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Comparative genomics of non-model invertebrates

Deliverables

First scientific publications drafted

First scientific publications drafted and prepared for submission.

International Scientific Conference and its report

International Scientific Conference conducted and its report published.

IGNITE logo, flyers, website

IGNITE logo, flyers, website established and available.

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Publications

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

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

Eukaryogenesis and oxygen in Earth history

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

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

Author(s): 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
Published in: Science Advances, 2021, ISSN 2375-2548
Publisher: 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

Author(s): 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
Published in: Genome Biology, 21/1, 2020, Page(s) 148, ISSN 1474-760X
Publisher: 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

Author(s): Tihelka E, Chenyang C, Giacomelli M, Pisani D, Donoghue PCJ
Published in: R Soc. Open Sciences, 2020, ISSN 2054-5703
Publisher: 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

Author(s): 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
Published in: The ISME Journal, 13/12, 2019, Page(s) 2938-2953, ISSN 1751-7362
Publisher: Nature Publishing Group
DOI: 10.1038/s41396-019-0482-0

Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult

Author(s): 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
Published in: Molecular Biology and Evolution, 2020, ISSN 1537-1719
Publisher: Society for Molecular Biology and Evolution
DOI: 10.1093/molbev/msaa314

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

Author(s): Nicola Conci, Gert Wörheide, Sergio Vargas
Published in: Genome Biology and Evolution, 11/11, 2019, Page(s) 3068-3081, ISSN 1759-6653
Publisher: 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

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

Computer vision for pattern detection in chromosome contact maps

Author(s): 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
Published in: Nature Communications, 11/1, 2020, Page(s) 5795, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-19562-7

Comparative genomics and the nature of placozoan species

Author(s): 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
Published in: PLOS Biology, 16/7, 2018, Page(s) e2005359, ISSN 1545-7885
Publisher: 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

Author(s): Jesus Lozano-Fernandez, Alastair R. Tanner, Mattia Giacomelli, Robert Carton, Jakob Vinther, Gregory D. Edgecombe, Davide Pisani
Published in: Nature Communications, 10/1, 2019, Page(s) 2295, ISSN 2041-1723
Publisher: 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

Author(s): 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
Published in: Genome Biology and Evolution, 11/8, 2019, Page(s) 2055-2070, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1093/gbe/evz097

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

Author(s): Lyubomir Penev, Mariya Dimitrova, Viktor Senderov, Georgi Zhelezov, Teodor Georgiev, Pavel Stoev, Kiril Simov
Published in: Publications, 7/2, 2019, Page(s) 38, ISSN 2304-6775
Publisher: MDPI
DOI: 10.3390/publications7020038

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

Author(s): Paschalis Natsidis, Philipp H. Schiffer, Irepan Salvador-Martínez, Maximilian J. Telford
Published in: Scientific Reports, 9/1, 2019, Page(s) 19477, ISSN 2045-2322
Publisher: 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

Author(s): Özgül Doğan, Michael Schrödl, Zeyuan Chen
Published in: PeerJ, 8, 2020, Page(s) e8603, ISSN 2167-8359
Publisher: PeerJ
DOI: 10.7717/peerj.8603

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

Author(s): Guiglielmoni N, Houtain A, Derzelle A, Van Doninck K, Flot J-F
Published in: BMC Bioinformatics, 2021, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859‐021‐04118‐3

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

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

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

Author(s): 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
Published in: Journal of the Geological Society, 2022, ISSN 0016-7649
Publisher: 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

Author(s): 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,
Published in: BMC Biology, 18/1, 2020, Page(s) Article number: 90, ISSN 1741-7007
Publisher: BioMed Central
DOI: 10.1186/s12915-020-00820-5

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

Author(s): 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
Published in: Nature Communications, 11/1, 2020, Page(s) 3676, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-17397-w

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

Author(s): Davide Pisani; Gert Wörheide; Michael Eitel; Maja Adamska; Marcin Adamski; Warren R. Francis; Walker Pett
Published in: Molecular Biology and Evolution, 36/4, 2019, Page(s) 643–649, ISSN 0737-4038
Publisher: 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

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

Integrated phylogenomicsand fossil data illuminatethe evolution of beetles

Author(s): 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
Published in: R. Soc Open Sciences, 2022, ISSN 2054-5703
Publisher: Royal Society
DOI: 10.1098/rsos.211771

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

Author(s): 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
Published in: Science, 2021, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abj2949

Anaerobic metabolism of Foraminifera thriving below the seafloor

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

Root Digger: a root placement program for phylogenetic trees.

Author(s): Ben Bettisworth; Alexandros Stamatakis; Alexandros Stamatakis
Published in: BMC Bioinformatics, 2021, ISSN 1471-2105
Publisher: 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

Author(s): 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
Published in: The ISME Journal, 14/1, 2020, Page(s) 322-322, ISSN 1751-7362
Publisher: 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

Author(s): 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
Published in: bioRxiv, 2022
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.01.07.475286

Empirical Analysis of Phylogenetic Quasi-Terraces

Author(s): Paula Breitling, Ben Bettisworth, Lukasz Reszczynski, Olga Chernomor, Alexandros Stamatakis
Published in: bioRxiv, 2019
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/810309

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

Author(s): Faure R, Guiglielmoni N, Flot J-F
Published in: bioRxiv, 2021
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2021.01.29.428779

A deep dive into genome assemblies of non-vertebrate animals

Author(s): Guiglielmoni N, Rivera-Vicéns R, Koszul R, Flot J-F
Published in: Preprints, 2021
Publisher: 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

Author(s): Ben Bettisworth, Alexandros Stamatakis
Published in: bioRxiv, 2020
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2021.06.24.449715

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

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

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

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

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

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

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

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

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

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