Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021 Mar 25;10(3):giab020.
doi: 10.1093/gigascience/giab020.

A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas

Carolina Peñaloza  1 , Alejandro P Gutierrez  1 , Lél Eöry  1 , Shan Wang  2 , Ximing Guo  2 , Alan L Archibald  1 , Tim P Bean  1 , Ross D Houston  1
Affiliations

A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas

Carolina Peñaloza et al. Gigascience. .

Abstract

Background: The Pacific oyster (Crassostrea gigas) is a bivalve mollusc with vital roles in coastal ecosystems and aquaculture globally. While extensive genomic tools are available for C. gigas, highly contiguous reference genomes are required to support both fundamental and applied research. Herein we report the creation and annotation of a chromosome-level assembly for C. gigas.

Findings: High-coverage long- and short-read sequence data generated on Pacific Biosciences and Illumina platforms were used to generate an initial assembly, which was then scaffolded into 10 pseudo-chromosomes using both Hi-C sequencing and a high-density linkage map. The assembly has a scaffold N50 of 58.4 Mb and a contig N50 of 1.8 Mb, representing a step advance on the previously published C. gigas assembly. Annotation based on Pacific Biosciences Iso-Seq and Illumina RNA-Seq resulted in identification of ∼30,000 putative protein-coding genes. Annotation of putative repeat elements highlighted an enrichment of Helitron rolling-circle transposable elements, suggesting their potential role in shaping the evolution of the C. gigas genome.

Conclusions: This new chromosome-level assembly will be an enabling resource for genetics and genomics studies to support fundamental insight into bivalve biology, as well as for selective breeding of C. gigas in aquaculture.

Keywords: DNA sequencing; Hi-C chromosome conformation capture; Pacific oyster; aquaculture; genome assembly.

PubMed Disclaimer

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1:
Figure 1:
Hi-C interaction analysis depicting the 11 super-scaffolds obtained after using the HiRise™ scaffolding software. The Hi-C contact map is visualized using Juicebox v1.11.08 [57].
Figure 2:
Figure 2:
A high concordance between the chromosome-level scaffolds and a high-density linkage map allowed the anchoring of 2 scaffolds (Sc2 and Sc11) to a single linkage group 2 (LG2). Scaffold (Sc) unit lengths are in Mb. Linkage group (LG) units of distance are expressed in cM. Ticks in each linkage group or scaffold indicate lengths in 25 cM or Mb, respectively. Plot generated using Circos v0.69–8 (Circos, RRID:SCR_011798) [58].
Figure 3:
Figure 3:
Circos plot depicting genome features across the 10 oyster chromosomes. (a) Oyster chromosomes (LG1–LG10 on an Mb scale). (b) Short-read coverage plot. Coverage within 2 SD of the mean is shown as grey circles. Abnormal sequence coverage (±2 SD from the mean) is indicated with a blue square or triangle, respectively. (c) GC content percentage (>35% in green; <31% in red). (d) Distribution of repeat elements: DNA transposons (light orange bar), retrotransposon TEs (red bar), and novel repeat elements (yellow bar). The location of centromeres is indicated with a green line. (e) Gene density (range: 50–150). For tracks (b) and (c), a window size of 0.1 Mb was used, whereas for tracks (d) and (e), the size was increased to 0.2 Mb.
Figure 4:
Figure 4:
Density of Helitrons identified across 4 molluscan genomes (orange bars), including maize as a reference species (grey bar). The reference genome assembled for C. gigas was compared to the king scallop (Pecten maximus; GCF_902652985.1), golden apple snail (Pomacea canaliculata; GCF_003073045.1), and Atlantic oyster (Crassostrea virginica; GCF_002022765.2), with maize included as a reference species (Zea mays; GCF_000005005.2). Helitron density is expressed as the number of conserved 3′-ends over genome size (in Mb).
See this image and copyright information in PMC

References

    1. Salvi D, Macali A, Mariottini P. Molecular phylogenetics and systematics of the bivalve family Ostreidae based on rRNA sequence-structure models and multilocus species tree. PLoS One. 2014;9(9):e108696. - PMC - PubMed
    1. Salvi D, Mariottini P. Molecular taxonomy in 2D: a novel ITS2 rRNA sequence-structure approach guides the description of the oysters' subfamily Saccostreinae and the genus Magallana (Bivalvia: Ostreidae). Zool J Linnean Soc. 2016;179:263–76.
    1. FAO. The State of World Fisheries and Aquaculture (SOFIA) 2020. Sustainability in action. Rome, Italy: 2020; 10.4060/ca9229en. - DOI
    1. Wang H, Qian L, Liu X, et al. Classification of a common cupped oyster from Southern China. J Shellfish Res. 2010;29(4):857–66.
    1. Robinson T, Griffiths C, Tonin A, et al. Naturalized populations of oysters, Crassostrea gigas along the South African coast: Distribution, abundance and population structure. J Shellfish Res. 2009;24:443–50.

Publication types