Four Tits Mitochondrial Genome Sequencing Passerine Mitochondrial Lineages Genome Analysis

Passeriformes have a great variety of species and large populations, with various morphology, and broadly widespreaded. The classification and phylogeny of Passeriformes have always been major concerns in ornithology. With the development of molecular biology and the application of computer technique, more and more DNA data were used into the classification and phylogeny of Passeriformes. There were a lot of studies of classification and phylogeny of Passeriformes in different orders or groups using mitochondrial genes such as Cytb, COI,12S rRNA,16S rRNA, ND1, ND2 and so on. Many results shows that different genes hasve disparate rates of evolution and discrepant information, more and more conflicting gene trees have been emerged, and has gradually become one of main problems in the reconstruction of molecular phylogeny. Believe it contains more information, mitochondrial genome may reflect the real phylogeny relationship better. Up to the end of April 2011, there have been 144 aves mitochondrial genomic sequences published in the GenBank database, only 24 of them are Passeriformes.We determined the complete mitochondrial genomic sequences of Parus cyanus, Parus major, Parus monticolus and Parus palustris by using long PCR amplification and primer walking sequencing approaches. The four mitochondrial genomic sequences were annotated and analyzed in details combining with the information of Gallus gallus, Taeniopygia guttata, Podoces hendersoni and Pseudopodoces humilis mitochondrial genomes. We reconstruct phylogeny of Passeriformes by combined the four new mtDNA sequences with orther Passeriformes species deposited in GenBank, Phylogenetic utility and performance of mitochondrial genes were also analysed with these data. The conclusions drawn from the study as follows:1. The mitochondrial genomes of Parus cyanus, Parus major, Parus monticolus and Parus palustris are 16,788 bp,16,773 bp,16,772 bp and 16,783 bp in length respectively. All of them encode 13 protein genes,2 rRNA genes,22 tRNA genes and 1 nocoding control region.2. The A+T content of Parus cyanus, Parus major, Parus monticolus and Parus palustris mitochondrial genome has no significent bias. The Nucleotide composition of ND6 gene is discrepant to the other 12 protein-coding genes (PCGs) for it's low content of cytosine (C). The content of guanine (G) is significantly low in all four aves'control region.3. All the tRNA genes of Parus cyanus, Parus major, Parus monticolus and Parus palustris mitochondrial genomes have the typical clover leaf structure except the tRNASer(AGN) gene, which is lack of the DHU arm in their secondary structure.4. The secondary structures of Parus cyanus, Parus major, Parus monticolus and Parus palustris rRNA had predicted. There are 4 domains,47 helices structures in 12S rRNA and 6 domains,60 helices structures in 16S rRNA. 5. The central conserved domain in the control region of passeriformes is analysed, the conserved sequence blocks B-F are determined. The control region lacked a heavy-strand replication origin (OH) like reported in mammal.6. The phylogeny of Passeriformes is analysed using MP, ML and BI methods, based on 5 datasets partitioned and combined of mitochondrial genes. The results support the monophyly of Passeriformes and Passerida. The results also show that menura novaehollandiae is neither belongs to Suboscine nor Oscine, but the sister group of Oscine.7. Through the study of phylogenetic utility and performance, the whole sequence of mitochondria genome, rRNA dataset, protein-coding gene dataset were proved to be more efficient, ND5,ND1,16S rRNA contain more phylogeny informations than other mitochondria genes or regions.