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Liu M, Hu SY, Li M, Sun H, Yuan ML. Comparative mitogenomic analysis provides evolutionary insights into Formica (Hymenoptera: Formicidae). PLoS One 2024; 19:e0302371. [PMID: 38857223 PMCID: PMC11164359 DOI: 10.1371/journal.pone.0302371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 04/02/2024] [Indexed: 06/12/2024] Open
Abstract
Formica is a large genus in the family Formicidae with high diversity in its distribution, morphology, and physiology. To better understand evolutionary characteristics of Formica, the complete mitochondrial genomes (mitogenomes) of two Formica species were determined and a comparative mitogenomic analysis for this genus was performed. The two newly sequenced Formica mitogenomes each included 37 typical mitochondrial genes and a large non-coding region (putative control region), as observed in other Formica mitogenomes. Base composition, gene order, codon usage, and tRNA secondary structure were well conserved among Formica species, whereas diversity in sequence size and structural characteristics was observed in control regions. We also observed several conserved motifs in the intergenic spacer regions. These conserved genomic features may be related to mitochondrial function and their highly conserved physiological constraints, while the diversity of the control regions may be associated with adaptive evolution among heterogenous habitats. A negative AT-skew value on the majority chain was presented in each of Formica mitogenomes, indicating a reversal of strand asymmetry in base composition. Strong codon usage bias was observed in Formica mitogenomes, which was predominantly determined by nucleotide composition. All 13 mitochondrial protein-coding genes of Formica species exhibited molecular signatures of purifying selection, as indicated by the ratio of non-synonymous substitutions to synonymous substitutions being less than 1 for each protein-coding gene. Phylogenetic analyses based on mitogenomic data obtained fairly consistent phylogenetic relationships, except for two Formica species that had unstable phylogenetic positions, indicating mitogenomic data are useful for constructing phylogenies of ants. Beyond characterizing two additional Formica mitogenomes, this study also provided some key evolutionary insights into Formica.
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Affiliation(s)
- Min Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Shi-Yun Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Min Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Hao Sun
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Ming-Long Yuan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
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Cardoso DC, Baldez BCL, Pereira AH, Kalapothakis E, Rosse IC, Cristiano MP. De novo assembly of the complete mitochondrial genome of Mycetophylax simplex Emery, 1888 through organelle targeting revels no substantial expansion of gene spacers, but rather some slightly shorter genes. Mol Genet Genomics 2024; 299:16. [PMID: 38411741 DOI: 10.1007/s00438-024-02099-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 12/10/2023] [Indexed: 02/28/2024]
Abstract
Mitochondria play a key role in cell biology and have their own genome, residing in a highly oxidative environment that induces faster changes than the nuclear genome. Because of this, mitochondrial markers have been exploited to reconstruct phylogenetic and phylogeographic relationships in studies of adaptation and molecular evolution. In this study, we determined the complete mitogenome of the fungus-farming ant Mycetophylax simplex (Hymenoptera, Formicidae) and conducted a comparative analysis among 29 myrmicine ant mitogenomes. Mycetophylax simplex is an endemic ant that inhabits sand dunes along the southern Atlantic coast. Specifically, the species occur in the ecosystem known as "restinga", within the Atlantic Forest biome. Due to habitat degradation, land use and decline of restinga habitats, the species is considered locally extinct in extremely urban beaches and is listed as vulnerable on the Brazilian Red List (ICMBio). We employed a mitochondrion-targeting approach to obtain the complete mitogenome through high-throughput DNA sequencing technology. This method allowed us to determine the mitogenome with high performance, coverage and low cost. The circular mitogenome has a length of 16,367 base pairs enclosing 37 genes (13 protein-coding genes, 22 tRNAs and 2 rRNAs) along with one control region (CR). All the protein-coding genes begin with a typical ATN codon and end with the canonical stop codons. All tRNAs formed the fully paired acceptor stems and fold into the typical cloverleaf-shaped secondary structures. The gene order is consistent with the shared Myrmicinae structure, and the A + T content of the majority strand is 81.51%. Long intergenic spacers were not found but some gene are slightly shorter. The phylogenetic relationships based on concatenated nucleotide and amino acid sequences of the 13 protein-coding genes, using Maximum Likelihood and Bayesian Inference methods, indicated that mitogenome sequences were useful in resolving higher-level relationship within Formicidae.
