The Mitochondrial Genome of the Imperiled Goliath Grouper Epinephelus itajara: Selective Pressures in Protein Coding Genes, Secondary Structure of tRNA Genes, and Phylogenetic Placement

TL;DR

This study sequenced the mitochondrial genome of the endangered Goliath Grouper, revealing its genetic structure and evolutionary relationships to aid conservation efforts.

Contribution

The complete mitochondrial genome of Epinephelus itajara is reported, including insights into gene structure, selection pressures, and phylogenetic placement.

Findings

The mitochondrial genome of Epinephelus itajara is 16,561 bp with conserved gene order and A+T-rich codon usage.

All protein-coding genes are under purifying selection, with cox1 and nad4 showing the strongest and weakest selection, respectively.

Phylogenetic analysis suggests a sister relationship between Epinephelus itajara and Epinephelus lanceolatus.

Abstract

The goliath grouper
Epinephelus itajara
(Perciformes: Epinephelidae) is a large, critically endangered fish distributed across coastal habitats in the western Atlantic Ocean, from Florida to southern Brazil, and with additional populations in the eastern Pacific basin. Conservation concerns for this species stem from historical overfishing, habitat loss, and life‐history traits such as slow growth and late sexual maturity. In this study, to aid conservation efforts, we assembled and characterized the complete mitochondrial genome of
E. itajara
. The mitochondrial genome of
Epinephelus itajara
is 16,561 bp long and comprises 13 protein‐coding genes (PCGs), two ribosomal RNA genes (12S and 16S rRNA), 22 transfer RNA (tRNA) genes, and an 856 bp control region. Gene order is identical to that reported for other congeneric species. The overall A + T content is 56%, and codon usage shows a preference for A + T‐rich codons. All PCGs were found to be under purifying selection, with variation in selective pressure among genes; cox1 and nad4 were under the strongest and weakest selection, respectively. Secondary structure analysis of the tRNA genes displayed typical cloverleaf secondary structures, except for trnS1, which lacked a complete D‐arm. Comparative analyses between MiTFi and RASP2 revealed that MiTFi provided more accurate predictions of tRNA secondary structures. The control region exhibited a high A + T content (69.9%), multiple microsatellite motifs, and one tandem repeat, along with hairpin secondary structures. These features mirror findings in closely related species. A maximum likelihood phylogenetic analysis based on translated PCGs did not support the monophyletic status of the genus Epinephelus and indicated a sister relationship between
Epinephelus itajara
and
Epinephelus lanceolatus
, another large‐bodied grouper from the Indo‐Pacific Ocean. The newly sequenced mitochondrial genome of
Epinephelus itajara
provides a new genomic resource that can support future conservation efforts.

This study presents the complete mitochondrial genome of the critically endangered Goliath Grouper (
Epinephelus itajara
), totaling 16,561 bp and comprising 13 protein‐coding genes, 22 tRNAs, and two rRNAs. Genomic analysis revealed conserved gene order, A + T‐rich codon usage, and purifying selection across all protein‐coding genes, providing valuable resources for conservation genetics and species identification. Photograph by Albert Kok, used with permission.

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