The Sequencing And Analysis Of Complete Mitochondrial Genomes Of Seven Avians In Galliformes, Passeriformes And Gruiformes

In comparison with nuclear genome, the mitochondrial genome has small molecularsize, simple structrue, close gene arrangement, strict matrilinear inheritance, fastsubstitution rate and no tissue specificity. In recent years, mitochondrial DNA(mtDNA)has been considered as an important tool for inferring phylogenetic relationships at manytaxonomic levels. In this study, we sequenced the complete mtDNA of Tragopancaboti,Crossoptilon auritum, Phasianus colchicus, Luscinia calliope, Cyanoptilacyanomelana, Ficedula zanthopygia and Gallinula chloropus by LA-PCR and nestedPCR. Combined with previous reports about avian complete mitochondrial genomesequences, we tried to address (1) the characteristic of mitochondrial genome of Tragopancaboti,Crossoptilon auritum and Phasianus colchicus in Galliformes,(2) thecharacteristic of mitochondrial genome of Luscinia calliope, Cyanoptila cyanomelanaand Ficedula zanthopygia of Passeriformes,(3) the characteristic of mitochondrialgenome of Gallinula chloropus in Gruiformes,(4) the phylogenetic analyses ofGaliiformes,(5) the divergence times for major lineages of galliformes birds. The resultswere summarized as follows：1. The analysis of complete mitochondrial genome sequences of Crossoptilonauritum and Phasianus colchicusAccroding to the results we got, the total length of Tragopan caboti,Crossoptilonauritum and Phasianus colchicus are16,727bp,16,687bp and16,692bp, respectively,which contains13protein-coding genes,22tRNAs genes,2rRNA genes and a noncodingcontrol region. There is an extra“C” in nad3gene of Crossoptilon auritum and Phasianuscolchicus. The length of Crossoptilon auritum and Phasianus colchicus control region are1,177bp,1,146bp and1,147bp, respectively, which were divided into three domains:domainI~III. Their structure of genome, base composition and gene orders are similar tothat of other species in Galliformes.2. The analysis of complete mitochondrial genome sequences of Luscinia calliope,Cyanoptila cyanomelana and Ficedula zanthopygiaIn this analysis, the total length of Luscinia calliope, Cyanoptila cyanomelana andFicedula zanthopygia are16,841bp，16,802bp and16,794bp, respectively, with13 protein-coding genes,22tRNAs genes,2rRNA genes and a noncoding control region.There are no an extra“C” in nad3genes of their mitochondrial genomes. They have onlyone control region and their length are1,257bp,1,241bp and1,213bp, respectively,which are different from some species of Passeriformes. Also, they have the similar basecomposition and gene order to other species of Passeriformes.3. The analysis of complete mitochondrial genome sequences of GallinulachloropusAs our results showed, the total length of Gallinula chloropus is17,016bp, including13protein-coding genes,22tRNAs genes,2rRNA genes and a noncoding control region.There is an extra“C” in nad3gene of Gallinula chloropus, and the start codons of nad3gene and cox1gene are ATT and GTG respectively, which is different from other genes ofGallinula chloropus. The structure of genome, base coposition and gene orders are similarto other species in Gruiformes.4. The phylogenetic analyses of GaliiformesWe sampled37species of Galliformes as ingroups, and took two species ofAnseriformes as outgroups in our study. We built phylogenetic trees of39aves with threemethods: MP, ML and BI. The results as follows:(1) Perdix is found as a sister group toLophura with high support.(2) Megapode was proved to be a well supported sister groupto all other Galliformes.(3)The monophyly of Galliformes and Phasianidae were stronglysupported(nucleotide and amino acid: posterior probabilities1.00in BI, bootsrap value=100%in MP ang ML), while Phasianinae was not a monphyly lineage according to therebuilt trees.(4)The turkey was embedded not only in the Phasianidae, but also in thePhasianinae.5. Estimation of divergence times for major lineages of galliformes birdsIn this study, we used relaxed molecular clocks to evaluate the divergence time ofmajor lineages of Galliformes based on complete mitochondrial genomes. A nucleotidedataset of13concatenated protein-coding genes from22species of Galliformes was usedto investigate the evolutionary divergences within the group, using Gallus bravardi,Schaubortyx and Gallinuloides fossils as calibration points. All the various relaxed clockmethods indicated that (1) Megapodiidae originated in the Late Cretaceous;(2) Numididae,Phasianidae, Arborophilinae and Coturnicinae originated in the Eocene of Paleogene;(3)Pavoninae and Gallininae originated at the Eocene-Oligocene boundary;(4) the estimateddivergence times among most genera of Phasianidae were much older than those of theprevious studies. Our results might provide a more likely time scale for evolutionaryhistory of the galliform birds.