De novo assembly and annotation of the European abalone Haliotis tuberculata transcriptome
00000 International audience The European abalone Haliotis tuberculata is a delicacy and consequently a commercially valuable gastropod species. Aquaculture production and wild populations are subjected to multiple climate-associated stressors and anthropogenic pressures, including rising sea-surfac...
Published in: | Marine Genomics |
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Online Access: | https://hal.archives-ouvertes.fr/hal-01483234 https://doi.org/10.1016/j.margen.2016.03.002 |
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ftccsdartic:oai:HAL:hal-01483234v1 2023-05-15T17:51:26+02:00 De novo assembly and annotation of the European abalone Haliotis tuberculata transcriptome Harney, Ewan Dubief, Bruno Boudry, Pierre Basuyaux, Olivier Schilhabel, Markus B. Huchette, Sylvain Paillard, Christine Nunes, Flavia L. D. Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR) Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM) Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS) Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne) Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER) Synergie MEr et Littoral (SMEL) Institute of Clinical Molecular Biology Kiel University Scea France Haliotis ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010) 2016-08 https://hal.archives-ouvertes.fr/hal-01483234 https://doi.org/10.1016/j.margen.2016.03.002 en eng HAL CCSD Elsevier info:eu-repo/semantics/altIdentifier/doi/10.1016/j.margen.2016.03.002 hal-01483234 https://hal.archives-ouvertes.fr/hal-01483234 doi:10.1016/j.margen.2016.03.002 ISSN: 1874-7787 Marine Genomics https://hal.archives-ouvertes.fr/hal-01483234 Marine Genomics, Elsevier, 2016, 28, pp.11-16. ⟨10.1016/j.margen.2016.03.002⟩ Vibrio harveyi ACL Climate change Development Gastropoda mollusca RNA-seq [SDE.BE]Environmental Sciences/Biodiversity and Ecology info:eu-repo/semantics/article Journal articles 2016 ftccsdartic https://doi.org/10.1016/j.margen.2016.03.002 2021-12-19T02:37:37Z 00000 International audience The European abalone Haliotis tuberculata is a delicacy and consequently a commercially valuable gastropod species. Aquaculture production and wild populations are subjected to multiple climate-associated stressors and anthropogenic pressures, including rising sea-surface temperatures, ocean acidification and an emerging pathogenic Vibrio infection. Transcript expression data provides a valuable resource for understanding abalone responses to variation in the biotic and abiotic environment. To generate an extensive transcriptome, we performed next-generation sequencing of RNA on larvae exposed to temperature and pH variation and on haemolymph of adults from two wild populations after experimental infection with Vibrio harveyi. We obtained more than 1.5 billion raw paired-end reads, which were assembled into 328,519 contigs. Filtration and clustering produced a transcriptome of 41,099 transcripts, of which 10,626 (25.85%) were annotated with Blast hits, and 7380 of these were annotated with Gene Ontology (GO) terms in Blast2Go. A differential expression analysis comparing all samples from the two life stages identified 5690 and 10,759 transcripts with significantly higher expression in larvae and adult haemolymph respectively. This is the greatest sequencing effort yet in the Haliotis genus, and provides the first high-throughput transcriptomic resource for H. tuberculata. Article in Journal/Newspaper Ocean acidification Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) Marine Genomics 28 11 16 |
institution |
Open Polar |
collection |
Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) |
op_collection_id |
ftccsdartic |
language |
English |
topic |
Vibrio harveyi ACL Climate change Development Gastropoda mollusca RNA-seq [SDE.BE]Environmental Sciences/Biodiversity and Ecology |
spellingShingle |
Vibrio harveyi ACL Climate change Development Gastropoda mollusca RNA-seq [SDE.BE]Environmental Sciences/Biodiversity and Ecology Harney, Ewan Dubief, Bruno Boudry, Pierre Basuyaux, Olivier Schilhabel, Markus B. Huchette, Sylvain Paillard, Christine Nunes, Flavia L. D. De novo assembly and annotation of the European abalone Haliotis tuberculata transcriptome |
topic_facet |
Vibrio harveyi ACL Climate change Development Gastropoda mollusca RNA-seq [SDE.BE]Environmental Sciences/Biodiversity and Ecology |
description |
00000 International audience The European abalone Haliotis tuberculata is a delicacy and consequently a commercially valuable gastropod species. Aquaculture production and wild populations are subjected to multiple climate-associated stressors and anthropogenic pressures, including rising sea-surface temperatures, ocean acidification and an emerging pathogenic Vibrio infection. Transcript expression data provides a valuable resource for understanding abalone responses to variation in the biotic and abiotic environment. To generate an extensive transcriptome, we performed next-generation sequencing of RNA on larvae exposed to temperature and pH variation and on haemolymph of adults from two wild populations after experimental infection with Vibrio harveyi. We obtained more than 1.5 billion raw paired-end reads, which were assembled into 328,519 contigs. Filtration and clustering produced a transcriptome of 41,099 transcripts, of which 10,626 (25.85%) were annotated with Blast hits, and 7380 of these were annotated with Gene Ontology (GO) terms in Blast2Go. A differential expression analysis comparing all samples from the two life stages identified 5690 and 10,759 transcripts with significantly higher expression in larvae and adult haemolymph respectively. This is the greatest sequencing effort yet in the Haliotis genus, and provides the first high-throughput transcriptomic resource for H. tuberculata. |
author2 |
Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR) Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM) Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS) Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne) Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER) Synergie MEr et Littoral (SMEL) Institute of Clinical Molecular Biology Kiel University Scea France Haliotis ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010) |
format |
Article in Journal/Newspaper |
author |
Harney, Ewan Dubief, Bruno Boudry, Pierre Basuyaux, Olivier Schilhabel, Markus B. Huchette, Sylvain Paillard, Christine Nunes, Flavia L. D. |
author_facet |
Harney, Ewan Dubief, Bruno Boudry, Pierre Basuyaux, Olivier Schilhabel, Markus B. Huchette, Sylvain Paillard, Christine Nunes, Flavia L. D. |
author_sort |
Harney, Ewan |
title |
De novo assembly and annotation of the European abalone Haliotis tuberculata transcriptome |
title_short |
De novo assembly and annotation of the European abalone Haliotis tuberculata transcriptome |
title_full |
De novo assembly and annotation of the European abalone Haliotis tuberculata transcriptome |
title_fullStr |
De novo assembly and annotation of the European abalone Haliotis tuberculata transcriptome |
title_full_unstemmed |
De novo assembly and annotation of the European abalone Haliotis tuberculata transcriptome |
title_sort |
de novo assembly and annotation of the european abalone haliotis tuberculata transcriptome |
publisher |
HAL CCSD |
publishDate |
2016 |
url |
https://hal.archives-ouvertes.fr/hal-01483234 https://doi.org/10.1016/j.margen.2016.03.002 |
genre |
Ocean acidification |
genre_facet |
Ocean acidification |
op_source |
ISSN: 1874-7787 Marine Genomics https://hal.archives-ouvertes.fr/hal-01483234 Marine Genomics, Elsevier, 2016, 28, pp.11-16. ⟨10.1016/j.margen.2016.03.002⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1016/j.margen.2016.03.002 hal-01483234 https://hal.archives-ouvertes.fr/hal-01483234 doi:10.1016/j.margen.2016.03.002 |
op_doi |
https://doi.org/10.1016/j.margen.2016.03.002 |
container_title |
Marine Genomics |
container_volume |
28 |
container_start_page |
11 |
op_container_end_page |
16 |
_version_ |
1766158582323085312 |