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Guo C, Wang Y, Li W, Cao J. The mitochondrial genome of Neoperla bimaculata (Li et al. 2021) (plecoptera: perlidae) from Tibet of southwest China and its phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:381-384. [PMID: 38529109 PMCID: PMC10962291 DOI: 10.1080/23802359.2024.2333564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/15/2024] [Indexed: 03/27/2024] Open
Abstract
The complete mitochondrial genome (mitogenome) of Neoperla bimaculata was sequenced and annotated in this study. We found that the mitogenome of N. bimaculata is 15,774 bp in length with an A + T content of 64.3%. It exhibits the classic structure of a mitogenome. Most protein-coding genes (PCGs) of the mitogenome initiate with the standard start codon ATN. Ten PCGs use the standard stop codon TAA/TAG, while the COI, COII, and ND5 genes terminate with a single T nucleotide. Phylogenetic analyses suggested that N. bimaculata, along with two unpublished Neoperla species, formed a cluster within the phylogenetic tree. Our results indicated that the genus Neoperla and Neoperlops were sister groups. Meanwhile, the monophyly of Perlinae and Acroneuriinae was supported in the mitochondrial phylogeny.
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Affiliation(s)
- Caiyue Guo
- Henan International Joint Laboratory of Taxonomy and Systematic Evolution of Insecta, Henan Institute of Science and Technology, Xinxiang, China
| | - Ying Wang
- Henan International Joint Laboratory of Taxonomy and Systematic Evolution of Insecta, Henan Institute of Science and Technology, Xinxiang, China
| | - Weihai Li
- Henan International Joint Laboratory of Taxonomy and Systematic Evolution of Insecta, Henan Institute of Science and Technology, Xinxiang, China
| | - Jinjun Cao
- Henan International Joint Laboratory of Taxonomy and Systematic Evolution of Insecta, Henan Institute of Science and Technology, Xinxiang, China
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Wang Y, Liu G, Wang J, Sun Z, Wang N. The complete mitochondrial genome of Dolichopus galeatus Loew, 1871 (Diptera: Dolichopodidae). Mitochondrial DNA B Resour 2023; 8:1041-1044. [PMID: 37810615 PMCID: PMC10552610 DOI: 10.1080/23802359.2023.2262691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 09/19/2023] [Indexed: 10/10/2023] Open
Abstract
The long-legged fly Dolichopus galeatus Loew, 1871 belongs to the subfamily Dolichopodinae (Diptera: Dolichopodidae). This work presents the mitochondrial genome (mitogenome) of D. galeatus for the first time. The mitogenome has a total length of 15,268 bp, 13 protein-coding genes, two ribosomal RNA (rRNA) genes, and 22 transfer RNA genes (tRNAs) that make up the genome. All genes have comparable positions and strands to those found in earlier reported fly mitogenomes. The nucleotide composition is tilted toward A and T, which account for 75.1% of the total. Phylogenetic approach shows that Lichtwardtia is the sister group of Dolichopus and that the Dolichopodidae are monophyletic.
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Affiliation(s)
- Yuanyuan Wang
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Guangming Liu
- College of Prataculture, Qingdao Agricultural University, Qingdao, China
| | - Jiayu Wang
- Grassland Station of Xilin Gol League Forestry and Grassland Bureau, Xilin Gol League, China
| | - Zhipeng Sun
- Grassland Station of Xilin Gol League Bordered Yellow Banner Forestry and Grassland Bureau, Xilin Gol League, China
| | - Ning Wang
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
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Rehman A, Huo QB, Du YZ. The First Complete Mitochondrial Genome of Genus Isocapnia (Plecoptera: Capniidae) and Phylogenetic Assignment of Superfamily Nemouroidea. Genes (Basel) 2023; 14:genes14050965. [PMID: 37239326 DOI: 10.3390/genes14050965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Capniidae are a family of stoneflies, also known as snow flies, who emerge in winter. The phylogeny of Capniidae is widely accepted to be based on morphological analysis. Until now, only five Capniidae mitochondrial genomes have been sequenced so far. In addition, sampling is required to determine an accurate phylogenetic association because the generic classification of this family is still controversial and needs to be investigated further. In this study, the first mitogenome of genus Isocapnia was sequenced with a length of 16,200 bp and contained 37 genes, including a control region, two rRNAs, 22 tRNAs, and 13 PCGs, respectively. Twelve PCGs originated with the common start codon ATN (ATG, ATA, or ATT), while nad5 used GTG. Eleven PCGs had TAN (TAA or TAG) as their last codon; however, cox1 and nad5 had T as their final codon due to a shortened termination codon. All tRNA genes demonstrated the cloverleaf structure, which is distinctive for metazoans excluding the tRNASer1 (AGN) that missed the dihydrouridine arm. A Phylogenetic analysis of the superfamily Nemouroidea was constructed using thirteen PCGs from 32 formerly sequenced Plecoptera species. The Bayesian inference and maximum likelihood phylogeny tree structures derived similar results across the thirteen PCGs. Our findings strongly supported Leuctridae + ((Capniidae + Taeniopterygidae) + (Nemouridae + Notonemouridae)). Ultimately, the best well-supported generic phylogenetic relationship within Capniidae is as follows; (Isocapnia + (Capnia + Zwicknia) + (Apteroperla + Mesocapnia)). These findings will enable us to better understand the evolutionary relationships within the superfamily Nemouroidea and the generic classification and mitogenome structure of the family Capniidae.
