn, Matthew W %A Stephen Richards %K Animals %K Arthropods %K DNA Methylation %K Evolution, Molecular %K Genetic Speciation %K Genetic Variation %K Phylogeny %XBACKGROUND: 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.
%B Genome Biol %V 21 %P 15 %8 2020 Jan 23 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/31969194?dopt=Abstract %R 10.1186/s13059-019-1925-7 %0 Journal Article %J BMC Biol %D 2020 %T Genome-enabled insights into the biology of thrips as crop pests. %A Rotenberg, Dorith %A Baumann, Aaron A %A Ben-Mahmoud, Sulley %A Christiaens, Olivier %A Dermauw, Wannes %A Ioannidis, Panagiotis %A Jacobs, Chris G C %A Vargas Jentzsch, Iris M %A Oliver, Jonathan E %A Poelchau, Monica F %A Rajarapu, Swapna Priya %A Schneweis, Derek J %A Snoeck, Simon %A Taning, Clauvis N T %A Wei, Dong %A Widana Gamage, Shirani M K %A Hughes, Daniel S T %A Murali, Shwetha C %A Bailey, Samuel T %A Bejerman, Nicolas E %A Holmes, Christopher J %A Jennings, Emily C %A Rosendale, Andrew J %A Rosselot, Andrew %A Hervey, Kaylee %A Schneweis, Brandi A %A Cheng, Sammy %A Childers, Christopher %A Simão, Felipe A %A Dietzgen, Ralf G %A Chao, Hsu %A Dinh, Huyen %A Harshavardhan Doddapaneni %A Dugan, Shannon %A Yi Han %A Lee, Sandra L %A Donna M Muzny %A Qu, Jiaxin %A Kim C Worley %A Benoit, Joshua B %A Friedrich, Markus %A Jones, Jeffery W %A Panfilio, Kristen A %A Park, Yoonseong %A Robertson, Hugh M %A Smagghe, Guy %A Ullman, Diane E %A Van der Zee, Maurijn %A Van Leeuwen, Thomas %A Veenstra, Jan A %A Waterhouse, Robert M %A Weirauch, Matthew T %A Werren, John H %A Whitfield, Anna E %A Zdobnov, Evgeny M %A Richard A Gibbs %A Stephen Richards %K Animals %K Crops, Agricultural %K Feeding Behavior %K Food Chain %K Genome, Insect %K Immunity, Innate %K Life History Traits %K Perception %K Phylogeny %K Reproduction %K Thysanoptera %K Transcriptome %XBACKGROUND: The western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set.
RESULTS: We report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~ 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta.
CONCLUSIONS: Analysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species.
%B BMC Biol %V 18 %P 142 %8 2020 Oct 19 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/33070780?dopt=Abstract %R 10.1186/s12915-020-00862-9 %0 Journal Article %J Genome Biol Evol %D 2020 %T Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera. %A Oeyen, Jan Philip %A Baa-Puyoulet, Patrice %A Benoit, Joshua B %A Beukeboom, Leo W %A Bornberg-Bauer, Erich %A Buttstedt, Anja %A Calevro, Federica %A Cash, Elizabeth I %A Chao, Hsu %A Charles, Hubert %A Chen, Mei-Ju May %A Childers, Christopher %A Cridge, Andrew G %A Dearden, Peter %A Dinh, Huyen %A Harshavardhan Doddapaneni %A Dolan, Amanda %A Donath, Alexander %A Dowling, Daniel %A Dugan, Shannon %A Duncan, Elizabeth %A Elpidina, Elena N %A Friedrich, Markus %A Geuverink, Elzemiek %A Gibson, Joshua D %A Grath, Sonja %A Grimmelikhuijzen, Cornelis J P %A Große-Wilde, Ewald %A Gudobba, Cameron %A Yi Han %A Hansson, Bill S %A Hauser, Frank %A Hughes, Daniel S T %A Ioannidis, Panagiotis %A Jacquin-Joly, Emmanuelle %A Jennings, Emily C %A Jones, Jeffery W %A Klasberg, Steffen %A Lee, Sandra L %A Lesný, Peter %A Lovegrove, Mackenzie %A Martin, Sebastian %A Martynov, Alexander G %A Mayer, Christoph %A Montagné, Nicolas %A Moris, Victoria C %A Munoz-Torres, Monica %A Murali, Shwetha