Comparative Genomics of Non-Model Invertebrates

Resources

Publications

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

Lyubomir Penev, Mariya Dimitrova, Viktor Senderov, Georgi Zhelezov, Teodor Georgiev, Pavel Stoev, Kiril Simov
YEAR: 2019
PUBLISHER/PLACE: MDPI
JOURNAL: Publications
VOLUME/ISSUE: 7(2)
PAGES: 38
URL/DOI: https://www.mdpi.com/2304-6775/7/2/38

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

Özgül Doğan, Michael Schrödl, Zeyuan Chen
YEAR: 2020
PUBLISHER/PLACE: PeerJ
JOURNAL: PeerJ
VOLUME/ISSUE: 8
PAGES: e8603
URL/DOI: https://peerj.com/articles/8603/

A deep dive into genome assemblies of non-vertebrate animals

Guiglielmoni, Nadège; Rivera-Vicéns, Ramón; Koszul, Romain; Flot, Jean-François
YEAR: 2022
JOURNAL: Peer Community Journal
URL/DOI: https://peercommunityjournal.org/articles/10.24072/pcjournal.128/

How many single-copy orthologous genes from whole genomes reveal deep gastropod relationships?

Zeyuan Chen​, Michael Schrödl
YEAR: 2022
JOURNAL: PeerJ
URL/DOI: https://doi.org/10.7717/peerj.13285

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

Mariya Dimitrova, Raïssa Meyer, Pier Luigi Buttigieg, Teodor Georgiev, Georgi Zhelezov, Seyhan Demirov, Vincent S. Smith, Lyubomir Penev
YEAR: 2020
PUBLISHER/PLACE: Pensoft Publishers
JOURNAL: Biodiversity Information Science and Standards
VOLUME/ISSUE: 4
PAGES: e59041
URL/DOI: https://doi.org/10.3897/biss.4.59041

Infrastructure and Population of the OpenBiodiv Biodiversity Knowledge Graph

Mariya Dimitrova, Viktor E Senderov, Teodor Georgiev, Georgi Zhelezov, Lyubomir Penev
YEAR: 2021
JOURNAL: Biodiversity Data Journal
VOLUME/ISSUE: 9: e67671
URL/DOI: https://doi.org/10.3897/BDJ.9.e67671

Biomedical Potential of the Neglected Molluscivorous and Vermivorous Conus Species

Yihe Zhao, Agostinho Antunes
YEAR: 2022
JOURNAL: Marine Drugs
URL/DOI: https://doi.org/10.3390/md20020105

Actinoporin-like Proteins Are Widely Distributed in the Phylum Porifera

Kenneth Sandoval, Grace P. McCormack
YEAR: 2022
JOURNAL: Mar. Drugs
URL/DOI: https://doi.org/10.3390/md20010074

Comparative genomics and the nature of placozoan species

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
YEAR: 2018
PLACE: San Francisco
PUBLISHER/PLACE: Public Library of Science
JOURNAL: PLOS Biology
VOLUME/ISSUE: 16/7
PAGES: e2005359
URL/DOI: https://doi. org/10.1371/journal.pbio.2005359

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

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
YEAR: 2020
PUBLISHER/PLACE: BioMed Central
JOURNAL: Genome Biology
VOLUME/ISSUE: 21/1
PAGES: 148
URL/DOI: https://doi.org/10.1186/s13059-020-02041-z

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

Claude Rispe, Fabrice Legeai, Paul D. Nabity, et al.
YEAR: 2020
PUBLISHER/PLACE: BioMed Central
JOURNAL: BMC Biology
VOLUME/ISSUE: 18/1
PAGES: 90
URL/DOI: https://doi.org/10.1186/s12915-020-00820-5

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

Sarah Farhat, Eric Bonnivard, Emmanuelle Pales Espinosa
YEAR: 2022
JOURNAL: BMC Genomics
URL/DOI: https://doi.org/10.1186/s12864-021-08262-1

