Black-tailed Jays And The Silver Face Long-tailed Tit Mitochondrial Genome Sequencing And Phylogenetic Analysis

Because of the characteristics of easy obtained, length and genetic constitution relatively stable, rapid evolution rate and maternal inheritance, mtDNA has been widely used in the fields of phylogeny, phylogeography and population structure.Up to the end of February 2010, there have been 110 birds mitochondrial genomic sequences published in the NCBI. Passeriformes is the largest group in aves, but it has only 11 mt genomic sequences sequenced. Due to its extremely rich in species, large numbers of individuals, morphological diversity, behavioral complexity, classification of Passeriformes birds is very difficult. The origin and evolution of Passeriformes have always been major arguments in ornithology. The increasing evidence from gene-comparison studies has demonstrated that the phylogenetic performance may vary among different genes. A single gene may not be representative of the whole mitogenome and can provide a misleading inference of the true inter-specific evolutionary relationships.In order to study the genome structures and sequence characters of mitochondrial genome in Passeriformes and providing new genomic information for research on phylogenetic relationships within Passeriformes, we determined the complete sequences of Podoces hendersoni and Aegithalos fuliginosus mitochondrial genomes by using long PCR and conserved primer walking approaches. The assemblyed sequences were annotated and analyzed in details according information of Gallus gallus, Corvus frugilegus, and Sylvia atricapilla mitochondrial genomes. We reconstruct phylogeny of Passeriformes by combined the two new mtDNA sequences with orther Passeriformes species deposited in GenBank, as well as other completed mitochondrial genome were sequenced in our laboratory. The conclusions drawn from the study as follows:1. The mitochondrial genomes of Podoces hendersoni and Aegithalos fuliginosus are 16,867 bp and 17,953 bp respectively. They all encode 13 protein genes,22 tRNA genes,2 rRNA genes and a control region. The differences between the two genomes are, Aegithalos fuliginosus has aΨcontrol region, and the gene order of Podoces hendersoni is the same as typical bird, but Aegithalos fuliginosus is the same as the Sylvia atricapilla, which has a special gene order:Cyt b/tRNAThr/CR/tRNAPro/ND6/tRNAGlu/ΨCR, between ND5 and 12S rRNA.2. COI gene, which uses GTG and ATG as initiation codon respectively in Podoces hendersoni and Aegithalos fuliginosus.The other 12 PCGs use the start codon ATG. Most protein genes use the typical and complete stop codon TAA,AGG or AGA, except COⅢand ND4 gene of Podoces hendersoni and Aegithalos fuliginosus, which use the incomplete stop codons T.3. The secondary structures of 20 tRNAs could form typical cloverleaf in Podoces hendersoni except for tRNASer(AGY),which had an absence of the DHU arm and tRNALeu(CUN) which anticodon-loop was consist of nine bases, other than the standard 7 bases. All 21 tRNA genes of Aegithalos fuliginosus mitochondrial genomes have a typical clover leaf structure except tRNASer(AGY), which is lack the DHU arm. The secondary structures of 22 tRNAs have all some unmatched base pairs, The G-U pairs are the main mismatches.4. The secondary structures of Podoces hendersoni and Aegithalos fuliginosus rRNA had predicted. There are 4 domains,43 helices structures in 12S rRNA and 6 domains,55 helices structures in 16SrRNA.5. F-box, D-box, C-box, B-box, Bird similarity-box and CSB1-box, which found in the control region of other birds, were also exist in Podoces hendersoni and Aegithalos fuliginosus. The control region, which lacked heavy-strand replication origin (OH) and the bidirectional transcription promoter (LSP/HSP), is speculated that these two species may form special space structures to carry out these tasks.6. The phylogenotic relationships among 16 Passeriformes species based on datasets of NADH dehydrogenase subunit genes(ND2, ND4, ND5), rRNA(12S rRNA,16S rRNA) and 21 tRNA (except tRNASer(AGY)) were reconstructed using maximum parsimony(MP), maximum likelihood(ML) and Bayesian methods. The presented results from the three methods congruence with morphology and DNA-DNA hybridisation data, which divided Passeriformes to Oscine and Suboscine. But the result of phylogenetic analysis suggest that lyrebirds belong to the Oscines, not the Suboscine as traditional views. Corvida was not supported as monophyletic groups. Longtailed Tits shoud be listed into familay. Pseudopodoces humilis should be listed into Paridae.