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Affiliation(s)
- Danon Clemes Cardoso
- Genetics and Evolution of Ants Research Group - GEF, Universidade Federal de Ouro Preto, Ouro Preto, Mina Gerais, 35400-000, Brazil.
| | - Brenda Carla Lima Baldez
- Programa de Pós-Graduação em Ecologia de Biomas Tropicais, Universidade Federal de Ouro Preto, Ouro Preto, Mina Gerais, 35400-000, Brazil
| | - Adriana Heloísa Pereira
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-010, Brazil
| | - Evanguedes Kalapothakis
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-010, Brazil
| | - Izinara Cruz Rosse
- Departamento de Farmácia, Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, 35400-000, Brazil
| | - Maykon Passos Cristiano
- Genetics and Evolution of Ants Research Group - GEF, Universidade Federal de Ouro Preto, Ouro Preto, Mina Gerais, 35400-000, Brazil
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Cao JJ, Wang Y, Murányi D, Cui JX, Li WH. Mitochondrial genomes provide insights into the Euholognatha (Insecta: Plecoptera). BMC Ecol Evol 2024; 24:16. [PMID: 38297210 PMCID: PMC10832105 DOI: 10.1186/s12862-024-02205-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/22/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Euholognatha is a monophyletic group within stoneflies comprised by a superfamily Nemouroidea and a family Scopuridae. Based on morphological data, the family-level phylogenetic relationships within Euholognatha are widely accepted, but there is still controversy among different molecular studies. To better understand the phylogeny of all six extant euholognathan families, we sequenced and analyzed seven euholognathan mitogenomes. RESULTS The sequence heterogeneity analysis observed a low degree of compositional heterogeneity in euholognathan mitogenomes. Meanwhile, leuctrid mitogenomes were more heterogeneous than other euholognathan families, which may affect the phylogenetic reconstruction. Phylogenetic analyses with various datasets generated three topologies. The Leuctridae was recovered as the earliest branching lineage, and the sister relationship of Capniidae and Taeniopterygidae was supported by most tree topologies and FcLM analyses. When separately excluding sparsely sampled Scopuridae or high heterogeneity leuctrid taxa, phylogenetic analyses under the same methods generated more stable and consistent tree topologies. Finally, based on the results of this study, we reconstructed the relationships within Euholognatha as: Leuctridae + (Scopuridae + ((Taeniopterygidae + Capniidae) + (Nemouridae + Notonemouridae))). CONCLUSION Our research shows the potential of data optimizing strategies in reconstructing phylogeny within Euholognatha and provides new insight into the phylogeny of this group.
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Affiliation(s)
- Jin-Jun Cao
- Henan International Joint Laboratory of Taxonomy and Systematic Evolution of Insecta, Henan Institute of Science and Technology, Henan, 453003, China
| | - Ying Wang
- Henan International Joint Laboratory of Taxonomy and Systematic Evolution of Insecta, Henan Institute of Science and Technology, Henan, 453003, China.
| | - Dávid Murányi
- Department of Zoology, Eszterházy Károly Catholic University, Leányka u. 6, Eger, H-3300, Hungary.
| | - Jian-Xin Cui
- Henan International Joint Laboratory of Taxonomy and Systematic Evolution of Insecta, Henan Institute of Science and Technology, Henan, 453003, China
| | - Wei-Hai Li
- Henan International Joint Laboratory of Taxonomy and Systematic Evolution of Insecta, Henan Institute of Science and Technology, Henan, 453003, China.