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

Nadège Guiglielmoni, Antoine Houtain, Alessandro Derzelle, Karine Van Doninck, Jean-François Flot
YEAR: 2021
PUBLISHER/PLACE: BioMed Central
JOURNAL: BMC Bioinformatics
VOLUME/ISSUE: 22
PAGES: 303
URL/DOI: https://doi.org/10.1186/s12859-021-04118-3

RootDigger: a root placement program for phylogenetic trees

Ben Bettisworth, Alexandros Stamatakis
YEAR: 2021
JOURNAL: BMC Bioinformatics
URL/DOI: https://doi.org/10.1186/s12859-021-03956-5

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

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 Wolf, Cong Liang, Ana Hernández-Plaza,Carlos P. Cantalapiedra, Kaia Achim, Nicole L. Schieber,Leslie Pan, Fabian Ruperti, Warren R. Francis, Sergio Vargas, Svenja Kling, Maike Renkert, Maxim Polikarpov, Gleb Bourenkov, Roberto Feuda, Imre Gaspar, Pawel Burkhardt, Bo Wang, Peer Bork, Martin Beck, Thomas R. Schneider, Anna Kreshuk, Gert Wörheide, Jaime Huerta-Cepas, Yannick Schwab, Leonid L. Moroz, Detlev Arendt
YEAR: 2021
JOURNAL: Science
URL/DOI: https://doi.org/10.1126/science.abj2949

Lack of support for Deuterostomia prompts reinterpretation of the first Bilateria

Paschalia Kapli, Paschalis Natsidis, Daniel J. Leite, Maximilian Fursman, Nadia Jeffrie, Imran A. Rahman, Hervé Philippe, Richard R. Copley, and Maximilian J. Telford
YEAR: 2021
JOURNAL: Science Advances
VOLUME/ISSUE: 7/12
URL/DOI: https://doi.org/10.1126/sciadv.abe2741

Transcriptomic response of Cinachyrella cf. cavernosa sponges to spatial competition

Aabha Deshpande, Ramón E. Rivera-Vicéns, Narsinh L. Thakur, Gert Wörheide
YEAR: 2021
JOURNAL: bioRxiv
URL/DOI: https://doi.org/10.1101/2021.07.05.451097

TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly

Ramón E. Rivera-Vicéns,Catalina A. Garcia-Escudero,Nicola Conci,Michael Eitel,Gert Wörheide
YEAR: 2021
JOURNAL: bioRxiv
URL/DOI: https://doi.org/10.1101/2021.02.18.431773

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

Roland Faure, ProfileNadège Guiglielmoni, ProfileJean-François Flot
YEAR: 2021
JOURNAL: bioRxiv
URL/DOI: https://doi.org/10.1101/2021.01.29.428779

Homologous chromosomes in asexual rotifer Adineta vaga suggest automixis

Paul Simion, Jitendra Narayan, Antoine Houtain, Alessandro Derzelle, Lyam Baudry, Emilien Nicolas, Marie Cariou, Nadège Guiglielmoni, Djampa KL Kozlowski, Florence Rodriguez Gaudray, Matthieu Terwagne, Julie Virgo, Benjamin Noel, Patrick Wincker, Etienne GJ Danchin, Martial Marbouty, Bernard Hallet, Romain Koszul, Antoine Limasset, Jean-François Flot, Karine Van Doninck
YEAR: 2020
JOURNAL: bioRxiv
URL/DOI: https://doi.org/10.1101/2020.06.16.155473

Integrated phylogenomics and fossil data illuminate the evolution of beetles

Chenyang Cai, Erik Tihelka, Mattia Giacomelli, John F. Lawrence, Adam Ślipiński, Robin Kundrata, Shûhei Yamamoto, Margaret K. Thayer, Alfred F. Newton, Richard A. B. Leschen, Matthew L. Gimmel, Liang Lü, Michael S. Engel, Patrice Bouchard, Diying Huang, Davide Pisani and Philip C. J. Donoghue
YEAR: 2022
JOURNAL: R. Soc. open sci.
URL/DOI: https://doi.org/10.1098/rsos.211771

