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. 2019 Jul 1;8(7):giz067.
doi: 10.1093/gigascience/giz067.

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

Chang-Ming Bai  1 , Lu-Sheng Xin  1 , Umberto Rosani  2   3 , Biao Wu  1 , Qing-Chen Wang  1 , Xiao-Ke Duan  4 , Zhi-Hong Liu  1 , Chong-Ming Wang  1
Affiliations

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

Chang-Ming Bai et al. Gigascience. .

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.

Keywords: Hi-C; PacBio; ark shell; chromosomal assembly; genomic.

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Figures

Figure 1:
Figure 1:
Example of a Scapharca (Anadara) broughtonii, the blood clam.
Figure 2:
Figure 2:
Hi-C interaction heat map for Scapharca (Anadara) broughtonii.
Figure 3:
Figure 3:
Gene ontology (GO) annotation of the predicted genes. The horizontal axis indicates classes of the second-level GO annotation. The vertical axis indicates the number and percentage of genes in each class.
Figure 4:
Figure 4:
Eukaryotic Orthologous Groups (KOG) classification of the predicted genes. Results are summarized in 24 function classes according to their functions. The horizontal axis represents each class, and the vertical axis represents the frequency of the classes.
See this image and copyright information in PMC

References

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