Characteristics Of Mitochondrial Genomes Of Acrididea And Their Application In Phylogenetic Analysis

Mitochondrial genomes have generally been used in studies of comparative genomics,phylogeny,and population genetics,for their abundance in cells,maternal inheritance,lack of recombination,absence of introns,and rapid evolutionary rate.Acrididea(Orthoptera:Caelifera)composes Acridomorpha and Tetrigoidea,with eight superfamilies and more than 11,500 described species,among which are some pests of importance in agriculture,forestry and animal husbandry.To date,a fairly limited number of species are known of their mitogenomes and these species are unevenly distributed among the superfamilies.To enrich mitogenome data of Acrididea for better understanding the evolution of grasshopper mitogenomes,we characterized mitogenomes of 20 species using the traditional sequencing(Sanger)method,with 11 species from Acridoidea,1 from Pyrgomorphoidea,and 8 from Tetrigoidea.We then made a comparative analysis of basic mitogenomic structure,nucleic acid composition,basic characteristics of protein-coding genes,secondary structure of tRNAs,and gene order.In addition,we compared the mitochondrial genomes of 111 species and reconstructed phylogenetic relationships using mitogenomes for taxa Oxya,Catantopinae and Tetrigoidea.The main results and conclusions were summarized as below.1.Basic characteristics of new mitochondrial genomesWe characterised mitogenome sequences of 20 species,among which 12 from Acridomorpha were complete mitogenomes and 8 from Tetrigoidea partial mitogenomes.All complete sequences were closed and double-stranded circular DNA,being composed of 37 genes including 13 protein-coding genes(PCGs),two ribosomal RNAgenes(rRNAs),22 transfer RNA genes(tRNAs)and one AT-region.The orientation and gene order of all complete mitogenomes were consistent.Simultaneously,the sequences were relatively compact and contained a different number of overlapping regions.Except the mitogenome of Traulia nigritibialis,stable gene overlapping sequences were located at ATP8-ATP6 and ND4-ND4L with 7 bp.All partial sequences were double-stranded circular DNA,and the orientation and gene order were consistent.The tRNATyr between tRNACys and COI of Falconius longicornis was not determined.The partial sequences were not compactly arranged with long fragment spacers.2.Characteristics of mitochondrial genomes of Oxya and their application in phylogenetic analysisThe comparetive mitogenomic analysis of five species(Oxya japonica,Oxya hainanensis,Oxya agavisa,Oxya chinensis,Oxya intricata)was performed.There was little difference in the length of each type of genes among the five species.Except Oxya chinensis,the length of PCGs of the other four species were consistent(11,191 bp).Different types of genes showed highly similar nucleotide composition biases towards A+T nucleotides,and the difference between the five species was very small.Predicted initiation codons of PCGs of all five species examined were the typical ATN,and the same gene was very conservative between different species.All T-stretches in the mitogenomes of the five Oxya grasshoppers were 10 bp in size,and inserted in the stem-loop sequence,which was rather conserved.The results from our phylogenetic analysis showed that Oxya was more closely related to the clade between Caryanda and Pseudoxya than to others.Among the five species in Oxya,the following relationship was reconstructed with the support of solid molecular information and high nodal values:(O.intricata+((O.agavisa+O.japonica)+(O.hainanensis+O.chinensis))).3.Characteristics of mitochondrial genomes of Catantopinae and their application in phylogenetic analysisMitogenome length of the seven species ranged from 15,574 bp to 16,293 bp.The sequence of Choroedocus capensis was the longest with 20 non-coding regions(1553 bp),except for the AT-region(1434 bp),with the largest spacer region between tRNASer(UCN)and ND1.The difference in length of different gene types were random without showing a close relationship.The A+T content followed downside in amount as:AT-region>rRNAs>tRNAs>PCGs.A wide variation in nuleic acid was shown in N-strand of tRNAPro,tRNAPhe,tRNAVal and tRNATyr while it was more consistent in J-strand,tRNASer(UCN),tRNAAsn,tRNASer(AGN),tRNALeu(UUR)and tRNAAsp had high nucleic acid identity.Our analysis suggest that the Catantopinae species were not clustered as a monophyletic group.Phylogenetic analysis showed that the seven species of Catantopinae were divided into three branches:two Choroedocus species were one,and Stenocatantops splendens and Xenocatantops brachycerus were a sister group,the three Traulia species were clustered into one,and at the base of the clade consisting of Acridinae,Gomphocerinae,and Oedipodinae.4.Characteristics of mitochondrial genomes of Tetrigoidea and their application in phylogenetic analysisThere was a gene spacer between tRNASer(UCN)and ND1,with a big difference in length.Formosatettix qinlingensis was the shortest(12 bp),Zhengitettix curvispinus the longest(945 bp).The gene overlaps between the genes ATP8-ATP6 and ND4-ND4L were completely identical among the species.The start and stop codons of PCGs were relatively conserved,with ATG as the primary initiation codon,TAA as the primary stop codon,and only a few species with atypical codons.Phylogenetic analysis confirmed that Tetriginae was a more evolved group in Tetrigoidea,and Scelimeninae was not a monophyletic group.The phylogenetic trees showed the following groups among 8 genera from Scelimeninae:((((Thoradonta+Loxilobus)+Eucriotettix)+Criotettix)+((Paragavialidium+Scelimena)+Falconius))+Zhengitettix).5.Comparetive analysis of mitochondrial genomes of AcridideaThe comparetive mitogenomic analysis of Acrididea showed following results.?The order of tRNA genes between CO? and ATP8 was reverse,as opposed to the arrangement inferred in ancestral insects,in which tRNALys precedes tRNAAsp.We assume that the rearrangement may be an important evolutionary feature of the mitogenome of Acrididea.? The full length of the mitogenome sequences was mainly concentrated at about 15,600 bp.The total length of PCGs,tRNAs and rRNAs varied very little between species,while the length of AT-region(the longest non-coding region)was quite different,with a major consquence on the length of mitogenome.? The content of the four bases in the complete mitogenomes was obviously uneven,and the nucleotide composition was downside A to T to C to G and had an obvious AT bias.? The largest change in the length of PCGs was ATP8,and relatively small change was ND4.The genetic distance of COI was the smallest and the evolution rate was the slowest,while ND6 had the largest genetic distance and the fastest evolution rate.? The initiation codons of the 13 PCGs were mainly ATN(ATA,ATT,ATG and ATC),and the stop codons mainly TAA,TAG and T(TA).The start codons of COI and ND6 were diversified,while the stop codons of ND5 were diversified.The start codon of ND4L had obvious group differentiation,and all of Acridomorpha started with ATG,while all of Tetrigoidea started with ATT.? The typical 22 tRNA genes,generally occurred in all Acrididea mitogenomes,and the anti-codons of tRNAs between different species were identical.The secondary structures of tRNAs and rRNAs were mainly based on normal base pairs.And there were multiple base mismatches,G-U mismatch was the most common.? The largest intergenic region in the mitogenomes was generally located between tRNASer(UCN)and ND1.There was a most conserved overlapping region between ATP8 and ATP6,and the overlapping fragment of most species was ATGATAA.