Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas
Background: The Portuguese oyster Crassostrea angulata and the Pacific oyster C. gigas are two major Crassostrea species that are naturally distributed along the Northwest Pacific coast and possess great ecological and economic value. Here, we report the construction and comparative analysis of the...
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OXFORD UNIV PRESS
2023
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ftchinacasciocas:oai:ir.qdio.ac.cn:337002/184677 2024-06-23T07:52:16+00:00 Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas Qi, Haigang Cong, Rihao Wang, Yanjun Li, Li Zhang, Guofan 2023-10-03 http://ir.qdio.ac.cn/handle/337002/184677 https://doi.org/10.1093/gigascience/giad077 英语 eng OXFORD UNIV PRESS GIGASCIENCE http://ir.qdio.ac.cn/handle/337002/184677 doi:10.1093/gigascience/giad077 oyster Crassostrea angulata Crassostrea gigas trio-binning haplotype-resolved genome Life Sciences & Biomedicine - Other Topics Science & Technology - Other Topics Biology Multidisciplinary Sciences ALIGNMENT DIVERGENCE ACCURATE SEARCH 期刊论文 2023 ftchinacasciocas https://doi.org/10.1093/gigascience/giad077 2024-05-27T23:36:17Z Background: The Portuguese oyster Crassostrea angulata and the Pacific oyster C. gigas are two major Crassostrea species that are naturally distributed along the Northwest Pacific coast and possess great ecological and economic value. Here, we report the construction and comparative analysis of the chromosome-level haplotype-resolved g enomes of the two oyster congeners. Findings: Based on a trio-binning strategy, the PacBio high-fidelity and Illumina Hi-C reads of the offspring of the hybrid cross C. angulata (male) x C. gigas (female) were partitioned and independently assembled to construct two chromosome-level fully phased genomes. The assembly size (contig N50 size, BUSCO completeness) of the two genomes were 582.4 M (12.8 M, 99.1%) and 606.4 M (5.46 M, 98.9%) for C. angulata and C. gigas, respectively, ranking at the top of mollusk genomes with high contiguity and integrity. The general features of the two genomes were highly similar, and 15,475 highly conserved ortholog gene pairs shared identical gene structures and similar genomic locations. Highly similar sequences can be primarily identified in the coding regions, whereas most noncoding regions and introns of genes in the same ortholog group contain substantial small genomic and/or structural variations. Based on population resequencing analysis, a total of 2,756 species-specific single-nucleotide polymorphisms and 1,088 genes possibly under selection were identified. Conclusions: This is the first report of trio-binned fully phased chromosome-level genomes in marine invertebrates. The study provides fundamental resources for the research on mollusk genetics, comparative genomics, and molecular evolution. Report Crassostrea gigas Pacific oyster Institute of Oceanology, Chinese Academy of Sciences: IOCAS-IR Pacific GigaScience 12 |
institution |
Open Polar |
collection |
Institute of Oceanology, Chinese Academy of Sciences: IOCAS-IR |
op_collection_id |
ftchinacasciocas |
language |
English |
topic |
oyster Crassostrea angulata Crassostrea gigas trio-binning haplotype-resolved genome Life Sciences & Biomedicine - Other Topics Science & Technology - Other Topics Biology Multidisciplinary Sciences ALIGNMENT DIVERGENCE ACCURATE SEARCH |
spellingShingle |
oyster Crassostrea angulata Crassostrea gigas trio-binning haplotype-resolved genome Life Sciences & Biomedicine - Other Topics Science & Technology - Other Topics Biology Multidisciplinary Sciences ALIGNMENT DIVERGENCE ACCURATE SEARCH Qi, Haigang Cong, Rihao Wang, Yanjun Li, Li Zhang, Guofan Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas |
topic_facet |
oyster Crassostrea angulata Crassostrea gigas trio-binning haplotype-resolved genome Life Sciences & Biomedicine - Other Topics Science & Technology - Other Topics Biology Multidisciplinary Sciences ALIGNMENT DIVERGENCE ACCURATE SEARCH |
description |
Background: The Portuguese oyster Crassostrea angulata and the Pacific oyster C. gigas are two major Crassostrea species that are naturally distributed along the Northwest Pacific coast and possess great ecological and economic value. Here, we report the construction and comparative analysis of the chromosome-level haplotype-resolved g enomes of the two oyster congeners. Findings: Based on a trio-binning strategy, the PacBio high-fidelity and Illumina Hi-C reads of the offspring of the hybrid cross C. angulata (male) x C. gigas (female) were partitioned and independently assembled to construct two chromosome-level fully phased genomes. The assembly size (contig N50 size, BUSCO completeness) of the two genomes were 582.4 M (12.8 M, 99.1%) and 606.4 M (5.46 M, 98.9%) for C. angulata and C. gigas, respectively, ranking at the top of mollusk genomes with high contiguity and integrity. The general features of the two genomes were highly similar, and 15,475 highly conserved ortholog gene pairs shared identical gene structures and similar genomic locations. Highly similar sequences can be primarily identified in the coding regions, whereas most noncoding regions and introns of genes in the same ortholog group contain substantial small genomic and/or structural variations. Based on population resequencing analysis, a total of 2,756 species-specific single-nucleotide polymorphisms and 1,088 genes possibly under selection were identified. Conclusions: This is the first report of trio-binned fully phased chromosome-level genomes in marine invertebrates. The study provides fundamental resources for the research on mollusk genetics, comparative genomics, and molecular evolution. |
format |
Report |
author |
Qi, Haigang Cong, Rihao Wang, Yanjun Li, Li Zhang, Guofan |
author_facet |
Qi, Haigang Cong, Rihao Wang, Yanjun Li, Li Zhang, Guofan |
author_sort |
Qi, Haigang |
title |
Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas |
title_short |
Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas |
title_full |
Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas |
title_fullStr |
Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas |
title_full_unstemmed |
Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas |
title_sort |
construction and analysis of the chromosome-level haplotype-resolved genomes of two crassostrea oyster congeners: crassostrea angulata and crassostrea gigas |
publisher |
OXFORD UNIV PRESS |
publishDate |
2023 |
url |
http://ir.qdio.ac.cn/handle/337002/184677 https://doi.org/10.1093/gigascience/giad077 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_relation |
GIGASCIENCE http://ir.qdio.ac.cn/handle/337002/184677 doi:10.1093/gigascience/giad077 |
op_doi |
https://doi.org/10.1093/gigascience/giad077 |
container_title |
GigaScience |
container_volume |
12 |
_version_ |
1802643534159806464 |