Chromosome genome assembly and annotation of the yellowbelly pufferfish with PacBio and Hi-C sequencing data

Yitao Zhou,Zhiyu Liu,Xuefeng Hu,Yunhai Guo,Yijun Xiao,Yanding Zhang,Youqiang Chen,Yanting Chen,Gang Lin,Shijun Xiao,Zhen Huang,Jianhua Chen,Ting Xue,Duo Chen,Jianxing Zhong,Wan Cen

doi:10.1038/s41597-019-0279-z

Abstract

Pufferfish are ideal models for vertebrate chromosome evolution studies. The yellowbelly pufferfish, Takifugu flavidus, is an important marine fish species in the aquaculture industry and ecology of East Asia. The chromosome assembly of the species could facilitate the study of chromosome evolution and functional gene mapping. To this end, 44, 27 and 50 Gb reads were generated for genome assembly using Illumina, PacBio and Hi-C sequencing technologies, respectively. More than 13 Gb full-length transcripts were sequenced on the PacBio platform. A 366 Mb genome was obtained with the contig of 4.4 Mb and scaffold N50 length of 15.7 Mb. 266 contigs were reliably assembled into 22 chromosomes, representing 95.9% of the total genome. A total of 29,416 protein-coding genes were predicted and 28,071 genes were functionally annotated. More than 97.7% of the BUSCO genes were successfully detected in the genome. The genome resource in this work will be used for the conservation and population genetics of the yellowbelly pufferfish, as well as in vertebrate chromosome evolution studies.

Highlights

Background & SummaryThe yellowbelly pufferfish (FishBase ID: 24266), Takifugu flavidus, is an economically and ecologically important fish species in coastal regions of East Asia, including the East China Sea, Yellow Sea and Bohai Bay[1,2]
A genome of Takifugu flavidus was published in 201411; this genome was a fragmented draft with contig and scaffold N50 lengths of 2.7 kb and 305.7 kb, respectively
A total of 29,416 protein-coding genes were predicted in the assembled genome, and more than 95% of those genes were successfully functionally annotated

Summary

Introduction

Background & SummaryThe yellowbelly pufferfish (FishBase ID: 24266), Takifugu flavidus, is an economically and ecologically important fish species in coastal regions of East Asia, including the East China Sea, Yellow Sea and Bohai Bay[1,2]. The yellowbelly pufferfish genome has been published, the genome was constructed using short reads from SOLiD next-generation sequencing, and the sequences have not been assembled at the chromosomal level[11]. We applied a combined strategy involving Illumina, PacBio and Hi-C technologies to generate sequencing data for chromosomal genome construction for the yellowbelly pufferfish (Fig. 1).

Results

Conclusion