A genome resource for the marine annelid Platynereis dumerilii .

Autor: Mutemi KN; European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany., Simakov O; Department for Neurosciences and Developmental Biology, University of Vienna, Austria., Pan L; European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany., Santangeli L; European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany., Null R; Current: Department of Biology, Washington University in Saint Louis, MO, USA 63139 Previous: Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA. 02543. USA., Handberg-Thorsager M; Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany., Vellutini BC; Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany., Peterson KJ; Department of Biological Sciences Dartmouth College Hanover NH 03755 USA., Fromm B; The Arctic University Museum of Norway, Tromsø, NO., Larsson T; Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. Current: Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden., Savage E; European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Current: Centre for Organismal Studies, University of Heidelberg, Heidelberg., Lopez MO; European Molecular Biology Laboratory, Genomics Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany., Hercog R; European Molecular Biology Laboratory, Genomics Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany. - not at EMBL anymore, do not know current address., Provaznik J; European Molecular Biology Laboratory, Genomics Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany., Ordoñez-Rueda D; European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany., Azevedo N; European Molecular Biology Laboratory, Genomics Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany. - not at EMBL anymore, do not know current address., Gazave E; Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France., Vervoort M; Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France., Tomancak P; Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany., Tan W; Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany., Winkler S; Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany., Benes V; EMBL, Genomics Core Facility, Meyerhofstr. 1, 69117 Heidelberg, Germany., Hui J; School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong., Helm C; Animal Evolution and Biodiversity, University of Göttingen, Untere Karspüle 2, 37073 Göttingen, Germany., Özpolat BD; Current: Department of Biology, Washington University in Saint Louis, MO, USA 63139 Previous: Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA. 02543. USA., Arendt D; European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.; Centre for Organismal Studies (COS) University of Heidelberg, 69120 Heidelberg, Germany.
Jazyk: angličtina
Zdroj: BioRxiv : the preprint server for biology [bioRxiv] 2024 Nov 11. Date of Electronic Publication: 2024 Nov 11.
DOI: 10.1101/2024.06.21.600153
Abstrakt: The marine annelid Platynereis dumerilii is a model organism used in many research areas including evolution and development, neurobiology, ecology and regeneration. Here we present the genomes of P. dumerilii (laboratory culture reference and a single individual assembly) and of the closely related P. massiliensis and P. megalops (single individual assembly) to facilitate comparative genomic approaches and help explore Platynereis biology. We used long-read sequencing technology and chromosomal-conformation capture along with extensive transcriptomic resources to obtain and annotate a draft genome assembly of ~1.47 Gbp for P. dumerilii , of which more than half represent repeat elements. We predict around 29,000 protein-coding genes, with relatively large intron sizes, over 38,000 non-coding genes, and 105 miRNA loci. We further explore the high genetic variation (~3% heterozygosity) within the Platynereis species complex. Gene ontology reveals the most variable loci to be associated with pigmentation, development and immunity. The current work sets the stage for further development of Platynereis genomic resources.
Databáze: MEDLINE