Project

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Genomic innovations underlying arthropod success and diversity

Applicant Waterhouse Robert
Number 202669
Funding scheme SNSF Professorships
Research institution Department of Ecology and Evolution University of Lausanne
Institution of higher education University of Lausanne - LA
Main discipline Genetics
Start/End 01.09.2021 - 31.08.2023
Approved amount 796'455.00
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All Disciplines (2)

Discipline
Genetics
Molecular Biology

Keywords (6)

function; arthropods; genomics; biodiversity; evolution; ecology

Lay Summary (French)

Lead
L’Homme est une créature curieuse, qui ne peut s'empêcher d'examiner et de comparer les autres animaux avec lesquels il partage la planète. En observant les similitudes et les différences de morphologie, de cycle de vie et d'écologie des différentes espèces, nous affinons notre compréhension de leurs interactions et apprenons à connaître leur biologie et leur évolution. Grâce aux progrès des technologies de séquençage, nous pouvons désormais comparer les espèces de manière très détaillée au niveau de leur génome et de leur ADN. La diversité dont font preuve les insectes, et plus généralement les arthropodes, en font un système d'étude idéal pour étudier les changements génétiques et génomiques à l'origine de la splendeur de la biodiversité animale.
Lay summary
La possibilité d'obtenir les cartes génétiques de nombreuses espèces, sous la forme de séquences de génomes entiers comportant des milliers de gènes et des milliards de nucléotides (ADN), accroît grandement la résolution de nos observations. Comparer ces génomes permet d’identifier les similitudes et les différences génétiques entre les espèces et de démêler les liens complexes les unissant. Cela permet également de faire progresser la compréhension des fonctions biologiques et des processus d'évolution à l’échelle des molécules, des organismes et des écosystèmes. La diversité des organismes sur Terre est la preuve de solutions évolutives nombreuses et variées aux défis de la vie. L’origine commune des espèces signifie qu’une approche comparative offre la possibilité de reconstruire l'histoire des événements qui ont abouti à la diversité génomique et biologique actuellement observable. En tant que groupe d'animaux terrestres le plus abouti, les arthropodes font preuve d'un vaste éventail d'adaptations évolutives pour exploiter des niches écologiques dans de nombreux écosystèmes différents. Cette diversité, ainsi que leur impact sur les humains et le rôle essentiel qu’ils jouent dans le maintien d'une planète saine, les rend fascinants à étudier comme modèles pour la compréhension des processus biologiques fondamentaux. Ce projet de recherche cherche à répondre aux questions suivantes : (i) quels types de changements ou innovations génomiques conduisent à ou facilitent la diversification des espèces ainsi que certains types d'adaptations du cycle de vie ? Et (ii) quelles sont les règles ou les contraintes qui régissent l'évolution génomique et maintiennent la viabilité des espèces tout en permettant, voire en favorisant, l’augmentation de la diversité biologique ?
Direct link to Lay Summary Last update: 07.07.2021

Responsible applicant and co-applicants

Employees

Publications

Publication
Anopheles mosquitoes reveal new principles of 3D genome organization in insects
Lukyanchikova Varvara, Nuriddinov Miroslav, Belokopytova Polina, Taskina Alena, Liang Jiangtao, Reijnders Maarten J. M. F., Ruzzante Livio, Feron Romain, Waterhouse Robert M., Wu Yang, Mao Chunhong, Tu Zhijian, Sharakhov Igor V., Fishman Veniamin (2022), Anopheles mosquitoes reveal new principles of 3D genome organization in insects, in Nature Communications, 13(1), 1960-1960.
CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation
Reijnders Maarten J. M. F., Waterhouse Robert M. (2022), CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation, in PLOS Computational Biology, 18(5), e1010075-e1010075.
Long-distance dispersal of pigeons and doves generated new ecological opportunities for host-switching and adaptive radiation by their parasites
Boyd Bret M., Nguyen Nam-Phuong, Allen Julie M., Waterhouse Robert M., Vo Kyle B., Sweet Andrew D., Clayton Dale H., Bush Sarah E., Shapiro Michael D., Johnson Kevin P. (2022), Long-distance dispersal of pigeons and doves generated new ecological opportunities for host-switching and adaptive radiation by their parasites, in Proceedings of the Royal Society B: Biological Sciences, 289(1970), 1.
Exploring new genomic territories with emerging model insects
Feron Romain, Waterhouse Robert M. (2022), Exploring new genomic territories with emerging model insects, in Current Opinion in Insect Science, 100902-100902.
Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes
Feron Romain, Waterhouse Robert M (2022), Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes, in GigaScience, 11, giac006.
Functional constraints on insect immune system components govern their evolutionary trajectories
Ruzzante Livio, Feron Romain, Reijnders Maarten J M F, Thiébaut Antonin, Waterhouse Robert M (2021), Functional constraints on insect immune system components govern their evolutionary trajectories, in Molecular Biology and Evolution, 1.

