Projekt

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Insect (meta)genomics

Titel Englisch Insect (meta)genomics
Gesuchsteller/in Zdobnov Evgeny
Nummer 143936
Förderungsinstrument Projektförderung (Abt. I-III)
Forschungseinrichtung Institut Suisse de Bioinformatique Centre Médical Universitaire Université de Genève
Hochschule Swiss Institute of Bioinformatics - SIB
Hauptdisziplin Genetik
Beginn/Ende 01.01.2013 - 30.06.2016
Bewilligter Betrag 605'700.00
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Keywords (2)

comparative analysis; genomics

Lay Summary (Französisch)

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.

Direktlink auf Lay Summary Letzte Aktualisierung: 22.01.2013

Lay Summary (Englisch)

Lead
Lay summary

Insects are the most diverse and successful terrestrial animals, encompassing by far the largest number of species. Thus, insect DNA provide an exceptional opportunity to explore the evolutionary processes acting on genes to understand how these processes translate into the incredible adaptations in insects, such as the emergence of wings or metamorphosis.

Direktlink auf Lay Summary Letzte Aktualisierung: 01.01.0001

Verantw. Gesuchsteller/in und weitere Gesuchstellende

Mitarbeitende

Publikationen

Publikation
Genome Sequencing of the Phytoseiid Predatory Mite Metaseiulus occidentalis Reveals Completely Atomized Hox Genes and Superdynamic Intron Evolution.
(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.
(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.
(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.
(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.
(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.
(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.
(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.
(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.
(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.
(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.
(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.
(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.
(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.
(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.
(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.
(2013), The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment., in The Journal of heredity, 104(5), 595-600.

Zusammenarbeit

Gruppe / Person Land
Formen der Zusammenarbeit
Misof Bernhard and Niehuis Oliver Deutschland (Europa)
- Publikation