Canchi %A Donna M Muzny %A Oppert, Brenda %A Parisot, Nicolas %A Pauli, Thomas %A Peters, Ralph S %A Petersen, Malte %A Pick, Christian %A Persyn, Emma %A Podsiadlowski, Lars %A Poelchau, Monica F %A Provataris, Panagiotis %A Qu, Jiaxin %A Reijnders, Maarten J M F %A von Reumont, Björn Marcus %A Rosendale, Andrew J %A Simão, Felipe A %A Skelly, John %A Sotiropoulos, Alexandros G %A Stahl, Aaron L %A Sumitani, Megumi %A Szuter, Elise M %A Tidswell, Olivia %A Tsitlakidis, Evangelos %A Vedder, Lucia %A Waterhouse, Robert M %A Werren, John H %A Wilbrandt, Jeanne %A Kim C Worley %A Yamamoto, Daisuke S %A van de Zande, Louis %A Zdobnov, Evgeny M %A Ziesmann, Tanja %A Richard A Gibbs %A Stephen Richards %A Hatakeyama, Masatsugu %A Misof, Bernhard %A Niehuis, Oliver %K Amino Acid Sequence %K Animals %K Conserved Sequence %K DNA Transposable Elements %K Female %K Gene Dosage %K Genetic Speciation %K Genome, Insect %K Glycoproteins %K Herbivory %K Host-Parasite Interactions %K Hymenoptera %K Immunity %K Insect Proteins %K Male %K Multigene Family %K Receptors, Odorant %K Social Behavior %K Vision, Ocular %XThe 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.
%B Genome Biol Evol %V 12 %P 1099-1188 %8 2020 Jul 01 %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/32442304?dopt=Abstract %R 10.1093/gbe/evaa106 %0 Journal Article %J Database (Oxford) %D 2019 %T Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community. %A Saha, Surya %A Hosmani, Prashant S %A Villalobos-Ayala, Krystal %A Miller, Sherry %A Shippy, Teresa %A Flores, Mirella %A Rosendale, Andrew %A Cordola, Chris %A Bell, Tracey %A Mann, Hannah %A DeAvila, Gabe %A DeAvila, Daniel %A Moore, Zachary %A Buller, Kyle %A Ciolkevich, Kathryn %A Nandyal, Samantha %A Mahoney, Robert %A Voorhis, Joshua Van %A Dunlevy, Megan %A Farrow, David %A Hunter, David %A Morgan, Taylar %A Shore, Kayla %A Guzman, Victoria %A Izsak, Allison %A Dixon, Danielle E %A Cridge, Andrew %A Cano, Liliana %A Cao, Xiaolong %A Jiang, Haobo %A Leng, Nan %A Johnson, Shannon %A Cantarel, Brandi L %A Stephen Richards %A English, Adam %A Shatters, Robert G %A Childers, Chris %A Chen, Mei-Ju %A Hunter, Wayne %A Cilia, Michelle %A Mueller, Lukas A %A Munoz-Torres, Monica %A Nelson, David %A Poelchau, Monica F %A Benoit, Joshua B %A Wiersma-Koch, Helen %A D'Elia, Tom %A Brown, Susan J %B Database (Oxford) %V 2019 %8 2019 Jan 01 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/30820572?dopt=Abstract %R 10.1093/database/baz035 %0 Journal Article %J Genome Biol %D 2019 %T Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. %A Panfilio, Kristen A %A Vargas Jentzsch, Iris M %A Benoit, Joshua B %A Erezyilmaz, Deniz %A Suzuki, Yuichiro %A Colella, Stefano %A Robertson, Hugh M %A Poelchau, Monica F %A Waterhouse, Robert M %A Ioannidis, Panagiotis %A Weirauch, Matthew T %A Hughes, Daniel S T %A Murali, Shwetha C %A Werren, John H %A Jacobs, Chris G C %A Duncan, Elizabeth J %A Armisén, David %A Vreede, Barbara M I %A Baa-Puyoulet, Patrice %A Berger, Chloé S %A Chang, Chun-Che %A Chao, Hsu %A Chen, Mei-Ju M %A Chen, Yen-Ta %A Childers, Christopher P %A Chipman, Ariel D %A Cridge, Andrew G %A Crumière, Antonin J J %A Dearden, Peter K %A Didion, Elise M %A Dinh, Huyen %A Harshavardhan Doddapaneni %A Dolan, Amanda %A Dugan, Shannon %A Extavour, Cassandra G %A Febvay, Gérard %A Friedrich, Markus %A Ginzburg, Neta %A Yi Han %A Heger, Peter %A Holmes, Christopher J %A Horn, Thorsten %A Hsiao, Yi-Min %A Jennings, Emily C %A Johnston, J Spencer %A Jones, Tamsin E %A Jones, Jeffery W %A Khila, Abderrahman %A Koelzer, Stefan %A Kovacova, Viera %A Leask, Megan %A Lee, Sandra L %A Lee, Chien-Yueh %A Lovegrove, Mackenzie R %A Lu, Hsiao-Ling %A Lu, Yong %A Moore, Patricia J %A Munoz-Torres, Monica C %A Donna M Muzny %A Palli, Subba R %A Parisot, Nicolas %A Pick, Leslie %A Porter, Megan L %A Qu, Jiaxin %A Refki, Peter N %A Richter, Rose %A Rivera-Pomar, Rolando %A Rosendale, Andrew J %A Roth, Siegfried %A Sachs, Lena %A Santos, M Emília %A Seibert, Jan %A Sghaier, Essia %A Shukla, Jayendra N %A Stancliffe, Richard J %A Tidswell, Olivia %A Traverso, Lucila %A Van der Zee, Maurijn %A Viala, Sèverine %A Kim C Worley %A Zdobnov, Evgeny M %A Richard A Gibbs %A Stephen Richards %K Amino Acid Sequence %K Animals %K CYS2-HIS2 Zinc Fingers %K Evolution, Molecular %K Feeding Behavior %K Gene Dosage %K Gene Expression Profiling %K Gene Transfer, Horizontal %K Genes, Homeobox %K Genome, Insect %K Hemiptera %K Pigmentation %K Smell %K Transcription Factors %XBACKGROUND: The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae.
RESULTS: The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding.
CONCLUSIONS: With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.
%B Genome Biol %V 20 %P 64 %8 2019 Apr 02 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/30935422?dopt=Abstract %R 10.1186/s13059-019-1660-0 %0 Journal Article %J BMC Genomics %D 2018 %T The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water. %A Armisén, David %A Rajakumar, Rajendhran %A Friedrich, Markus %A Benoit, Joshua B %A Robertson, Hugh M %A Panfilio, Kristen A %A Ahn, Seung-Joon %A Poelchau, Monica F %A Chao, Hsu %A Dinh, Huyen %A Harshavardhan Doddapaneni %A Dugan, Shannon %A Richard A Gibbs %A Hughes, Daniel S T %A Yi Han %A Lee, Sandra L %A Murali, Shwetha C %A Donna M Muzny %A Qu, Jiaxin %A Worley, Kim C %A Munoz-Torres, Monica %A Abouheif, Ehab %A Bonneton, François %A Chen, Travis %A Chiang, Li-Mei %A Childers, Christopher P %A Cridge, Andrew G %A Crumière, Antonin J J %A Decaras, Amelie %A Didion, Elise M %A Duncan, Elizabeth J %A Elpidina, Elena N %A Favé, Marie-Julie %A Finet, Cédric %A Jacobs, Chris G C %A Cheatle Jarvela, Alys M %A Jennings, Emily C %A Jones, Jeffery W %A Lesoway, Maryna P %A Lovegrove, Mackenzie R %A Martynov, Alexander %A Oppert, Brenda %A Lillico-Ouachour, Angelica %A Rajakumar, Arjuna %A Refki, Peter Nagui %A Rosendale, Andrew J %A Santos, Maria Emilia %A Toubiana, William %A Van der Zee, Maurijn %A Vargas Jentzsch, Iris M %A Lowman, Aidamalia Vargas %A Viala, Sèverine %A Richards, Stephen %A Khila, Abderrahman %K Adaptation, Physiological %K Animals %K Evolution, Molecular %K Genome %K Genomics %K Heteroptera %K Insect Proteins %K Phenotype %K Phylogeny %XBACKGROUND: Having conquered water surfaces worldwide, the semi-aquatic bugs occupy ponds, streams, lakes, mangroves, and even open oceans. The diversity of this group has inspired a range of scientific studies from ecology and evolution to developmental genetics and hydrodynamics of fluid locomotion. However, the lack of a representative water strider genome hinders our ability to more thoroughly investigate the molecular mechanisms underlying the processes of adaptation and diversification within this group.
