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...

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Autores principales: Peñaloza, Carolina, Gutierrez, Alejandro P, Eöry, Lél, Wang, Shan, Guo, Ximing, Archibald, Alan L, Bean, Tim P, Houston, Ross D
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
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.
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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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