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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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2
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Zhang C, Mao B, Wang H, Dai L, Huang Y, Chen Z, Huang J. The Complete Mitogenomes of Three Grasshopper Species with Special Notes on the Phylogenetic Positions of Some Related Genera. INSECTS 2023; 14:85. [PMID: 36662013 PMCID: PMC9865218 DOI: 10.3390/insects14010085] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 06/17/2023]
Abstract
Clarifying phylogenetic position and reconstructing robust phylogeny of groups using various evidences are an eternal theme for taxonomy and systematics. In this study, the complete mitogenomes of Longzhouacris mirabilis, Ranacris albicornis, and Conophyma zhaosuensis were sequenced using next-generation sequencing (NGS), and the characteristics of the mitogenomes are presented briefly. The mitogenomes of the three species are all circular molecules with total lengths of 16,164 bp, 15,720 bp, and 16,190 bp, respectively. The gene structures and orders, as well as the characteristics of the mitogenomes, are similar to those of other published mitogenomes in Caelifera. The phylogeny of the main subfamilies of Acrididae with prosternal process was reconstructed using a selected dataset of mitogenome sequences under maximum likelihood (ML) and Bayesian inference (BI) frameworks. The results showed that the genus Emeiacris consistently fell into the subfamily Melanoplinae rather than Oxyinae, and the genus Choroedocus had the closest relationship with Shirackiacris of the subfamily Eyprepocnemidinae in both phylogenetic trees deduced from mitogenome protein coding genes (PCGs). This finding is entirely consistent with the morphological characters, which indicate that Emeiacris belongs to Melanoplinae and Choroedocus belongs to Eyprepocnemidinae. In addition, the genera Conophymacris and Xiangelilacris, as well as Ranacris and Menglacris, are two pairs of the closest relatives, but their phylogenetic positions need further study to clarify.
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Affiliation(s)
- Chulin Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Changsha 410004, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin 541004, China
- Key Laboratory of Forest Bio-Resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha 410004, China
| | - Benyong Mao
- College of Agriculture and Biological Science, Dali University, Dali 671003, China
| | - Hanqiang Wang
- Shanghai Entomological Museum, Chinese Academy of Sciences, Shanghai 200032, China
| | - Li Dai
- Shanghai Entomological Museum, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Zhilin Chen
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin 541004, China
| | - Jianhua Huang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Changsha 410004, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin 541004, China
- Key Laboratory of Forest Bio-Resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha 410004, China
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Qian H, Altanchimeg D, Naizab N, Wang S, Wen S, Lin C. The complete mitochondrial genome of Eclipophleps carinata (Orthoptera: Acridoidea: Gomphoceridae). Mitochondrial DNA B Resour 2021; 6:1310-1312. [PMID: 33855185 PMCID: PMC8018437 DOI: 10.1080/23802359.2021.1907803] [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: 11/18/2022] Open
Abstract
The complete Eclipophleps carinata mitogenome was sequenced through Illumina HiSeq 2500 platform and the resulting data were analyzed in this paper. The mitochondrial genome of E. carinata is a typical circular DNA molecule of 15,781 bp with 37 genes and 74.5% A + T content, which encoded 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and the control region. The E. carinata mitochondrial genome and 27 mitochondrial genomes (downloaded from NCBI) were employed to construct phylogenetic tree, in which Ruspolia dubia and Teleogryllus occipitails were the outgroups. Phylogenetic reconstruction validated the taxonomic status of E. carinata, which was placed in the monophyletic Gomphocerinae in Acrididae.
