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Wang L, Chen J, Xue X, Qin G, Gao Y, Li K, Zhang Y, Li XJ. Comparative analysis of mitogenomes among three species of grasshoppers (Orthoptera: Acridoidea: Gomphocerinae) and their phylogenetic implications. PeerJ 2023; 11:e16550. [PMID: 38111661 PMCID: PMC10726767 DOI: 10.7717/peerj.16550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 11/09/2023] [Indexed: 12/20/2023] Open
Abstract
Whole mitochondrial genomes have been widely used in phylogenetic analysis, population genetics and biogeography studies. This study sequenced and characterized three complete mitochondrial genomes (Dasyhippus peipingensis, Myrmeleotettix palpalis, Aeropedellus prominemarginis) and determined their phylogenetic position in Acrididae. The length of the mitochondrial genomes ranged from 15,621-15,629 bp and composed of 13 PCGs, 2 rRNA, 22 tRNA genes and an AT control region. The arrangement and structure of the mitochondrial genomes were similar to those of other invertebrates. Comparative genomics revealed that the three mitochondrial genomes were highly conserved in terms of gene size, structure, and codon usage, all PCGs were purified selections with an ATN start codon and a TAN stop codon. All tRNAs could be folded into the typical clover-leaf structure, except tRNA Ser (AGN) that lacked a dihydrouridine (DHU) arm. Phylogenetic analysis based on 13 PCGs of 34 Acrididae species and seven outgroup species revealed that differences in the shape of antennae within the family Acrididae should be given less weight as a taxonomic character for higher-level classification. Moreover, the divergence time estimates indicates that in Gomphocerinae, the species with clubbed antennae were formed within the nearest 18 Mya, and Pacris xizangensis is more ancient.
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Affiliation(s)
- Li Wang
- The Key Laboratory of Zoological Systematics and Application, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Jianyu Chen
- The Key Laboratory of Zoological Systematics and Application, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Xiaobao Xue
- The Key Laboratory of Zoological Systematics and Application, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Guoqing Qin
- The Key Laboratory of Zoological Systematics and Application, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Yuanyi Gao
- The Key Laboratory of Zoological Systematics and Application, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Kai Li
- The Key Laboratory of Zoological Systematics and Application, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Yulong Zhang
- The Key Laboratory of Zoological Systematics and Application, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Xin-Jiang Li
- The Key Laboratory of Zoological Systematics and Application, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
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Amorim IC, Melo ADS, Silva AFD, Wallau GDL, Moura RDCD. Characterization of the mitogenome of Rhammatocerus brasiliensis and phylogenetic analysis of the family Acrididae (Orthoptera). Gene 2020; 731:144362. [DOI: 10.1016/j.gene.2020.144362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 11/30/2022]
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Chang H, Qiu Z, Yuan H, Wang X, Li X, Sun H, Guo X, Lu Y, Feng X, Majid M, Huang Y. Evolutionary rates of and selective constraints on the mitochondrial genomes of Orthoptera insects with different wing types. Mol Phylogenet Evol 2020; 145:106734. [PMID: 31972240 DOI: 10.1016/j.ympev.2020.106734] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 12/30/2022]
Abstract
Orthoptera is the most diverse order of polyneopterans, and the forewing and hindwing of its members exhibit extremely variability from full length to complete loss in many groups; thus, this order provides a good model for studying the effects of insect flight ability on the evolutionary constraints on and evolutionary rate of the mitochondrial genome. Based on a data set of mitochondrial genomes from 171 species, including 43 newly determined, we reconstructed Orthoptera phylogenetic relationships and estimated the divergence times of this group. The results supported Caelifera and Ensifera as two monophyletic groups, and revealed that Orthoptera originated in the Carboniferous (298.997 Mya). The date of divergence between the suborders Caelifera and Ensifera was 255.705 Mya, in the late Permian. The major lineages of Acrididae seemed to have radiated in the Cenozoic, and the six patterns of rearrangement of 171 Orthoptera mitogenomes mostly occurred in the Cretaceous and Cenozoic. Based on phylogenetic relationships and ancestral state reconstruction, we analysed the evolutionary selection pressure on and evolutionary rate of mitochondrial protein-coding genes (mPCGs). The results indicated that during approximately 300 Mya of evolution, these genes experienced purifying selection to maintain their function. Flightless orthopteran insects accumulated more non-synonymous mutations than flying species and experienced more relaxed evolutionary constraints. The different wing types had different evolutionary rates, and the mean evolutionary rate of Orthoptera mitochondrial mPCGs was 13.554 × 10-9 subs/s/y. The differences in selection pressures and evolutionary rates observed between the mitochondrial genomes suggested that functional constraints due to locomotion play an important role in the evolution of mitochondrial DNA in orthopteran insects with different wing types.