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Fausto AM, Taddei AR, Belardinelli MC, Ceci M, Gambellini G, Fochetti R. Sperm models in European Plecoptera. ARTHROPOD STRUCTURE & DEVELOPMENT 2023; 77:101311. [PMID: 37852030 DOI: 10.1016/j.asd.2023.101311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/20/2023]
Abstract
Systematic issues regarding Plecoptera are still debated, and the molecular data seem to be unable to definitively clarify the relationships within the order. Spermatozoa are under constant evolutionary pressure, and comparative spermatology can be useful in carrying systematic and phylogenetic information. In the present paper we describe the sperm structure, using light, scanning and transmission electron and immunofluorescence microscopy, of six Euholognatha species belonging to genera not analyzed in our previous studies, i.e. Capnopsis, Amphinemura, Rhabdiopteryx, Tyrrhenoleuctra, Zwicknia and Protonemura. The spermatozoa of all the species examined are fîliform and have a flagellum characterized by an axoneme with 9 + 9+2 pattern and two mitochondrial derivatives. Their ultrastructure shows a degree of heterogeneity within the order. On the contrary, morphological features of sperm are well conserved inside a single Euholognathan family, and the species share a general family sperm model, even if different interspecific or intergeneric characters can be identified and used for systematic inferences. Among Nemouroidea, Taeniopterygidae, showing a peculiar sperm model, seems to have an isolated phylogenetic position. Nemouridae, with a mono-layered acrosome, are isolated among the remaining families, while we can hypothesize a sister taxa relationship between Leuctridae and Capniidae. As regards Perloidea, the sperm characters suggest a closer relationship between Chloroperlidae and Perlodidae, rather than between Perlidae and Perlodidae, as commonly hypothesized.
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Affiliation(s)
- Anna Maria Fausto
- Department for Innovation in Biological, Agro-food and Forest Systems, Tuscia University, Largo dell'Università snc, 01100, Viterbo, Italy
| | - Anna Rita Taddei
- Center of Large Equipments, Section of Electron Microscopy, Tuscia University, Largo dell' Università snc, 01100, Viterbo, Italy
| | - Maria Cristina Belardinelli
- Department for Innovation in Biological, Agro-food and Forest Systems, Tuscia University, Largo dell'Università snc, 01100, Viterbo, Italy
| | - Massimo Ceci
- Department for Innovation in Biological, Agro-food and Forest Systems, Tuscia University, Largo dell'Università snc, 01100, Viterbo, Italy
| | - Gabriella Gambellini
- Center of Large Equipments, Section of Electron Microscopy, Tuscia University, Largo dell' Università snc, 01100, Viterbo, Italy
| | - Romolo Fochetti
- Department for Innovation in Biological, Agro-food and Forest Systems, Tuscia University, Largo dell'Università snc, 01100, Viterbo, Italy.
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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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Gao S, Wang G, Wang X, Yuan H, Wang Y. The mitochondrial genome analysis of a stonefly, Nemoura longicercia Okamoto, 1922 (Plecoptera: Nemouridae). Mitochondrial DNA B Resour 2022; 7:1867-1869. [PMID: 36325293 PMCID: PMC9621250 DOI: 10.1080/23802359.2022.2135397] [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: 11/05/2022] Open
Abstract
To better understand the diversity and phylogeny of Nemouridae, we sequenced and annotated the complete mitochondrial genome (mitogenome) of Nemoura longicercia Okamoto, 1922. The entire mitochondrial genome of N. longicercia was 15,728 bp. It contained 37 representative genes (22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and two ribosomal RNA genes (rRNAs)) and a control region. In this genome, 23 genes were found on the heavy strand (H-strand) and 14 genes were on the light strand (L-strand). All PCGs began with the initiation codon ATN. Eleven PCGs stopped with the termination codon TAA or TAG, while COII and ND5 genes stopped with incomplete codon T. Bayesian’s inference (BI) and maximum-likelihood (ML) methods generated the identical tree topology across the PCGR dataset (13 PCGs plus two rRNAs). The monophyly of each subfamily was well-supported. This analysis supported the clade N. longicercia plus N. papilla as sister taxon to the clade N. meniscata plus N. nankinensis.
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Affiliation(s)
- Shuo Gao
- 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
| | - Xuan Wang
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Hao Yuan
- 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 Henan Institute of Science and Technology, Xinxiang453003, China
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Li M, Liu M, Hu SY, Luo FZ, Yuan ML. Comparative mitogenomic analyses provide evolutionary insights into the retrolateral tibial apophysis clade (Araneae: Entelegynae). Front Genet 2022; 13:974084. [PMID: 36186478 PMCID: PMC9515440 DOI: 10.3389/fgene.2022.974084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
The retrolateral tibial apophysis (RTA) clade is the largest spider lineage within Araneae. To better understand the diversity and evolution, we newly determined mitogenomes of ten RTA species from six families and performed a comparative mitogenomics analysis by combining them with 40 sequenced RTA mitogenomes available on GenBank. The ten mitogenomes encoded 37 typical mitochondrial genes and included a large non-coding region (putative control region). Nucleotide composition and codon usage were well conserved within the RTA clade, whereas diversity in sequence length and structural features was observed in control region. A reversal of strand asymmetry in nucleotide composition, i.e., negative AT-skews and positive GC-skews, was observed in each RTA species, likely resulting from mitochondrial gene rearrangements. All protein-coding genes were evolving under purifying selection, except for atp8 whose Ka/Ks was larger than 1, possibly due to positive selection or selection relaxation. Both mutation pressure and natural selection might contribute to codon usage bias of 13 protein-coding genes in the RTA lineage. Phylogenetic analyses based on mitogenomic data recovered a family-level phylogeny within the RTA; {[(Oval calamistrum clade, Dionycha), Marronoid clade], Sparassidae}. This study characterized RTA mitogenomes and provided some new insights into the phylogeny and evolution of the RTA clade.
