First insight into the whole genome shotgun sequence of the endangered noble pen shell Pinna nobilis: a giant bivalve undergoing a mass mortality event
| Autor: | Danijela Joksimović, Nardo Vicente, Stéphane Coupé, Jean-Luc Bonnefont, Robert Bunet, José Rafa García-March, Rajko Martinović, Jean-Marc Prévot, Jose Tena-Medialdea |
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| Přispěvatelé: | Institut Océanographique Paul Ricard, Université de Toulon (UTLN), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Universidad Catolica de Valencia (UCV), University of Montenegro (UCG), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN) |
| Rok vydání: | 2021 |
| Předmět: |
0106 biological sciences
0301 basic medicine biology Shotgun sequencing Endangered species Zoology Aquatic Science biology.organism_classification 010603 evolutionary biology 01 natural sciences Mass mortality [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics 03 medical and health sciences 030104 developmental biology Animal Science and Zoology 14. Life underwater ComputingMilieux_MISCELLANEOUS Pinna nobilis Sequence (medicine) |
| Zdroj: | Journal of Molluscan Studies Journal of Molluscan Studies, 2021, 87 (1), pp.eyaa04. ⟨10.1093/mollus/eyaa041⟩ Journal of Molluscan Studies, Oxford University Press (OUP), 2021, ⟨10.1093/mollus/eyaa041⟩ |
| ISSN: | 1464-3766 0260-1230 |
| DOI: | 10.1093/mollus/eyaa041 |
| Popis: | The noble pen shell Pinna nobilis is a Mediterranean endemic and emblematic giant bivalve. Already considered by the late 20th century to be an endangered species, it is facing a dramatic and rapidly expanding epizooty that has decimated populations since mid-2016. The ecological importance of P. nobilis has prompted important investigations for conservation purposes. Here, we report a first analysis of the whole genome sequencing of this animal. This was performed on an Illumina HiSeq X platform using a single paired-end library of short fragments (2 × 150 bp). The de novo contig assembly had a total size of 584 Mb (96,738 contigs, N50 = 7.6 kb, with 0.4% of ambiguous nucleotides), representing 77.5% of the predicted genome size of 754 Mb. The P. nobilis genome is highly AT-rich, with a GC content of 35.6%. At 1%, heterozygosity was in the range of other bivalves with sequenced genomes. Over one-third (36.2%) of the genome consisted of repeated elements with a surprising larger number of short interspersed nuclear elements compared to other molluscan genomes. We were also able to reconstruct the full mitochondrial genome (c. 19 kb, with 12 protein-coding genes, 2 rRNA and 22 tRNA genes). In the context of the epizootic outbreak affecting P. nobilis, a first insight into the innate immune and stress-related genes found in the sequence is provided. |
| Databáze: | OpenAIRE |
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