Study On Genetic Diversity Of Katsuwonus Pelamis Populations And Phylogeny Of Tribe Thunnini Fishes

Tunas, refer to the tribe Thunnini fishes, in general, belonging to the Perciformes, Scombridae. Tunas are highly migratory pelagic species. This study has sequenced four complete mitogenomes, including Auxis thazard, Auxis rochei, Thunnus albacares, Thunnus alalunga. The structrue of the mitogenome of Thunnus alalunga is analysised in detail. Phylogenetic analysis is based on complete mitogenomes of 13 tribe Thunnini species. What’s more, Katsuwonus pelamis is one of important economic tunas. The sequences of Katsuwonus pelamis are also analyzed to explore genetic diversity of Katsuwonus pelamis populations. Those data can provide help for the effective management of fishery resources. 1. Analysis of genetic diversity of Katsuwonus pelamis based on Cytb seqencesIn this study, we obtained 92 Cytb sequences of Katsuwonus pelamis. Analysis with 139 Cytb sequences from Gen Bank, we got 205 distinct haplotypes. Haplotype diversity of five populations（S17, HN, S19, NSX, S21） was the highest, and S1 was the lowest. Nucleotide diversity of NSA is the lowest, and HN was the highest. The higher frequencies of the 1020 th base is A on the premise that the 1017 th base of K. pelamis Cytb sequences is G. Estimates of evolutionary divergence over sequence pairs between and within groups based on Cytb sequences, divergence of S19 was the largest. Neighbor-joining tree showed that 12 populations were clustered into two branches. 11 populations（except S19） were clustered one branch. Tajima’s D neutral test showed that S19, KS, S14 and NSF were significantly deviated from the equilibrium. Fu’s Fs test showed that the 11 groups（except HN） were significantly deviated from the neutral equilibrium. Mismatch distributions showed multiple peaks, indicating that the 11 populations（except HN） may not experience population expansion. 2. Analysis of genetic diversity of Katsuwonus pelamis based on D-loop sequencesWe obtained 238 distinct haplotypes based on analysis of 241 D-loop sequences. Nucleotide diversity of S14 is the highest. KS diverged from equation curve fitting h-S, blow the curve. Evolutionary divergence of S14 was the largest between populations, and HN is the lowest. Genetic distances between S14 and S21, S11 and S14 is the largest. NJ tree showed that 11 populations（except S14） were clustered one branch.Mismatch distribution showed multi peak, indicating that 11 populations（except HN） may not experience population expansion. 3. Analysis of the structrue of the mitogenome of Thunnus alalunga13 pairs of primers for polymerase chain reaction amplification were designed to sequence the complete mitogenome of T. alalunga. The complete mitogenome was 16,527 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes, and two non-coding regions: the light-strand replication origin（OL） and the control region（CR）. The overall nucleotide base composition of T. alalunga is A, 28.37%; G, 16.69%; T, 25.46%; and C, 29.49%, with the A+T content of 53.83%, showing an obvious anti-G bias. Among 13 protein-coding genes and control region sequences, base composition of G were 11.90%（ATP8）¹8.50%（COXI）, showing an obvious anti-G bias. Sequences coding protein, t RNA, r RNA, and control region showed obvious AT bias, especially D-loop sequences. Except for initiation codon of COXI gene beginning with GTG, all other protein-coding genes started with ATG. There were two types of complete stop codons: nine genes ended with TAA and one gene（ND6） ended with TAG. Three genes（COXII, ND4 and Cytb） had an incomplete stop codon: T. There were some overlaps existing in T. alalunga mitogenome. Compared with T. alalunga（Gen Bank accession number NC₀05317）, their mitogenome sequences have the same length, but 95 different nucleotide bases, which appear in CR, 16 S r RNA, ND1, ND2, COXI, COXII, ATP6, COXIII, ND3, ND4 L, ND4, ND5, ND6, Cytb, and the 4695 th nucleotide bases. Most distinct nucleotide bases consisted in the sequence of control region. 4. Phylogeny of tribe Thunnini fishes based on complete mitogenomesWe have sequenced four complete mitogenomes, including A. thazard, A. rochei, T. albacares, T. alalunga. Phylogenetic analysis was based on complete mitogenomes of 13 tribe Thunnini species. Four kinds of fishes which G + C content more than 47% live in tropical waters, and Thunnus maccoyii who live in the temperate waters, G + C content was only 46%. Fishes living in tropical and subtropical waters with the higher content of G+C may be related to their living environment. Maximum Likelihood tree built under GTR+G+I model and NJ tree based on the Kimura two parameter model showed 13 tribe Thunnini species clustered two clade. Eight Thunnus species clustered together, the confidence level of 100%. Auxis, Euthynnus and Katsuwonus species formed a clade, the confidence level of 100%. T. alalunga and Thunnus orientalis clustered together, as the sister species.