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...
Published in: | GigaScience |
---|---|
Main Authors: | , , , , |
Format: | Text |
Language: | English |
Published: |
Oxford University Press
2023
|
Subjects: | |
Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10546077/ http://www.ncbi.nlm.nih.gov/pubmed/37787064 https://doi.org/10.1093/gigascience/giad077 |
id |
ftpubmed:oai:pubmedcentral.nih.gov:10546077 |
---|---|
record_format |
openpolar |
spelling |
ftpubmed:oai:pubmedcentral.nih.gov:10546077 2023-11-05T03:41:30+01:00 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC10546077/ http://www.ncbi.nlm.nih.gov/pubmed/37787064 https://doi.org/10.1093/gigascience/giad077 en eng Oxford University Press http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10546077/ http://www.ncbi.nlm.nih.gov/pubmed/37787064 http://dx.doi.org/10.1093/gigascience/giad077 © The Author(s) 2023. 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 (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Gigascience Data Note Text 2023 ftpubmed https://doi.org/10.1093/gigascience/giad077 2023-10-08T01:03:34Z 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 genomes 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 (♂) × C. gigas (♀) 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. Text Crassostrea gigas Pacific oyster PubMed Central (PMC) GigaScience 12 |
institution |
Open Polar |
collection |
PubMed Central (PMC) |
op_collection_id |
ftpubmed |
language |
English |
topic |
Data Note |
spellingShingle |
Data Note 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 |
Data Note |
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 genomes 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 (♂) × C. gigas (♀) 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 |
Text |
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 University Press |
publishDate |
2023 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10546077/ http://www.ncbi.nlm.nih.gov/pubmed/37787064 https://doi.org/10.1093/gigascience/giad077 |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_source |
Gigascience |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10546077/ http://www.ncbi.nlm.nih.gov/pubmed/37787064 http://dx.doi.org/10.1093/gigascience/giad077 |
op_rights |
© The Author(s) 2023. 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 (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
op_doi |
https://doi.org/10.1093/gigascience/giad077 |
container_title |
GigaScience |
container_volume |
12 |
_version_ |
1781697901429260288 |