RESULTS: Here we report the sequencing and manual annotation of the Gerris buenoi (G. buenoi) genome; the first water strider genome to be sequenced thus far. The size of the G. buenoi genome is approximately 1,000 Mb, and this sequencing effort has recovered 20,949 predicted protein-coding genes. Manual annotation uncovered a number of local (tandem and proximal) gene duplications and expansions of gene families known for their importance in a variety of processes associated with morphological and physiological adaptations to a water surface lifestyle. These expansions may affect key processes associated with growth, vision, desiccation resistance, detoxification, olfaction and epigenetic regulation. Strikingly, the G. buenoi genome contains three insulin receptors, suggesting key changes in the rewiring and function of the insulin pathway. Other genomic changes affecting with opsin genes may be associated with wavelength sensitivity shifts in opsins, which is likely to be key in facilitating specific adaptations in vision for diverse water habitats.
CONCLUSIONS: Our findings suggest that local gene duplications might have played an important role during the evolution of water striders. Along with these findings, the sequencing of the G. buenoi genome now provides us the opportunity to pursue exciting research opportunities to further understand the genomic underpinnings of traits associated with the extreme body plan and life history of water striders.
%B BMC Genomics %V 19 %P 832 %8 2018 Nov 21 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/30463532?dopt=Abstract %R 10.1186/s12864-018-5163-2 %0 Journal Article %J Environ Sci Technol %D 2018 %T The Toxicogenome of Hyalella azteca: A Model for Sediment Ecotoxicology and Evolutionary Toxicology. %A Poynton, Helen C %A Hasenbein, Simone %A Benoit, Joshua B %A Sepulveda, Maria S %A Poelchau, Monica F %A Hughes, Daniel S T %A Murali, Shwetha C %A Chen, Shuai %A Glastad, Karl M %A Goodisman, Michael A D %A Werren, John H %A Vineis, Joseph H %A Bowen, Jennifer L %A Friedrich, Markus %A Jones, Jeffery %A Robertson, Hugh M %A Feyereisen, René %A Mechler-Hickson, Alexandra %A Mathers, Nicholas %A Lee, Carol Eunmi %A Colbourne, John K %A Biales, Adam %A Johnston, J Spencer %A Wellborn, Gary A %A Rosendale, Andrew J %A Cridge, Andrew G %A Munoz-Torres, Monica C %A Bain, Peter A %A Manny, Austin R %A Major, Kaley M %A Lambert, Faith N %A Vulpe, Chris D %A Tuck, Padrig %A Blalock, Bonnie J %A Lin, Yu-Yu %A Smith, Mark E %A Ochoa-Acuña, Hugo %A Chen, Mei-Ju May %A Childers, Christopher P %A Qu, Jiaxin %A Dugan, Shannon %A Lee, Sandra L %A Chao, Hsu %A Dinh, Huyen %A Yi Han %A Harshavardhan Doddapaneni %A Worley, Kim C %A Donna M Muzny %A Richard A Gibbs %A Richards, Stephen %K Amphipoda %K Animals %K Ecotoxicology %K Geologic Sediments %K North America %K Toxicity Tests %K Water Pollutants, Chemical %XHyalella 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.
