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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2019.01211

Nanopore sequencing and de novo assembly of a black-shelled Pacific oyster (Crassostrea gigas) genome

 Xiaotong Wang1*, Wenjie Xu2, Lei Wei1,  Chenglong Zhu2, Cheng He1, Hongce Song1, Zhongqiang Cai3, Wenchao Yu1, Qiuyun Jiang1, Lingling Li1, Kun Wang2 and  Chenguang Feng2*
  • 1Ludong University, China
  • 2Northwestern Polytechnical University, China
  • 3Chinese Academy of Fishery Sciences (CAFS), China

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 time between black-shelled and the previous published Pacific oyster genome was estimated at about 2.2 million years ago, which implied 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 bivalve.

Keywords: Crassostrea gigas, black-shelled Pacific oyster, evolution, genome assembly, nanopore sequencing

Received: 01 Sep 2019; Accepted: 04 Nov 2019.

Copyright: © 2019 Wang, Xu, Wei, Zhu, He, Song, Cai, Yu, Jiang, Li, Wang and Feng. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Dr. Xiaotong Wang, Ludong University, Yantai, 264025, Shandong Province, China, wangxiaotong999@163.com
Dr. Chenguang Feng, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi Province, China, fcg1989@126.com