The Sequencing And Analysis Of The Complete Mitochondrial Genomes Of13Passeriformes Species

Passeriformes is the biggest order of aves, has a great variety of species. Thespecies in Passeriformes show a diversity of morphology, and distribute widely.Now, there are big issues in the classification and phylogenetic relationships ofPasseriformes, which is the hot topic of ornithologist’s research. Compared tonuclear genomes, the mitochondrial genomes have some advantages as follow:small in size, closed gene arrangement, no duplicate copies of the same gene, strictmaternally inherited, no tissue specificity, and fast mutation rate. So, themitochondrial DNA widely used as the molecular markers in the study ofphylogenetic relationships.In this study, we cloned and sequenced the complete mitochondrial genomesof13species in8families by LA-PCR (Long and accurate polymerase chainreaction) and nested PCR, which are Sturnidae (Sturnus sericeus, Sturnuscineraceus, Acridotheres cristatellus, Acridotheres tristis, Gracupica nigricollis,and Gracula religiosa), Alaudidae (Alauda arvensis), Passeridae (Passer montanus),Fringillidae (Fringilla montifringilla), Leiothrichidae (Garrulax canorus),Oriolidae (Oriolus chinensis), Laniidae (Lanius tephronotus), and Campephagidae(Pericrocotus ethologus). Based on these data we sequenced, combined thereleased complete mitochondrial genome sequences of other birds in the GenBank,our study addressed two following questions:(1) the characteristic of mitochondrialgenomes of the species studied in this study,(2) The phylogenetic relationships ofPasseriformes based on complete mitochondrial genomes. The main resultssummarized as follows:1. The analysis of complete mitochondrial genomes of13species inPasseriformesThe results are as follows:(1) The total length of complete mitochondrialgenomes sequenced in this study range from16803bp（Oriolus chinensis）to17785bp（Garrulax canorus）；(2) They both including two rRNA genes (12S rRNA and16S rRNA),22tRNA genes,13protein-coding genes, and one or two noncodingcontrol regions (Among them, Garrulax canorus and Alauda arvensis have twononcoding control regions, and the others just contain one).(3) All of these geneswere coded on the H-strand, except for one protein-coding gene (nad6) and eighttRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer（UCN）, tRNAProand tRNAGlu).(4) There are three types of control region:①the single controlregion with the representative of6species in the family Sturnidae, Pericrocotusethologus, Lanius tephronotus, Passer montanus, Fringilla montifringilla andOriolus chinensis;②the2almost identical copies of CR (CR1+CR2) with therepresentative of Garrulax canorus;③two extensive heteroplasmic controlregions with the representative of Alauda arvensis.(5)The structures, basecompositions, codon usage and other features of those genomes are similar to otherreported Passeriformes species.(6) All tRNA genes have the potential to fold intotypical clover-leaf structure.(7) According to sequence alignment, the stop codonof cox2gene in Passer montanus and L.tephronotus is CAA.2. The phylogenetic relationships of Passeriformes based on completemitochondrial genomesIn this study, we used the complete mitochondrial genome sequences of13species we acquired, combined the62released complete mitochondrial genomesequences of Passeriformes species as ingroups, and used2Coraciiformes and2Piciformes species as outgroups. Based on the13protein-coding genes and thecorresponding amino acid datasets, we built the phylogenetic trees using MP, BIand ML method, respectively. The results as follows:(1) The monophyly ofPasseriformes was supported.(2) Paridae should be separated from the superfamilySylvioidea, and placed within the superfamily Muscicapoidea.(3) The familyMuscicapidae in superfamily Muscicapoidea is not monophyletic.(4) The familyPetroicidae in superfamily Muscicapoidea is at the basal place of Passerida.(5)Corvida is paraphyly, not the monophyly.