Hoy Marjorie A, Waterhouse Robert M, Wu Ke, Estep Alden S, Ioannidis Panagiotis, Palmer William J, Pomerantz Aaron F, Simão Felipe A, Thomas Jainy, Jiggins Francis M, Murphy Terence D, Pritham Ellen J, Robertson Hugh M, Zdobnov Evgeny M, Gibbs Richard A, Richards Stephen (2016), Genome Sequencing of the Phytoseiid Predatory Mite Metaseiulus occidentalis Reveals Completely Atomized Hox Genes and Superdynamic Intron Evolution., in Genome biology and evolution
, 8(6), 1762-75.
Gulia-Nuss Monika, Nuss Andrew B, Meyer Jason M, Sonenshine Daniel E, Roe R Michael, Waterhouse Robert M, Sattelle David B, de la Fuente José, Ribeiro Jose M, Megy Karine, Thimmapuram Jyothi, Miller Jason R, Walenz Brian P, Koren Sergey, Hostetler Jessica B, Thiagarajan Mathangi, Joardar Vinita S, Hannick Linda I, Bidwell Shelby, Hammond Martin P, Young Sarah, Zeng Qiandong, Abrudan Jenica L, Almeida Francisca C, Ayllón Nieves (2016), Genomic insights into the Ixodes scapularis tick vector of Lyme disease., in Nature communications
, 7, 10507-10507.
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 (2016), Unique features of a global human ectoparasite identified through sequencing of the bed bug genome., in Nature communications
, 7, 10165-10165.
Anstead Clare A, Korhonen Pasi K, Young Neil D, Hall Ross S, Jex Aaron R, Murali Shwetha C, Hughes Daniel S T, Lee Siu F, Perry Trent, Stroehlein Andreas J, Ansell Brendan R E, Breugelmans Bert, Hofmann Andreas, Qu Jiaxin, Dugan Shannon, Lee Sandra L, Chao Hsu, Dinh Huyen, Han Yi, Doddapaneni Harsha V, Worley Kim C, Muzny Donna M, Ioannidis Panagiotis, Waterhouse Robert M, Zdobnov Evgeny M (2015), Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions., in Nature communications
, 6, 7344-7344.
Simão Felipe A, Waterhouse Robert M, Ioannidis Panagiotis, Kriventseva Evgenia V, Zdobnov Evgeny M (2015), BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs., in Bioinformatics (Oxford, England)
, 31(19), 3210-2.
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 (2015), Social evolution. Genomic signatures of evolutionary transitions from solitary to group living., in Science (New York, N.Y.)
, 348(6239), 1139-43.
Barribeau Seth M, Sadd Ben M, du Plessis Louis, Brown Mark J F, Buechel Severine D, Cappelle Kaat, Carolan James C, Christiaens Olivier, Colgan Thomas J, Erler Silvio, Evans Jay, Helbing Sophie, Karaus Elke, Lattorff H Michael G, Marxer Monika, Meeus Ivan, Näpflin Kathrin, Niu Jinzhi, Schmid-Hempel Regula, Smagghe Guy, Waterhouse Robert M, Yu Na, Zdobnov Evgeny M, Schmid-Hempel Paul (2015), A depauperate immune repertoire precedes evolution of sociality in bees., in Genome biology
, 16, 83-83.
Sadd Ben M, Barribeau Seth M, Bloch Guy, de Graaf Dirk C, Dearden Peter, Elsik Christine G, Gadau Jürgen, Grimmelikhuijzen Cornelis J P, Hasselmann Martin, Lozier Jeffrey D, Robertson Hugh M, Smagghe Guy, Stolle Eckart, Van Vaerenbergh Matthias, Waterhouse Robert M, Bornberg-Bauer Erich, Klasberg Steffen, Bennett Anna K, Câmara Francisco, Guigó Roderic, Hoff Katharina, Mariotti Marco, Munoz-Torres Monica, Murphy Terence, Santesmasses Didac (2015), The genomes of two key bumblebee species with primitive eusocial organization., in Genome biology
, 16, 76-76.
Zhao Chaoyang, Escalante Lucio Navarro, Chen Hang, Benatti Thiago R, Qu Jiaxin, Chellapilla Sanjay, Waterhouse Robert M, Wheeler David, Andersson Martin N, Bao Riyue, Batterton Matthew, Behura Susanta K, Blankenburg Kerstin P, Caragea Doina, Carolan James C, Coyle Marcus, El-Bouhssini Mustapha, Francisco Liezl, Friedrich Markus, Gill Navdeep, Grace Tony, Grimmelikhuijzen Cornelis J P, Han Yi, Hauser Frank, Herndon Nicolae (2015), A massive expansion of effector genes underlies gall-formation in the wheat pest Mayetiola destructor., in Current biology : CB
, 25(5), 613-20.
Neafsey Daniel E, Waterhouse Robert M, Abai Mohammad R, Aganezov Sergey S, Alekseyev Max A, Allen James E, Amon James, Arcà Bruno, Arensburger Peter, Artemov Gleb, Assour Lauren A, Basseri Hamidreza, Berlin Aaron, Birren Bruce W, Blandin Stephanie A, Brockman Andrew I, Burkot Thomas R, Burt Austin, Chan Clara S, Chauve Cedric, Chiu Joanna C, Christensen Mikkel, Costantini Carlo, Davidson Victoria L M, Deligianni Elena (2014), Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes., in Science (New York, N.Y.)
