Construction of a chromosome-level genome and variation map for the Pacific oyster Crassostrea gigas.

Szczegóły
Abstrakt

Tytuł:: Construction of a chromosome-level genome and variation map for the Pacific oyster Crassostrea gigas.
Autorzy:: Qi H; Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.; National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, China.
Li L; Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.; National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, China.
Zhang G; Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.; National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, China.
Źródło:: Molecular ecology resources [Mol Ecol Resour] 2021 Jul; Vol. 21 (5), pp. 1670-1685. Date of Electronic Publication: 2021 Apr 18.
Typ publikacji:: Journal Article
Język:: English
Imprint Name(s):: Original Publication: Oxford, England : Blackwell
MeSH Terms:: Chromosome Mapping*
Crassostrea*/genetics
Genome*
Animals ; Chromosomes ; DNA Copy Number Variations ; INDEL Mutation ; Polymorphism, Single Nucleotide
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Grant Information:: 41876169 National Natural Science Foundation of China; 2019JZZY010813 Major scientific and technological innovation projects in Shandong Province; COMS2019Q06 Key Deployment Project of Centre for Ocean Mega-Research of Science, Chinese academy of science; CARS-49 The Earmarked Fund for China Agriculture Research System
Contributed Indexing:: Keywords: Crassostrea gigas; Pacific oyster; genome; resequencing; variation
Entry Date(s):: Date Created: 20210303 Date Completed: 20210818 Latest Revision: 20210818
Update Code:: 20240105
DOI:: 10.1111/1755-0998.13368
PMID:: 33655634
: Czasopismo naukowe

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The Pacific oyster (Crassostrea gigas) is a widely distributed marine bivalve of great ecological and economic importance. In this study, we provide a high-quality chromosome-level genome assembled using Pacific Bioscience long reads and Hi-C-based and linkage-map-based scaffolding technologies and a high-resolution variation map constructed using large-scale resequencing analysis. The 586.8 Mb genome consists of 10 pseudochromosome sequences ranging from 38.6 to 78.9 Mb, containing 301 contigs with an N50 size of 3.1 Mb. A total of 30,078 protein-coding genes were predicted, of which 22,757 (75.7%) were high-reliability annotations supported by a homologous match to a curated protein in the SWISS-PROT database or transcript expression. Although a medium level of repeat components (57.2%) was detected, the genomic content of the segmental duplications reached 26.2%, which is the highest among the reported genomes. By whole genome resequencing analysis of 495 Pacific oysters, a comprehensive variation map was built, comprised of 4.78 million single nucleotide polymorphisms, 0.60 million short insertions and deletions, and 49,333 copy number variation regions. The structural variations can lead to an average interindividual genomic divergence of 0.21, indicating their crucial role in shaping the Pacific oyster genome diversity. The large amount of mosaic distributed repeat elements, small variations, and copy number variations indicate that the Pacific oyster is a diploid organism with an extremely high genomic complexity at the intra- and interindividual level. The genome and variation maps can improve our understanding of oyster genome diversity and enrich the resources for oyster molecular evolution, comparative genomics, and genetic research.
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