Comparison on characteristics of tunicates mitochondrial genomes and molecular phylogeny
尾索动物线粒体基因组特征比较及分子系统发育

In this paper, a comprehensive analysis based on 12 tunicates mitochondrial genomes has been done and the basic characteristics of tunicates mitochondrial genomes are fully revealed. In tunicates mitochondrial genomes, all genes are encoded on the same DNA strand, which is significantly different with the genes distribution feature of vertebrates and amphioxus mitochondrial genomes. Compared with typical gene composition of metazoan mitochondrial genomes, there are increase of transfer RNA genes and missing of atp8 gene in some tunicates species. Gene order is extremely rearranged among tunicates mitochondrial genomes, there are gene rearrangement and gene loss of major genes even in same genus. There are differences in the start codon, stop codon and amino-acid number in protein-coding genes of tunicates mitochondrial genomes. The ratio of Ka/Ks of 12 protein-coding genes from 2 Ciona mitochondrial genomes is less than 1 (between 0.0927 and 0.6752), indicating a negative selection. In major coding genes, nad5 and nad4 genes have the largest number of different loci, which can be used as alternative molecular markers to analyze biodiversity among different tunicates species. The phylogenetic trees based on mitochondrial genomes support the relationship at family level: (((Pyuridae+Styelidae)+(((Polyclinidae+Didemnidae)+Clavelinidae)+Cionidae))+ Ascidiidae)+Doliolidae.