Comparative genomics of non-model invertebrates

Livrables

Popularization events and activities

Popularization events and activities documented

IGNITE logo, flyers, website

IGNITE logo, flyers, website established and available.

All data, workflows, algorithms & software released

All data, workflows, algorithms & software released to the public.

First scientific publications drafted

First scientific publications drafted and prepared for submission.

Phylogenies

Phylogenies published

Genome evolution reconstruction

Genome evolution reconstruction completed

Scientific publications published

Main scientific publications published

Lists of developmental, cell & tissue genes

Lists of developmental cell tissue genes published

Timetrees

Timetrees published

Lists of holobiont & bioproduct genes

Lists of holobiont bioproduct genes published

International Scientific Conference and its report

International Scientific Conference conducted and its report published.

Publications

Comparative proteomics of octocoral and scleractinian skeletomes and the evolution of coral calcification

Auteurs: Sergio Vargas; Gert Wörheide; Nicola Conci; Martin Lehmann
Publié dans: Genome Biology and Evolution, Numéro 12/9, 2020, Page(s) 1623–1635, ISSN 1759-6653
Éditeur: Oxford University Press
DOI: 10.1101/2019.12.30.891028

Eukaryogenesis and oxygen in Earth history

Auteurs: Mills DB, Boyle RA, Daines SJ, Sperling EA, Pisani D, Donoghue PCJ & Lenton TM
Publié dans: Nature Ecology and Evolution, 2022, ISSN 2397-334X
Éditeur: Springer Nature
DOI: 10.1038/s41559-022-01733-y

Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga

Auteurs: Simion P, Narayan J, Houtain A, Derzelle A, Baudry L, Nicolas E, Arora R, Cariou M, Cruaud C, Gaudray FR, Gilbert C, Guiglielmoni N, Hespeels B, Kozlowski DKL, Labadie K, Limasset A, Llirós M, Marbouty M, Terwagne M, Virgo J, Cordaux R, Danchin EGJ, Hallet B, Koszul R, Lenormand T, Flot J-F, Van Doninck K
Publié dans: Science Advances, 2021, ISSN 2375-2548
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/sciadv.abg4216

instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder

Auteurs: Lyam Baudry, Nadège Guiglielmoni, Hervé Marie-Nelly, Alexandre Cormier, Martial Marbouty, Komlan Avia, Yann Loe Mie, Olivier Godfroy, Lieven Sterck, J. Mark Cock, Christophe Zimmer, Susana M. Coelho, Romain Koszul
Publié dans: Genome Biology, Numéro 21/1, 2020, Page(s) 148, ISSN 1474-760X
Éditeur: BioMed Central
DOI: 10.1186/s13059-020-02041-z

Integrated phylogenomic and fossil evidence of stick and leaf insects (Phasmatodea) reveal a Permian–Triassic coorigination with insectivores

Auteurs: Tihelka E, Chenyang C, Giacomelli M, Pisani D, Donoghue PCJ
Publié dans: R Soc. Open Sciences, 2020, ISSN 2054-5703
Éditeur: Royal Society
DOI: 10.1098/rsos.201689

Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp. nov

Auteurs: J. Grace Klinges, Stephanie M. Rosales, Ryan McMinds, Elizabeth C. Shaver, Andrew A. Shantz, Esther C. Peters, Michael Eitel, Gert Wörheide, Koty H. Sharp, Deron E. Burkepile, Brian R. Silliman, Rebecca L. Vega Thurber
Publié dans: The ISME Journal, Numéro 13/12, 2019, Page(s) 2938-2953, ISSN 1751-7362
Éditeur: Nature Publishing Group
DOI: 10.1038/s41396-019-0482-0

Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult

Auteurs: Benoit Morel, Pierre Barbera, Lucas Czech, Ben Bettisworth, Lukas Hübner, Sarah Lutteropp, Dora Serdari, Evangelia-Georgia Kostaki, Ioannis Mamais, Alexey M Kozlov, Pavlos Pavlidis, Dimitrios Paraskevis, Alexandros Stamatakis
Publié dans: Molecular Biology and Evolution, 2020, ISSN 1537-1719
Éditeur: Society for Molecular Biology and Evolution
DOI: 10.1093/molbev/msaa314

New Non-Bilaterian Transcriptomes Provide Novel Insights into the Evolution of Coral Skeletomes