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Affiliation(s)
- Abdur Rehman
- College of Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou 225009, China
| | - Qing-Bo Huo
- College of Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou 225009, China
| | - Yu-Zhou Du
- College of Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education, Yangzhou University, Yangzhou 225009, China
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Liu HL, Chen S, Chen QD, Pu DQ, Chen ZT, Liu YY, Liu X. The First Mitochondrial Genomes of the Family Haplodiplatyidae (Insecta: Dermaptera) Reveal Intraspecific Variation and Extensive Gene Rearrangement. BIOLOGY 2022; 11:biology11060807. [PMID: 35741328 PMCID: PMC9219768 DOI: 10.3390/biology11060807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 05/17/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary The insect order Dermaptera is commonly known as earwigs. The earwigs have many interesting biological characteristics, such as epizoic on other small animals, viviparous, and maternal care on their eggs and young nymphs. The external morphology of earwigs has been studied in detail, but their genetic characteristics remain unclear. The phylogenetic position of Dermaptera among all insect orders and the inner relationship of Dermaptera are largely unsolved. To better understand the molecular characters of earwigs, we sequenced and analyzed two mitogenomes of an earwig species from the family Haplodiplatyidae. The results revealed the existence of intraspecific variation and extensive gene rearrangement events in the mitogenomes of earwigs. The phylogenetic results are partially similar to previous studies. The discoveries in this study could provide new information for the molecular diversity and mitogenomic evolution of earwigs. Abstract Haplodiplatyidae is a recently established earwig family with over 40 species representing a single genus, Haplodiplatys Hincks, 1955. The morphology of Haplodiplatyidae has been studied in detail, but its molecular characters remain unclear. In this study, two mitogenomes of Haplodiplatys aotouensis Ma & Chen, 1991, were sequenced based on two samples from Fujian and Jiangxi provinces, respectively. These represent the first mitogenomes for the family Haplodiplatyidae. The next-generation sequencing method and subsequent automatic assembly obtained two mitogenomes. The two mitogenomes of H. aotouensis were generally identical but still exhibit a few sequence differences involving protein-coding genes (PCGs), ribosomal RNA (rRNA) genes, control regions, and intergenic spacers. The typical set of 37 mitochondrial genes was annotated, while many transfer RNA (tRNA) genes were rearranged from their ancestral locations. The calculation of nonsynonymous (Ka) and synonymous (Ks) substitution rates in PCGs indicated the fastest evolving nd4l gene in H. aotouensis. The phylogenetic analyses supported the basal position of Apachyidae but also recovered several controversial clades.
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Affiliation(s)
- Hong-Ling Liu
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Ministry of Agriculture, Chengdu 610066, China; (H.-L.L.); (S.C.); (Q.-D.C.); (D.-Q.P.)
| | - Song Chen
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Ministry of Agriculture, Chengdu 610066, China; (H.-L.L.); (S.C.); (Q.-D.C.); (D.-Q.P.)
| | - Qing-Dong Chen
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Ministry of Agriculture, Chengdu 610066, China; (H.-L.L.); (S.C.); (Q.-D.C.); (D.-Q.P.)
| | - De-Qiang Pu
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Ministry of Agriculture, Chengdu 610066, China; (H.-L.L.); (S.C.); (Q.-D.C.); (D.-Q.P.)
| | - Zhi-Teng Chen
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China;
| | - Yue-Yue Liu
- Analysis and Testing Center, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China;
| | - Xu Liu
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Ministry of Agriculture, Chengdu 610066, China; (H.-L.L.); (S.C.); (Q.-D.C.); (D.-Q.P.)
- Correspondence:
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Complete Mitochondrial Genome of Malenka flexura (Plecoptera: Nemouridae) and Phylogenetic Analysis. Genes (Basel) 2022; 13:genes13050911. [PMID: 35627296 PMCID: PMC9142110 DOI: 10.3390/genes13050911] [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] [Received: 05/06/2022] [Revised: 05/15/2022] [Accepted: 05/18/2022] [Indexed: 11/17/2022] Open
Abstract
The genus-level relationships within the subfamily Amphinemurinae have been controversial, although attempts have been made based on morphology and limited molecular data. With the establishment of two new genera, the phylogenetic relationships within Amphinemurinae should be re-examined. In this study, the complete mitochondrial genome (mitogenome) of Malenka flexura of the genus Malenka was firstly sequenced and analyzed. The phylogeny of Amphinemurinae was also reconstructed using 13 proteincoding genes (PCGs) from previously published stoneflies. This mitogenome was 15,744 bp long and encoded the typical 37 genes, as well as a putative control region. The gene arrangement of M. flexura mitogenome is identical with the putative ancestral mitogenome in Drosophila yakuba. Most PCGs used standard ATN as start codons and TAA/TAG as termination codons. All tRNA genes exhibited the typical cloverleaf secondary structure, except for tRNASer(AGN), whose dihydrouridine (DHU) arm was lacking. Some structural elements in the control region were founded, such as tandem repeat regions, stemloop structures, polyN stretch and microsatellite structure, etc. Phylogenetic analyses of sequenced Amphinemurinae mitogenomes unsupported the sister relationship of Amphinemura and Malenka. Finally, the phylogenetic analyses inferred a relationship within Amphinemurinae: Amphinemura + (Malenka + (Protonemura + (Indonemoura + (Sphaeronemoura + Mesonemoura)))).
