期刊
FRONTIERS IN GENETICS
卷 10, 期 -, 页码 -出版社
FRONTIERS MEDIA SA
DOI: 10.3389/fgene.2019.01211
关键词
Crassostrea gigas; black-shelled pacific oyster; evolution; genome assembly; nanopore sequencing
资金
- National Key R&D Program of China [2018YFD0901400]
- National Natural Science Foundation of China [41876193, 41906088]
- Fundamental Research Funds for the Central Universities [19SH0304]
- Key R&D Program of Shandong Province, China [2018GHY115027]
- Special Funds for Taishan Scholars Project of Shandong Province, China [tsqn201812094]
- Shandong Provincial Natural Science Foundation, China [ZR2019MC002]
- Fine Agricultural Breeds Project of Shandong Province, China [2019LZGC020]
- Modern Agricultural Industry Technology System of Shandong Province, China [SDAIT-14-03]
- Key R&D Program of Yantai City, China [2017ZH054]
- Plan of Excellent Youth Innovation Team of Colleges and universities in Shandong Province, China [2019KJF004]
- Research Funds for Interdisciplinary subject, NWPU [19SH030408]
The Pacific oyster, Crassostrea gigas, belongs to one of the most species-rich phyla and provides important ecological and economical services. Here we present a genome assembly for a variety of this species, black-shelled Pacific oyster, using a combination of 61.8 Gb Nanopore long reads and 105.6 Gb raw BGI-seq short reads. The genome assembly comprised 3,676 contigs, with a total length of 587 Mb and a contig N50 of 581 kb. Annotation of the genome assembly identified 283 Mb (48.32%) of repetitive sequences and a total of 26,811 protein-coding genes. A long-term transposable element active, accompanied by recent expansion (1 million years ago), was detected in this genome. The divergence between black-shelled and the previous published Pacific oysters was estimated at about 2.2 million years ago, which implies that species C. gigas had great intraspecific genetic variations. Moreover, we identified 148/188 specifically expanded/contracted gene families in this genome. We believe this genome assembly will be a valuable resource for understanding the genetic breeding, conservation, and evolution of oysters and bivalves.
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