A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas
BACKGROUND: The Pacific oyster (Crassostrea gigas) is a bivalve mollusc with vital roles in coastal ecosystems and aquaculture globally. While extensive genomic tools are available for C. gigas, highly contiguous reference genomes are required to support both fundamental and applied research. Herein...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Oxford University Press
2021
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7992393/ https://www.ncbi.nlm.nih.gov/pubmed/33764468 http://dx.doi.org/10.1093/gigascience/giab020 |
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author | Peñaloza, Carolina Gutierrez, Alejandro P Eöry, Lél Wang, Shan Guo, Ximing Archibald, Alan L Bean, Tim P Houston, Ross D |
author_facet | Peñaloza, Carolina Gutierrez, Alejandro P Eöry, Lél Wang, Shan Guo, Ximing Archibald, Alan L Bean, Tim P Houston, Ross D |
author_sort | Peñaloza, Carolina |
collection | PubMed |
description | BACKGROUND: The Pacific oyster (Crassostrea gigas) is a bivalve mollusc with vital roles in coastal ecosystems and aquaculture globally. While extensive genomic tools are available for C. gigas, highly contiguous reference genomes are required to support both fundamental and applied research. Herein we report the creation and annotation of a chromosome-level assembly for C. gigas. FINDINGS: High-coverage long- and short-read sequence data generated on Pacific Biosciences and Illumina platforms were used to generate an initial assembly, which was then scaffolded into 10 pseudo-chromosomes using both Hi-C sequencing and a high-density linkage map. The assembly has a scaffold N50 of 58.4 Mb and a contig N50 of 1.8 Mb, representing a step advance on the previously published C. gigas assembly. Annotation based on Pacific Biosciences Iso-Seq and Illumina RNA-Seq resulted in identification of ∼30,000 putative protein-coding genes. Annotation of putative repeat elements highlighted an enrichment of Helitron rolling-circle transposable elements, suggesting their potential role in shaping the evolution of the C. gigas genome. CONCLUSIONS: This new chromosome-level assembly will be an enabling resource for genetics and genomics studies to support fundamental insight into bivalve biology, as well as for selective breeding of C. gigas in aquaculture. |
format | Online Article Text |
id | pubmed-7992393 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-79923932021-03-31 A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas Peñaloza, Carolina Gutierrez, Alejandro P Eöry, Lél Wang, Shan Guo, Ximing Archibald, Alan L Bean, Tim P Houston, Ross D Gigascience Data Note BACKGROUND: The Pacific oyster (Crassostrea gigas) is a bivalve mollusc with vital roles in coastal ecosystems and aquaculture globally. While extensive genomic tools are available for C. gigas, highly contiguous reference genomes are required to support both fundamental and applied research. Herein we report the creation and annotation of a chromosome-level assembly for C. gigas. FINDINGS: High-coverage long- and short-read sequence data generated on Pacific Biosciences and Illumina platforms were used to generate an initial assembly, which was then scaffolded into 10 pseudo-chromosomes using both Hi-C sequencing and a high-density linkage map. The assembly has a scaffold N50 of 58.4 Mb and a contig N50 of 1.8 Mb, representing a step advance on the previously published C. gigas assembly. Annotation based on Pacific Biosciences Iso-Seq and Illumina RNA-Seq resulted in identification of ∼30,000 putative protein-coding genes. Annotation of putative repeat elements highlighted an enrichment of Helitron rolling-circle transposable elements, suggesting their potential role in shaping the evolution of the C. gigas genome. CONCLUSIONS: This new chromosome-level assembly will be an enabling resource for genetics and genomics studies to support fundamental insight into bivalve biology, as well as for selective breeding of C. gigas in aquaculture. Oxford University Press 2021-03-25 /pmc/articles/PMC7992393/ /pubmed/33764468 http://dx.doi.org/10.1093/gigascience/giab020 Text en © The Author(s) 2021. Published by Oxford University Press GigaScience. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Data Note Peñaloza, Carolina Gutierrez, Alejandro P Eöry, Lél Wang, Shan Guo, Ximing Archibald, Alan L Bean, Tim P Houston, Ross D A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas |
title | A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas |
title_full | A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas |
title_fullStr | A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas |
title_full_unstemmed | A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas |
title_short | A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas |
title_sort | chromosome-level genome assembly for the pacific oyster crassostrea gigas |
topic | Data Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7992393/ https://www.ncbi.nlm.nih.gov/pubmed/33764468 http://dx.doi.org/10.1093/gigascience/giab020 |
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