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Mitochondrial Genomes of the Genus Claassenia (Plecoptera: Perlidae) and Phylogenetic Assignment to Subfamily Perlinae. Genes (Basel) 2021; 12:genes12121986. [PMID: 34946934 PMCID: PMC8701382 DOI: 10.3390/genes12121986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 11/29/2021] [Accepted: 12/10/2021] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial genomes of three stoneflies, e.g., Claassenia magna Wu, 1948, Claassenia sp. 2 and Claassenia xucheni Chen, 2019 were sequenced in this study with 15,774, 15,777 and 15,746 bp in length, respectively. Each mitogenome contained 37 genes including 22 tRNAs, two ribosomal RNAs, 13 protein-coding genes (PCGs), and a noncoding control region (CR). In general, standard ATN start and TAN termination codons were evident in the PCGs. Although the dihydrouridine arm was absent in trnSer, the remaining 21 tRNAs displayed the characteristic cloverleaf secondary structure. Stem-loop structures were identified in the CRs of all three mitogenomes, but tandem repeats were only apparent in Claassenia xucheni. The mitogenomes of three Claassenia species were analyzed and compared with mitogenomes in 21 other stoneflies from the Perlidae and three Euholognatha species (Rhopalopsole bulbifera, Capnia zijinshana and Amphinemura longispina) as outgroups. Phylogenetic analyses using maximum likelihood and Bayesian inference. Phylogenetic analysis supported that Claassenia was recovered as the sister group of other Perlinae and Claassenia+Perlinae emerged from the paraphyletic Acroneuriinae. The final results supported that Claassenia was classified into subfamily Perlinae and proposed Claassenia represent a transitional group of the subfamilies Acroneuriinae and Perlinae. This study provided new molecular evidence for exploring the debatable taxonomic position of the genus Claassenia in Perlidae.
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Wang Y, Cao J, Chen J, Li W. The mitochondrial genome of the stonefly Togoperla limbata Pictet (Plecoptera: Perlidae). Mitochondrial DNA B Resour 2020; 5:2809-2810. [PMID: 33457956 PMCID: PMC7782005 DOI: 10.1080/23802359.2020.1788465] [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: 11/17/2022] Open
Abstract
We sequenced the complete mitochondrial genomes of Togoperla limbata which is the unique species distributed in Japan to provide supplementary data for future study in phylogenetic studies of Perlidae. This complete mitogenome of T. limbata is 15,915 bp long, including 37 typical genes and a control region as other stoneflies. Through the data analysis, the A + T content of the whole mitogenome, PCGs, tRNAs, rRNAs, and control region was 63.7%, 61.3%, 68.7%, 66.8%, and 74.8%. Most PCGs used typical start or stop codon except COI, ND5, and ND1 used the exceptional start codon and the COII and ND5 used the single T as the stop codon. Phylogenetic tree was constructed by using Bayesian inference (BI) and maximum-likelihood (ML) analysis based on the sequences of the 13 PCGs and two rRNAs and the result showed that subfamily Perlinae was a monophyletic group and the clade Togoperla and Paragnetina had a closer relationship.
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Affiliation(s)
- Ying Wang
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Jinjun Cao
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Jiajia Chen
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Weihai Li
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
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8
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Shen Y, Du YZ. The complete mitochondrial genome of Flavoperla biocellata Chu, 1929 (Plecoptera: Perlidae) and the phylogenetic analyses of Plecoptera. PeerJ 2020; 8:e8762. [PMID: 32211236 PMCID: PMC7081787 DOI: 10.7717/peerj.8762] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 02/17/2020] [Indexed: 12/03/2022] Open
Abstract
Of the roughly 400 species of Perlidae in the world, most species are widely distributed in the northern hemisphere, but a few can be found in South Africa and South America. There are only five species in the genus Flavoperla of the family Perlidae in China. To gain a better understanding of the architecture and evolution of mitochondrial genome in Flavoperla, the entire mitochondrial genome (mitogenome) of a Chinese Flavoperla biocellata Chu, 1929 from family Perlidae (Insecta: Plecoptera) was sequenced. The 15,805-bp long mitochondrial genome of F. biocellata contained 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a putative control region (CR). The gene arrangement of F. biocellata was identical with that of other stoneflies and with the fly Drosophila yakuba. Most PCGs of F. biocellata used the standard ATN start codons and complete TAN termination codons. Twenty-one of the 22 tRNA genes exhibited cloverleaf secondary structures, but the dihydrouridine (DHU) arm of trnSer (AGN) was completely reduced. Phylogenetic analyses with both Bayesian inference (BI) and maximum likelihood methods (ML) generated similar topology, both supporting the monophyly of all stonefly families and the infraorder Systellognatha. The phylogenetic analysis based on mitochondrial genomic data from 30 stonefly species recovered a well-supported tree resolving higher-level relationships within Plecoptera. The northern hemisphere suborder Arctoperlaria divided into two groups, Euholognatha and Systellognatha. The southern hemisphere suborder Antarctoperlaria formed two clades: Eustheniidae+Diamphipnoidae and Austroperlidae+ Gripopterygidae; consistent with relationships proposed based on morphology. The final relationships within Plecoptera were recovered as (((Perlidae+(Perlodidae+Chloroperlidae))+(Pteronarcyidae+(Peltoperlidae+Styloperlidae))) +(Taeniopterygidae+(Capniidae+(Nemouridae+Notonemouridae))))+ (Gripopterygoidae+Eusthenioidae).
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Affiliation(s)
- Yue Shen
- School of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yu-Zhou Du
- School of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education, Yangzhou University, Yangzhou, China
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Hao C, Wang G, Li W, Cao J. The mitochondrial genome analysis of Flavoperla hatakeyamae (Plecoptera: Perlidae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:1023-1024. [PMID: 33366857 PMCID: PMC7748619 DOI: 10.1080/23802359.2020.1721350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In this study, we analyzed the entire mitochondrial genome of Flavoperla hatakeyamae, which has 15,730 bp in length. This complete mitochondrial genome possessed 13 protein coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region. The nucleotide composition of the complete sequence of mitochondrial genome was accounting for 35.0%, T for 31.3%, C for 21.2%, G for 12.5%, and A + T for 66.3%. Among the 13 protein-coding genes, the starting codon of 12 protein-coding genes was ATN except the starting codon of COII was ACC. In addition, 11 of the protein-coding genes used conservative termination codon TAA/TAG, except for COII and ND5 which terminated by a single T. Based on Bayesian (BI) and maximum-likelihood (ML) methods, we found that the genus Flavoperla and Niponiella were gathered into one branch and the species of Perlinae were clustered in one clade.