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

Erik Tihelka, Chenyang Cai, Mattia Giacomelli, Davide Pisani and Philip C. J. Donoghue
YEAR: 2020
JOURNAL: R. Soc. open sci.
URL/DOI: https://doi.org/10.1098/rsos.201689

The Role of Homology and Orthology in the Phylogenomic Analysis of Metazoan Gene Content

Walker Pett, Marcin Adamski, Maja Adamska, Warren R Francis, Michael Eitel, Davide Pisani, Gert Wörheide
YEAR: 2019
JOURNAL: Molecular Biology and Evolution
URL/DOI: https://doi.org/10.1093/molbev/msz013

Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult

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
YEAR: 2020
PUBLISHER/PLACE: Oxford University Press
JOURNAL: Molecular Biology and Evolution
PAGES: msaa314
URL/DOI: https://doi.org/10.1093/molbev/msaa314

A streamlined workflow for conversion, peer review, and publication of genomics metadata as omics data papers

Mariya Dimitrova, Raïssa Meyer, Pier Luigi Buttigieg, Teodor Georgiev, Georgi Zhelezov, Seyhan Demirov, Vincent Smith, Lyubomir Penev
YEAR: 2021
JOURNAL: GigaScience
VOLUME/ISSUE: 10/5
URL/DOI: https://doi.org/10.1093/gigascience/giab034

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

Nicola Conci, Gert Wörheide, Sergio Vargas
YEAR: 2019
JOURNAL: Genome Biology and Evolution
URL/DOI: https://doi.org/10.1093/gbe/evz199

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

Jesus Lozano-Fernandez, Mattia Giacomelli, James F. Fleming, Albert Chen, Jakob Vinther, Philip F. Thomsen, Henrik Glenner, Ferran Palero, David A. Legg, Thomas Iliffe, Davide Pisani, Jorgen Olsen
YEAR: 2019
PLACE: UK
PUBLISHER/PLACE: Oxford University Press
JOURNAL: Genome Biology and Evolution
VOLUME/ISSUE: 11/8
PAGES: 2055–2070
URL/DOI: https://doi.org/10.1093/gbe/evz097

Comparative Proteomics of Octocoral and Scleractinian Skeletomes and the Evolution of Coral Calcification

Nicola Conci, Martin Lehmann, Sergio Vargas, Gert Wörheide
YEAR: 2020
JOURNAL: Genome Biology and Evolution
URL/DOI: https://doi.org/10.1093/gbe/evaa162

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

Paschalis Natsidis, Philip H. Schiffer, Irepan Salvador-Martíne, Maximilian J. Telford
YEAR: 2019
PLACE: UK
PUBLISHER/PLACE: Nature Publishing Group
JOURNAL: Scientific Reports
VOLUME/ISSUE: 9/1
PAGES: 19477
URL/DOI: https://doi.org/10.1038/s41598-019-55573-1

Eukaryogenesis and oxygen in Earth history

Daniel B. Mills, Richard A. Boyle, Stuart J. Daines, Erik A. Sperling, Davide Pisani, Philip C. J. Donoghue & Timothy M. Lenton
YEAR: 2022
JOURNAL: Nat Ecol Evol
URL/DOI: https://doi.org/10.1038/s41559-022-01733-y

Computer vision for pattern detection in chromosome contact maps

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
YEAR: 2020
PUBLISHER/PLACE: Nature Publishing Group
JOURNAL: Nature Communications
VOLUME/ISSUE: 11/1
PAGES: 5795
URL/DOI: https://doi.org/10.1038/s41467-020-19562-7

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

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
YEAR: 2020
PUBLISHER/PLACE: Nature Publishing Group
JOURNAL: Nature Communication
VOLUME/ISSUE: 11/1
PAGES: 3676
URL/DOI: https://doi.org/10.1038/s41467-020-17397-w

