The complete mitochondrial genome of the hybrid grouper Epinephelus moara (♀)×Epinephelus tukula (♂), and phylogenetic analysis in subfamily Epinephelinae

• Published in: Acta oceanologica Sinica 2020-12, Vol.39 (12), p.65-75
• Main Authors: Li, Zhentong, Tian, Yongsheng, Cheng, Meiling, Wang, Linna, Zhang, Jingjing, Wu, Yuping, Pang, Zunfang, Ma, Wenhui, Zhai, Jieming
• Format: Article
• Language: English
• Subjects: Analysis; Bats; Breeding; Climatology; Codons; DNA; Earth and Environmental Science; Earth Sciences; Ecology; Engineering Fluid Dynamics; Environmental Chemistry; Epinephelus moara; Epinephelus tukula; Genes; Genomes; Marine & Freshwater Sciences; Marine fishes; Mitochondria; Molecular evolution; Nucleotide sequence; Nucleotides; Oceanography; Offspring; PCR; Phylogenetics; Phylogeny; Progeny; Protein structure; Proteins; Replication origins; rRNA; Secondary structure; Transfer RNA; tRNA; Vertebrates
• ISSN: 0253-505X; 1869-1099
• DOI: 10.1007/s13131-020-1689-7

The mitochondrial genome (mitogenome) of hybrid grouper Epinephelus moara (♀)× Epinephelus tukula (♂), a new hybrid progeny, can provide valuable information for analyzing phylogeny and molecular evolution. In this study, the mitogenome was analyzed using PCR amplification and sequenced, then the phylogenetic relationship of E. moara (♀)×E. tukula (♂) and 35 other species were constructed using Maximum Likelihood and Neighbor-Joining methods with the nucleotide sequences of 13 conserved protein-coding genes (PCGs). The complete mitogenome of E. moara (♀)×E. tukula (♂) was 16 695 bp in length, which contained 13 PCGs, 2 rRNA genes, 22 tRNA genes, a replication origin and a control region. The composition and order of these genes were consistent with most other vertebrates. Of the 13 PCGs, 12 PCGs were encoded on the heavy strand, and ND6 was encoded on the light strand. The mitogenome of the E. moara (♀)×E. tukula (♂) had a higher AT nucleotide content, a positive AT-skew and a negative GC-skew. All protein initiation codons were ATG, except for COX and ND4 (GTG), ATP6 (CTG), and ND3 (ATA). ND2, COXII, ND3, ND4 and Cytb had T as the terminating codon, COXIII’s termination codon was TA, and the remaining PCGs of that were TAA. All tRNA genes, except for the lacking DHU-arm of tRNA Ser (AGN) , were predicted to form a typical cloverleaf secondary structure. In addition, sequence similarity analysis (99% identity) and phylogenetic analysis (100% bootstrap value) indicated that the mitochondrial genome was maternally inherited. This study provides mitogenome data for studying genetic, phylogenetic relationships and breeding of grouper.