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Insect (meta)genomics

English title Insect (meta)genomics
Applicant Zdobnov Evgeny
Number 143936
Funding scheme Project funding (Div. I-III)
Research institution Institut Suisse de Bioinformatique Centre Médical Universitaire Université de Genève
Institution of higher education Swiss Institute of Bioinformatics - SIB
Main discipline Genetics
Start/End 01.01.2013 - 30.06.2016
Approved amount 605'700.00
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Keywords (2)

comparative analysis; genomics

Lay Summary (French)

Lead
Ce projet est centré sur l’étude des insectes, qui comprennent un grand nombre d’espèces, ainsi le génome des insectes fournit une excellente occasion d’explorer les processus évolutifs qui agissent sur les gènes et les génomes.
Lay summary

Ce projet est centré sur l’étude des insectes. Les insectes, qui comprennent un grand nombre d’espèces, sont des animaux jouissant de la plus grande diversité et distribution terrestre. Ainsi le génome des insectes fournit une excellente occasion d’explorer les processus évolutifs qui agissent sur les gènes et les génomes, et permet de comprendre comment ces processus se traduisent en nouvelles fonctions et nouveaux phénotypes. La génomique facilite un grand nombre d’études des processus cellulaires au niveau moléculaire. La diminution des coûts et l’augmentation des capacités de séquençage ouvrent de nouvelles opportunités accessibles à de nombreux groupes de recherche. Il est cependant évident que l’analyse d’une telle quantité de données nécessite la conception de méthodes computationnelles. Le coût de l’analyse des données dépasse déjà le coût de leur production, le plus grand défi de l’analyse étant de lier le génotype au phénotype. Les objectifs de cette étude sont: (a) séquencer les génomes de vingt insectes à la base de la phylogénie qui représente les insectes sans ailes (par exemple les collemboles et les poissons d’argent) et les insectes munis d’ailes (par exemple les libellules et les demoiselles) d’adresser la questions comme l’Evolution du vol et la métamorphose; (b) avancer les méthodes de pointe en génomique computationnelle.

Direct link to Lay Summary Last update: 22.01.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
Genome Sequencing of the Phytoseiid Predatory Mite Metaseiulus occidentalis Reveals Completely Atomized Hox Genes and Superdynamic Intron Evolution.
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.
Genomic insights into the Ixodes scapularis tick vector of Lyme disease.
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.
Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta.
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, 76, 118-47.
Unique features of a global human ectoparasite identified through sequencing of the bed bug genome.
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.
A depauperate immune repertoire precedes evolution of sociality in bees.
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.
A massive expansion of effector genes underlies gall-formation in the wheat pest Mayetiola destructor.
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.
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
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.
Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection.
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.
Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions.
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.
Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.
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.
The genomes of two key bumblebee species with primitive eusocial organization.
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.
Finding the missing honey bee genes: lessons learned from a genome upgrade.
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, 15, 86-86.
Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.
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.), 347(6217), 1258522-1258522.
OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software.
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, 43(Database i), 250-6.
Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality.
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, 23(8), 1235-47.
The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment.
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.

Collaboration

Group / person Country
Types of collaboration
Misof Bernhard and Niehuis Oliver Germany (Europe)
- Publication