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Kriventseva Evgenia V, Tegenfeldt Fredrik, Petty Tom J, Waterhouse Robert M, Simão Felipe A, Pozdnyakov Igor A, Ioannidis Panagiotis, Zdobnov Evgeny M (2014), OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software., in Nucleic acids research
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Elsik Christine G, Worley Kim C, Bennett Anna K, Beye Martin, Camara Francisco, Childers Christopher P, de Graaf Dirk C, Debyser Griet, Deng Jixin, Devreese Bart, Elhaik Eran, Evans Jay D, Foster Leonard J, Graur Dan, Guigo Roderic, Guigo Roderic, Hoff Katharina Jasmin, Holder Michael E, Hudson Matthew E, Hunt Greg J, Jiang Huaiyang, Joshi Vandita, Khetani Radhika S, Kosarev Peter, Kovar Christie L (2014), Finding the missing honey bee genes: lessons learned from a genome upgrade., in BMC genomics
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Simola Daniel F, Wissler Lothar, Donahue Greg, Waterhouse Robert M, Helmkampf Martin, Roux Julien, Nygaard Sanne, Glastad Karl M, Hagen Darren E, Viljakainen Lumi, Reese Justin T, Hunt Brendan G, Graur Dan, Elhaik Eran, Kriventseva Evgenia V, Wen Jiayu, Parker Brian J, Cash Elizabeth, Privman Eyal, Childers Christopher P, Muñoz-Torres Monica C, Boomsma Jacobus J, Bornberg-Bauer Erich, Currie Cameron R, Elsik Christine G (2013), Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality., in Genome research
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Kanost Michael R, Arrese Estela L, Cao Xiaolong, Chen Yun-Ru, Chellapilla Sanjay, Goldsmith Marian R, Grosse-Wilde Ewald, Heckel David G, Herndon Nicolae, Jiang Haobo, Papanicolaou Alexie, Qu Jiaxin, Soulages Jose L, Vogel Heiko, Walters James, Waterhouse Robert M, Ahn Seung-Joon, Almeida Francisca C, An Chunju, Aqrawi Peshtewani, Bretschneider Anne, Bryant William B, Bucks Sascha, Chao Hsu, Chevignon Germain (2016), Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta., in Insect biochemistry and molecular biology
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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 (2015), Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection., in Proceedings of the National Academy of Sciences of the United States of America
, 112(48), 14936-41.
i5K Consortium (2013), The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment., in The Journal of heredity
, 104(5), 595-600.
Genomics facilitates a remarkable array of studies of cellular processes at the molecular level. The decreasing costs and growing throughput of sequencing are providing unprecedented opportunities within the reach of many research groups. Beyond whole-genome sequencing of particular organisms, extracting and sequencing DNA directly from environmental samples, termed metagenomics, revolutionized our understanding of the microbial complexity and the role of animal’s microbiota in the biology of their hosts. Yet, the insect genomics revolution is still in its infancy, with fewer than 40 sequenced arthropods and only the very first steps being taken towards initiatives to scale it up to 5’000 (the i5K initiative). Importantly, the technology already allows reading the complete genome of insects together with their microbiomes, from fungi to bacteria to viruses, all in one go. Thus, the discovery snapshot we propose here is denoted as (meta)genomics, although understanding of the microbiome dynamics will require more focused longitudinal studies in the future. It is clear, however, that analysis of such tremendous amounts of data requires further elaboration of computational approaches, and the data analysis costs already outweigh the data generation costs, with the biggest analysis challenge being to link genotype-to-phenotype.
This project is focused on the study of insects. Insects are the most diverse and successful terrestrial animals, encompassing by far the largest number of species. Thus, insect genomes provide an exceptional opportunity to explore the evolutionary processes acting on genes and genomes to understand how these processes translate into new functions and phenotypes. The overarching question of genotype-to-phenotype mapping remains complex, yet it is becoming more feasible as both genotype and phenotype resources are expanding and the large-effect phenotypes of the incredible adaptations in insects, such as the emergence of wings or metamorphosis, provide a clear starting point.
The objectives of this proposal are to:
Aim 1: Sequence (meta)genomes of 20 basal insects representing wingless insects (e.g. springtails, bristletails, and silverfish) and basal winged insects (e.g. mayflies, dragonflies, and damselflies) to dramatically improve the genome sampling from this key phyletic radiation point, and to provide the basis for addressing the genotype-to-phenotype question through large-effect cases such as the evolution of flight and metamorphosis; and to
Aim 2: Advance the state-of-the-art methods in computational (meta)genomics through further development of our comparative toolbox (for analysis of gene orthology, families, ncRNAs, miRNAs and their targets, CNCs, genomic gene arrangements (microsynteny), high throughput phylogenomics, and microbiomes), and the implementation of these tools into pipelines accessible to the research community.
World-leading expertise and a reputation for delivering trustworthy results are key requirements sought after by international consortia. In such consortia, my laboratory led the evolutionary analyses of several recently sequenced animal genomes. This experience and established collaborations with the leading researchers in the field present a unique setting for this project, e.g. the biological material will be provided by our collaborators, the project is endorsed by the i5K consortium, and the Baylor College will advise us on sequencing (see the letters of support provided). Although the aims may appear ambitious, we will prioritise our intermediate targets for the highest potential impact.