Supporting data for "A chromosome-level genome assembly for the Pacific oyster ( Crassostrea gigas )"
The Pacific oyster ( Crassostrea gigas ) is a bivalve mollusc species 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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ftdatacite:10.5524/100875 2023-05-15T15:58:15+02:00 Supporting data for "A chromosome-level genome assembly for the Pacific oyster ( Crassostrea gigas )" Carolina, Peñaloza Alejandro, Gutierrez P Lel, Eory Shan, Wang Ximing, Guo Alan, Archibald Tim, Bean P Ross, Houston D 2021 https://dx.doi.org/10.5524/100875 http://gigadb.org/dataset/100875 en eng GigaScience Database https://dx.doi.org/10.1093/gigascience/giab020 Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode cc0-1.0 CC0 Genomic Transcriptomic pacific oyster genome assembly aquaculture dna sequencing hi-c chromosome conformation capture GigaDB Dataset dataset Dataset 2021 ftdatacite https://doi.org/10.5524/100875 https://doi.org/10.1093/gigascience/giab020 2022-02-08T12:42:49Z The Pacific oyster ( Crassostrea gigas ) is a bivalve mollusc species 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 the Pacific oyster. In the current study, high coverage long and short read sequence data generated on Pacific Biosciences and Illumina platforms from a single female individual specimen was used to generate an initial assembly, which was then scaffolded into 10 pseudo chromosomes using both Hi-C sequencing and a high density SNP linkage map. The final 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. The new assembly was annotated using Pacific Biosciences Iso-Seq and Illumina RNA-Seq data, identifying ~30K putative protein coding genes, with an average of 3.1 transcripts per gene. Annotation of putative repeat elements highlighted an inverse relationship with gene density and identified putative centromeres of the metacentric chromosomes. An enrichment of Helitron rolling circle transposable elements was observed, suggesting their potential role in shaping the evolution of the C. gigas genome. 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 genetic improvement of C. gigas in aquaculture breeding programmes. Dataset Crassostrea gigas Pacific oyster DataCite Metadata Store (German National Library of Science and Technology) Pacific |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
English |
topic |
Genomic Transcriptomic pacific oyster genome assembly aquaculture dna sequencing hi-c chromosome conformation capture |
spellingShingle |
Genomic Transcriptomic pacific oyster genome assembly aquaculture dna sequencing hi-c chromosome conformation capture Carolina, Peñaloza Alejandro, Gutierrez P Lel, Eory Shan, Wang Ximing, Guo Alan, Archibald Tim, Bean P Ross, Houston D Supporting data for "A chromosome-level genome assembly for the Pacific oyster ( Crassostrea gigas )" |
topic_facet |
Genomic Transcriptomic pacific oyster genome assembly aquaculture dna sequencing hi-c chromosome conformation capture |
description |
The Pacific oyster ( Crassostrea gigas ) is a bivalve mollusc species 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 the Pacific oyster. In the current study, high coverage long and short read sequence data generated on Pacific Biosciences and Illumina platforms from a single female individual specimen was used to generate an initial assembly, which was then scaffolded into 10 pseudo chromosomes using both Hi-C sequencing and a high density SNP linkage map. The final 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. The new assembly was annotated using Pacific Biosciences Iso-Seq and Illumina RNA-Seq data, identifying ~30K putative protein coding genes, with an average of 3.1 transcripts per gene. Annotation of putative repeat elements highlighted an inverse relationship with gene density and identified putative centromeres of the metacentric chromosomes. An enrichment of Helitron rolling circle transposable elements was observed, suggesting their potential role in shaping the evolution of the C. gigas genome. 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 genetic improvement of C. gigas in aquaculture breeding programmes. |
format |
Dataset |
author |
Carolina, Peñaloza Alejandro, Gutierrez P Lel, Eory Shan, Wang Ximing, Guo Alan, Archibald Tim, Bean P Ross, Houston D |
author_facet |
Carolina, Peñaloza Alejandro, Gutierrez P Lel, Eory Shan, Wang Ximing, Guo Alan, Archibald Tim, Bean P Ross, Houston D |
author_sort |
Carolina, Peñaloza |
title |
Supporting data for "A chromosome-level genome assembly for the Pacific oyster ( Crassostrea gigas )" |
title_short |
Supporting data for "A chromosome-level genome assembly for the Pacific oyster ( Crassostrea gigas )" |
title_full |
Supporting data for "A chromosome-level genome assembly for the Pacific oyster ( Crassostrea gigas )" |
title_fullStr |
Supporting data for "A chromosome-level genome assembly for the Pacific oyster ( Crassostrea gigas )" |
title_full_unstemmed |
Supporting data for "A chromosome-level genome assembly for the Pacific oyster ( Crassostrea gigas )" |
title_sort |
supporting data for "a chromosome-level genome assembly for the pacific oyster ( crassostrea gigas )" |
publisher |
GigaScience Database |
publishDate |
2021 |
url |
https://dx.doi.org/10.5524/100875 http://gigadb.org/dataset/100875 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_relation |
https://dx.doi.org/10.1093/gigascience/giab020 |
op_rights |
Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode cc0-1.0 |
op_rightsnorm |
CC0 |
op_doi |
https://doi.org/10.5524/100875 https://doi.org/10.1093/gigascience/giab020 |
_version_ |
1766393978893107200 |