Datasets

Supporting data for "Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes"

Author Feron, Romain; Waterhouse, Robert
Publication date 05.01.2022
Persistent Identifier (PID) 10.5524/100974
Repository GigaDB
Abstract
Ambitious initiatives to coordinate genome sequencing of Earth’s biodiversity mean that the accumulation of genomic data is growing rapidly. In addition to cataloguing biodiversity, these data provide the basis for understanding biological function and evolution. Accurate and complete genome assemblies offer a comprehensive and reliable foundation upon which to advance our understanding of organismal biology at genetic, species, and ecosystem levels. However, ever-changing sequencing technologies and analysis methods mean that available data are often heterogeneous in quality. In order to guide forthcoming genome generation efforts and promote efficient prioritisation of resources, it is thus essential to define and monitor taxonomic coverage and quality of the data.Here we present an automated analysis workflow that surveys genome assemblies from the United States National Center for Biotechnology Information (NCBI), assesses their completeness using the relevant Benchmarking Universal Single-Copy Orthologue (BUSCO) datasets, and collates the results into an interactively browsable resource. We apply our workflow to produce a community resource of available assemblies from the phylum Arthropoda, the Arthropoda Assembly Assessment Catalogue. Using this resource, we survey current taxonomic coverage and assembly quality at the NCBI, we examine how key assembly metrics relate to gene content completeness, and we compare results from using different BUSCO lineage datasets.These results demonstrate how the workflow can be used to build a community resource that enables large-scale assessments to survey species coverage and data quality of available genome assemblies, and to guide prioritisations for ongoing and future sampling, sequencing, and genome generation initiatives.

Collaboration

Group / person Country
Types of collaboration
Lemaitre Group, EPFL Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
University of Neuchâtel Institute of Biology Seminars Individual talk Reference Genomes for European Eukaryotic Biodiversity: How and Why? 28.04.2022 Neuchâtel, Switzerland Waterhouse Robert;
Biodiversity Genomics 2021 Talk given at a conference 3D-organisation of mosquito chromosomes in space and time 28.09.2021 Virtual, Great Britain and Northern Ireland Waterhouse Robert;
Basel Computational Biology Conference Talk given at a conference Evolutionary profiling identifies insect immune gene families that function in concert 14.09.2021 Basel, Switzerland Waterhouse Robert;


Knowledge transfer events

Active participation

Title Type of contribution Date Place Persons involved
Mosquito Immunogenomics MSc Genetics & Molecular Biology Workshop 23.05.2022 Rome, Italy Waterhouse Robert;


Associated projects

Number Title Start Funding scheme
198691 An interdisciplinary study of arthropod moulting: linking genotype, phenotype and life history evolution 01.03.2021 Sinergia
186397 An integrated evolutionary and functional characterisation of the Drosophila immune peptidic secretome 01.07.2019 Sinergia
170664 Exploiting evolutionary signatures to build an enhanced understanding of gene function 01.09.2017 SNSF Professorships
196125 Next-generation data mining of organismal and ecological trait data across Arthropoda 01.12.2020 Spark

Abstract

The comparative approach has been a cornerstone of biological research for centuries. By observing the similarities and differences in species morphologies, life histories, and ecologies, we have refined our understanding of species relationships and learned about their biology and evolution. The ability to obtain genetic blueprints in the form of whole genome sequences from many different species means that the resolution of our observations is now increasingly enhanced and extended: to thousands of genes and billions of nucleotides. Comparisons that identify genetic and genomic similarities and differences have disentangled complex species relationships and advanced understanding of biological function and evolutionary processes at molecular, organismal, and ecosystem levels. The diversity of organisms on Earth today represents many varied evolutionary solutions to life’s challenges. Their common ancestry means that the comparative approach offers the opportunity to reconstruct the history of events that have resulted in currently observable genomic and biological diversity. The questions that this research project therefore seeks to address centre on: (i) what kinds of genomic changes or innovations lead to or facilitate which kinds of life history adaptations and species diversifications? And (ii) what are the rules or constraints governing how genomic evolution proceeds in a manner that maintains viability while allowing or even promoting the generation of biological diversity?Studies exemplifying the state-of-the-art in the field of characterising the genomic basis of animal diversity show that complex gene repertoire evolutionary gain and loss dynamics likely provide the substrate from which diversity can emerge. Early radiations were accompanied by gene family innovations, conservation, and losses that likely underlie key functional shifts in multicellularity, development, homeostasis, and immunity. In younger lineages too, genetic and genomic changes can be associated with adaptations and diversifications such as enhanced immunity and trade-offs amongst vision, smell, and echolocation abilities of bats. As the most successful group of terrestrial animals, arthropods demonstrate a vast array of evolutionary adaptations to exploit ecological niches across many different ecosystems. This diversity makes their biology fascinating to study, as models for understanding fundamental biological processes, as well as because of the impacts they have on humans and their critical roles in maintaining a healthy planet. This, together with accumulating arthropod genomics resources, make them ideal for investigating how conservation or divergence and gains or losses of functional genomic elements give rise to the splendour of animal biology.This project therefore aims to (i) apply computational comparative approaches to infer evolutionary histories of genomic elements and quantify genomic innovations across arthropods; (ii) apply machine learning and text mining methods to enhance gene- and organismal-level functional characterisations; (iii) use these quantifications and characterisations to learn the rules governing how genomic evolution proceeds and how it generates functional-biological diversity; and (iv) apply the same challenges (infections) to multiple species of Drosophila flies to test the functional implications of genomic innovations in terms of gene expression on a system-level biological response, i.e. immunity.By addressing these aims, this project will establish a new set of quantifiable evolutionary features with which the field can characterise element evolutionary histories and genomic innovations in order to explore how these changes relate to observable phenotypic differences. The research will lead to advancements in the field on the one hand covering comparative genomics methodologies, and on the other providing insights into how evolution works and how biodiversity is generated and maintained. Results will demonstrate the importance and highlight the benefits of applying genomic technologies at increasingly complex scales to understand the diversity of life on Earth.
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