Auteurs: Nicola Conci, Gert Wörheide, Sergio Vargas
Publié dans: Genome Biology and Evolution, Numéro 11/11, 2019, Page(s) 3068-3081, ISSN 1759-6653
Éditeur: Oxford University Press
DOI: 10.1093/gbe/evz199

Author Correction: Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida

Auteurs: Jesus Lozano-Fernandez, Alastair R. Tanner, Mattia Giacomelli, Robert Carton, Jakob Vinther, Gregory D. Edgecombe, Davide Pisani
Publié dans: Nature Communications, Numéro 10/1, 2019, Page(s) 4534, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-019-12259-6

Computer vision for pattern detection in chromosome contact maps

Auteurs: Cyril Matthey-Doret, Lyam Baudry, Axel Breuer, Rémi Montagne, Nadège Guiglielmoni, Vittore Scolari, Etienne Jean, Arnaud Campeas, Philippe Henri Chanut, Edgar Oriol, Adrien Méot, Laurent Politis, Antoine Vigouroux, Pierrick Moreau, Romain Koszul, Axel Cournac
Publié dans: Nature Communications, Numéro 11/1, 2020, Page(s) 5795, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-020-19562-7

Comparative genomics and the nature of placozoan species

Auteurs: Michael Eitel, Warren R. Francis, Frédérique Varoqueaux, Jean Daraspe, Hans-Jürgen Osigus, Stefan Krebs, Sergio Vargas, Helmut Blum, Gray A. Williams, Bernd Schierwater, Gert Wörheide
Publié dans: PLOS Biology, Numéro 16/7, 2018, Page(s) e2005359, ISSN 1545-7885
Éditeur: Public Library of Science
DOI: 10.1371/journal.pbio.2005359

Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida

Auteurs: Jesus Lozano-Fernandez, Alastair R. Tanner, Mattia Giacomelli, Robert Carton, Jakob Vinther, Gregory D. Edgecombe, Davide Pisani
Publié dans: Nature Communications, Numéro 10/1, 2019, Page(s) 2295, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-019-10244-7

Pancrustacean Evolution Illuminated by Taxon-Rich Genomic-Scale Data Sets with an Expanded Remipede Sampling

Auteurs: Jesus Lozano-Fernandez, Mattia Giacomelli, James F Fleming, Albert Chen, Jakob Vinther, Philip Francis Thomsen, Henrik Glenner, Ferran Palero, David A Legg, Thomas M Iliffe, Davide Pisani, Jørgen Olesen
Publié dans: Genome Biology and Evolution, Numéro 11/8, 2019, Page(s) 2055-2070, ISSN 1759-6653
Éditeur: Oxford University Press
DOI: 10.1093/gbe/evz097

OpenBiodiv: A Knowledge Graph for Literature-Extracted Linked Open Data in Biodiversity Science

Auteurs: Lyubomir Penev, Mariya Dimitrova, Viktor Senderov, Georgi Zhelezov, Teodor Georgiev, Pavel Stoev, Kiril Simov
Publié dans: Publications, Numéro 7/2, 2019, Page(s) 38, ISSN 2304-6775
Éditeur: MDPI
DOI: 10.3390/publications7020038

Computational discovery of hidden breaks in 28S ribosomal RNAs across eukaryotes and consequences for RNA Integrity Numbers

Auteurs: Paschalis Natsidis, Philipp H. Schiffer, Irepan Salvador-Martínez, Maximilian J. Telford
Publié dans: Scientific Reports, Numéro 9/1, 2019, Page(s) 19477, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-019-55573-1

The complete mitogenome of Arion vulgaris Moquin-Tandon, 1855 (Gastropoda: Stylommatophora): mitochondrial genome architecture, evolution and phylogenetic considerations within Stylommatophora

Auteurs: Özgül Doğan, Michael Schrödl, Zeyuan Chen
Publié dans: PeerJ, Numéro 8, 2020, Page(s) e8603, ISSN 2167-8359
Éditeur: PeerJ
DOI: 10.7717/peerj.8603

Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms

Auteurs: Guiglielmoni N, Houtain A, Derzelle A, Van Doninck K, Flot J-F
Publié dans: BMC Bioinformatics, 2021, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859‐021‐04118‐3

Streamlined Conversion of Omics Metadata into Manuscript Facilitates Publishing and Reuse of Omics Data

Auteurs: Mariya Dimitrova, Raïssa Meyer, Pier Luigi Buttigieg, Teodor Georgiev, Georgi Zhelezov, Seyhan Demirov, Vincent Smith, Lyubomir Penev
Publié dans: Biodiversity Information Science and Standards, Numéro 4, 2020, Page(s) e59041, ISSN 2535-0897
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.4.59041

The Ediacaran origin of Ecdysozoa: integrating fossil and phylogenomic data.