%B Environ Sci Technol %V 52 %P 6009-6022 %8 2018 May 15 %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/29634279?dopt=Abstract %R 10.1021/acs.est.8b00837 %0 Journal Article %J Genome Biol %D 2017 %T Erratum to: The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species. %A Papanicolaou, Alexie %A Schetelig, Marc F %A Arensburger, Peter %A Atkinson, Peter W %A Benoit, Joshua B %A Bourtzis, Kostas %A Castañera, Pedro %A Cavanaugh, John P %A Chao, Hsu %A Childers, Christopher %A Curril, Ingrid %A Dinh, Huyen %A Harshavardhan Doddapaneni %A Dolan, Amanda %A Dugan, Shannon %A Friedrich, Markus %A Gasperi, Giuliano %A Geib, Scott %A Georgakilas, Georgios %A Richard A Gibbs %A Giers, Sarah D %A Gomulski, Ludvik M %A González-Guzmán, Miguel %A Guillem-Amat, Ana %A Yi Han %A Hatzigeorgiou, Artemis G %A Hernández-Crespo, Pedro %A Hughes, Daniel S T %A Jones, Jeffery W %A Karagkouni, Dimitra %A Koskinioti, Panagiota %A Lee, Sandra L %A Malacrida, Anna R %A Manni, Mosè %A Mathiopoulos, Kostas %A Meccariello, Angela %A Munoz-Torres, Monica %A Murali, Shwetha C %A Murphy, Terence D %A Donna M Muzny %A Oberhofer, Georg %A Ortego, Félix %A Paraskevopoulou, Maria D %A Poelchau, Monica %A Qu, Jiaxin %A Reczko, Martin %A Robertson, Hugh M %A Rosendale, Andrew J %A Rosselot, Andrew E %A Saccone, Giuseppe %A Salvemini, Marco %A Savini, Grazia %A Schreiner, Patrick %A Scolari, Francesca %A Siciliano, Paolo %A Sim, Sheina B %A Tsiamis, George %A Ureña, Enric %A S Vlachos, Ioannis %A Werren, John H %A Wimmer, Ernst A %A Worley, Kim C %A Zacharopoulou, Antigone %A Richards, Stephen %A Handler, Alfred M %B Genome Biol %V 18 %P 11 %8 2017 Jan 18 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/28100280?dopt=Abstract %R 10.1186/s13059-017-1155-9 %0 Journal Article %J Database (Oxford) %D 2017 %T Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community. %A Saha, Surya %A Hosmani, Prashant S %A Villalobos-Ayala, Krystal %A Miller, Sherry %A Shippy, Teresa %A Flores, Mirella %A Rosendale, Andrew %A Cordola, Chris %A Bell, Tracey %A Mann, Hannah %A DeAvila, Gabe %A DeAvila, Daniel %A Moore, Zachary %A Buller, Kyle %A Ciolkevich, Kathryn %A Nandyal, Samantha %A Mahoney, Robert %A Van Voorhis, Joshua %A Dunlevy, Megan %A Farrow, David %A Hunter, David %A Morgan, Taylar %A Shore, Kayla %A Guzman, Victoria %A Izsak, Allison %A Dixon, Danielle E %A Cridge, Andrew %A Cano, Liliana %A Cao, Xiaolong %A Jiang, Haobo %A Leng, Nan %A Johnson, Shannon %A Cantarel, Brandi L %A Richards, Stephen %A English, Adam %A Shatters, Robert G %A Childers, Chris %A Chen, Mei-Ju %A Hunter, Wayne %A Cilia, Michelle %A Mueller, Lukas A %A Munoz-Torres, Monica %A Nelson, David %A Poelchau, Monica F %A Benoit, Joshua B %A Wiersma-Koch, Helen %A D'Elia, Tom %A Brown, Susan J %K Animals %K Citrus %K Databases, Genetic %K Genome, Insect %K Hemiptera %K Insect Vectors %K Pest Control %K Plant Diseases %K Rhizobiaceae %Xhttps://citrusgreening.org/.