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Affiliation(s)
- Huihui Chang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
| | - Zhongying Qiu
- School of Basic Medical Sciences & Shaanxi Key Laboratory of Brain Disorders, Xi'an Medical University, Xi'an 710021, China
| | - Hao Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
| | - Xiaoyang Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
| | - Xuejuan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
| | - Huimin Sun
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
| | - Xiaoqiang Guo
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Yingchun Lu
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Xiaolei Feng
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
| | - Muhammad Majid
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
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Deng J, Yu Z, Ning J, Wang H, Lin X, Liu X. Complete mitochondrial genome and phylogenetic analysis of a Chorthippus fallax (Zuboxsky) isolated in rangeland of northwest region of China. Mitochondrial DNA B Resour 2020; 5:61-62. [PMID: 33366422 PMCID: PMC7720977 DOI: 10.1080/23802359.2019.1695549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
In this study, we assembled a complete 16,143 bp mitochondrial genome for Chorthippus fallax (Zuboxsky), which encodes 13 protein-coding genes, 22 tRNAs, 12S and 16S rRNAs and a 722 bp D-loop in the characteristic arrangement of superfamily Acrididae. The most common start codon for 13 PCGs is ATG and the most common termination codon is TAA. The overall A + T content was 75.13%. Phylogenetic analysis based on the entire mitochondrial genome indicated C. fallax (Zuboxsky) had more close relationship with Euchorthippus fusigeniculatus and Chorthippus chinensis in family Arcypteridae, and implied non-monophyly for the family. The data will be important for better understanding of the phylogenetic relationship of members in Acrididae superfamily.
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Affiliation(s)
- Jialu Deng
- College of Life Science, Huaibei Normal University, Huaibei, China
| | - Ziqi Yu
- College of Life Science, Huaibei Normal University, Huaibei, China
| | - Jie Ning
- College of Life Science, Huaibei Normal University, Huaibei, China
| | - Heng Wang
- College of Life Science, Huaibei Normal University, Huaibei, China
| | - Xinda Lin
- College of Life Science, Huaibei Normal University, Huaibei, China
| | - Xiaoli Liu
- College of Life Science, Huaibei Normal University, Huaibei, China
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Shah A, Hoffman JI, Schielzeth H. Transcriptome assembly for a colour-polymorphic grasshopper (Gomphocerus sibiricus) with a very large genome size. BMC Genomics 2019; 20:370. [PMID: 31088494 PMCID: PMC6518663 DOI: 10.1186/s12864-019-5756-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 04/30/2019] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The club-legged grasshopper Gomphocerus sibiricus is a Gomphocerinae grasshopper with a promising future as model species for studying the maintenance of colour-polymorphism, the genetics of sexual ornamentation and genome size evolution. However, limited molecular resources are available for this species. Here, we present a de novo transcriptome assembly as reference resource for gene expression studies. We used high-throughput Illumina sequencing to generate 5,070,036 paired-end reads after quality filtering. We then combined the best-assembled contigs from three different de novo transcriptome assemblers (Trinity, SOAPdenovo-trans and Oases/Velvet) into a single assembly. RESULTS This resulted in 82,251 contigs with a N50 of 1357 and a TransRate assembly score of 0.325, which compares favourably with other orthopteran transcriptome assemblies. Around 87% of the transcripts could be annotated using InterProScan 5, BLASTx and the dammit! annotation pipeline. We identified a number of genes involved in pigmentation and green pigment metabolism pathways. Furthermore, we identified 76,221 putative single nucleotide polymorphisms residing in 8400 contigs. We also assembled the mitochondrial genome and investigated levels of sequence divergence with other species from the genus Gomphocerus. Finally, we detected and assembled Wolbachia sequences, which revealed close sequence similarity to the strain pel wPip. CONCLUSIONS Our study has generated a significant resource for uncovering genotype-phenotype associations in a species with an extraordinarily large genome, while also providing mitochondrial and Wolbachia sequences that will be useful for comparative studies.
