The Complete Mitochondrial Genome And Molecular Phylogeny Of Three Shorebirds

The Charadriiformes could be classified into three sub-clades,Lari,Charadrii and Alcidrii,however there have been some different taxonomic opinions.The mitochondria genomes and molecular systematics are effective ways to solve the problem of classification.In this study we obtained the complete mitochondrial genome sequences of three Charadriiforme species which are Tringa erythropus,Tringa glareola,and Gallinago stenura through PCR,then made a comparative research on genome characteristics including the gene composition,arrangement,base composition,initiation codons,termination codons,the frequency of codons and so on by bioinformatics softwares.Based on the three complete mitochondrial genomes in this study and other 15 of Charadriiforme genomes from GenBank,we constructed the phylogenetic trees using bioinformatics softwares to confirm the classification status of these three Charadriiforme birds and try to clarify the controversial issues within Charadriiformes.The result can provide more useful information for the future research on molecular systematics of Charadriiformes.The main results indicate as follows.1.The length of complete mitochondrial genomes for three species of Charadriiformes(Tringa erythropus,Tringa glareola,and Gallinago stenura)was 16683 bp,16804 bp and 18153 bp.The complete mitochondrial genome contained 37 genomes:13 protein-coding genes(ND1,ND2,CO ?,CO ?,ATP8,ATP6,CO?,ND3,ND4L,ND4,ND5,Cyt b,ND6),22 tRNAs,2 rRNA genes(12S rRNA and 16S rRNA gene)and D-Loop region.2.The base composition of the mitochondrial genome for the three species was obviously AT bias,the content of AT was higher.Besides,that is all the same in the 12 PCG dataset(except for ND6),rRNA dataset(12S rRNA and 16S RNA)and D-Loop region.The initiation codons of the mitochondrial protein-encoding genes for these three species were mainly ATN and GTG,which was obviously distinct from other vertebrates.The stop codons of them were mainly TAA,AGG,AGA,T--and TAG,which were common stop codons for birds.3.The phylogenetic trees of 18 Charadriiformes indicate that the order of Charadriiformes was divided into three groups:Scolopaci,Lari,and Charadrii.The phylogenetic tree supported the gull birds as suborder,Lari,belonging to the Charadriiformes.Sandpiper was the latest one to be evolved.The Scolopaci contained Jacanidae and Scolopacidae,the Scolopacidae consisted of Tringa,Eurynorhynchus,Gallinago and Arenaria.Tringa erythropus and Tringa glareola belong to Tringa,had a close relationship,maybe differentiated from the same ancestor.Gallinago stenura belongs to Gallinago of Scolopacidae,differentiated from the Scolopacidae earlier time.4.The phylogenetic tree of long gene fragment show a high BCL value of the branches,which is suitable for the analysis of phylogenetic relationship for all taxon within Charadriiformes.Without mitochondrial complete genome sequences,we can use long protein-coding genes to study phylogenetic relationship of Charadriiformes.