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Affiliation(s)
- Hongge Qian
- Institute of Life Science and Technology, Inner Mongolia Normal University, Hohhot, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | | | - Non Naizab
- Institute of Life Science and Technology, Inner Mongolia Normal University, Hohhot, China
| | - Shusen Wang
- College of Desert Control Science and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Suyaletu Wen
- Wulatehou Banner Forestry Bureau, Bayannaoer, China
| | - Chen Lin
- Institute of Life Science and Technology, Inner Mongolia Normal University, Hohhot, China
- College of Plant Protection, China Agricultural University, Beijing, China
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4
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Zhongying Q, Huihui C, Hao Y, Yuan H, Huimeng L, Xia L, Xingchun G. Comparative mitochondrial genomes of four species of Sinopodisma and phylogenetic implications (Orthoptera, Melanoplinae). Zookeys 2020; 969:23-42. [PMID: 33013166 PMCID: PMC7515930 DOI: 10.3897/zookeys.969.49278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 08/14/2020] [Indexed: 11/12/2022] Open
Abstract
In this study, the whole mitochondrial genomes (mitogenomes) from four species were sequenced. The complete mitochondrial genomes of Sinopodisma pieli, S. houshana, S. qinlingensis, and S. wulingshanensis are 15,857 bp, 15,818 bp, 15,843 bp, and 15,872 bp in size, respectively. The 13 protein-coding genes (PCGs) begin with typical ATN codons, except for COXI in S. qinlingensis, which begins with ACC. The highest A+T content in all the sequenced orthopteran mitogenomes is 76.8% (S. qinlingensis), followed by 76.5% (S. wulingshanensis), 76.4% (S. pieli) and 76.4% (S. houshana) (measured on the major strand). The long polythymine stretches (T-stretch) in the A+T-rich region of the four species are not adjacent to the trnI locus but are inside the stem-loop sequences on the major strand. Moreover, several repeated elements are found in the A+T-rich region of the four species. Phylogenetic analysis based on 53 mitochondrial genomes using Bayesian Inference (BI) and Maximum Likelihood (ML) revealed that Melanoplinae (Podismini) was a monophyletic group; however, the monophyly of Sinopodisma was not supported. These data will provide important information for a better understanding of the phylogenetic relationship of Melanoplinae.
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Affiliation(s)
- Qiu Zhongying
- Shaanxi Key Laboratory of Brain Disorders &School of Basic Medical Sciences, Xi'an Medical University, Xi'an,710021, China Xi'an Medical University Xi'an China
| | - Chang Huihui
- Shaanxi Key Laboratory of Brain Disorders &School of Basic Medical Sciences, Xi'an Medical University, Xi'an,710021, China Xi'an Medical University Xi'an China
| | - Yuan Hao
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China Shaanxi Normal University Xi'an China
| | - Huang Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China Shaanxi Normal University Xi'an China
| | - Lu Huimeng
- Key Laboratory for Space Bioscience & Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China Northwestern Polytechnical University Xi'an China
| | - Li Xia
- Huizhou No.8 High School, Hui'zhou 516001, China Huizhou No.8 High School Hui'zhou China
| | - Gou Xingchun
- Shaanxi Key Laboratory of Brain Disorders &School of Basic Medical Sciences, Xi'an Medical University, Xi'an,710021, China Xi'an Medical University Xi'an China
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5
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Yuan H, Zhang X, Zhao L, Chang H, Yang C, Qiu Z, Huang Y. Characterization and analysis of full-length transcriptomes from two grasshoppers, Gomphocerus licenti and Mongolotettix japonicus. Sci Rep 2020; 10:14228. [PMID: 32848169 PMCID: PMC7450073 DOI: 10.1038/s41598-020-71178-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 08/06/2020] [Indexed: 11/09/2022] Open
Abstract
Acrididae are diverse in size, body shape, behavior, ecology and life history; widely distributed; easy to collect; and important to agriculture. They represent promising model candidates for functional genomics, but their extremely large genomes have hindered this research; establishing a reference transcriptome for a species is the primary means of obtaining genetic information. Here, two Acrididae species, Gomphocerus licenti and Mongolotettix japonicus, were selected for full-length (FL) PacBio transcriptome sequencing. For G. licenti and M. japonicus, respectively, 590,112 and 566,165 circular consensus sequences (CCS) were generated, which identified 458,131 and 428,979 full-length nonchimeric (FLNC) reads. After isoform-level clustering, next-generation sequencing (NGS) short sequences were used for error correction, and remove redundant sequences with CD-HIT, 17,970 and 16,766 unigenes were generated for G. licenti and M. japonicus. In addition, we obtained 17,495 and 16,373 coding sequences, 1,082 and 813 transcription factors, 11,840 and 10,814 simple sequence repeats, and 905 and 706 long noncoding RNAs by analyzing the transcriptomes of G. licenti and M. japonicus, respectively, and 15,803 and 14,846 unigenes were annotated in eight functional databases. This is the first study to sequence FL transcriptomes of G. licenti and M. japonicus, providing valuable genetic resources for further functional genomics research.
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Affiliation(s)
- Hao Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Xue Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Lina Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Huihui Chang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Chao Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China.,Shaanxi Institute of Zoology, Xi'an, China
| | - Zhongying Qiu
- School of Basic Medical Sciences, Xi'an Medical University, Xi'an, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China.