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Affiliation(s)
- Caihao Hao
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Guochang Wang
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Weihai Li
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Jinjun Cao
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
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Hou P, Wang L, Li X, Yang D. First mitochondrial genome of Euprosopia sp. (Diptera: Platystomatidae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:723-724. [PMID: 33366720 PMCID: PMC7748858 DOI: 10.1080/23802359.2020.1715274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Platystomatid flies, one of the largest families in Diptera. Here, we determined the complete mitogenome of Euprosopia sp., which is the first for the family Platystomatidae. The 16,266 base pair (bp) mitogenome comprises of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes, and a control region. The gene order and the orientation are similar to those of other sequenced Acalyptratae species except tRNASer(AGN) gene were substituted by another tRNAPhe gene. All PCGs start with ATN codons, except COI and ND1, and end with TAA or incomplete stop codon TA + tRNA. The 22 tRNAs have a typical cloverleaf secondary structure. Phylogenetic analyses base on 13 Diptera species supported the monophyly of Superfamily Tephritoidea.
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Affiliation(s)
- Peng Hou
- College of Life Science and Bioengineering, Shenyang University, Shenyang, China.,College of Plant Protection, China Agricultural University, Beijing, China
| | - Liang Wang
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Xin Li
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Ding Yang
- College of Plant Protection, China Agricultural University, Beijing, China
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Wei X, Cao J, Wang P, Wang Y, Li W. The mitochondrial genome analysis of Paragnetina indentata (Plecoptera: Perlidae). Mitochondrial DNA B Resour 2020; 5:44-45. [PMID: 33366414 PMCID: PMC7720948 DOI: 10.1080/23802359.2019.1693927] [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
In this study, the entire mitochondrial genome of Paragnetina indentata was sequenced. The circular mitochondrial genome was the first mitochondrial genome representing the genus Paragnetina, which consists of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region with the length of 15,885 bp. In the complete sequence, the A + T content for 64.1% (A for 33.6%, T for 30.5%, C for 23.3%, and G for 12.7%). Among the 13 PCGs, 11 start codons is ATN and the start codon of ND1, ND2, and ND5 genes is TTG, GTG, and GTG, respectively. In addition, 11 of the PCGs used conservative termination codon TAA or TAG, except for COII and ND5 which terminated by the single T. By using the Bayesian inference (BI) and maximum-likelihood (ML) methods, the phylogenetic relationship showed that P. indentata was closely related to Togoperla sp. and the species of Perlinae were clustered in a clade.
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Affiliation(s)
- Xiping Wei
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Jinjun Cao
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Pengcheng Wang
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Ying Wang
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Weihai Li
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
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Chen M, Cao J, Li W, Wang Y. The mitochondrial genome from the stonefly: Claassenia sp. (Plecoptera: Perlidae). Mitochondrial DNA B Resour 2019; 4:3790-3791. [PMID: 33366193 PMCID: PMC7710317 DOI: 10.1080/23802359.2019.1681918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 10/13/2019] [Indexed: 11/06/2022] Open
Abstract
Claasseniini is the apparent sister group to all the other groups of Perlidae, and the small tribe Claasseniini has only one genus includes 12 species in the world. Only five mitochondrial genomes in the Perlinae have previously been reported. In this study, we sequenced the mitochondrial genome of Claassenia sp. Wu in genus Claassenia for the first time. The total length of the mitochondrial genome is 15,774 bp, and the DNA base composition is 34.0% A, 27.4% T, 25.6% C and 13.0% G. The whole genome contains 37 genes and one control region, which is similar to other published stoneflies. All PCG started with ATN except CCG for COI gene, TTG for ND1 gene, GTG for ND4 and ND5 genes. The termination codon of 11 PCGs used the normal complete codon TAA or TAG, and the COII and ND5 genes were terminated by a single T. All tRNAs except tRNASer(AGN) fold into a classic clover structure. The phylogenetic tree by Maximum likelihood (ML) and Bayesian (BI) methods supported that Claassenia sp. was the basal taxa of the Perlidae clade. This study provides new data for further mitochondrial genome study on the Perlidae.
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Affiliation(s)
- Mengdan Chen
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Jinjun Cao
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Weihai Li
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Ying Wang
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
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Chen J, Cao J, Li W, Wang Y. Characterization of the complete mitochondrial genome of a stonefly species, Kamimuria klapaleki (Plecoptera: Pelidae). Mitochondrial DNA B Resour 2019; 4:3416-3417. [PMID: 33366019 PMCID: PMC7710318 DOI: 10.1080/23802359.2019.1674722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
We have sequenced and analyzed complete mitochondrial genome (mitogenomes) of the Kamimuria klapaleki, the third mitochondrial genome in the genus Kamimuria, which belongs to the family Pelidae in this paper. The mitogenome of K. klapaleki is circular with the length of 16,077 bp, which possessed 37 genes and a control region like other stonefly. The A + T content of the whole mitogenome was 67.1%. All PCGs were 11,217 bp in length, accounting for 65.3% of the content of A + T. The A + T content of lrRNA and srRNA were 72.3% and 66.4%. The highest A + T content was in the control region (76.2%). There are 15 gene overlaps and 9 gene intergenic spacers in this mitochondrial genome. In addition, we performed phylogenetic analysis by using the Bayesian (BI) and Maximum Likelihood (ML) methods based on the concatenated data set of PCGs from 11 species in Pelidae and two species in Styloperlidae (outgroups). The clade K. chungnanshana + K. wangi was a sister group to K. klapaleki, which is consistent with the traditional morphological classification.
