Phylogenetic Studies Of The Sinipercid Fishes (Perciformes:Sinipercidae) Based On Threee Complete Mitochondrial DNA Sequences

The Sinipercids are a group of12species of freshwater percoid fish endemic to East Asia. Molecular phylogenetics, also known as molecular systematics, is the use of the structure of molecules to gain information on an organism’s evolutionary relationships. With its small size, high abundance in the cell, maternal inheritance and rapid evolutionary rate, mitochondrial genome has been considered as a natural marker and being widely applied in population genetic and evolutionary studies. In this paper, we described the complete sequencing of mitochondrial genomes of Siniperca chuatsi, Siniperca kneri and Siniperca scherzeri and analyzed the genome organization and gene arrangement of these mitogenomes. Phylogenetic analysis was performed using the mitochondrial genomes of39fish species from the representatives of Scombridae, Cichlidae, Terapontidae, Lutjanidae, sinipercidae, Kyphosidae, Centrarchidae, Pomacanthidae, Oplegnathidae, Sparidae and Labridae. From the mitochondrial sequence data, two different data sets were analyzed:(1) concatenated protein-coding nucleotide sequence;(2) each of the protein-coding nucleotide sequence. Each of the data sets was aligned using clustal X and analyzed by neighbor-joining (N-J) in MEGA4.0and bootstrap analysis was performed with1000replications.1. We used14sets of primers to amplify contiguous, overlapping segments of the complete mitochondrial genome of three Sinipercid fishes. The amplified DNA fragments were purified via spin columns and sequenced with an ABI3730automated DNA sequencer (Applied Biosystems, Foster City, CA, USA) following the manufacturer’s protocol. The S. chuatsi, S. kneri and S. scherzeri mitochondrial genomes were reported for the first time and there were16,496,17,002, and16,585bp in length with accession numbers of JF972568, JN378751and JN084101, respectively. The result shows that the primers we shoosed were appropriate for amplify the mitochondrial genome of Sinipercid fishes. The organization of the three mitochondrial genomes is similar to those reported from other fish mitochondrial genomes, which contains37genes (13protein-coding genes,2ribosomal RNAs, and22transfer RNAs) and a major non-coding control region.2. Among the total mtDNA, the base composition of the three Sinipercid fishes were have lower proportion of G.The base composition of the13mitochondrial protein-coding genes of the three Sinipercid fishes is similarity to each other. In the protein-coding genes, the proportion of G at the first position of the codons has no obvious bias, but was relatively low at the second and third position. Especially at the third position, the G was found with only7.1%,7.1%,8.2%of the codons in S. chuatsi, S. kneri and S. scherzer, respectively. Among the13protein-coding genes of the three sinipercid fishes, overlaps of three reading frames are found on the same strand:ATP8and ATP6overlap by10nucleotides, and ND4and ND4L overlapp by7nucleotides, and ND5and ND6overlap by3nucleotidesSequence analyses revealed that all three sinipercid fishes mitogenomes contain22tRNA genes, including two pairs of double style genes (tRNA-leuUUA(R)and tRNA-leuCUA(N); tRNA-SerUAN(A) and tRNA-SerAGY(C) and18single style genes. The three tRNA clusters-IQM(isoleucine, glutamine and methionine), WANCY(tryptophan, alanine, asparagine, cysteine and tyrosine) and HSL (histidine, serine and leucine) are conserved among the three sinipercid fishes.The non-coding control region located between the tRNA-Pro and tRNA-Phe genes contains the heavy strand origin of replication (OH). A smaller control region containing the putative light strand origin of replication is found between tRNA-Asn and tRNA-Cys genes, which was5’-GCCGG-3’3. Phylogenetic analysis was performed using the mitochondrial genomes of39fish species from the representatives of Scombridae, Cichlidae, Terapontidae, Lutjanidae, sinipercidae, Kyphosidae. Centrarchidae, Pomacanthidae, Oplegnathidae, Sparidae and Labridae. From the mitochondrial sequence data, two different data sets were analyzed:(1) concatenated protein-coding nucleotide sequence;(2) each of the protein-coding nucleotide sequence. Each of the data sets was aligned using clustal X and analyzed by neighbor-joining (N-J) in MEGA4.0and bootstrap analysis was performed with1000replications. According to there tests, mitochondrial protein-coding genes can be roughly classified into four groups, good (ND5, ND4and ATP6)、better(CO3, ND2, CYTB and ND6)、medium(C02, ND4L,CO1) and poor(ND1,ND3and ATP8).The result of phylogenetic analysis showed sinipercine fishes was a monophyletic group. S.chuast and S.kneri were sister species. The reconstructed phylogenetic relationship showed S.scherzeri were primitive. Among the CYTB genes,67nucleotide sites were variable between the three Sinipercid fishes. Of the variable sites,44(46.3%) were transitions between C←�'T,23(24.2%) were transitions between A←�'G.