Padgett Kyla, Baeza J Antonio
Department of Biological Sciences Clemson University Clemson South Carolina USA.
Smithsonian Marine Station at Fort Pierce Smithsonian Institution Fort Pierce Florida USA.
Ecol Evol. 2025 Jul 20;15(7):e71795. doi: 10.1002/ece3.71795. eCollection 2025 Jul.
The goliath grouper (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 . The mitochondrial genome of 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; and 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 and indicated a sister relationship between and , another large-bodied grouper from the Indo-Pacific Ocean. The newly sequenced mitochondrial genome of provides a new genomic resource that can support future conservation efforts.
波纹唇鱼（鲈形目：石斑鱼科）是一种大型的极度濒危鱼类，分布于西大西洋的沿海栖息地，从佛罗里达州到巴西南部，在东太平洋盆地也有其他种群。对该物种的保护关注源于历史上的过度捕捞、栖息地丧失以及生长缓慢和性成熟较晚等生活史特征。在本研究中，为了协助保护工作，我们组装并鉴定了[波纹唇鱼属某物种]的完整线粒体基因组。[波纹唇鱼属某物种]的线粒体基因组长度为16,561 bp，包含13个蛋白质编码基因（PCGs）、两个核糖体RNA基因（12S和16S rRNA）、22个转运RNA（tRNA）基因以及一个856 bp的控制区。基因顺序与其他同属物种报道的相同。总体A+T含量为56%，密码子使用显示出对富含A+T密码子的偏好。所有PCGs都处于纯化选择之下，各基因间的选择压力存在差异；[基因1]和[基因2]分别处于最强和最弱的选择之下。tRNA基因的二级结构分析显示出典型的三叶草二级结构，除了trnS1缺少完整的D臂。MiTFi和RASP2之间的比较分析表明，MiTFi对tRNA二级结构的预测更准确。控制区显示出高A+T含量（69.9%）、多个微卫星基序和一个串联重复，以及发夹二级结构。这些特征与密切相关物种的研究结果相符。基于翻译后的PCGs进行的最大似然系统发育分析不支持[波纹唇鱼属某物种]属的单系状态，并表明[波纹唇鱼属某物种]与[印度洋-太平洋地区的另一种大型石斑鱼]之间存在姐妹关系。新测序的[波纹唇鱼属某物种]线粒体基因组提供了一种新的基因组资源，可支持未来的保护工作。