Auteurs: Howard RJ, Giacomelli M, Lozano-Fernandez J, Edgecombe GD, Fleming JF, Kristensen RM, Ma X, Olesen J, Sørensen MV, Thomsen PF, Wills MA, Donoghue PCJ, Pisani D
Publié dans: Journal of the Geological Society, 2022, ISSN 0016-7649
Éditeur: Geological Society Publishing House
DOI: 10.1144/jgs2021-107

The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest

Auteurs: Claude Rispe, Fabrice Legeai, Paul D. Nabity, Rosa Fernández, Arinder K. Arora, Patrice Baa-Puyoulet, Celeste R. Banfill, Leticia Bao, Miquel Barberà, Maryem Bouallègue, Anthony Bretaudeau, Jennifer A. Brisson, Federica Calevro, Pierre Capy, Olivier Catrice, Thomas Chertemps, Carole Couture, Laurent Delière, Angela E. Douglas, Keith Dufault-Thompson, Paula Escuer, Honglin Feng, Astrid Forneck,
Publié dans: BMC Biology, Numéro 18/1, 2020, Page(s) Article number: 90, ISSN 1741-7007
Éditeur: BioMed Central
DOI: 10.1186/s12915-020-00820-5

Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri

Auteurs: Nathan J. Kenny, Warren R. Francis, Ramón E. Rivera-Vicéns, Ksenia Juravel, Alex de Mendoza, Cristina Díez-Vives, Ryan Lister, Luis A. Bezares-Calderón, Lauren Grombacher, Maša Roller, Lael D. Barlow, Sara Camilli, Joseph F. Ryan, Gert Wörheide, April L. Hill, Ana Riesgo, Sally P. Leys
Publié dans: Nature Communications, Numéro 11/1, 2020, Page(s) 3676, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-020-17397-w

The role of homology and orthology in the phylogenomic analysis of metazoan gene content

Auteurs: Davide Pisani; Gert Wörheide; Michael Eitel; Maja Adamska; Marcin Adamski; Warren R. Francis; Walker Pett
Publié dans: Molecular Biology and Evolution, Numéro 36/4, 2019, Page(s) 643–649, ISSN 0737-4038
Éditeur: Oxford University Press
DOI: 10.1093/molbev/msz013

Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks

Auteurs: Farhat S, Bonnivard E, Pales Espinosa E, Tanguy A, Boutet I, Guiglielmoni N, Flot J-F, Allam B
Publié dans: BMC Genomics, 2022, ISSN 1471-2164
Éditeur: BioMed Central
DOI: 10.1186/s12864-021-08262-1

Integrated phylogenomicsand fossil data illuminatethe evolution of beetles

Auteurs: Cai C, Tihelka E, Giacomelli M, Lawrence JF, Ślipiński A, Kundrata R, Yamamoto S, Thayer MK, Newton AF, Leschen RAB, Gimmel ML, Lü L, Engel MS, Bouchard P, Huang D, Pisani D, Donoghue PCJ
Publié dans: R. Soc Open Sciences, 2022, ISSN 2054-5703
Éditeur: Royal Society
DOI: 10.1098/rsos.211771

Profiling cellular diversity in sponges informs animal cell type and nervous system evolution

Auteurs: Jacob M. Musser, Klaske J. Schippers, Michael Nickel, Giulia Mizzon, Andrea B. Kohn,Constantin Pape, Paolo Ronchi, Nikolaos Papadopoulos, Alexander J. Tarashansky,Jörg U. Hammel, Florian Wolf2, Cong Liang, Ana Hernández-Plaza, Carlos P. Cantalapiedra,Kaia Achim, Nicole L. Schieber6, Leslie Pan, Fabian Ruperti, Warren R. Francis, Sergio Vargas,Svenja Kling, Maike Renkert, Maxim Polikarpov, Gleb B
Publié dans: Science, 2021, ISSN 0036-8075
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/science.abj2949

Anaerobic metabolism of Foraminifera thriving below the seafloor

Auteurs: William D. Orsi, Raphaël Morard, Aurele Vuillemin, Michael Eitel, Gert Wörheide, Jana Milucka, Michal Kucera
Publié dans: The ISME Journal, Numéro 14/10, 2020, Page(s) 2580-2594, ISSN 1751-7362
Éditeur: Nature Publishing Group
DOI: 10.1038/s41396-020-0708-1

Root Digger: a root placement program for phylogenetic trees.

