Nanopore Sequencing and De Novo Assembly of a Black-Shelled Pacific Oyster (Crassostrea gigas) Genome.

Xiaotong Wang,Hongce Song,Kun Wang,Wenjie Xu,Lingling Li,Chenglong Zhu,Cheng He,Zhongqiang Cai,Lei Wei,Qiuyun Jiang,Chenguang Feng,Wenchao Yu

doi:10.3389/fgene.2019.01211

Xiaotong Wang, Hongce Song + Show 10 more

Open Access

https://doi.org/10.3389/fgene.2019.01211

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Abstract

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.

Highlights

Fossil records show that oysters appeared about 200 million years ago (Upper Triassic; Stott, 2004)
For the 23-mer analysis, K_num was 83,754,003,275 and K_depth was estimated as 141, giving an estimated genome size of c. 594 Mb (Table S2). This genome size is within the range of 545–637 Mb reported by (Zhang et al, 2012)
The heterozygous peak was much higher than the second, homozygous peak, indicating that the Black-shelled Pacific oyster (BPO) had a diploid genome with a high level of heterozygosity

Summary

Introduction

Fossil records show that oysters appeared about 200 million years ago (Upper Triassic; Stott, 2004). They began their work of filtering the oceans. Because of their “advanced” defense mechanism (thick shells), which confers strong resistance to desiccation and sunlight exposure, they underwent a large increase during the following 70 million years (from the Jurassic to the Cretaceous). By about 135 million years ago, oysters were the predominant shellfish in the world’s ocean (Stott, 2004). The oyster is of great significance to marine ecology (Beck et al, 2011)

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