Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C. Issue 7 (9th July 2019)

• Record Type: Journal Article
• Authors: Bai, Chang-Ming; Xin, Lu-Sheng; Rosani, Umberto; Wu, Biao; Wang, Qing-Chen; Duan, Xiao-Ke; Liu, Zhi-Hong; Wang, Chong-Ming
• Is Part Of: GigaScience. Volume 8:Issue 7(2019)
• Publication Date: 2019-07-09
• Subjects: ark shell -- PacBio -- Hi-C -- genomic -- chromosomal assembly; Information storage and retrieval systems -- Research -- Periodicals; Biology -- Research -- Periodicals; Medical sciences -- Research -- Periodicals; Database management -- Periodicals; 570.285
• DOI: 10.1093/gigascience/giz067
• Languages: English
• ISSNs: 2047-217X

Abstract

Abstract: 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 86× 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.