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

By

Liu, Lu
Liu, Qi
Gao, Tianxiang

Type

Article

Date of Publication

2022

Original Publication

ZooKeys

Volume

1129

Pages

55--72

Subjects

Chirolophinae , draft genome , genome assembly , genome evolution , Next-Generation Sequencing , Stichaeidae , Zoarcales

Contributed by

Pensoft Publishers

Language

English

Published by

Sofia, Bulgaria Pensoft Publishers

Identifiers

DOI: https://doi.org/10.3897/zookeys.1129.91543

 

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, Chirolophis japonicus, 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 Anarrhichthys ocellatus, Cebidichthys violaceus, and Pholis gunnellus. The results provide more thorough genetic information of C. japonicus and a theoretical basis and reference for further genome-wide analysis.