Comparative genomics of non-model invertebrates

Informazioni relative al progetto

IGNITE

ID dell’accordo di sovvenzione: 764840

DOI 10.3030/764840

Progetto chiuso

Data della firma CE 2 Agosto 2017

Data di avvio 1 Gennaio 2018

Data di completamento 30 Giugno 2022

Finanziato da

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Costo totale € 3 810 631,42

Contributo UE € 3 810 631,42

Coordinato da

LUDWIG-MAXIMILIANS-UNIVERSITAET MUENCHEN
Germany

Risultati finali

Websites, patent fillings, videos etc. (2)

Popularization events and activities

Popularization events and activities documented

IGNITE logo, flyers, website

IGNITE logo, flyers, website established and available.

Other (1)

All data, workflows, algorithms & software released

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

Documents, reports (8)

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.

Pubblicazioni

Peer reviewed articles (28)

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

Autori: Sergio Vargas; Gert Wörheide; Nicola Conci; Martin Lehmann
Pubblicato in: Genome Biology and Evolution, Numero 12/9, 2020, Pagina/e 1623–1635, ISSN 1759-6653
Editore: Oxford University Press
DOI: 10.1101/2019.12.30.891028

Eukaryogenesis and oxygen in Earth history

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

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

Autori: 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
Pubblicato in: Science Advances, 2021, ISSN 2375-2548
Editore: 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

Autori: 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
Pubblicato in: Genome Biology, Numero 21/1, 2020, Pagina/e 148, ISSN 1474-760X
Editore: 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

Autori: Tihelka E, Chenyang C, Giacomelli M, Pisani D, Donoghue PCJ
Pubblicato in: R Soc. Open Sciences, 2020, ISSN 2054-5703
Editore: 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

Autori: 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
Pubblicato in: The ISME Journal, Numero 13/12, 2019, Pagina/e 2938-2953, ISSN 1751-7362
Editore: Nature Publishing Group
DOI: 10.1038/s41396-019-0482-0

Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult

Autori: 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
Pubblicato in: Molecular Biology and Evolution, 2020, ISSN 1537-1719
Editore: Society for Molecular Biology and Evolution
DOI: 10.1093/molbev/msaa314

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

Autori: Nicola Conci, Gert Wörheide, Sergio Vargas
Pubblicato in: Genome Biology and Evolution, Numero 11/11, 2019, Pagina/e 3068-3081, ISSN 1759-6653
Editore: 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

Autori: Jesus Lozano-Fernandez, Alastair R. Tanner, Mattia Giacomelli, Robert Carton, Jakob Vinther, Gregory D. Edgecombe, Davide Pisani
Pubblicato in: Nature Communications, Numero 10/1, 2019, Pagina/e 4534, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-019-12259-6

Computer vision for pattern detection in chromosome contact maps

Autori: 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
Pubblicato in: Nature Communications, Numero 11/1, 2020, Pagina/e 5795, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-020-19562-7

Comparative genomics and the nature of placozoan species

Autori: 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
Pubblicato in: PLOS Biology, Numero 16/7, 2018, Pagina/e e2005359, ISSN 1545-7885
Editore: 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

Autori: Jesus Lozano-Fernandez, Alastair R. Tanner, Mattia Giacomelli, Robert Carton, Jakob Vinther, Gregory D. Edgecombe, Davide Pisani
Pubblicato in: Nature Communications, Numero 10/1, 2019, Pagina/e 2295, ISSN 2041-1723
Editore: 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

Autori: 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
Pubblicato in: Genome Biology and Evolution, Numero 11/8, 2019, Pagina/e 2055-2070, ISSN 1759-6653
Editore: Oxford University Press
DOI: 10.1093/gbe/evz097

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

Autori: Lyubomir Penev, Mariya Dimitrova, Viktor Senderov, Georgi Zhelezov, Teodor Georgiev, Pavel Stoev, Kiril Simov
Pubblicato in: Publications, Numero 7/2, 2019, Pagina/e 38, ISSN 2304-6775
Editore: MDPI
DOI: 10.3390/publications7020038

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

Autori: Paschalis Natsidis, Philipp H. Schiffer, Irepan Salvador-Martínez, Maximilian J. Telford
Pubblicato in: Scientific Reports, Numero 9/1, 2019, Pagina/e 19477, ISSN 2045-2322
Editore: 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

Autori: Özgül Doğan, Michael Schrödl, Zeyuan Chen
Pubblicato in: PeerJ, Numero 8, 2020, Pagina/e e8603, ISSN 2167-8359
Editore: PeerJ
DOI: 10.7717/peerj.8603

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

Autori: Guiglielmoni N, Houtain A, Derzelle A, Van Doninck K, Flot J-F
Pubblicato in: BMC Bioinformatics, 2021, ISSN 1471-2105
Editore: BioMed Central
DOI: 10.1186/s12859‐021‐04118‐3

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

Autori: Mariya Dimitrova, Raïssa Meyer, Pier Luigi Buttigieg, Teodor Georgiev, Georgi Zhelezov, Seyhan Demirov, Vincent Smith, Lyubomir Penev
Pubblicato in: Biodiversity Information Science and Standards, Numero 4, 2020, Pagina/e e59041, ISSN 2535-0897
Editore: Pensoft Publishers
DOI: 10.3897/biss.4.59041