%B Database (Oxford) %V 2017 %8 2017 Jan 01 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/29220441?dopt=Abstract %R 10.1093/database/bax032 %0 Journal Article %J Genome Biol %D 2016 %T Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface. %A McKenna, Duane D %A Scully, Erin D %A Pauchet, Yannick %A Hoover, Kelli %A Kirsch, Roy %A Geib, Scott M %A Mitchell, Robert F %A Waterhouse, Robert M %A Ahn, Seung-Joon %A Arsala, Deanna %A Benoit, Joshua B %A Blackmon, Heath %A Bledsoe, Tiffany %A Bowsher, Julia H %A Busch, André %A Calla, Bernarda %A Chao, Hsu %A Childers, Anna K %A Childers, Christopher %A Clarke, Dave J %A Cohen, Lorna %A Demuth, Jeffery P %A Dinh, Huyen %A Harshavardhan Doddapaneni %A Dolan, Amanda %A Duan, Jian J %A Dugan, Shannon %A Friedrich, Markus %A Glastad, Karl M %A Goodisman, Michael A D %A Haddad, Stephanie %A Yi Han %A Hughes, Daniel S T %A Ioannidis, Panagiotis %A Johnston, J Spencer %A Jones, Jeffery W %A Kuhn, Leslie A %A Lance, David R %A Lee, Chien-Yueh %A Lee, Sandra L %A Lin, Han %A Lynch, Jeremy A %A Moczek, Armin P %A Murali, Shwetha C %A Donna M Muzny %A Nelson, David R %A Palli, Subba R %A Panfilio, Kristen A %A Pers, Dan %A Poelchau, Monica F %A Quan, Honghu %A Qu, Jiaxin %A Ray, Ann M %A Rinehart, Joseph P %A Robertson, Hugh M %A Roehrdanz, Richard %A Rosendale, Andrew J %A Shin, Seunggwan %A Silva, Christian %A Torson, Alex S %A Jentzsch, Iris M Vargas %A Werren, John H %A Worley, Kim C %A Yocum, George %A Zdobnov, Evgeny M %A Richard A Gibbs %A Richards, Stephen %K Animals %K Coleoptera %K Evolution, Molecular %K Gene Transfer, Horizontal %K Genome, Insect %K Host-Parasite Interactions %K Introduced Species %K Larva %K Sequence Analysis, DNA %K Trees %XBACKGROUND: Relatively little is known about the genomic basis and evolution of wood-feeding in beetles. We undertook genome sequencing and annotation, gene expression assays, studies of plant cell wall degrading enzymes, and other functional and comparative studies of the Asian longhorned beetle, Anoplophora glabripennis, a globally significant invasive species capable of inflicting severe feeding damage on many important tree species. Complementary studies of genes encoding enzymes involved in digestion of woody plant tissues or detoxification of plant allelochemicals were undertaken with the genomes of 14 additional insects, including the newly sequenced emerald ash borer and bull-headed dung beetle.
RESULTS: The Asian longhorned beetle genome encodes a uniquely diverse arsenal of enzymes that can degrade the main polysaccharide networks in plant cell walls, detoxify plant allelochemicals, and otherwise facilitate feeding on woody plants. It has the metabolic plasticity needed to feed on diverse plant species, contributing to its highly invasive nature. Large expansions of chemosensory genes involved in the reception of pheromones and plant kairomones are consistent with the complexity of chemical cues it uses to find host plants and mates.
CONCLUSIONS: Amplification and functional divergence of genes associated with specialized feeding on plants, including genes originally obtained via horizontal gene transfer from fungi and bacteria, contributed to the addition, expansion, and enhancement of the metabolic repertoire of the Asian longhorned beetle, certain other phytophagous beetles, and to a lesser degree, other phytophagous insects. Our results thus begin to establish a genomic basis for the evolutionary success of beetles on plants.