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Affiliation(s)
- Jiajia Chen
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Jinjun Cao
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Weihai Li
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Ying Wang
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China,CONTACT Ying Wang Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang453003, China
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Cao J, Wang Y, Zhang G, Yi S, Li W. The characterization of the mitochondrial genome of Calineuria stigmatica (Plecoptera: Perlidae). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2796-2797. [PMID: 33365732 PMCID: PMC7706896 DOI: 10.1080/23802359.2019.1659119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/30/2022]
Abstract
The nearly complete sequence of the mitochondrial DNA of Calineuria stigmatica has been completed and annotated in this study. The circular genome is 15,070 bp in length with an A + T content of 61.8% and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes. The control region can only be assembled partially. All PCGs use normal start codon ATN, while COI, ND1, and ND5 use CCG, TTG, and GTG as start codon, respectively. Meanwhile, 10 PCGs use the typical termination codons TAN, except COII, ND4, ND5, which stopped with the incomplete terminaton signal T--. Based on 13 PCGs and two rRNAs using the Bayesian (BI) method supported that C. stigmatica was closely grouped with four other Acroneuriinae species. Our results provide basic data for further study of phylogeny in Plecoptera.
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Affiliation(s)
- Jinjun Cao
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Ying Wang
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Guoqiang Zhang
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Shanqing Yi
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Weihai Li
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
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15
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Gao S, Dong H, Yang D. The mitochondrial genome of Hilara sp. (Diptera: Empididae). Mitochondrial DNA B Resour 2019; 4:2723-2724. [PMID: 33365700 PMCID: PMC7706997 DOI: 10.1080/23802359.2019.1644563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 07/10/2019] [Indexed: 11/05/2022] Open
Abstract
The dance fly Hilara sp. belongs to the subfamily Empidinae of Empididae. The mitogenome (GenBank accession number: MN064659) of Hilara sp. was sequenced, the new representative of the mitogenome of the subfamily. The nearly complete mitogenome is 14,927 bp totally, consisting of 13 protein-coding genes, 2 rRNAs, and 22 transfer RNAs. All genes have the similar locations and strands with that of other published species of Empididae. The nucleotide composition biases towards A and T, which together made up 75.7%of the entirety. Bayesian inference analysis strongly supported the monophyly of Empidoidea, Empididae, and Dolichopodidae. It is clear that the phylogenetic relationship within Empidoidea: Dolichopodinae was the sister group to Neurigoninae, and Empidinae was the sister group to Trichopezinae, and the clade that contains Dolichopodinae and Neurigoninae was assigned to the sister group to the clade that contains Empidinae and Trichopezinae.
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Affiliation(s)
- Shang Gao
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Hui Dong
- College of Plant Protection, China Agricultural University, Beijing, China
- Key Laboratory of Southern Subtropical Plant Diversity, Fairylake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen, China
| | - Ding Yang
- College of Plant Protection, China Agricultural University, Beijing, China
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16
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Liu Z, Wang Y, Li W, Cao J. The complete mitochondrial genome of a stonefly species, Etrocorema hochii (Plecoptera: Pelidae). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2690-2691. [PMID: 33365685 PMCID: PMC7706475 DOI: 10.1080/23802359.2019.1644565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The mitochondrial genome of Etrocorema hochii (Wu, 1938), the first representative of Etrocorema, was sequenced and annotated in this study. The complete circular mitochondrial genome (mitogenome) was 15,854 bp in length using Illumina sequencing and harboured 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), two ribosomal RNA genes (rRNA), and one control region in the typical stonefly gene order. The nucleotide composition of this genome is A (36.0%), T (31.4%), C (20.9%), and G (11.7%). All PCGs use the typical start codon ATN, except ND1, ND2, and COI, which start with TTG, GTG, and ACC, respectively. Only the ND5 genes terminated with single T--, and the rest use the stop codon TAA/TAG. We used this new nucleotide information under Bayesian and maximum-likelihood analyses to explore the relationships of Pelidae. Phylogenetic analyses showed that E. hochii is closely related to the clade (Togoperla + Kamimuria), which is widely accepted view.
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Affiliation(s)
- Zhuangzhuang Liu
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Ying Wang
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China.,Postdoctoral Research Base, Henan Institute of Science and Technology, Xinxiang, China
| | - Weihai Li
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Jinjun Cao
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
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17
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Ding S, Li W, Wang Y, Cameron SL, Murányi D, Yang D. The phylogeny and evolutionary timescale of stoneflies (Insecta: Plecoptera) inferred from mitochondrial genomes. Mol Phylogenet Evol 2019; 135:123-135. [PMID: 30876966 DOI: 10.1016/j.ympev.2019.03.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/09/2019] [Accepted: 03/11/2019] [Indexed: 10/27/2022]
Abstract
Phylogenetic analysis based on mitochondrial genomic data from 25 stonefly species recovered a well-supported tree resolving higher-level relationships within Plecoptera (stoneflies). The monophyly of both currently recognized suborders was strongly supported, concordant with previous molecular analyses of Plecoptera. The southern hemisphere suborder Antarctoperlaria formed two clades: Eustheniidae + Diamphipnoidae and Austroperlidae + Gripopterygidae; consistent with relationships proposed based on morphology. The largely northern hemisphere suborder Arctoperlaria also divided into two groups, Euholognatha and Systellognatha, each composed of the five families traditionally assigned to each infraorder (the placement Scopuridae by mt genome data remains untested at this time). Within Euholognatha, strong support for the clade Nemouridae + Notonemouridae confirmed the northern origin of the currently southern hemisphere restricted Notonemouridae. Other family level relationships within the Arctoperlaria differ from those recovered by previous morphology and molecular based analyses. A fossil-calibrated divergence estimation suggests the formation of two suborders dates back to the Jurassic (181 Ma), with subsequent diversification of most stonefly families during the Cretaceous. This result confirms the hypothesis that initial divergence between the suborders was driven by the breakup of the supercontinent Pangaea into Laurasia and Gondwanaland (commencing 200 Ma and complete by 150 Ma).
