广东农业科学2026，Vol.53Issue(5)：137-149,13.DOI:10.16768/j.issn.1004-874X.2026.05.011
黑鞍鳃棘鲈线粒体基因组全序列测定及分析
Complete Mitochondrial Genome Sequencing and Analysis of Plectropomus laevis
摘要
Abstract
[Objective]This study aims to characterize the mitochondrial genome of Plectropomus laevis and provide key molecular data for phylogenetic analysis,genetic diversity assessment,and germplasm conservation of this species.[Method]The complete mitochondrial genome of P.laevis was sequenced and annotated for the first time.Illumina sequencing technology was employed to obtain the whole-genome sequence.After assembly and annotation,bioinformatics analyses were performed,including base composition,codon usage bias,tRNA secondary structure prediction,and phylogenetic reconstruction based on 13 protein-coding genes(PCGs).[Result]The results showed that the complete mitochondrial genome of P.laevis is 16771 bp in length,containing 13 PCGs,2 rRNA genes,22 tRNA genes,and a control region containing the heavy-strand origin(OH).No gene loss or rearrangement was detected,indicating a highly conserved structure.Base composition analysis revealed an overall AT content of 56.93％,with an AT-skew of 0.0120 and a GC-skew of-0.2318,which are typical characteristics of vertebrate mitochondrial bias.Except for cox1(GTG)and atp6(CTG),all other PCGs start with ATG.Among amino acids,leucine(Leu)showed the highest proportion(16.0％),while cysteine(Cys)had the lowest(1.6％).Relative synonymous codon usage(RSCU)analysis indicated that highly preferred codons predominantly end with A/U,and the codon usage pattern is highly similars to those of its congeneric species P.leopardus and P.areolatus,revealing conserved codon usage within the genus.Among the 22 tRNAs,all except trnS1 exhibited a complete typical cloverleaf secondary structure;the dihydrouridine arm stem of trnS1 retained only 2 base pairs,showing a highly reduced structure,a feature rarely reported in the family Epinephelidae.Phylogenetic trees constructed using neighbor-joining and maximum likelihood methods based on the 13 PCGs consistently supported the monophyly of the genus Plectropomus and suggested that Plectropomus may represent an early-diverging lineage within Epinephelidae.[Conclusion]The mitochondrial genome of P.laevis is highly conserved in structure and exhibits typical vertebrate nucleotide bias.Its codon usage pattern is highly conserved within the genus.The DHU arm of trnS1 is highly reduced,a feature rarely documented in Epinephelidae.Phylogenetic analysis confirmed the monophyly of Plectropomus and its placement as an early-diverging lineage.关键词
黑鞍鳃棘鲈/线粒体基因组/全序列分析/密码子使用偏好/tRNA二级结构/系统发育Key words
Plectropomus laevis/mitochondrial genome/complete sequence analysis/codon usage bias/tRNA secondary structure/phylogeny分类
农业科技引用本文复制引用
陈宗馥,林蠡,吴锦辉,秦真东,秦海鹏,肖佑鹏,甘昭龙,黎烽,赵艳飞,陈冰,陈燕,甘松永..黑鞍鳃棘鲈线粒体基因组全序列测定及分析[J].广东农业科学,2026,53(5):137-149,13.基金项目
广东省现代化海洋牧场适养品种核心技术攻关项目(2025-MRB-00-001) （2025-MRB-00-001）
