Genome-wide survey reveals the phylogenomic relationships of Chirolophisjaponicus Herzenstein, 1890 (Stichaeidae, Perciformes)

Lu Liu; Qi Liu; Tianxiang Gao

doi:10.3897/zookeys.1129.91543

Genome-wide survey reveals the phylogenomic relationships of Chirolophisjaponicus Herzenstein, 1890 (Stichaeidae, Perciformes)

Zookeys. 2022 Nov 11:1129:55-72. doi: 10.3897/zookeys.1129.91543. eCollection 2022.

Authors

Lu Liu¹, Qi Liu², Tianxiang Gao^{3

4}

Affiliations

¹ Naval Architecture and Port Engineering College, Shandong Jiaotong University, Weihai, China Shandong Jiaotong University Weihai China.
² Wuhan Onemore-tech Co., Ltd. Wuhan, Hubei, China Wuhan Onemore-tech Co., Ltd Wuhan China.
³ Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang, China Zhejiang Ocean University Zhoushan China.
⁴ Zhejiang Provincial Key Laboratory of Mariculture and Enhancement, Zhejiang Marine Fisheries Research Institute, Zhoushan, China Zhejiang Marine Fisheries Research Institute Zhoushan China.

Abstract

Fish are the largest vertebrate group, consisting of more than 30 000 species with important ecological and economical value, while less than 3% of fish genomes have been published. Herein, a fish, Chirolophisjaponicus, was sequenced using the next-generation sequencing. Approximately 595.7 megabase pair of the C.japonicus genome was assembled (49 901 contigs with 42.61% GC contents), leading to a prediction of 46 729 protein-coding gene models. A total of 554 136 simple sequence repeats was identified in the whole genome of C.japonicus, and dinucleotide microsatellite motifs were the most abundant, accounting for 59.49%. Phylogenomic analysis of 16 genomes based on the 694 single-copy genes suggests that C.japonicus is closely related with Anarrhichthysocellatus, Cebidichthysviolaceus, and Pholisgunnellus. The results provide more thorough genetic information of C.japonicus and a theoretical basis and reference for further genome-wide analysis.

Keywords: Chirolophinae; Stichaeidae; Zoarcales; draft genome; genome assembly; genome evolution; next-generation sequencing.

Lu Liu, Qi Liu, Tianxiang Gao.

Grants and funding

This study was supported by the Province Key Research and Development Program of Zhejiang: 2021C02047; The Doctoral Research Foundation of Shandong Jiaotong University, Grant/Award Numbers: BS201902051.