Wissenschaftliche Veranstaltungen

Aktiver Beitrag

Titel Art des Beitrags Titel des Artikels oder Beitrages Datum Ort Beteiligte Personen
BITS 2016 - 13th Annual Meeting of the Bioinformatics Italian Society Poster OrthoDB: genome annotation and interpretation through orthology 15.07.2016 Salerno, Italien Manni Mosé;
Belgrade BioInformatics Conference Vortrag im Rahmen einer Tagung 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, Schweiz Ioannidis Panagiotis;
SIB Days 2016 Poster BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs 07.06.2016 Biel, Schweiz Simao Neto Felipe Aristides;
SIB Days 2016 Vortrag im Rahmen einer Tagung PhyloSIB resources and tools: OrthoDB and BUSCO 07.06.2016 Biel, Schweiz Waterhouse Robert;
invited speaker Einzelvortrag Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes 15.01.2016 • UC Riverside, Center for Disease Vector Research, Vereinigte Staaten von Amerika Waterhouse Robert;
Plant and Animal Genome Conference XXIV Vortrag im Rahmen einer Tagung BUSCO: Assessing Genome Assembly and Annotation Completeness with Single-Copy Orthologs 08.01.2016 San Diego , Vereinigte Staaten von Amerika Simao Neto Felipe Aristides;
Séminaire Symbiose, INRIA/Irisa Vortrag im Rahmen einer Tagung Orthology-based genome annotation and interpretation 03.12.2015 Université de Rennes-1, Frankreich Waterhouse Robert;
American Committee of Medical Entomology Vortrag im Rahmen einer Tagung Comparative genomics of fundamental processes in vector taxa 25.10.2015 Philadelphia, Vereinigte Staaten von Amerika Waterhouse Robert;
Department of Genetic Medicine and Development Seminar Series Einzelvortrag Sequencing the genome of a 'basal' insect: the damselfly Calopteryx splendens 06.10.2015 Geneva, Schweiz Ioannidis Panagiotis;
SIB Training Network PhD retreat Vortrag im Rahmen einer Tagung BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs 02.07.2015 Bern, Schweiz Simao Neto Felipe Aristides;
7th International Meeting on Molecular & Population Biology of Mosquitoes & Other Disease Vectors Vortrag im Rahmen einer Tagung Evolutionary systems biology in a collaborative analysis and visualisation environment 24.06.2015 Crete, Griechenland Waterhouse Robert;
9th Annual Arthropod Genomics Symposium Vortrag im Rahmen einer Tagung i5k at OrthoDB 17.06.2015 Manhattan, Kansas, Vereinigte Staaten von Amerika Waterhouse Robert;
9th Annual Arthropod Genomics Symposium Poster BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs 17.06.2015 Manhattan, Kansas, Vereinigte Staaten von Amerika Simao Neto Felipe Aristides;
9th Annual Arthropod Genomics Symposium Poster Genome sequencing of the damselfly Calopteryx splendens (Arthropoda:Odonata) 17.06.2015 Manhattan, Kansas, Vereinigte Staaten von Amerika Ioannidis Panagiotis;
PhyloSIB 2015 Vortrag im Rahmen einer Tagung BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs 07.06.2015 Basel, Schweiz Simao Neto Felipe Aristides;
QfO 2015 Vortrag im Rahmen einer Tagung OrthoDB in 2015: scaling up the data and the user experience 25.05.2015 Barselona, Spanien Zdobnov Evgeny;
Department of Genetic Medicine and Development Seminar Series Einzelvortrag Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes 10.03.2015 Geneva, Schweiz Waterhouse Robert;
Entomological Soc. Am., The Futures of Insect Genomics: A Grand Challenge of Entomology Vortrag im Rahmen einer Tagung Towards a complete catalogue of functional genomic elements from multiple Anopheles genomes 16.11.2014 Portland, Vereinigte Staaten von Amerika Waterhouse Robert;
Department of Genetic Medicine and Development Seminar Series Einzelvortrag Intron dynamics of the in the predatory mite Metaseiulus occidentalis (Acari:Phytoseiidae) 23.09.2014 Geneva, Schweiz 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, Niederlande Simao Neto Felipe Aristides;
Seventh International Symposium on Molecular Insect Science Poster Genome sequencing of Calopteryx splendens (Odonata) and Thermobia domestica (Zygentoma) 13.07.2014 Amsterdam, Niederlande Ioannidis Panagiotis;
Seventh International Symposium on Molecular Insect Science Vortrag im Rahmen einer Tagung Towards a complete catalogue of functional genomic elements from multiple Anopheles genomes 13.07.2014 Amsterdam, Niederlande Waterhouse Robert;
SIB Training Network PhD retreat Poster BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs 07.07.2014 Bern, Schweiz Simao Neto Felipe Aristides;
ALPHY/PhyloSIB 2014, Swiss-French meeting on Bioinformatics and Evolutionary Genomics Vortrag im Rahmen einer Tagung Phylogeny of the hessian fly, Mayetiola destructor 04.02.2014 Geneva, Schweiz Ioannidis Panagiotis;
SIB Days 2014 Poster BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs 27.01.2014 Biel, Schweiz Simao Neto Felipe Aristides;
The Broad Institute of Harvard & MIT Einzelvortrag Orthology-based genome annotation and interpretation 07.11.2013 Cambridge, Vereinigte Staaten von Amerika Waterhouse Robert;
Biological Sciences, University of Massachusetts Einzelvortrag Genome biology of disease-vector insects and other bugs 25.09.2013 Lowell, Vereinigte Staaten von Amerika Waterhouse Robert;
Quest for Orthologs III Vortrag im Rahmen einer Tagung OrthoDB: latest developments 24.07.2013 Lausanne, Schweiz Zdobnov Evgeny;
6th International Meeting on Molecular & Population Biology of Mosquitoes & Other Disease Vectors Vortrag im Rahmen einer Tagung Towards a complete catalogue of functional genomic elements from multiple Anopheles genomes 17.07.2013 Crete, Griechenland Waterhouse Robert;
Alexander Koenig Research Museum Einzelvortrag Genome biology of disease-vector insects and other arthropods 04.07.2013 Bonn, Deutschland Waterhouse Robert;
7th Annual Arthropod Genomics Symposium Vortrag im Rahmen einer Tagung Orthology-based genome annotation and interpretation 15.06.2013 Notre Dame, Indiana, Vereinigte Staaten von Amerika Waterhouse Robert;


Kommunikation mit der Öffentlichkeit

Kommunikation Titel Medien Ort Jahr
Medienarbeit: Radio, Fernsehen CQFD Westschweiz 2016
Medienarbeit: Printmedien, Online-Medien Des Suisses décodent le génome de la tique. Westschweiz 2016
Medienarbeit: Printmedien, Online-Medien Genome of the predatory mite Metaseiulus occidentalis International 2016
Neue Medien (Web, Blogs, Podcasts, NewsFeed, usw.) BUSCO tool for assessing assembly completeness International 2015
Medienarbeit: Printmedien, Online-Medien Les génomes des bourdons créent le buzz dans le domaine de la pollinisation Westschweiz 2015
Medienarbeit: Radio, Fernsehen Genomes of 16 Anopheles mosquitoes International 2014

Verbundene Projekte

Nummer Titel Start Förderungsinstrument
170664 Exploiting evolutionary signatures to build an enhanced understanding of gene function 01.09.2017 SNF-Förderungsprofessuren
125350 Computational insect genomics 01.01.2010 Projektförderung (Abt. I-III)
118375 Computational identification of microRNA genes and their targets 01.01.2008 ProDoc (Forschungsmodul, FM)
112588 Computational comparative analysis of insect genomes 01.04.2006 Projektförderung (Abt. I-III)
127347 Investigation of vertebrate CNC repertoire expansion and neofunctionalization 01.02.2011 ProDoc (Forschungsmodul, FM)

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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