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Affiliation(s)
- Shuangmei Ding
- Department of Entomology, China Agricultural University, Beijing, China; Department of Entomology, Purdue University, West Lafayette, IN, USA
| | - Weihai Li
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Ying Wang
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Stephen L Cameron
- Department of Entomology, Purdue University, West Lafayette, IN, USA
| | - Dávid Murányi
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Herman Ottó út 15, Budapest H-1022, Hungary; Department of Zoology, Hungarian Natural History Museum, Baross u. 13, Budapest H-1088, Hungary
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing, China.
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18
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Hou P, Qilemoge, Li X, Yang D. The mitochondrial genome of Syntormon pallipes (Diptera: Dolichopodidae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1604093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Peng Hou
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Qilemoge
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Xin Li
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Ding Yang
- College of Plant Protection, China Agricultural University, Beijing, China
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19
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Li J, Cao J, Wang Y, Kong F. The mitochondrial genome analysis of a stonefly, Niponiella limbatella (Plecoptera: Perlidae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1607591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Jianfeng Li
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Jinjun Cao
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Ying Wang
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Fanbin Kong
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
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20
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Hou P, Gao S, Li X, Yang D, Zhang C. The mitochondrial genome of Janthicuomyia sp. (Diptera, Tachinidae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1604092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Peng Hou
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Shang Gao
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Xin Li
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Ding Yang
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Chuntian Zhang
- College of Life Science, Shenyang Normal University, Shenyang, China
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21
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Wang Y, Cao JJ, Li N, Ma GY, Li WH. The first mitochondrial genome from Scopuridae (Insecta: Plecoptera) reveals structural features and phylogenetic implications. Int J Biol Macromol 2018; 122:893-902. [PMID: 30412754 DOI: 10.1016/j.ijbiomac.2018.11.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 09/04/2018] [Accepted: 11/04/2018] [Indexed: 01/10/2023]
Abstract
This study determined the first complete mitochondrial genome (mitogenome) of a stonefly, Scopura longa (Plecoptera: Scopuridae), and reconstructed a phylogeny based on two datasets of mitogenomes in eighteen available stoneflies to examine the relationships among Plecoptera. The complete mitogenome of S. longa is a circular molecule of 15,798bp in size. It contains 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a control region (CR). Most PCGs used standard ATN start codons and TAN stop codons. All tRNAs could be folded as typical cloverleaf secondary structures except tRNASer(AGN), with the dihydrouridine (DHU) arm missing. Tandem repeat regions, two potential stem-loop (SL) structures, Poly T structures and G+C-rich regions are detected in the control region. Finally, the phylogenetic relationships among the families within the Arctoperlaria were reconstructed. The topological structures of the two trees were almost identical. The present phylogenetic analysis shows that S. longa belongs to the infraorder Euholognatha. The monophyly of each family is generally well supported based on nucleotide sequences. The Pteronarcyidae is sister to ((Peltoperlidae+Styloperlidae)+(Perlidae+(Perlodidae+Chloroperlidae))).
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Affiliation(s)
- Ying Wang
- Department of Plant Protection, Henan Institute of Science and Technology, Henan 453003, China
| | - Jin-Jun Cao
- Department of Plant Protection, Henan Institute of Science and Technology, Henan 453003, China
| | - Ni Li
- Department of Plant Protection, Henan Institute of Science and Technology, Henan 453003, China
| | - Gao-Yan Ma
- Department of Plant Protection, Henan Institute of Science and Technology, Henan 453003, China
| | - Wei-Hai Li
- Department of Plant Protection, Henan Institute of Science and Technology, Henan 453003, China.
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22
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Hou P, Ding S, Li X, Yang D, Zhang C, Wang Q. The mitochondrial genome of Drino Sp. (Diptera, Tachinidae). Mitochondrial DNA B Resour 2018; 3:886-887. [PMID: 33474354 PMCID: PMC7799928 DOI: 10.1080/23802359.2018.1501318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 07/08/2018] [Indexed: 11/20/2022] Open
Abstract
The tachinid fly Drino sp. belongs to the subfamily Exoristinae of Tachinidae. We sequenced and annotated the mitogenome of Drino sp. which makes this species first representative of the tribe Eryciini (Tachinidae: Exoristinae) with nearly complete mitochondrial data. This mitogenome is 15437 bp in total, which consists of 22 transfer RNAs, 13 protein-coding genes, 2 ribosomal RNAs and non-coding control region. All genes have the conservational arrangement with other published species of Tachinidae. The nucleotide composition biases toward A and T, the overall A + T% was up to 80.4% of the entire mitogenome. Bayesian inference analysis strongly supported the monophyly of Tachinidae and Exoristinae. Our results also suggested that Exoristinae is the sister group to Phasiinae, and Dexiinae is the sister group to the clade of Phasiinae + Exoristinae.