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6
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Comparative analysis of mitogenomes among six species of grasshoppers (Orthoptera: Acridoidea: Catantopidae) and their phylogenetic implications in wing-type evolution. Int J Biol Macromol 2020; 159:1062-1072. [PMID: 32416301 DOI: 10.1016/j.ijbiomac.2020.05.058] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 04/16/2020] [Accepted: 05/09/2020] [Indexed: 11/22/2022]
Abstract
The degree of wing development has a close relationship with insects' movement ability and range, and it should also be closely related to mitochondrial-related genes. The complete mitochondrial genomes of six species of Catantopidae were sequenced, annotated and analyzed. Then, combined with 37 mitogenomes of grasshoppers, the ratio of nonsynonymous substitution to synonymous substitution (Ka/Ks) of the combined sequences of protein coding genes (PCGs) was calculated by DnaSP5, and the phylogenetic relationships were reconstructed by maximum likelihood (ML) and Bayesian (BI) methods based on PCGs+rRNAs. The results showed that the sizes of the six complete mitogenomes are Stenocatantops mistshenkoi Willemse F., 1968, 15,573 bp; Traulia lofaoshana Tinkham, 1940, 15,645 bp; Sinopodisma rostellocerca You, 1980, 15,622 bp; Anapodisma miramae Dovnar-Zapolskij, 1932, 15,189 bp; Qinlingacris elaeodes Yin & Chou, 1979, 15,221 bp; and Eozubovskya planicaudata Zhang & Jin, 1985, 15,830 bp; their structures are the same as those of Acridoidea. The AT bias of the wing-degenerated group (lobiform and apterous) is higher than that of the longipennate group, and more nonsynonymous substitutions accumulated in the wing-degenerated group than in the longipennate group (P = 0.000), which indicates that the wing-degenerated group has undergone weaker evolutionary selection than the longipinnate group. The phylogenetic tree shows that the wing-degenerated group in the Catantopidae are multiorigin and present parallel evolution.
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Hawlitschek O, Morinière J, Lehmann GUC, Lehmann AW, Kropf M, Dunz A, Glaw F, Detcharoen M, Schmidt S, Hausmann A, Szucsich NU, Caetano-Wyler SA, Haszprunar G. DNA barcoding of crickets, katydids and grasshoppers (Orthoptera) from Central Europe with focus on Austria, Germany and Switzerland. Mol Ecol Resour 2016; 17:1037-1053. [PMID: 27863033 DOI: 10.1111/1755-0998.12638] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/28/2016] [Accepted: 11/10/2016] [Indexed: 12/21/2022]
Abstract
We present a DNA barcoding study on the insect order Orthoptera that was generated in collaboration between four barcoding projects in three countries, viz. Barcoding Fauna Bavarica (Germany), German Barcode of Life, Austrian Barcode of Life and Swiss Barcode of Life. Our data set includes 748 COI sequences from 127 of the 162 taxa (78.4%) recorded in the three countries involved. Ninety-three of these 122 species (76.2%, including all Ensifera) can be reliably identified using DNA barcodes. The remaining 26 caeliferan species (families Acrididae and Tetrigidae) form ten clusters that share barcodes among up to five species, in three cases even across different genera, and in six cases even sharing individual barcodes. We discuss incomplete lineage sorting and hybridization as most likely causes of this phenomenon, as the species concerned are phylogenetically young and hybridization has been previously observed. We also highlight the problem of nuclear mitochondrial pseudogenes (numts), a known problem in the barcoding of orthopteran species, and the possibility of Wolbachia infections. Finally, we discuss the possible taxonomic implications of our barcoding results and point out future research directions.
