Dataset Information

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 Chirolophisjaponicus 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, 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 r ...[more]

PMID: 36761850

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Project description:Introduction: Xinjiang Brown cattle are a famous dual-purpose (dairy-beef) cultivated breed in China that occupy a pivotal position within the cattle breeding industry in Xinjiang, China. However, little information is available on the genetic background of this breed. To fill this research gap, we conducted a whole-genome screen using specific-locus amplified fragment sequencing to examine the genetic structure and diversity of 130 Xinjiang Brown cattle-grazing type (XBG, traditional type) cattle. Methods: A subsequent joint analysis incorporating two ancestral breeds, specifically 19 Brown Swiss (BS) foreign and nine Kazakh (KZ) Chinese cattle, as well as 20 Xinjiang Brown cattle-housing type (XBH) cattle, was used to explore the genetic background of the Xinjiang Brown cattle. Results: The results showed that, after nearly a century of crossbreeding, XBG cattle formed a single population with a stable genetic performance. The genetic structure, genetic diversity, and selection signature analysis of the two ancestral types showed highly different results compared to that of XBH cattle. Local ancestry inference showed that the average proportions of XGB cattle within the BS and KZ cattle lineages were 37.22% and 62.78%, respectively, whereas the average proportions of XBH cattle within the BS and KZ cattle lineages were 95.14% and 4.86%, respectively. Thus, XGB cattle are more representative of all Xinjiang Brown cattle, in line with their breeding history, which involves crossbreeding. Two complementary approaches, fixation index and mean nucleotide diversity, were used to detect selection signals in the four aforementioned cattle breeds. Finally, the analysis of 26 candidate genes in Xinjiang Brown cattle revealed significant enrichment in 19 Gene Ontology terms, and seven candidate genes were enriched in three pathways related to disease resistance (CDH4, SIRPB1, and SIRPα) and the endocrine system (ADCY5, ABCC8, KCNJ11, and KCNMA1). Finally, development of the core SNPs in XBG cattle yielded 8,379 loci. Conclusion: The results of this study detail the evolutionary process of crossbreeding in Xinjiang Brown cattle and provide guidance for selecting and breeding new strains of this species.

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Dataset Information

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

Publications

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

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Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

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