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Affiliation(s)
- Min Li
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Min Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Shi-Yun Hu
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Fang-Zhen Luo
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Ming-Long Yuan
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
- *Correspondence: Ming-Long Yuan,
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Ge X, Zang H, Ye X, Peng L, Wang B, Lian G, Sun C. Comparative Mitogenomic Analyses of Hydropsychidae Revealing the Novel Rearrangement of Protein-Coding Gene and tRNA (Trichoptera: Annulipalpia). INSECTS 2022; 13:759. [PMID: 36135460 PMCID: PMC9501032 DOI: 10.3390/insects13090759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/17/2022] [Accepted: 08/20/2022] [Indexed: 06/16/2023]
Abstract
Gene rearrangement of the mitochondrial genome of insects, especially the rearrangement of protein-coding genes, has long been a hot topic for entomologists. Although mitochondrial gene rearrangement is common within Annulipalpia, protein-coding gene rearrangement is relatively rare. As the largest family in Annulipalpia, the available mitogenomes from Hydropsychidae Curtis, 1835 are scarce, and thus restrict our interpretation of the mitogenome characteristic. In this study, we obtained 19 novel mitogenomes of Hydropsychidae, of which the mitogenomes of the genus Arctopsyche are published for the first time. Coupled with published hydropsychid mitogenome, we analyzed the nucleotide composition evolutionary rates and gene rearrangements of the mitogenomes among subfamilies. As a result, we found two novel gene rearrangement patterns within Hydropsychidae, including rearrangement of protein-coding genes. Meanwhile, our results consider that the protein-coding gene arrangement of Potamyia can be interpreted by the tandem duplication/random loss (TDRL) model. In addition, the phylogenetic relationships within Hydropsychidae constructed by two strategies (Bayesian inference and maximum likelihood) strongly support the monophyly of Arctopscychinae, Diplectroninae, Hydropsychinae, and Macronematinae. Our study provides new insights into the mechanisms and patterns of mitogenome rearrangements in Hydropsychidae.
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Affiliation(s)
- Xinyu Ge
- Lab of Taxonomy & Aquatic Insects, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Haoming Zang
- Lab of Taxonomy & Aquatic Insects, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoyun Ye
- Environmental Monitoring Station of Qingtian County, Lishui 323999, China
| | - Lang Peng
- Lab of Taxonomy & Aquatic Insects, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Beixin Wang
- Lab of Taxonomy & Aquatic Insects, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Gang Lian
- Zhejiang Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control, Zhejiang Province Ecological Environment Monitoring Centre, Hangzhou 310012, China
| | - Changhai Sun
- Lab of Taxonomy & Aquatic Insects, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
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Wang Y, Cao J, Guo X, Guo C, Li W, Murányi D. Comparative analysis of mitochondrial genomes among the family Peltoperlidae (Plecoptera: Systellognatha) and phylogenetic implications. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.979847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nowadays, the position of Peltoperlidae in Systellognatha has been resolved based on morphological analyses. However, there are different opinions based on molecular data. To date, only three peltoperlid mitogenomes are available, and more sampling is needed to obtain precise phylogenetic relationships. In this study, we obtained the complete mitogenomes of Cryptoperla kawasawai (15,832 bp) and Peltoperlopsis sagittata (15,756 bp). Our results show that gene content, gene order, DmTTF binding site, nucleotide composition, codon usage, ribonucleic acid (RNA) structure, and structural elements in the control region are highly conserved in peltoperlids. Heatmap analysis of codon usage shows that the AT-rich codons UUA, AUU, UUU, and AUA were commonly used codons in the Peltoperlidae. Evolutionary rate analyses of protein-coding genes reveal that different genes have been subject to different rates of molecular evolution correlated with the GC content. All tRNA genes in peltoperlid mitogenomes have a canonical cloverleaf secondary structure except for trnS1, whose dihydrouridine arm simply forms a loop. The control region of the family has several distinct structural characteristics and has the potential to serve as effective phylogenetic markers. Phylogenetic analyses support the monophyly of Perloidea, but the monophyly of Pteronarcyoidea is still not supported. The Peltoperlidae is placed as the earliest branch within the Systellognatha, and the estimated phylogenetic relationship is: Peltoperlidae + {(Styloperlidae + Pteronarcyidae) + [Perlidae + (Chloroperlidae + Perlodidae)]}. Our results provide new insight into the phylogeny of this group.