Auteurs: Ben Bettisworth; Alexandros Stamatakis; Alexandros Stamatakis
Publié dans: BMC Bioinformatics, 2021, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.5445/ir/1000133165

Correction: Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp. nov

Auteurs: J. Grace Klinges, Stephanie M. Rosales, Ryan McMinds, Elizabeth C. Shaver, Andrew A. Shantz, Esther C. Peters, Michael Eitel, Gert Wörheide, Koty H. Sharp, Deron E. Burkepile, Brian R. Silliman, Rebecca L. Vega Thurber
Publié dans: The ISME Journal, Numéro 14/1, 2020, Page(s) 322-322, ISSN 1751-7362
Éditeur: Nature Publishing Group
DOI: 10.1038/s41396-019-0509-6

Chromosome-level genome assembly and annotation of two lineages of the ant Cataglyphis hispanica: steppingstones towards genomic studies of hybridogenesis and thermal adaptation in desert ants

Auteurs: Darras H, Araujo N de S, Baudry L, Guiglielmoni N, Lorite P, Marbouty M, Rodriguez F, Arkhipova I, Koszul R, Flot J-F, Aron S
Publié dans: bioRxiv, 2022
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.01.07.475286

Empirical Analysis of Phylogenetic Quasi-Terraces

Auteurs: Paula Breitling, Ben Bettisworth, Lukasz Reszczynski, Olga Chernomor, Alexandros Stamatakis
Publié dans: bioRxiv, 2019
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/810309

GraphUnzip: unzipping assembly graphs with long reads and Hi-C

Auteurs: Faure R, Guiglielmoni N, Flot J-F
Publié dans: bioRxiv, 2021
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2021.01.29.428779

A deep dive into genome assemblies of non-vertebrate animals

Auteurs: Guiglielmoni N, Rivera-Vicéns R, Koszul R, Flot J-F
Publié dans: Preprints, 2021
Éditeur: Multidisciplinary Digital Publishing Institute
DOI: 10.20944/preprints202111.0170.v1

Phylourny: Predicting the Knock-out-phase of Tournaments via Phylogenetic Methods by example of the UEFA EURO 2020

Auteurs: Ben Bettisworth, Alexandros Stamatakis
Publié dans: bioRxiv, 2020
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2021.06.24.449715

OpenBiodiv-O Ontology: Bridging the Gap Between Biodiversity Data and Biodiversity Publishing

Auteurs: Mariya Dimitrova, Viktor Senderov, Kiril Simov, Teodor Georgiev, Lyubomir Penev
Publié dans: Biodiversity Information Science and Standards, Numéro 3, 2019, Page(s) e35773, ISSN 2535-0897
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.3.35773

Data Auditing, Cleaning and Quality Assurance Workflows from the Experience of a Scholarly Publisher

Auteurs: Lyubomir Penev, Teodor Georgiev, Mariya Dimitrova, Yasen Mutafchiev, Pavel Stoev, Robert Mesibov
Publié dans: Biodiversity Information Science and Standards, Numéro 3, 2019, Page(s) e35019, ISSN 2535-0897
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.3.35019

The Pensoft Data Publishing Workflow: The FAIRway from articles to Linked Open Data

Auteurs: Lyubomir Penev, Teodor Georgiev, Viktor Senderov, Mariya Dimitrova, Pavel Stoev
Publié dans: Biodiversity Information Science and Standards, Numéro 3, 2019, Page(s) e35902, ISSN 2535-0897
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.3.35902

Mobilizing Data from Taxonomic Literature for an Iconic Species (Dinosauria, Theropoda, Tyrannosaurus rex)

Auteurs: Jeremy Miller, Yanell Braumuller, Puneet Kishor, David Shorthouse, Mariya Dimitrova, Guido Sautter, Donat Agosti
Publié dans: Biodiversity Information Science and Standards, Numéro 3, 2019, Page(s) e37078, ISSN 2535-0897
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.3.37078

OpenBiodiv: Linking Type Materials, Institutions, Locations and Taxonomic Names Extracted From Scholarly Literature

Auteurs: Mariya Dimitrova, Viktor Senderov, Teodor Georgiev, Georgi Zhelezov, Lyubomir Penev
Publié dans: Biodiversity Information Science and Standards, Numéro 3, 2019, Page(s) e35089, ISSN 2535-0897
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.3.35089

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