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


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.

SUBMITTER: Liu L 

PROVIDER: S-EPMC9836534 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Genome-wide survey reveals the phylogenomic relationships of <i>Chirolophisjaponicus</i> Herzenstein, 1890 (Stichaeidae, Perciformes).

Liu Lu L   Liu Qi Q   Gao Tianxiang T  

ZooKeys 20221111


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, <i>Chirolophisjaponicus</i>, was sequenced using the next-generation sequencing. Approximately 595.7 megabase pair of the <i>C.japonicus</i> 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 r  ...[more]

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