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Wang Y, Cao J, Murányi D, Guo X, Guo C, Li W. Family–level phylogeny of infraorder Systellognatha (Insecta: Plecoptera) inferred from mitochondrial genomes. ZOOL SCR 2022. [DOI: 10.1111/zsc.12555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ying Wang
- 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
| | - Dávid Murányi
- Plant Protection Institute, Centre for Agricultural Research Hungarian Academy of Sciences Budapest Hungary
- Department of Zoology Hungarian Natural History Museum Budapest Hungary
| | - Xuan Guo
- Henan International Joint Laboratory of Taxonomy and Systematic Evolution of Insecta Henan Institute of Science and Technology Xinxiang China
| | - Caiyue Guo
- 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
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Mitochondrial Genome of Strophopteryx fasciata (Plecoptera: Taeniopterygidae), with a Phylogenetic Analysis of Nemouroidea. Genes (Basel) 2022; 13:genes13071116. [PMID: 35885898 PMCID: PMC9322138 DOI: 10.3390/genes13071116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 12/10/2022] Open
Abstract
Taeniopterygidae is a medium-sized family of stoneflies. The phylogeny of Taeniopterygidae was widely accepted based on the morphological analyses. However, there are different opinions based on molecular data. To date, only two taeniopterygid mitochondrial genomes (mitogenomes) were available, and more sampling is needed to obtain precise phylogenetic relationships. In this research, the Strophopteryx fasciata mitogenome was sequenced and analyzed. The complete mitogenome of S. fasciata was 15,527 bp in length and contained 37 genes and a non-coding control region. Among taeniopterygid mitogenomes, the length variation was minimal in protein-coding genes (PCGs), transfer RNA genes (tRNAs) and ribosomal RNA genes (rRNAs), but very different in the control region. Similar to mitogenomes of other taeniopterygid species, the S. fasciata mitogenome was consistently AT biased and displayed positive AT- and negative GC-skews of the whole mitogenome. Most PCGs used ATN as the start codon and TAA/TAG as the stop codon. The stop codons were far less variable than the start codons in taeniopterygid mitogenomes. All Ka/Ks ratios were less than 1, indicating the presence of purifying selection in these genes. The secondary structures of transfer and ribosomal RNA genes of S. fasciata mitogenome are highly conserved with other taeniopterygid species. In the control region of the S. fasciata mitogenome, some essential elements (tandem repeats, stem–loop structures, and poly−N stretch, etc.) were observed. Two phylogenetic trees were inferred from Bayesian inference (BI) and Maximum Likelihood (ML) methods generated the identical topology across the PCGR dataset. The relationships of five families in Nemouroidea were recovered as Leuctridae + ((Capniidae + Taeniopterygidae) + (Nemouridae + Notonemouridae)). These results will help us understand the mitogenome structure of taeniopterygid species and the evolutionary relationship within Plecoptera.
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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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Wang Y, Cao J, Murányi D, Chen X, Yan F. The complete mitochondrial genome of Amphinemura bulla Shimizu, 1997 (Plecoptera: Nemouridae) from Japan. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:846-847. [PMID: 33796652 PMCID: PMC7971268 DOI: 10.1080/23802359.2021.1884029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The genus Amphinemura belongs to the family Nemouridae (Plecoptera) and has 205 species in the Holarctic and Oriental Regions. We sequenced the fourth complete mitochondrial genome of A. bulla Shimizu, 1997. The mitogenome is 15,827 bp long with 37 genes plus a control region with an A + T content of 68.9%. There are 10 intergenic spacers (75 bp total) and 13 gene overlaps (43 bp total). All protein-coding genes (PCGs) use normal initiation codons, except ND1 and ND5 which begin with TTG and GTG. Two PCGs (COII and ND5) use a single T as a partial termination codon. Phylogenetic analyses showed that Nemoura and Amphinemura were sister group resulting in a paraphyletic Amphinemurinae different from the morphological classification.
