A chromosome-level genome assembly of the potato grouper (Epinephelus tukula)

Wang, Linna; Li, Zhentong; Liu, Yang; Chen, Shuai; Li, Linlin; Duan, Pengfei; Wang, Xinyi; Li, Wensheng; Wang, Qingbin; Zhai, Jieming; Tian, Yongsheng

doi:10.1016/j.ygeno.2022.110473

Cited by 5 publications

(3 citation statements)

References 45 publications

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“…In conclusion, groupers hold significant ecological aimportance and commercial value. In recent years, several high-quality chromosome-level assemblies of grouper reference genomes have been assembled, including seven species of the Epinephelus genus [5][6][7][8][9][10][11][12][13] , one species of the Plectropomus genus [14][15][16][17] , one species of the Cromileptes genus 18 , and one species of the Cephalopholis genus 19 , which provide important genomic resources for evolutionary analysis, molecular-assisted breeding, and germplasm conservation of groupers. Phylogenetic studies show that Epinephelus species in the western Pacific Ocean have diverged into two genetic clades with variations in body size 20,21 , implying the potential presence of independent evolutionary trajectories during the course of adaptation.…”

Section: Background and Summarymentioning

confidence: 99%

“…Phylogenetic studies show that Epinephelus species in the western Pacific Ocean have diverged into two genetic clades with variations in body size 20,21 , implying the potential presence of independent evolutionary trajectories during the course of adaptation. However, a significant limitation exists, as reference genomes are available for seven species within the large-bodied clade 5,[7][8][9][10][11][12][13]18 , whereas the small-bodied clade has an accessible reference genome for only one Library construction and sequencing. All the DNA extraction, library construction and sequencing procedures were performed by the Nextomics Biosciences (Wuhan, China) according to the manufacturer's protocols.…”

Section: Background and Summarymentioning

confidence: 99%

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Chromosome-level genome assembly and annotation of the yellow grouper, Epinephelus awoara

Zhang,

Yang,

Hua

et al. 2024

Sci Data

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Epinephelus awoara, as known as yellow grouper, is a significant economic marine fish that has been bred artificially in China. However, the genetic structure and evolutionary history of yellow grouper remains largely unknown. Here, this work presents the high-quality chromosome-level genome assembly of yellow grouper using PacBio single molecule sequencing technique (SMRT) and High-through chromosome conformation capture (Hi-C) technologies. The 984.48 Mb chromosome-level genome of yellow grouper was assembled, with a contig N50 length of 39.77 Mb and scaffold N50 length of 41.39 Mb. Approximately 99.76% of assembled sequences were anchored into 24 pseudo-chromosomes with the assistance of Hi-C reads. Furthermore, approximately 41.17% of the genome was composed of repetitive elements. In total, 24,541 protein-coding genes were predicted, of which 22,509 (91.72%) genes were functionally annotated. The highly accurate, chromosome-level reference genome assembly and annotation are crucial to the understanding of population genetic structure, adaptive evolution and speciation of the yellow grouper.

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Section: Background and Summarymentioning

confidence: 99%

Section: Background and Summarymentioning

confidence: 99%

Chromosome-level genome assembly and annotation of the yellow grouper, Epinephelus awoara

Zhang,

Yang,

Hua

et al. 2024

Sci Data

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show abstract

“…Genome sequencing technology has enabled the reconstruction of phylogenetic and evolutionary histories of species using whole-genome data ( Berthelot et al, 2014 ). While several reference genomes have been assembled and used to analyze phylogeny in Epinephelus , including the genomes of E. lanceolatus ( Zhou et al, 2019a ), E. tukula ( Wang et al, 2022a ), and E. fuscoguttatus ( Yang et al, 2022 ), large-scale orthologous gene detection remains limited due to challenges in obtaining annotated high-quality genomes. Phylotranscriptomics (transcriptome-based phylogenetic inference) is a cost-effective and powerful tool for identifying orthologous genes and reconstructing phylogenetic relationships among group species ( Cheon et al, 2020 ; Morales-Briones et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Genetic mechanism of body size variation in groupers: Insights from phylotranscriptomics

Zhang,

Weng,

Wang

et al. 2024

Zoological Research

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Animal body size variation is of particular interest in evolutionary biology, but the genetic basis remains largely unknown. Previous studies have shown the presence of two parallel evolutionary genetic clusters within the fish genus Epinephelus with evident divergence in body size, providing an excellent opportunity to investigate the genetic basis of body size variation in vertebrates. Herein, we performed phylotranscriptomic analysis and reconstructed the phylogeny of 13 epinephelids originating from the South China Sea. Two genetic clades with an estimated divergence time of approximately 15.4 million years ago were correlated with large and small body size, respectively. A total of 180 rapidly evolving genes and two positively selected genes were identified between the two groups. Functional enrichment analyses of these candidate genes revealed distinct enrichment categories between the two groups. These pathways and genes may play important roles in body size variation in groupers through complex regulatory networks. Based on our results, we speculate that the ancestors of the two divergent groups of groupers may have adapted to different environments through habitat selection, leading to genetic variations in metabolic patterns, organ development, and lifespan, resulting in body size divergence between the two locally adapted populations. These findings provide important insights into the genetic mechanisms underlying body size variation in groupers and species differentiation.

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Decoding the fish genome opens a new era in important trait research and molecular breeding in China

Zhou,

Wang,

et al. 2024

Sci. China Life Sci.

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A chromosome-level genome assembly of the potato grouper (Epinephelus tukula)

Cited by 5 publications

References 45 publications

Chromosome-level genome assembly and annotation of the yellow grouper, Epinephelus awoara

Chromosome-level genome assembly and annotation of the yellow grouper, Epinephelus awoara

Genetic mechanism of body size variation in groupers: Insights from phylotranscriptomics

Decoding the fish genome opens a new era in important trait research and molecular breeding in China

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