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Affiliation(s)
- Peng Hou
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Shuangmei Ding
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Xin Li
- College of Life Science, Shenyang Normal University, Shenyang, China
| | - Ding Yang
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Chuntian Zhang
- College of Life Science, Shenyang Normal University, Shenyang, China
| | - Qiang Wang
- Shanghai Entry-Exit Inspection and Quarantine Bureau of China, Technical Center for Animal Plant and Food Inspection and Quarantine, Shanghai, China
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23
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Wang Y, Cao J, Murányi D, Li W. Comparison of two complete mitochondrial genomes from Perlodidae (Plecoptera: Perloidea) and the family-level phylogenetic implications of Perloidea. Gene 2018; 675:254-264. [DOI: 10.1016/j.gene.2018.06.093] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 06/24/2018] [Accepted: 06/26/2018] [Indexed: 10/28/2022]
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24
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Qilemoge, Gao S, Tang C, Wang N, Yang D. The mitochondrial genome of Diostracus lamellatus (Diptera: Dolichopodidae). MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:346-347. [PMID: 33537413 PMCID: PMC7831357 DOI: 10.1080/23802359.2018.1450662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The long-legged fly Diostracus lamellatus Wei et Liu belongs to the subfamily Hydrophorinae of Dolichopodidae. The mitogenome of D. lamellatus was sequenced, the first representative of the mitogenome of the subfamily. The mitogenome is 14,143 bp totally, consisting of 13 protein-coding genes, two rRNAs, and 22 transfer RNAs. All genes have the similar locations and strands with that of other published species of Dolichopodidae. The nucleotide composition biases towards A and T, which together made up 75.8% of the entirety. Bayesian inference analysis strongly supported the monophyly of Dolichopodidae. It suggested that the Hydrophorinae is the sister group to the clade of Sciapodinae + Dolichopodinae.
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Affiliation(s)
- Qilemoge
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Shang Gao
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Chufei Tang
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Ning Wang
- College of Plant Protection, China Agricultural University, Beijing, China.,Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Ding Yang
- College of Plant Protection, China Agricultural University, Beijing, China
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25
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Wang Y, Cao JJ, Li WH. Complete Mitochondrial Genome of Suwallia teleckojensis (Plecoptera: Chloroperlidae) and Implications for the Higher Phylogeny of Stoneflies. Int J Mol Sci 2018; 19:E680. [PMID: 29495588 PMCID: PMC5877541 DOI: 10.3390/ijms19030680] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 02/20/2018] [Accepted: 02/24/2018] [Indexed: 11/21/2022] Open
Abstract
Stoneflies comprise an ancient group of insects, but the phylogenetic position of Plecoptera and phylogenetic relations within Plecoptera have long been controversial, and more molecular data is required to reconstruct precise phylogeny. Herein, we present the complete mitogenome of a stonefly, Suwallia teleckojensis, which is 16146 bp in length and consists of 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and a control region (CR). Most PCGs initiate with the standard start codon ATN. However, ND5 and ND1 started with GTG and TTG. Typical termination codons TAA and TAG were found in eleven PCGs, and the remaining two PCGs (COII and ND5) have incomplete termination codons. All transfer RNA genes (tRNAs) have the classic cloverleaf secondary structures, with the exception of tRNASer(AGN), which lacks the dihydrouridine (DHU) arm. Secondary structures of the two ribosomal RNAs were shown referring to previous models. A large tandem repeat region, two potential stem-loop (SL) structures, Poly N structure (2 poly-A, 1 poly-T and 1 poly-C), and four conserved sequence blocks (CSBs) were detected in the control region. Finally, both maximum likelihood (ML) and Bayesian inference (BI) analyses suggested that the Capniidae was monophyletic, and the other five stonefly families form a monophyletic group. In this study, S. teleckojensis was closely related to Sweltsa longistyla, and Chloroperlidae and Perlidae were herein supported to be a sister group.
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Affiliation(s)
- Ying Wang
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang 453003, Henan, China.
| | - Jin-Jun Cao
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang 453003, Henan, China.
| | - Wei-Hai Li
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang 453003, Henan, China.
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26
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Li X, Ding S, Li X, Hou P, Tang C, Yang D. The complete mitochondrial genome analysis of Eristalis tenax (Diptera, Syrphidae). Mitochondrial DNA B Resour 2017; 2:654-655. [PMID: 33490470 PMCID: PMC7800263 DOI: 10.1080/23802359.2017.1375875] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 09/01/2017] [Indexed: 11/24/2022] Open
Abstract
The complete mitochondrial genome of Eristalis tenax (Linnaeus, 1758) (Diptera, Syrphidae) is reported here. This is the first sequenced mitogenome from the subfamily Milesiinae. The whole mitochondrial genome is 16,091 bp in length and contains 37 canonical genes, which include 22 transfer RNA genes, 13 protein-coding genes and two ribosomal RNA genes, the control region is 1125 bp in length. Most PCGs start with standard ATN codons, while CO1 and ND1 use TTG, CO3 uses TGG as start codons. All PCGs terminate in the common stop codons TAA. In addition, the nucleotide composition of the coding region was 40.0% of A, 40.1% of T, 11.2% of C, 8.7% of G and 80.1% of A + T content. The phylogenetic tree shows that Syrphidae is the sister group of Pipunculidae.