%B Genome Biol %V 17 %P 227 %8 2016 Nov 11 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/27832824?dopt=Abstract %R 10.1186/s13059-016-1088-8 %0 Journal Article %J Mitochondrial DNA B Resour %D 2016 %T The mitogenome of the bed bug (Hemiptera: Cimicidae). %A Kolokotronis, Sergios-Orestis %A Foox, Jonathan %A Rosenfeld, Jeffrey A %A Brugler, Mercer R %A Reeves, Darryl %A Benoit, Joshua B %A Booth, Warren %A Robison, Grant %A Steffen, Michael %A Sakas, Zoe %A Palli, Subba R %A Schal, Coby %A Richards, Stephen %A Narechania, Apurva %A Baker, Richard H %A Sorkin, Louis N %A Amato, George %A Mason, Christopher E %A Siddall, Mark E %A DeSalle, Rob %XWe report the extraction of a bed bug mitogenome from high-throughput sequencing projects originally focused on the nuclear genome of . The assembled mitogenome has a similar AT nucleotide composition bias found in other insects. Phylogenetic analysis of all protein-coding genes indicates that is clearly a member of a paraphyletic Cimicomorpha clade within the Order Hemiptera.
%B Mitochondrial DNA B Resour %V 1 %P 425-427 %8 2016 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/27617305?dopt=Abstract %R 10.1080/23802359.2016.1180268 %0 Journal Article %J Nat Commun %D 2016 %T Unique features of a global human ectoparasite identified through sequencing of the bed bug genome. %A Benoit, Joshua B %A Adelman, Zach N %A Reinhardt, Klaus %A Dolan, Amanda %A Poelchau, Monica %A Jennings, Emily C %A Szuter, Elise M %A Hagan, Richard W %A Gujar, Hemant %A Shukla, Jayendra Nath %A Zhu, Fang %A Mohan, M %A Nelson, David R %A Rosendale, Andrew J %A Derst, Christian %A Resnik, Valentina %A Wernig, Sebastian %A Menegazzi, Pamela %A Wegener, Christian %A Peschel, Nicolai %A Hendershot, Jacob M %A Blenau, Wolfgang %A Predel, Reinhard %A Johnston, Paul R %A Ioannidis, Panagiotis %A Waterhouse, Robert M %A Nauen, Ralf %A Schorn, Corinna %A Ott, Mark-Christoph %A Maiwald, Frank %A Johnston, J Spencer %A Gondhalekar, Ameya D %A Scharf, Michael E %A Peterson, Brittany F %A Raje, Kapil R %A Hottel, Benjamin A %A Armisén, David %A Crumière, Antonin Jean Johan %A Refki, Peter Nagui %A Santos, Maria Emilia %A Sghaier, Essia %A Viala, Sèverine %A Khila, Abderrahman %A Ahn, Seung-Joon %A Childers, Christopher %A Lee, Chien-Yueh %A Lin, Han %A Hughes, Daniel S T %A Duncan, Elizabeth J %A Murali, Shwetha C %A Qu, Jiaxin %A Dugan, Shannon %A Lee, Sandra L %A Chao, Hsu %A Dinh, Huyen %A Yi Han %A Harshavardhan Doddapaneni %A Worley, Kim C %A Donna M Muzny %A Wheeler, David %A Panfilio, Kristen A %A Vargas Jentzsch, Iris M %A Vargo, Edward L %A Booth, Warren %A Friedrich, Markus %A Weirauch, Matthew T %A Anderson, Michelle A E %A Jones, Jeffery W %A Mittapalli, Omprakash %A Zhao, Chaoyang %A Zhou, Jing-Jiang %A Evans, Jay D %A Attardo, Geoffrey M %A Robertson, Hugh M %A Zdobnov, Evgeny M %A Ribeiro, Jose M C %A Richard A Gibbs %A Werren, John H %A Palli, Subba R %A Schal, Coby %A Richards, Stephen %K Animals %K Bedbugs %K Ectoparasitic Infestations %K Feeding Behavior %K Gene Transfer, Horizontal %K Genome %K Host-Parasite Interactions %K Humans %K Insecticide Resistance %K Insecticides %K Sequence Analysis, DNA %XThe 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.