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

Jesus Lozano-Fernandez, Alastair R. Tanner, Mattia Giacomelli, Robert Carton, Jakob Vinther, Gregory D. Edgecombe, Davide Pisani
YEAR: 2019
PUBLISHER/PLACE: Nature Publishing Group
JOURNAL: Nature Communications
VOLUME/ISSUE: 10/1
PAGES: 4534
URL/DOI: https://doi.org/10.1038/s41467-019-12259-6

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

Jesus Lozano-Fernandez, Alastair R. Tanner, Mattia Giacomelli, Robert Carton, Jakob Vinther, Gregory D. Edgecombe, Davide Pisani
YEAR: 2019
PLACE: UK
PUBLISHER/PLACE: Nature Publishing Group
JOURNAL: Nature Communications
VOLUME/ISSUE: 10/1
PAGES: 2295
URL/DOI: https://doi.org/10.1038/s41467-019-10244-7

Anaerobic metabolism of Foraminifera thriving below the seafloor.

William D. Orsi, Raphaël Morard, Aurele Vuillemin
YEAR: 2020
JOURNAL: ISME J
URL/DOI: https://doi.org/10.1038/s41396-020-0708-1

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

J. Grace Klinges, Stephanie M. Rosales, Ryan McMinds et al.
YEAR: 2020
JOURNAL: ISME J
URL/DOI: https://doi.org/10.1038/s41396-019-0509-6

Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite

J. Grace Klinges, Stephanie M. Rosales, Ryan McMinds et al.
YEAR: 2019
JOURNAL: ISME J
URL/DOI: https://doi.org/10.1038/s41396-019-0482-0

Systematic errors in orthology inference and their effects on evolutionary analyses

Paschalis Natsidis, Paschalia Kapli, Philipp H. Schiffer, Maximilian J. Telford
YEAR: 2021
PUBLISHER/PLACE: Cell Press
JOURNAL: iScience
VOLUME/ISSUE: 24/2
PAGES: 102110
URL/DOI: https://doi.org/10.1016/j.isci.2021.102110

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

Jeremy A. Miller, Yanell Braumuller, Puneet Kishor, David Peter Shorthouse, Mariya Dimitrova, Guido Sautter, Donat Agosti
YEAR: 2019
PLACE: Bulgaria
PUBLISHER/PLACE: Pensoft Publishers
JOURNAL: Biodiversity Information Science and Standards
VOLUME/ISSUE: 3
PAGES: e37078
URL/DOI: https://biss.pensoft.net/article/37078/

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

Lyubomir Penev, Teodor Georgiev, Viktor Senderov, Mariya Dimitrova, Pavel Stoev
YEAR: 2019
PLACE: Bulgaria
PUBLISHER/PLACE: Pensoft Publishers
JOURNAL: Biodiversity Information Science and Standards
VOLUME/ISSUE: 3
PAGES: e35902
URL/DOI: https://biss.pensoft.net/article/35902/

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

Mariya Dimitrova, Viktor Senderov, Kiril Simov, Teodor Georgiev, Lyubomir Penev
YEAR: 2019
PLACE: Bulgaria
PUBLISHER/PLACE: Pensoft Publishers
JOURNAL: Biodiversity Information Science and Standards
VOLUME/ISSUE: 3
PAGES: e35773
URL/DOI: https://biss.pensoft.net/article/35773/list/8/

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

Mariya Dimitrova, Viktor Senderov, Teodor Georgiev, Georgi Zhelezov, Lyubomir Penev
YEAR: 2019
PLACE: Bulgaria
PUBLISHER/PLACE: Pensoft Publishers
JOURNAL: Biodiversity Information Science and Standards
VOLUME/ISSUE: 3
PAGES: e35089
URL/DOI: https://biss.pensoft.net/article/35089/

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

Lyubomir Penev, Teodor Georgiev, Mariya Dimitrova, Yasen Mutafchiev, Pavel Stoev, Robert Mesibov
YEAR: 2019
PLACE: Bulgaria
PUBLISHER/PLACE: Pensoft Publishers
JOURNAL: Biodiversity Information Science and Standards
VOLUME/ISSUE: 3
PAGES: e35019
URL/DOI: https://biss.pensoft.net/article/35019/list/8/