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Affiliation(s)
- O Hawlitschek
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany.,Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta 37, 08003, Barcelona, Spain
| | - J Morinière
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - G U C Lehmann
- Department of Biology, Behavioural Physiology, Humboldt University Berlin, Invalidenstr. 43, 10115, Berlin, Germany
| | - A W Lehmann
- Orthoptera Working Group Brandenburg and Berlin, Friedensallee 37, 14532, Stahnsdorf, Germany
| | - M Kropf
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences (BOKU), Gregor Mendel-Str. 33, 1180, Vienna, Austria
| | - A Dunz
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - F Glaw
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - M Detcharoen
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - S Schmidt
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - A Hausmann
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - N U Szucsich
- 3rd Zoological Dep., Natural History Museum Vienna, Burgring 7, 1010, Vienna, Austria
| | - S A Caetano-Wyler
- Université de Genève, Département de Génétique et Evolution, Quai Ernest Ansermet 30, 1211, Geneva 4, Switzerland
| | - G Haszprunar
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany.,Department Biology II and GeoBio-Center of Ludwig-Maximilians-Universität München, Groβhaderner Str. 2, 82152, Planegg-Martinsried, Germany
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Kang AR, Kim MJ, Park IA, Kim KY, Kim I. Extent and divergence of heteroplasmy of the DNA barcoding region in Anapodisma miramae (Orthoptera: Acrididae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3405-14. [PMID: 25835040 DOI: 10.3109/19401736.2015.1022730] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
A partial sequence of the mitochondrial cytochrome oxidase subunit I (COI) gene is widely used as a molecular marker for species identification in animals, also termed a DNA barcode. However, the presence of more than one sequence type in a single individual, also known as heteroplasmy, is one of the shortcomings of barcode identification. In this study, we examined the extent and divergence of COI heteroplasmy, including nuclear-encoded mitochondrial pseudogenes (NUMTs), at the genomic-DNA level from 13 insect species including orthopteran Anapodisma miramae, and a long fragment of mitochondrial DNA and cDNA from A. miramae as templates. When multiple numbers of clones originated from genomic DNA were sequenced, heteroplasmy was prevalent in all species and NUMTs were observed in five species. Long fragment DNA (∼13.5 kb) also is a source of heteroplasmic amplification, but the divergent haplotypes and NUMTs obtained from genomic DNA were not detected in A. miramae. On the other hand, cDNA was relatively heteroplasmy-free. Consistently, one dominant haplotype was always obtained from the genomic DNA-origin clones in all species and also from the long fragment- and cDNA-origin clones in the two tested individuals of A. miramae. Furthermore, the dominant haplotype was identical in sequence, regardless of the DNA source in A. miramae. Thus, one possible solution to avoid the barcoding problem in relationship to heteroplasmy could be the acquisition of multiple numbers of barcoding sequences to determine a dominant haplotype that can be assigned as barcoding sequence for a given species.
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Affiliation(s)
- Ah Rang Kang
- a College of Agriculture & Life Sciences, Chonnam National University , Gwangju , Korea and
| | - Min Jee Kim
- a College of Agriculture & Life Sciences, Chonnam National University , Gwangju , Korea and
| | - In Ah Park
- a College of Agriculture & Life Sciences, Chonnam National University , Gwangju , Korea and
| | - Kee Young Kim
- b Department of Agricultural Biology , National Academy of Agricultural Science , Wanju-gun , Korea
| | - Iksoo Kim
- a College of Agriculture & Life Sciences, Chonnam National University , Gwangju , Korea and
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Song H, Amédégnato C, Cigliano MM, Desutter‐Grandcolas L, Heads SW, Huang Y, Otte D, Whiting MF. 300 million years of diversification: elucidating the patterns of orthopteran evolution based on comprehensive taxon and gene sampling. Cladistics 2015; 31:621-651. [DOI: 10.1111/cla.12116] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2015] [Indexed: 10/23/2022] Open
Affiliation(s)
- Hojun Song
- Department of Biology University of Central Florida Orlando FL USA
- Department of Entomology Texas A&M University College Station TX USA
| | - Christiane Amédégnato
- Département Systématique et Évolution Muséum National d ‘Histoire Naturelle’ ISYEB, UMR7205 CNRS MNHN UPMC EPHE Paris France
| | | | - Laure Desutter‐Grandcolas
- Département Systématique et Évolution Muséum National d ‘Histoire Naturelle’ ISYEB, UMR7205 CNRS MNHN UPMC EPHE Paris France
| | - Sam W. Heads
- Illinois Natural History Survey University of Illinois at Urbana‐Champaign Champaign IL USA
| | - Yuan Huang
- Institute of Zoology Shaanxi Normal University Xi'an China
| | - Daniel Otte
- Department of Biodiversity, Earth & Environmental Science Academy of Natural Sciences of Drexel University Philadelphia PA USA
| | - Michael F. Whiting
- Department of Biology and M. L. Bean Museum Brigham Young University Provo UT USA
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10
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Zhi Y, Liu B, Han G, Yin H, Zhang D. The complete mitochondrial genome of Kingdonella bicollina (Orthoptera: Acridoidea: Catantopidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:391-2. [PMID: 24617489 DOI: 10.3109/19401736.2014.896000] [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 complete mitochondrial genome of Kingdonella bicollina, which was collected from the Tibetan Plateau, is determined here. It is 15,630 bp in length and contains 75.6% AT. All 13 mitochondrial PCGs share the start codon ATN, except for cox1 (CCG start codon). The termination codons include TAA, TAG and T. All tRNA genes could be folded into the typical cloverleaf secondary structure, except trnS(AGN) lacking of dihydrouridine arm. The sizes of the large and small ribosomal RNA genes are 1312 and 859 bp, respectively. The A+T-rich region is 739 bp in length contains 79.7% AT content.