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Affiliation(s)
- Ying Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China.,Postdoctoral Research Base, Henan Institute of Science and Technology, Xinxiang, China
| | - Jinjun Cao
- Postdoctoral Research Base, Henan Institute of Science and Technology, Xinxiang, China
| | - Dávid Murányi
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary.,Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
| | - Xiling Chen
- Postdoctoral Research Base, Henan Institute of Science and Technology, Xinxiang, China
| | - Fenming Yan
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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Li R, Lei Z, Li W, Zhang W, Zhou C. Comparative Mitogenomic Analysis of Heptageniid Mayflies (Insecta: Ephemeroptera): Conserved Intergenic Spacer and tRNA Gene Duplication. INSECTS 2021; 12:170. [PMID: 33669334 PMCID: PMC7920270 DOI: 10.3390/insects12020170] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 02/07/2023]
Abstract
Large intergenic spacers and tRNA gene duplications have been reported in several insect groups, although little is known about mitogenomes of mayflies. Here, we determined complete mitogenomes of ten heptageniid species and systemically analyzed their mitogenomic features. Both a conserved intergenic spacer (IGS) and trnM duplication were detected in those mitogenomes. The IGS, which was observed in heptageniids, could be further folded into a stable stem-loop structure. The tRNA gene duplication was found in almost all analyzed mitogenomes, and a unique gene block trnI-trnM-trnQ-trnM-ND2 was also discovered. Our analysis demonstrates that the heptageniid gene arrangement pattern can be explained by the tandem duplication-random loss (TDRL) model. Phylogenetic analyses using both Bayesian inference (BI) and maximum likelihood (ML) methods based on the nucleotide and amino acid sequence data recovered the genus Epeorus as monophyletic with strong support. Our results provide a better understanding of mitogenomic evolution in Heptageniidae, as well as novel molecular markers for species identification of mayflies.
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Affiliation(s)
| | | | | | | | - Changfa Zhou
- The Key Laboratory of Jiangsu Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (R.L.); (Z.L.); (W.L.); (W.Z.)
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Cao J, Wang Y, Guo X, Wang G, Li W, Murányi D. Two Complete Mitochondrial Genomes From Leuctridae (Plecoptera: Nemouroidea): Implications for the Phylogenetic Relationships Among Stoneflies. JOURNAL OF INSECT SCIENCE (ONLINE) 2021; 21:6137693. [PMID: 33590866 PMCID: PMC7885146 DOI: 10.1093/jisesa/ieab009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Indexed: 06/01/2023]
Abstract
The family-level relationships within Plecoptera have been a focused area of research for a long time. Its higher classification remains unstable, and the phylogenetic relationships within Plecoptera should be re-examined. Here, we sequenced and analyzed two complete mitochondrial genomes (mitogenomes) of Paraleuctra cercia and Perlomyia isobeae of the family Leuctridae. We reconstructed the phylogeny of Plecoptera based on 13 protein-coding genes (PCGs) from published stoneflies. Our results showed that the Bayesian inference and maximum-likelihood tree had similar topological structures except for the positions of two families, Peltoperlidae and Scopuridae. The Plecoptera is divided into two clades, the suborder Antarctoperlaria and the suborder Arctoperlaria. The two suborders subsequently formed two groups, Eusthenioidea and Gripopterygoidea, and Euholognatha and Systellognatha, which is consistent with the results of morphological studies. In addition, the Leuctridae is the earliest branch within the superfamily Nemouroidea. But the monophyly of Perloidea and Pteronarcyoidea are still not well supported.