%B Nat Commun %V 7 %P 10165 %8 2016 Feb 02 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/26836814?dopt=Abstract %R 10.1038/ncomms10165 %0 Journal Article %J Genome Biol %D 2016 %T The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species. %A Papanicolaou, Alexie %A Schetelig, Marc F %A Arensburger, Peter %A Atkinson, Peter W %A Benoit, Joshua B %A Bourtzis, Kostas %A Castañera, Pedro %A Cavanaugh, John P %A Chao, Hsu %A Childers, Christopher %A Curril, Ingrid %A Dinh, Huyen %A Harshavardhan Doddapaneni %A Dolan, Amanda %A Dugan, Shannon %A Friedrich, Markus %A Gasperi, Giuliano %A Geib, Scott %A Georgakilas, Georgios %A Richard A Gibbs %A Giers, Sarah D %A Gomulski, Ludvik M %A González-Guzmán, Miguel %A Guillem-Amat, Ana %A Yi Han %A Hatzigeorgiou, Artemis G %A Hernández-Crespo, Pedro %A Hughes, Daniel S T %A Jones, Jeffery W %A Karagkouni, Dimitra %A Koskinioti, Panagiota %A Lee, Sandra L %A Malacrida, Anna R %A Manni, Mosè %A Mathiopoulos, Kostas %A Meccariello, Angela %A Munoz-Torres, Monica %A Murali, Shwetha C %A Murphy, Terence D %A Donna M Muzny %A Oberhofer, Georg %A Ortego, Félix %A Paraskevopoulou, Maria D %A Poelchau, Monica %A Qu, Jiaxin %A Reczko, Martin %A Robertson, Hugh M %A Rosendale, Andrew J %A Rosselot, Andrew E %A Saccone, Giuseppe %A Salvemini, Marco %A Savini, Grazia %A Schreiner, Patrick %A Scolari, Francesca %A Siciliano, Paolo %A Sim, Sheina B %A Tsiamis, George %A Ureña, Enric %A Vlachos, Ioannis S %A Werren, John H %A Wimmer, Ernst A %A Worley, Kim C %A Zacharopoulou, Antigone %A Richards, Stephen %A Handler, Alfred M %K Animals %K Animals, Genetically Modified %K Biological Evolution %K Ceratitis capitata %K Genome, Insect %K High-Throughput Nucleotide Sequencing %K Humans %K Introduced Species %K Molecular Sequence Annotation %K Pest Control, Biological %XBACKGROUND: The Mediterranean fruit fly (medfly), Ceratitis capitata, is a major destructive insect pest due to its broad host range, which includes hundreds of fruits and vegetables. It exhibits a unique ability to invade and adapt to ecological niches throughout tropical and subtropical regions of the world, though medfly infestations have been prevented and controlled by the sterile insect technique (SIT) as part of integrated pest management programs (IPMs). The genetic analysis and manipulation of medfly has been subject to intensive study in an effort to improve SIT efficacy and other aspects of IPM control.
RESULTS: The 479 Mb medfly genome is sequenced from adult flies from lines inbred for 20 generations. A high-quality assembly is achieved having a contig N50 of 45.7 kb and scaffold N50 of 4.06 Mb. In-depth curation of more than 1800 messenger RNAs shows specific gene expansions that can be related to invasiveness and host adaptation, including gene families for chemoreception, toxin and insecticide metabolism, cuticle proteins, opsins, and aquaporins. We identify genes relevant to IPM control, including those required to improve SIT.
CONCLUSIONS: The medfly genome sequence provides critical insights into the biology of one of the most serious and widespread agricultural pests. This knowledge should significantly advance the means of controlling the size and invasive potential of medfly populations. Its close relationship to Drosophila, and other insect species important to agriculture and human health, will further comparative functional and structural studies of insect genomes that should broaden our understanding of gene family evolution.
%B Genome Biol %V 17 %P 192 %8 2016 Sep 22 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/27659211?dopt=Abstract %R 10.1186/s13059-016-1049-2