Four Kinds Of Passeriformes Birds Mitochondrial Genome And Long-tailed Tits Belong To Compare Mitochondrial Genome Studies

As the largest taxon in Aves, Passeriformes was an hotspot in the research of ornithology, due to its morphological diversity and behavioral complexity. Now, the phylogeny of Passeriformes and some taxa within it remained to be unsloved. As the smallest genome in animals, the mitochondrial genome was often used to reconstruct the relationship between different categories. Many phylogenetic analyses in Passeriformes used mitochondrial genes. In order to avoid the error caused by the analysis of a single gene, the complete sequence of mitochondrial genomes were selected to reconstructed the phylogenetic relationships of relevant categories.The gene arrangement of animal mitochondrial genomes was considered to be stable in certain categories. But some rearrangement events occurred in certain animal mitochondrial genomes. The mechanism and frenquency of rearrangement in mitochondrial genomes were the hotspots concerned by many researchers.In this research, we sequenced the complete mitochondrial genome of Sylviparus modestus, Aegithalos concinnus talifuensis, Aegithalos bonvaloti and Aegithalos caudatus by the PCR methods of L-PCR, sub-PCR and sequencing technologies of direct and primer walking. The complete mitochondrial genome of four species were annotated and analysed with Gallus gallus, Pseudopodoces humilis and Sylvia atricapilla. Besides, we used another32complete mitochondrial genome sequences of Passeriformes,25of which were downloaded form NCBI and the rest were unpublished data that were accomplished by our laboratory, to reconstructed the phylogenetic relationships of Passeriformes. And we also briefly summarized the mitochondrial genome rearrangement in Vertebrates. The main points derived form this research were listed below:1. The length of four complete mitochondrial genomes was17086bp(S.modestus),17940bp (A.c. talifuensis),17953bp (A.bonvaloti),17938bp (A.caudatus). All of the four genomes encoded37genes including13PCGs,2rRNA genes and22tRNA genes. As the gene arrangement of Gallus gallus, S.modestus had only one non-coding region which was called control region and located between tRNAGluand tRNAPhe. Unlike S.modestus, the species in Aegithalos had the same gene arrangement with Sylvia atricapilla, which was a new arrangement in birds. Besides the traditional control region between tRNAGlu and tRNAphe, this arrangement had anther control region between tRNAThr and tRNAPro, the sequence of which was almost the same as the typical one.2. In these four species, the start condon of most PCGs were ATG except COI of S.modestus and ND3of the genus Aegithalos. The former was GTG, while the latter was ATA. Most of the stop condons were TAR and AGR, which were seen as the typical stop condon for Vertebrates. Two exceptions were COIII and ND4, whose stop condons were incomplete condon T. 3. The functional RNA of the four species included tRNAs and rRNAs. Nearly all of the tRNAs could formed the classical structure clover leaf structure, while Ser-AGY was excluded for its DHU arm was lost. Most of the mispaired base pairs in tRNAs were G-U mispair. The secondary structure of the two rRNAs was conserved. The secondary structure of12Sr RNA contained4domains and43helices, while the secondary structure of16S rRNA contained6domains and55helices.4. The mitochondrion comparative genome analysis of the genus Aegithalos showed that, this genus could be divided into3groups, one is A.concinnus, an other is A.caudatus, the rest one contained A.bonvaloti and A.fuliginosus; the variable sites between A.c.concinnus and A.c.talifuensis were so large that the number was formerly considered as the level of species, at the same time, the variable sites between A.bonvaloti and A.fuliginosus were only41; in genus Aegithalos, the evolution rates were different in different functional regions, the rates of control region and PCGs were faster, while the rates of tRNA and rRNA were slower; the amino acid sequence of PCGs showed that the numbers of S sites in A.caudatus were larger than other taxon, we guessed that this may be related to its unique living environment.5. We reorganized the37mitochondrial genes into3data sets, and reconstructed the phylogenetic relationships in Passeriformes by the methods of MP, ML and Bayesian Inference. The results showed that the positions of refleman and superb lyrebird were different form the traditional classification system. The former was the sister group of the whole Passeriformes, the latter was the sister group of Oscine. The position of Paridae was ambiguous, but it was clear that it should be removed form Sylvioidea, but its sister group remained unknown. The genus Aegithalos had a close relationship with Sylviidae or Pycnonotidae.6. The primary analysis of the mitochondrial gene arrangement indicated that rearrangement was not rare in Vertebrates. The hotspot of rearrangement was concentrated in the regions adjacent to the two replicate orgins. So we guessed that the appearance of rearrangements was probably related to the incorrect replication led by the replicate orgins, or the cutting sites of the Restriction Enzyme could be found near the hotspot. In the two rearrangement models, we considered that the tandem replication and random loss model could explained the rearrangement events occoured in exchange of adjacent genes, and the recombination model could excellent interpreted the complex arrangement such as the shift of long fragments.