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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
| | - Xuan Guo
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Guoquan Wang
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, Agricultural College, Guangxi University, Nanning, China
| | - Weihai Li
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, Agricultural College, Guangxi University, Nanning, China
| | - Dávid Murányi
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
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Wang J, Tian T, Zhou M, Li W, Cao J. The complete mitochondrial genome of a stonefly species, Protonemura datongensis (plecoptera: Nemouridae). Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1756957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Jie Wang
- Department of Biological Center, Harbin Academy of Agricultural Sciences, Harbin, China
| | - Tian Tian
- Department of Biological Center, Harbin Academy of Agricultural Sciences, Harbin, China
| | - Meng Zhou
- Department of Biological Center, Harbin Academy of Agricultural Sciences, Harbin, 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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Wei X, Cao J, Kong F, Wang Y. The mitochondrial genome analysis of Sphaeronemoura elephas (Plecoptera: Nemouridae) from Jiangxi Province of southeastern China. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:1107-1108. [PMID: 33366895 PMCID: PMC7748612 DOI: 10.1080/23802359.2020.1726226] [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: 10/28/2022]
Abstract
We sequenced and annotated the species of Sphaeronemoura elephas which represents the first record for continental China from Jiangxi Province in this study to provide mitochondrial genome data for future studies. The entire mitochondrial genome of S. elephas harbored 37 typical code genes and one control region with 15,846 bp in length. The A + T account of total nucleotide, PCGs, tRNAs, rRNAs and control region were 67.1, 64.5, 70.5, 71.0, 82.4%, respectively and the A + T content was the highest in control region. The start codon of all PCGs used ATN except ND5 and ND1 started with GTG and TTG. Eleven PCGs used typical terminal codon TAA or TAG while the COII and ND5 stopped with the single T. Based on 13 PCGs by using Bayesian (BI) and maximum-likelihood (ML) methods, we found that the genus Sphaeronemoura and Mesonemoura were sister groups and the species of Amphinemurinae was monophyletic group.
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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
| | - Fanbin Kong
- 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 S, Cao J, Li W, Wang Y. Characterization of the complete mitochondrial genome of Nemoura meniscata Li & yang (Plecoptera: Nemouridae) from China. Mitochondrial DNA B Resour 2020; 5:1052-1053. [PMID: 33366870 PMCID: PMC7748651 DOI: 10.1080/23802359.2020.1721370] [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: 01/16/2020] [Accepted: 01/19/2020] [Indexed: 11/24/2022] Open
Abstract
We sequenced the third complete mitochondrial genome of Nemoura meniscataby using the high-throughput sequencing method. The mitochondrial genome harbored 37 typical code genes and a control region with 15,895 bp in length was a double-stranded and circular genome. The nucleotide composition is partial to A and T. Seventy-eight nucleotides were dispersed in 10 intergenic spacers and gene overlaps were also found at 13 gene junctions with 48 nucleotides. In phylogenetic trees, the 13 Nemouridae species form a clade diverged from the outgroup clade. The genus Nemoura and Amphinemura were sister groups which is consistent with the previous study.
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Affiliation(s)
- Sijin Chen
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Jinjun Cao
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - 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
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Chen M, Wang Y, Chen J, Cao J. The complete mitochondrial genome of a stonefly species, Indonemoura auriformis (Plecoptera: Nemouridae). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:3392-3393. [PMID: 33366008 PMCID: PMC7707255 DOI: 10.1080/23802359.2019.1674723] [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: 12/04/2022]
Abstract
One new mitochondrial genome of Indonemoura auriformis from the family Nemouridae (Insecta: Plecoptera) was sequenced in the study. The mitochondrial genome has the length of 15,718 bp, encoding 37 genes: 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and 2 ribosomal RNA (rRNA) genes. The whole nucleotide composition biased adenine and thymine with A + T accounting for 69.9%. Nine PCGs and 14 tRNA genes are encoded in the J chain, the other four PCGs, eight tRNAs, and two rRNA genes are encoded in the chain of N. The mitochondrial genome includes 13 gene overlaps and 12 intergenic spacers. Most PCGs strictly use the ATN as start codon, and terminate with traditional stop codon (TAA and TAG). Except the tRNASer(AGN) seems to lack dihydrogen glycine arm, all tRNA genes of the mitochondrial genome are the typical clover secondary structure. The phylogenetic tree of PCGs dataset based on bayesian inference (BI) and maximum likelihood (ML) analysis show the same tree topology. Both ML and BI analysis support the sister-group relationship between Amphinemuria and Nemoura. Meanwhile, Capniidae is closely related to Taeniopterygidae.
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Affiliation(s)
- Mengdan Chen
- 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
| | - 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
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