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Affiliation(s)
- Xiaoli Li
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Shuangmei Ding
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Xin Li
- College of Plant Protection, China Agricultural University, Beijing, China
- College of Life Science, Shenyang Normal University, Shenyang, China
| | - Peng Hou
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Chufei Tang
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Ding Yang
- College of Plant Protection, China Agricultural University, Beijing, China
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27
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Wang L, Yang D, Ding S, Li X, Zhang J, Tao M. Complete mitochondrial genome of Hydrellia griseola (Diptera, Ephydridae). Mitochondrial DNA B Resour 2017; 2:591-592. [PMID: 33473913 PMCID: PMC7799989 DOI: 10.1080/23802359.2017.1372703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The complete mitochondrial genome (mitogenome) of Hydrellia griseola has been reported in this study. This is the first sequenced complete mitogenome of the family Ephydridae. The complete mitogenome is 16,159 bp in length, including 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and a partial sequence of the AT-rich region, and the AT-rich region contains several characteristic repeated sequences. In addition, the nucleotide composition of the coding region was 38.7% of A, 37.0% of T, 14.2% of C, 10.1% of G, 75.7% of A + T content. Four complete mitochondrial genome data of related species are download from GenBank, and all of them are used in Neighbor-Join analyses. The result consistently supports the monophyly of Ephydroidea.
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Affiliation(s)
- Liang Wang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China.,College of Plant Protection, China Agricultural University, Beijing, China
| | - Ding Yang
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Shuangmei Ding
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Xin Li
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Junhua Zhang
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Mei Tao
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
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28
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Li X, Ding S, Hou P, Liu X, Zhang C, Yang D. Mitochondrial genome analysis of Ectophasia roundiventris (Diptera, Tachinidae). Mitochondrial DNA B Resour 2017; 2:457-458. [PMID: 33490457 PMCID: PMC7800338 DOI: 10.1080/23802359.2017.1357447] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
The mitochondrial genome of Ectophasia roundiventris (Loew, 1858), the first representative of subfamily Phasiinae, was sequenced and annotated. So far, there are four Tachinidae mitochondrial genomes, here, all of them are used in Neighbour-Join and Maximum Likelihood analyses. The nucleotide composition of Ectophasia roundiventris mitochondrial genome was 40.4% of A, 39.0% of T, 11.8% of C, 8.8% of G, 79.4% of A + T content. The codon ATG was the most popular start codon. The conservative stop codon was TAA, COX2, and ND5 terminated with an incomplete stop codon T, while the gene ND4 was ended with stop codon TA.
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Affiliation(s)
- Xin Li
- College of Life Science, Shenyang Normal University, Shenyang, China.,College of Plant Protection, China Agricultural University, Beijing, China
| | - Shuangmei Ding
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Peng Hou
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Xiaoyan Liu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chuntian Zhang
- College of Life Science, Shenyang Normal University, Shenyang, China
| | - Ding Yang
- College of Plant Protection, China Agricultural University, Beijing, China
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29
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Zhou Q, Ding S, Li X, Zhang T, Yang D. Complete mitochondrial genome of Allognosta vagans (Diptera, Stratiomyidae). Mitochondrial DNA B Resour 2017; 2:461-462. [PMID: 33473862 PMCID: PMC7800880 DOI: 10.1080/23802359.2017.1357450] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
The complete mitochondrial genome (mitogenome) of Allognosta vagans (Loew, 1873) has been reported in this study. This is the first sequenced mitogenome of the subfamily Beridinae. The genome is 15,982 bp in length, including 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a partial sequence of the AT-rich region, and the AT-rich region contains several characteristic repeated sequences. In addition, the nucleotide composition of the coding region was 38.8% of A, 38.7% of T, 9.4% of C, 13.1% of G, 77.5% of A + T content. So far, five complete mitochondrial genome data of related species are available in our lab, all of them are used in Maximum Likelihood and Neighbour-Join analyses. The result supported that Xylomyidae and Stratiomyidae are sister group.
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Affiliation(s)
- Qingxia Zhou
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Shuangmei Ding
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Xin Li
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Tingting Zhang
- Department of Entomology, Shandong Agricultural University, Taian, China
| | - Ding Yang
- College of Plant Protection, China Agricultural University, Beijing, China
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30
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Chen ZT, Du YZ. First Mitochondrial Genome from Nemouridae (Plecoptera) Reveals Novel Features of the Elongated Control Region and Phylogenetic Implications. Int J Mol Sci 2017; 18:ijms18050996. [PMID: 28475163 PMCID: PMC5454909 DOI: 10.3390/ijms18050996] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/03/2017] [Accepted: 05/04/2017] [Indexed: 11/16/2022] Open
Abstract
The complete mitochondrial genome (mitogenome) of Nemoura nankinensis (Plecoptera: Nemouridae) was sequenced as the first reported mitogenome from the family Nemouridae. The N. nankinensis mitogenome was the longest (16,602 bp) among reported plecopteran mitogenomes, and it contains 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes and two ribosomal RNA (rRNA) genes. Most PCGs used standard ATN as start codons, and TAN as termination codons. All tRNA genes of N. nankinensis could fold into the cloverleaf secondary structures except for trnSer (AGN), whose dihydrouridine (DHU) arm was reduced to a small loop. There was also a large non-coding region (control region, CR) in the N. nankinensis mitogenome. The 1751 bp CR was the longest and had the highest A+T content (81.8%) among stoneflies. A large tandem repeat region, five potential stem-loop (SL) structures, four tRNA-like structures and four conserved sequence blocks (CSBs) were detected in the elongated CR. The presence of these tRNA-like structures in the CR has never been reported in other plecopteran mitogenomes. These novel features of the elongated CR in N. nankinensis may have functions associated with the process of replication and transcription. Finally, phylogenetic reconstruction suggested that Nemouridae was the sister-group of Capniidae.
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Affiliation(s)
- Zhi-Teng Chen
- School of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou 225009, China.
| | - Yu-Zhou Du
- School of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education, Yangzhou University, Yangzhou 25009, China.
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