Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C

文献类型： 外文期刊

第一作者： Bai, Chang-Ming

作者： Bai, Chang-Ming;Xin, Lu-Sheng;Wu, Biao;Wang, Qing-Chen;Liu, Zhi-Hong;Wang, Chong-Ming;Bai, Chang-Ming;Xin, Lu-Sheng;Wu, Biao;Wang, Qing-Chen;Liu, Zhi-Hong;Wang, Chong-Ming;Bai, Chang-Ming;Xin, Lu-Sheng;Wu, Biao;Wang, Qing-Chen;Liu, Zhi-Hong;Wang, Chong-Ming;Bai, Chang-Ming;Xin, Lu-Sheng;Wu, Biao;Wang, Qing-Chen;Liu, Zhi-Hong;Wang, Chong-Ming;Rosani, Umberto;Rosani, Umberto;Duan, Xiao-Ke

作者机构：

关键词： ark shell; PacBio; Hi-C; genomic; chromosomal assembly

期刊名称：GIGASCIENCE （ 影响因子：6.524； 五年影响因子：8.702 ）

ISSN： 2047-217X

年卷期： 2019 年 8 卷 7 期

页码：

收录情况： SCI

摘要： Background: The blood clam, Scapharca (Anadara) broughtonii, is an economically and ecologically important marine bivalve of the family Arcidae. Efforts to study their population genetics, breeding, cultivation, and stock enrichment have been somewhat hindered by the lack of a reference genome. Herein, we report the complete genome sequence of S. broughtonii, a first reference genome of the family Arcidae. Findings: A total of 75.79 Gb clean data were generated with the Pacific Biosciences and Oxford Nanopore platforms, which represented approximately 86x coverage of the S. broughtonii genome. De novo assembly of these long reads resulted in an 884.5-Mb genome, with a contig N50 of 1.80 Mb and scaffold N50 of 45.00 Mb. Genome Hi-C scaffolding resulted in 19 chromosomes containing 99.35% of bases in the assembled genome. Genome annotation revealed that nearly half of the genome (46.1%) is composed of repeated sequences, while 24,045 protein-coding genes were predicted and 84.7% of them were annotated. Conclusions: We report here a chromosomal-level assembly of the S. broughtonii genome based on long-read sequencing and Hi-C scaffolding. The genomic data can serve as a reference for the family Arcidae and will provide a valuable resource for the scientific community and aquaculture sector.

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