Complete mitogenomes of four Trichiurus species: A taxonomic review of the T.lepturus species complex

Abstract

Four Trichiurus species, T.japonicus, T.lepturus, T.nanhaiensis, and T.brevis, from the coasts of the China Seas, have been identified and their entire mitochondrial genomes (mitogenomes) have been sequenced by next-generation sequencing technology. A comparative analysis of five mitogenomes was conducted, including the mitogenome of T.gangeticus. The mitogenomes contained 16.568-16.840 bp and encoded 36 typical mitochondrial genes (13 protein-coding, 2 ribosomal RNA-coding, and 21 transfer RNA-coding genes) and two typical noncoding control regions. Although tRNA^Pro is absent from Trichiurus mitogenomes, when compared with the 22 tRNAs reported in other vertebrates, the gene arrangements in the mitogenomes of the studied species are consistent with those in most teleost mitogenomes. The full-length sequences and protein-coding genes (PCGs) in the mitogenomes of the five species had obvious AT biases and negative GC skew values. Our study indicate that the specimens in the Indian Ocean are neither T.lepturus nor T.nanhaiensis but they are T.gangeticus; the Trichiurus species composition in the Indian Ocean is totally different from that in Pacific and Atlantic oceans; there are at least two Trichiurus species in Indian Ocean; and the worldwide systematics and diversity of the genus Trichiurus need to be reviewed.

Keywords: Characterization; Trichiurus; mitogenome; molecular tool; phylogeny; taxonomy.

Figure 1.

A Eighteen sampling localities of the genus the Trichiurus along the Chinese coast and the species composition after our surveys. Refer to Suppl. material 1: Table S1 for the abbreviations of localities. B The maximum-likelihood (ML) tree of these four Trichiurus species along the coast based on the COI gene. The numbers at the nodes are bootstrap values of the ML and NJ (neighbor-joining) analyses. The sampling size (n) indicated in parentheses C The photographs of four Trichiurus species used in the mitogenomes analyses.

Figure 2.

Positions of 14 (a–n) landmarks used to contrast the morphological differences between Trichiurus species.

Figure 3.

The maximum-likelihood (ML) tree of the Trichiuridae based on the sequences of mitogenome (excluding d-loop). The numbers at the nodes are bootstrap values of the ML and NJ (neighbor-joining) analyses.

Figure 4.

The maximum-likelihood (ML) tree of six Trichiurus species in the world based on the COI gene. The numbers at the nodes are bootstrap values of the ML and NJ (neighbor-joining) analyses.

Figure 5.

The simple regression and the boxplot analysis in T.japonicus (blue), T.lepturus (orange) and T.nanhaiensis (grey) A Total length [D(i,n)] and Preanal length [D(i,m)] B Caudal length [D(m,n)] and Body depth at anus [D(e,f)] C Head depth [D(d,o)] and Orbital length [D(j,k)] and D Head length [D(i,l)] and Head depth [D(d,o)]. The landmarks are illustrated in Fig. 2.

Figure 6.

A AT-skew in 13genes. B GC-skew in in 13 genes.

Figure 7.

A Mean evolutionary rates for each protein coding gene in mitogenomes of five Trichiurus species B Evolutionary rates of ND6 gene of five Trichiurus species. C Evolutionary rates of Ka/Ks in ATP8 gene of five Trichiurus species. Indicated the rates of non-synonymous substitutions to the rate of synonymous substitutions (ka/ks). T.japonicus (TJ), T.lepturus (TL), T.nanhaiensis (TN), T.gangeticus (TG) and T.brevis (TB).

Figure 8.

Relative synonymous codon usage (RSCU) of the mitogenomes of the five Trichiurus species; the stop codon is not included. T.japonicus (TJ), T.lepturus (TL), T.nanhaiensis (TN), T.gangeticus (TG) and T.brevis (TB).

Figure 9.

Frequencies of different amino acids in the mitogenomes of the five Trichiurus species; the stop codon is not included.

Figure 10

. The mean partwise interspecific (gray) and intergeneric (black) p-distance in each gene.