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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ftunivstirling:oai:dspace.stir.ac.uk:1893/32667 2023-05-15T15:58:01+02:00 A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas Penaloza, Carolina Gutierrez, Alejandro P Eory, Lel Wang, Shan Guo, Ximing Archibald, Alan L Bean, Tim P Houston, Ross D Biotechnology and Biological Sciences Research Council Natural Environment Research Council University of Edinburgh Rutgers, The State University of New Jersey 2021-03 application/pdf http://hdl.handle.net/1893/32667 https://doi.org/10.1093/gigascience/giab020 http://dspace.stir.ac.uk/retrieve/03d3744f-0ac0-4f05-870f-248afd06b1e2/giab020.pdf en eng Oxford University Press Penaloza C, Gutierrez AP, Eory L, Wang S, Guo X, Archibald AL, Bean TP & Houston RD (2021) A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas. Gigascience, 10 (3), Art. No.: giab020. https://doi.org/10.1093/gigascience/giab020 giab020 http://hdl.handle.net/1893/32667 doi:10.1093/gigascience/giab020 33764468 WOS:000637267600011 2-s2.0-85103480555 1729809 http://dspace.stir.ac.uk/retrieve/03d3744f-0ac0-4f05-870f-248afd06b1e2/giab020.pdf © The Author(s) 2021. Published by Oxford University Press GigaScience. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. http://creativecommons.org/licenses/by/4.0/ CC-BY : Pacific oyster genome assembly aquaculture DNA sequencing Hi-C chromosome conformation capture Journal Article VoR - Version of Record 2021 ftunivstirling https://doi.org/10.1093/gigascience/giab020 2022-06-13T18:44:25Z 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. Article in Journal/Newspaper Crassostrea gigas Pacific oyster University of Stirling: Stirling Digital Research Repository Pacific GigaScience 10 3 |
institution |
Open Polar |
collection |
University of Stirling: Stirling Digital Research Repository |
op_collection_id |
ftunivstirling |
language |
English |
topic |
: Pacific oyster genome assembly aquaculture DNA sequencing Hi-C chromosome conformation capture |
spellingShingle |
: Pacific oyster genome assembly aquaculture DNA sequencing Hi-C chromosome conformation capture Penaloza, Carolina Gutierrez, Alejandro P Eory, Lel Wang, Shan Guo, Ximing Archibald, Alan L Bean, Tim P Houston, Ross D A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas |
topic_facet |
: Pacific oyster genome assembly aquaculture DNA sequencing Hi-C chromosome conformation capture |
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. |
author2 |
Biotechnology and Biological Sciences Research Council Natural Environment Research Council University of Edinburgh Rutgers, The State University of New Jersey |
format |
Article in Journal/Newspaper |
author |
Penaloza, Carolina Gutierrez, Alejandro P Eory, Lel Wang, Shan Guo, Ximing Archibald, Alan L Bean, Tim P Houston, Ross D |
author_facet |
Penaloza, Carolina Gutierrez, Alejandro P Eory, Lel Wang, Shan Guo, Ximing Archibald, Alan L Bean, Tim P Houston, Ross D |
author_sort |
Penaloza, Carolina |
title |
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_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_sort |
chromosome-level genome assembly for the pacific oyster crassostrea gigas |
publisher |
Oxford University Press |
publishDate |
2021 |
url |
http://hdl.handle.net/1893/32667 https://doi.org/10.1093/gigascience/giab020 http://dspace.stir.ac.uk/retrieve/03d3744f-0ac0-4f05-870f-248afd06b1e2/giab020.pdf |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_relation |
Penaloza C, Gutierrez AP, Eory L, Wang S, Guo X, Archibald AL, Bean TP & Houston RD (2021) A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas. Gigascience, 10 (3), Art. No.: giab020. https://doi.org/10.1093/gigascience/giab020 giab020 http://hdl.handle.net/1893/32667 doi:10.1093/gigascience/giab020 33764468 WOS:000637267600011 2-s2.0-85103480555 1729809 http://dspace.stir.ac.uk/retrieve/03d3744f-0ac0-4f05-870f-248afd06b1e2/giab020.pdf |
op_rights |
© The Author(s) 2021. Published by Oxford University Press GigaScience. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. http://creativecommons.org/licenses/by/4.0/ |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1093/gigascience/giab020 |
container_title |
GigaScience |
container_volume |
10 |
container_issue |
3 |
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1766393739339628544 |