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
BITS 2016 - 13th Annual Meeting of the Bioinformatics Italian Society Poster OrthoDB: genome annotation and interpretation through orthology 15.07.2016 Salerno, Italy Manni Mosé;
Belgrade BioInformatics Conference Talk given at a conference OrthoDB: an evolutionary perspective to interpreting genomics data 24.06.2016 Belgrade, Serbien Waterhouse Robert;
SIB Days 2016 Poster The draft genome of the damselfly Calopteryx splendens reveals unique features of early-divergent insect lineages 07.06.2016 biel, Switzerland Ioannidis Panagiotis;
SIB Days 2016 Poster BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs 07.06.2016 Biel, Switzerland Simao Neto Felipe;
SIB Days 2016 Talk given at a conference PhyloSIB resources and tools: OrthoDB and BUSCO 07.06.2016 Biel, Switzerland Waterhouse Robert;
invited speaker Individual talk Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes 15.01.2016 • UC Riverside, Center for Disease Vector Research, United States of America Waterhouse Robert;
Plant and Animal Genome Conference XXIV Talk given at a conference BUSCO: Assessing Genome Assembly and Annotation Completeness with Single-Copy Orthologs 08.01.2016 San Diego , United States of America Simao Neto Felipe;
Séminaire Symbiose, INRIA/Irisa Talk given at a conference Orthology-based genome annotation and interpretation 03.12.2015 Université de Rennes-1, France Waterhouse Robert;
American Committee of Medical Entomology Talk given at a conference Comparative genomics of fundamental processes in vector taxa 25.10.2015 Philadelphia, United States of America Waterhouse Robert;
Department of Genetic Medicine and Development Seminar Series Individual talk Sequencing the genome of a 'basal' insect: the damselfly Calopteryx splendens 06.10.2015 Geneva, Switzerland Ioannidis Panagiotis;
SIB Training Network PhD retreat Talk given at a conference BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs 02.07.2015 Bern, Switzerland Simao Neto Felipe;
7th International Meeting on Molecular & Population Biology of Mosquitoes & Other Disease Vectors Talk given at a conference Evolutionary systems biology in a collaborative analysis and visualisation environment 24.06.2015 Crete, Greece Waterhouse Robert;
9th Annual Arthropod Genomics Symposium Talk given at a conference i5k at OrthoDB 17.06.2015 Manhattan, Kansas, United States of America Waterhouse Robert;
9th Annual Arthropod Genomics Symposium Poster BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs 17.06.2015 Manhattan, Kansas, United States of America Simao Neto Felipe;
9th Annual Arthropod Genomics Symposium Poster Genome sequencing of the damselfly Calopteryx splendens (Arthropoda:Odonata) 17.06.2015 Manhattan, Kansas, United States of America Ioannidis Panagiotis;
PhyloSIB 2015 Talk given at a conference BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs 07.06.2015 Basel, Switzerland Simao Neto Felipe;
QfO 2015 Talk given at a conference OrthoDB in 2015: scaling up the data and the user experience 25.05.2015 Barselona, Spain Zdobnov Evgeny;
Department of Genetic Medicine and Development Seminar Series Individual talk Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes 10.03.2015 Geneva, Switzerland Waterhouse Robert;
Entomological Soc. Am., The Futures of Insect Genomics: A Grand Challenge of Entomology Talk given at a conference Towards a complete catalogue of functional genomic elements from multiple Anopheles genomes 16.11.2014 Portland, United States of America Waterhouse Robert;
Department of Genetic Medicine and Development Seminar Series Individual talk Intron dynamics of the in the predatory mite Metaseiulus occidentalis (Acari:Phytoseiidae) 23.09.2014 Geneva, Switzerland Ioannidis Panagiotis;
Seventh International Symposium on Molecular Insect Science Poster BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs 13.07.2014 Amsterdam, Netherlands Simao Neto Felipe;
Seventh International Symposium on Molecular Insect Science Poster Genome sequencing of Calopteryx splendens (Odonata) and Thermobia domestica (Zygentoma) 13.07.2014 Amsterdam, Netherlands Ioannidis Panagiotis;
Seventh International Symposium on Molecular Insect Science Talk given at a conference Towards a complete catalogue of functional genomic elements from multiple Anopheles genomes 13.07.2014 Amsterdam, Netherlands Waterhouse Robert;
SIB Training Network PhD retreat Poster BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs 07.07.2014 Bern, Switzerland Simao Neto Felipe;
ALPHY/PhyloSIB 2014, Swiss-French meeting on Bioinformatics and Evolutionary Genomics Talk given at a conference Phylogeny of the hessian fly, Mayetiola destructor 04.02.2014 Geneva, Switzerland Ioannidis Panagiotis;
SIB Days 2014 Poster BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs 27.01.2014 Biel, Switzerland Simao Neto Felipe;
The Broad Institute of Harvard & MIT Individual talk Orthology-based genome annotation and interpretation 07.11.2013 Cambridge, United States of America Waterhouse Robert;
Biological Sciences, University of Massachusetts Individual talk Genome biology of disease-vector insects and other bugs 25.09.2013 Lowell, United States of America Waterhouse Robert;
Quest for Orthologs III Talk given at a conference OrthoDB: latest developments 24.07.2013 Lausanne, Switzerland Zdobnov Evgeny;
6th International Meeting on Molecular & Population Biology of Mosquitoes & Other Disease Vectors Talk given at a conference Towards a complete catalogue of functional genomic elements from multiple Anopheles genomes 17.07.2013 Crete, Greece Waterhouse Robert;
Alexander Koenig Research Museum Individual talk Genome biology of disease-vector insects and other arthropods 04.07.2013 Bonn, Germany Waterhouse Robert;
7th Annual Arthropod Genomics Symposium Talk given at a conference Orthology-based genome annotation and interpretation 15.06.2013 Notre Dame, Indiana, United States of America Waterhouse Robert;


Communication with the public

Communication Title Media Place Year
Media relations: radio, television CQFD Western Switzerland 2016
Media relations: print media, online media Des Suisses décodent le génome de la tique. Western Switzerland 2016
Media relations: print media, online media Genome of the predatory mite Metaseiulus occidentalis International 2016
New media (web, blogs, podcasts, news feeds etc.) BUSCO tool for assessing assembly completeness International 2015
Media relations: print media, online media Les génomes des bourdons créent le buzz dans le domaine de la pollinisation Western Switzerland 2015
Media relations: radio, television Genomes of 16 Anopheles mosquitoes International 2014

Associated projects

Number Title Start Funding scheme
170664 Exploiting evolutionary signatures to build an enhanced understanding of gene function 01.09.2017 SNSF Professorships
125350 Computational insect genomics 01.01.2010 Project funding (Div. I-III)
118375 Computational identification of microRNA genes and their targets 01.01.2008 ProDoc
112588 Computational comparative analysis of insect genomes 01.04.2006 Project funding (Div. I-III)
127347 Investigation of vertebrate CNC repertoire expansion and neofunctionalization 01.02.2011 ProDoc

Abstract

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 toAim 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.
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