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Affiliation(s)
- Abhijeet Shah
- Institute of Ecology and Evolution, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany
| | - Joseph I. Hoffman
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany
| | - Holger Schielzeth
- Institute of Ecology and Evolution, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany
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Lin LL, Li XJ, Zhang HL, Zheng ZM. Mitochondrial genomes of three Tetrigoidea species and phylogeny of Tetrigoidea. PeerJ 2017; 5:e4002. [PMID: 29158966 PMCID: PMC5694214 DOI: 10.7717/peerj.4002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 10/17/2017] [Indexed: 11/20/2022] Open
Abstract
The mitochondrial genomes (mitogenomes) of Formosatettix qinlingensis, Coptotettix longjiangensis and Thoradonta obtusilobata (Orthoptera: Caelifera: Tetrigoidea) were sequenced in this study, and almost the entire mitogenomes of these species were determined. The mitogenome sequences obtained for the three species were 15,180, 14,495 and 14,538 bp in length, respectively, and each sequence included 13 protein-coding genes (PCGs), partial sequences of rRNA genes (rRNAs), tRNA genes (tRNAs) and a A + T-rich region. The order and orientation of the gene arrangement pattern were identical to that of most Tetrigoidea species. Some conserved spacer sequences between trnS(UCN) and nad1 were useful to identify Tetrigoidea and Acridoidea. The Ka/Ks value of atp8 between Trachytettix bufo and other four Tetrigoidea species indicated that some varied sites in this gene might be related with the evolution of T. bufo. The three Tetrigoidea species were compared with other Caelifera. At the superfamily level, conserved sequences were observed in intergenic spacers, which can be used for superfamily level identification between Tetrigoidea and Acridoidea. Furthermore, a phylogenomic analysis was conducted based on the concatenated data sets from mitogenome sequences of 24 species of Orthoptera in the superorders Caelifera and Ensifera. Both maximum likelihood and bayesian inference analyses strongly supported Acridoidea and Tetrigoidea as forming monophyletic groups. The relationships among six Tetrigoidea species were (((((Tetrix japonica, Alulatettix yunnanensis), Formosatettix qinlingensis), Coptotettix longjiangensis), Trachytettix bufo), Thoradonta obtusilobata).
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Affiliation(s)
- Li-Liang Lin
- College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, China
| | - Xue-Juan Li
- College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, China
| | - Hong-Li Zhang
- School of Life Sciences, Datong University, Datong, Shanxi, China
| | - Zhe-Min Zheng
- College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, China
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Zhou F, Huang Y. The complete mitochondrial genome of Spathosternum prasiniferum sinense Uvarov, 1931 (Orthoptera: Acridoidea: Acrididae). Mitochondrial DNA A DNA Mapp Seq Anal 2016; 27:1932-1933. [PMID: 25329291 DOI: 10.3109/19401736.2014.971293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The complete mitogenome of Spathosternum prasiniferum sinense was sequenced and annotated in this work. It is 15,591 bp in size and contains 37 typical animal mitochondrial genes, meanwhile, A + T content is high as 74.1%. All protein-coding genes (PCGs) use standard ATN initiation codons. Twelve PCGs utilize complete termination codons TAG or TAA, except for DN5 gene uses an incomplete stop codon TA. tRNA genes were predicted with a characteristic cloverleaf secondary structure except trnS(AGN). The sizes of the lrRNA and srRNA genes are 1315 and 788 bp, respectively. The AT content of the A + T-rich region is 86.5%.
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Affiliation(s)
- Fei Zhou
- a College of Life Sciences, Shaanxi Normal University , Xi'an , Shaanxi Province , P.R. China
| | - Yuan Huang
- a College of Life Sciences, Shaanxi Normal University , Xi'an , Shaanxi Province , P.R. China
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Guo C, Zhang Q, Huang Y. The complete mitochondrial genome of the Oedaleus infernalis sauss (Orthoptera: Oedipodidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:89-90. [PMID: 26709737 DOI: 10.3109/19401736.2015.1110812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Oedaleus infernalis sauss (Orthoptera: Oedipodidae) is one of the main pests at the rice production area in China, and they mainly feed on leaves and grain of rice. The mitogenome was 15 898 bp long and composed of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one putative control region. Most protein-coding genes started with a traditional ATN codon, and terminated with the mitochondria stop codon (TAA/TAG) or a single T-- base. The average A + T content of the O. infernalis sauss mitochondrial genome protein-coding sequence, rRNA, tRNA gene, and A + T-rich region was corresponding well to the A + T bias generally observed in insect mitochondrial genomes. Using the 12 protein-coding genes of O. infernalis sauss in this study, together with 15 other closely species, a preliminary phylogenetic analysis has been carried out.
