Determination And Comparison Of Four Mites Mitochondrial Genomes And Lineage Genomics Analysis

With the extensive application of mitochondrial genome data in phylogenetic studies,gene-based studies have been unable to address the need for deep phylogenetic relationships.Therefore,phylogenomics has become main research methods in molecular phylogenetics.The increase in mitochondrial genomic data of Caelifera will provide new data for studying the evolutionary and comparative mitochondrial genomics and building a more robust phylogenetic tree.In this study,the Long-PCR and Sub-PCR amplification and Sanger sequencing were used to obtain the mitochondrial genomes of four Acridoidea species,Hieroglyphus tonkinensis,Oxya adentata,Pternoscirta caliginosa and Omocestus haemorrhoidalis.After assembling,annotating and analyzing characteristics of these new determined mitogenomes,we conducted a comprehensive comparative genomics analyses for 142 Orthopteran species.In additions,phylogenetic relationships of 15 Oedipodidae,31 Catantopidae species,8 Arcypteridae species and 100 Caelifera species were reconstructed based on datasets of mitogenomes.The main conclusions are summarized as following:1.The complete mitogenomes of H.tonkinensis,O.adentata,P.caliginosa and O.haemorrhoidalisare 15 625bp,15 447bp,15 598bp,15 600bp in size,respectively.All four mitogenomes contain 37 genes and genes order have typical KD inversion.AT biase is found in each part of the four mitogenomes.2.In addition to the start condons of COX1 in H.tonkinensis and O.adentata are ACC,the other protein coding genes all use the typical ATN as initiation condons.Except the stop condons of ND5 in O.adentata and P.caliginosa are the incomplete termination codon T,the other protein coding genes all use the typical TAA and TAG as termination condons.Among the available codons,the most frequently used codons is UUA,the lesser are CGC,CUC and AGC;the highest among the amino acid composition is Leu(Leucine),the least is Cys(Cysteine).3.21 of the 22 tRNAs were well folded into a clover-leaf secondary structure,except trnSAGN,which lacked the DHU stem in the four species.The anti-codon is consistent with most insects.The secondary structure of rRNA genes is similar to the other caeliferan species.The conserved sequence blocks of Block A,Block B,Block C and Block G,except Block D,exist in the D-Loop region of the four species.In D-Loop regions,one repeat element is found in H.tonkinensis,four repeat elements is found in P.caliginosa and no repeat element is found in O.adentata and O.haemorrhoidalis.4.The results of comparative mitogenomics analysis in 142 Orthoptera mitochondrial genomes indicated that the mitogenomes are about 15.6kb in length.The nucleotide composition is A>T>C>G,with a significant AT biase.The largest gene length change is ATP8,the smallest is COX1;the proportion of KD rearrangement in Caelifera is 95%,and there is no other form;the proportion of KD rearrangement in Ensifera is 46%,except KD rearrangement,the proportion of gene rearrangement is 36%.The larger overlapping regions of Orthoptera mitochondrial genes are in trnC-trnY?COX1-trnLUUR and ND4L-trnT,the larger intergenic region is between ND1 and trnLCUN.The initiation codon of COX1 is relatively diverse,the other 12 protein coding genes are mainly typical ATN,in addition to the typical stop codon:TAA and TAG,there are incomplete termination codon T and TA.The most abundant amino acids is leucine,followed by isoleucine,serine,and phenylalanine.TrnSAGN are deficient in the DHU arm of almost all Orthoptera species.Not all Orthoptera insects has conserved regions and poly-T in the D-loop region,and the number of repeat elements is not the same.5.Based on the results of datasets analysis,data partitioning and model selection,the phylogenetic trees of Oedipodidae,Catantopidae,Arcypteridae and Caelifera were constructed by BI and ML method for different datasets.The phylogenetic trees of Oedipodidae show that Compsorhipis davidiana and Bryodeminae may have a close relationship.The phylogenetic positions of Traulia,Xenocatantops,Sinopodisma and Pedopodisma were varied with differient methods or datasets,the other species position are basically unchanged,only the branch support is different.The topology and branch support of phylogenetic trees of Arcypteridae were same in all cases,and divided into two branches,Ceracrinae and Arcypteridae,respectively.The phylogenetic analyses based on 100 Caeliferan mitogenome sequences show that the relationships among subfamilies were:(Tridactyloidea +(Tetrigoidea +(Eumastacoidea +(Tanaoceroidea +(Pneumoroidea +(Acridoidea + Pyrgomorphoidea)))))).The phylogenetic trees support the monophyly of Caelifera,Acridoidea,Eumastacoidea,Tetrigoidea,Acrididea,Pamphagidae,Pyrgomorphidae and Oxyinae;but don not support the monophyly of Oedipodidae,Arcypteridae,Acrididae,Gomphoceridae and Romaleidae.There is a close genetic relationship between Chrotogonidae and Pyrgomorphidae.Lentulidae?Lithidiidae?Romaleidae,Ommexechidae and Tristiridae also has a close relationship,...