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Affiliation(s)
- Yongchao Zhi
- a College of Life Sciences, Hebei University , Baoding , Hebei , P.R. China and
| | - Bing Liu
- b School of Computer Science, Southwest Petroleum University , Chengdu , Sichuan , P.R. China
| | - Gaofeng Han
- a College of Life Sciences, Hebei University , Baoding , Hebei , P.R. China and
| | - Hong Yin
- a College of Life Sciences, Hebei University , Baoding , Hebei , P.R. China and
| | - Daochuan Zhang
- a College of Life Sciences, Hebei University , Baoding , Hebei , P.R. China and
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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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12
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Leavitt JR, Hiatt KD, Whiting MF, Song H. Searching for the optimal data partitioning strategy in mitochondrial phylogenomics: A phylogeny of Acridoidea (Insecta: Orthoptera: Caelifera) as a case study. Mol Phylogenet Evol 2013; 67:494-508. [DOI: 10.1016/j.ympev.2013.02.019] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 02/10/2013] [Accepted: 02/15/2013] [Indexed: 11/24/2022]
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Zhang HL, Zhao L, Zheng ZM, Huang Y. Complete Mitochondrial Genome ofGomphocerus sibiricus(Orthoptera: Acrididae) and Comparative Analysis in Four Gomphocerinae Mitogenomes. Zoolog Sci 2013; 30:192-204. [DOI: 10.2108/zsj.30.192] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Zhang HL, Zeng HH, Huang Y, Zheng ZM. The complete mitochondrial genomes of three grasshoppers, Asiotmethis zacharjini, Filchnerella helanshanensis and Pseudotmethis rubimarginis (Orthoptera: Pamphagidae). Gene 2013; 517:89-98. [PMID: 23291499 DOI: 10.1016/j.gene.2012.12.080] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 12/02/2012] [Accepted: 12/19/2012] [Indexed: 11/17/2022]
Abstract
The complete mitogenomes of Asiotmethis zacharjini, Filchnerella helanshanensis and Pseudotmethis rubimarginis are 15,660 bp, 15,657 bp and 15,661 bp in size, respectively. All three mitogenomes contain a standard set of 13 protein - coding genes, 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and an A+T-rich region in the same order as those of the other analysed caeliferan species, including the rearrangement of trnAsp and trnLys. The putative initiation codon for the cox1 gene in the three species is CCG. The long polythymine stretch (T-stretch) in the A+T-rich region of the three species is not adjacent to the trnIle but inside the stem-loop sequence in the majority strand. The mitogenomes of F. helanshanensis and P. rubimarginis have higher overall similarities. The characterization of the three mitogenomes will enrich our knowledge on the Pamphagidae mitogenome. The phylogenetic analyses indicated that within the Caelifera, Pyrgomorphoidea is a sister group to Acridoidea. The species from the Pamphagidae form a monophyletic group, as is the case for Acrididae. Furthermore, the two families cluster as sister groups, supporting the monophyly of Acridoidea. The relationships among eight acridid subfamilies were (Cyrtacanthacridinae+(Calliptaminae+(Catantopinae+(Oxyinae+(Melanopline+(Acridinae+(Oedipodinae+Gomphocerinae).
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Affiliation(s)
- Hong-Li Zhang
- Institute of Zoology, Shaanxi Normal University, Xi'an 710062, China
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Yin H, Zhi Y, Jiang H, Wang P, Yin X, Zhang D. The complete mitochondrial genome of Gomphocerus tibetanus Uvarov, 1935 (Orthoptera: Acrididae: Gomphocerinae). Gene 2012; 494:214-8. [DOI: 10.1016/j.gene.2011.12.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 12/10/2011] [Accepted: 12/10/2011] [Indexed: 10/14/2022]
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