Analysis On Complete Mitochondrial Genome And Phylogenetic Of Gruiformes And Charadriiformes

In this study,we used the next-generation sequencing method to sequence Porzana fusca,Porzana pusilla,Porzana paykullii,Rallus aquaticus and Gallirallus striatus in Gruiformes,and Hydrophasianus chirurgus in Charadriiformes.Analyzed and compared the mitochondrial DNA?mtDNA?structure,phylogeny,and taxonomic origin of the Gruiformes and Charadriiformes,the main results were as follows:1)Based on sequencing,splicing,and annotating the mtDNA of six birds,the results showed that lengths of mtDNA in six birds were 16,935 bp in Porzana fusca16,978 bp in Porzana pusilla,16955 bp in Porzana paykullii,17149 bp in Rallus,17647 bp in Gallirallus striatus and 16855 bp in Hydrophasianus chirurgus,respectively.All their mitochondrial genomes contained 37 coding genes and a control region?CR?.All 22 tRNA genes in six species were from 63 to 80 bp in length,which included IQM,WANCY and HSL regions.These sequences could be folded into canonical cloverleaf secondary structure,except for tRNA^Ser?AGY?,which lost its“DHU”arm.The CR in the six species of mitochondrial genomes was different in length.But their main structure and function were similar,which included three major regions according to the difference in base composition and nucleotide frequency.2)The base compositions were A>C>T>G in 73 species complete mitochondrial sequences in Gruiformes and Charadriiformes.The total AT content in the 73 species was larger than that of GC.The start codons in protein-coding genes?PCGs?included ATG,GTG,ATT,ATC and ATA,while its stop codons included TAA,TAG,AGG,AGA and the incomplete cipher T.In PCGs,the highest frequency of codon was CTA?Leu?.The highest frequency of amino acids was Leu,whereas the lowest was Cys.3)The Ralli branchesmainly consisted of the species in Rallidae,where Porzana was closest to Porphyrio.Gallirallus striatus and Lewinia muelleri consisted a sister group,while Rallus aquaticus was a seperate branch.Hydrophasianus chirurgus?Charadriiformes;Jacanidae?was closely related to Rostratulidae.Different to the traditional taxonomy,Gallicrex cinerea and Amaurornis phoenicurus consist a sister group and should be classified as Amaurornis,and Gallirallus striatus was more closely related to Lewinia muelleri and should be grouped into genus of Lewinia,and Gelochelidon nilotica,Thalasseus bengalensis and Sterna hirundo consisted a sister group,which should be classified as Sternidae;Pluvianellus socialis and Chionis minor formed a sister group,which should be classified as Chionididae.In addition,Rhynochetos jubatus and Larus vegae were in a single branch,respectively,and their classification status remained to be discussed.4)According to the estimation of divergent time corrected by fossil records of related birds and compared with previous studies,the base divergent time of Gruiformes was 56.57 Ma?62.26⁴6.05 Ma?,and the emergence time of the suborders Grui was about 19.59 Ma?30.35¹2.12 Ma?,and the emergence time of the suborders of the Ralli was about 40.18 Ma?46.63²2.70 Ma?.The divergent time was 11.17 Ma?14.80⁶.85 Ma?among Porzana fusca,Porzana pusilla and Porzana paykullii.Rallus aquaticus belonged to the genus of Porzana,whose divergence time was 19.60 Ma?26.23¹0.78 Ma?.The divergent time of Gallirallus striatus separated from the genus Gallirallus was 15.78 Ma?20.16⁸.61Ma?.The origin time of Charadriiformes was about 56.34 Ma?62.75⁴4.78Ma?.The origin time of the Charadrii was 44.52 Ma?52.66²3.55 Ma?.The divarication time of Lari was 40.09 Ma?46.35²2.14 Ma?.The divarication time of Scolopaci was37.99 Ma?44.34²7.75 Ma?.The divergent time of Hydrophasianus chirurgus was12.56 Ma?18.59⁴.28 Ma?.