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

Autori: 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
Pubblicato in: Journal of the Geological Society, 2022, ISSN 0016-7649
Editore: 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

Autori: 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,
Pubblicato in: BMC Biology, Numero 18/1, 2020, Pagina/e Article number: 90, ISSN 1741-7007
Editore: BioMed Central
DOI: 10.1186/s12915-020-00820-5

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

Autori: 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
Pubblicato in: Nature Communications, Numero 11/1, 2020, Pagina/e 3676, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-020-17397-w

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

Autori: Davide Pisani; Gert Wörheide; Michael Eitel; Maja Adamska; Marcin Adamski; Warren R. Francis; Walker Pett
Pubblicato in: Molecular Biology and Evolution, Numero 36/4, 2019, Pagina/e 643–649, ISSN 0737-4038
Editore: 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

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

Integrated phylogenomicsand fossil data illuminatethe evolution of beetles

Autori: 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
Pubblicato in: R. Soc Open Sciences, 2022, ISSN 2054-5703
Editore: Royal Society
DOI: 10.1098/rsos.211771

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

Autori: 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
Pubblicato in: Science, 2021, ISSN 0036-8075
Editore: American Association for the Advancement of Science
DOI: 10.1126/science.abj2949

Anaerobic metabolism of Foraminifera thriving below the seafloor

Autori: William D. Orsi, Raphaël Morard, Aurele Vuillemin, Michael Eitel, Gert Wörheide, Jana Milucka, Michal Kucera
Pubblicato in: The ISME Journal, Numero 14/10, 2020, Pagina/e 2580-2594, ISSN 1751-7362
Editore: Nature Publishing Group
DOI: 10.1038/s41396-020-0708-1

Root Digger: a root placement program for phylogenetic trees.

Autori: Ben Bettisworth; Alexandros Stamatakis; Alexandros Stamatakis
Pubblicato in: BMC Bioinformatics, 2021, ISSN 1471-2105
Editore: 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

Autori: 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
Pubblicato in: The ISME Journal, Numero 14/1, 2020, Pagina/e 322-322, ISSN 1751-7362
Editore: Nature Publishing Group
DOI: 10.1038/s41396-019-0509-6

Other (5)

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

Autori: 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
Pubblicato in: bioRxiv, 2022
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.01.07.475286

Empirical Analysis of Phylogenetic Quasi-Terraces

Autori: Paula Breitling, Ben Bettisworth, Lukasz Reszczynski, Olga Chernomor, Alexandros Stamatakis
Pubblicato in: bioRxiv, 2019
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/810309

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

Autori: Faure R, Guiglielmoni N, Flot J-F
Pubblicato in: bioRxiv, 2021
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2021.01.29.428779

A deep dive into genome assemblies of non-vertebrate animals

Autori: Guiglielmoni N, Rivera-Vicéns R, Koszul R, Flot J-F
Pubblicato in: Preprints, 2021
Editore: 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

Autori: Ben Bettisworth, Alexandros Stamatakis
Pubblicato in: bioRxiv, 2020
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2021.06.24.449715

Non-peer reviewed articles (5)

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

Autori: Mariya Dimitrova, Viktor Senderov, Kiril Simov, Teodor Georgiev, Lyubomir Penev
Pubblicato in: Biodiversity Information Science and Standards, Numero 3, 2019, Pagina/e e35773, ISSN 2535-0897
Editore: Pensoft Publishers
DOI: 10.3897/biss.3.35773

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

Autori: Lyubomir Penev, Teodor Georgiev, Mariya Dimitrova, Yasen Mutafchiev, Pavel Stoev, Robert Mesibov
Pubblicato in: Biodiversity Information Science and Standards, Numero 3, 2019, Pagina/e e35019, ISSN 2535-0897
Editore: Pensoft Publishers
DOI: 10.3897/biss.3.35019

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

Autori: Lyubomir Penev, Teodor Georgiev, Viktor Senderov, Mariya Dimitrova, Pavel Stoev
Pubblicato in: Biodiversity Information Science and Standards, Numero 3, 2019, Pagina/e e35902, ISSN 2535-0897
Editore: Pensoft Publishers
DOI: 10.3897/biss.3.35902

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

Autori: Jeremy Miller, Yanell Braumuller, Puneet Kishor, David Shorthouse, Mariya Dimitrova, Guido Sautter, Donat Agosti
Pubblicato in: Biodiversity Information Science and Standards, Numero 3, 2019, Pagina/e e37078, ISSN 2535-0897
Editore: Pensoft Publishers
DOI: 10.3897/biss.3.37078

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

Autori: Mariya Dimitrova, Viktor Senderov, Teodor Georgiev, Georgi Zhelezov, Lyubomir Penev
Pubblicato in: Biodiversity Information Science and Standards, Numero 3, 2019, Pagina/e e35089, ISSN 2535-0897
Editore: Pensoft Publishers
DOI: 10.3897/biss.3.35089