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Affiliation(s)
- Chunan Guo
- a College of Life Science, Shaanxi Normal University , Xi'an , People's Republic of China
| | - Qin Zhang
- a College of Life Science, Shaanxi Normal University , Xi'an , People's Republic of China
| | - Yuan Huang
- a College of Life Science, Shaanxi Normal University , Xi'an , People's Republic of China
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Hao J, Liu N, Zhou F, Huang Y. The complete mitochondrial genome of Bryodema miramae (Orthoptera: Oedipodidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2500-1. [PMID: 26024137 DOI: 10.3109/19401736.2015.1036248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete circular mitochondrial genome (mitogenome) of Bryodema miramae is 15,919 bp in length, containing 37 typical genes and 1 non-coding AT-rich region. The AT content of the AT-rich region is 84.7%. All protein-coding genes (PCGs) start with standard ATN initiation codon and end with complete termination codons TAG or TAA except for cox1 gene using an incomplete stop codon T. tRNA genes are predicted with a characteristic cloverleaf secondary structure except for trnS(AGN), whose dihydrouridine (DHU) arm is replaced by a simple loop. The lengths of the large and small ribosomal RNA genes are 1319 and 836 bp, respectively. Phylogenetic analysis found: (i) Bryodema miramae has a close relationship with Bryodema luctuosum luctuosum, but with low credibility, the bootstrap value was under 50% and (ii) the Bryodema clade forms a sister group with another clade containing Orinhippus tibetanus and Pacris xizangensis.
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Affiliation(s)
- Jing Hao
- a College of Life Sciences, Shaanxi Normal University , Xi'an , People's Republic of China
| | - Nian Liu
- a College of Life Sciences, Shaanxi Normal University , Xi'an , People's Republic of China
| | - Fei Zhou
- a College of Life Sciences, Shaanxi Normal University , Xi'an , People's Republic of China
| | - Yuan Huang
- a College of Life Sciences, Shaanxi Normal University , Xi'an , People's Republic of China
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Zhang HL, Huang Y, Lin LL, Wang XY, Zheng ZM. The phylogeny of the Orthoptera (Insecta) as deduced from mitogenomic gene sequences. Zool Stud 2013. [DOI: 10.1186/1810-522x-52-37] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
Background
The phylogeny of the Orthoptera was analyzed based on 6 datasets from 47 orthopteran mitochondrial genomes (mitogenomes). The phylogenetic signals in the mitogenomes were rigorously examined under analytical regimens of maximum likelihood (ML) and Bayesian inference (BI), along with how gene types and different partitioning schemes influenced the phylogenetic reconstruction within the Orthoptera. The monophyly of the Orthoptera and its two suborders (Caelifera and Ensifera) was consistently recovered in the analyses based on most of the datasets we selected, regardless of the optimality criteria.
Results
When the seven NADH dehydrogenase subunits were concatenated into a single alignment (NADH) and were analyzed; a near-identical topology to the traditional morphological analysis was recovered, especially for BI_NADH. In both the concatenated cytochrome oxidase (COX) subunits and COX + cytochrome b (Cyt b) datasets, the small extent of sequence divergence seemed to be helpful for resolving relationships among major Orthoptera lineages (between suborders or among superfamilies). The conserved and variable domains of ribosomal (r)RNAs performed poorly when respectively analyzed but provided signals at some taxonomic levels.
Conclusions
Our findings suggest that the best phylogenetic inferences can be made when moderately divergent nucleotide data from mitogenomes are analyzed, and that the NADH dataset was suited for studying orthopteran phylogenetic relationships at different taxonomic levels, which may have been due to the larger amount of DNA sequence data and the larger number of phylogenetically informative sites.
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