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Pang S, Zhang Q, Liang L, Qin Y, Li S, Bian X. Comparative Mitogenomics and Phylogenetic Implications for Nine Species of the Subfamily Meconematinae (Orthoptera: Tettigoniidae). INSECTS 2024; 15:413. [PMID: 38921128 PMCID: PMC11204050 DOI: 10.3390/insects15060413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/27/2024]
Abstract
Currently, the subfamily Meconematinae encompasses 1029 species, but whole-mitochondrial-genome assemblies have only been made available for 13. In this study, the whole mitochondrial genomes (mitogenomes) of nine additional species in the subfamily Meconematinae were sequenced. The size ranged from 15,627 bp to 17,461 bp, indicating double-stranded circular structures. The length of the control region was the main cause of the difference in mitochondrial genome length among the nine species. All the mitogenomes including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and a control region (CR). The majority strand encoded 23 genes, and the minority strand encoded 14 genes. A phylogenetic analysis reaffirmed the monophyletic status of each subfamily, but the monophysitism of Xizicus, Xiphidiopsis and Phlugiolopsis was not supported.
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Affiliation(s)
- Siyu Pang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin 541006, China; (S.P.); (Q.Z.); (L.L.); (Y.Q.); (S.L.)
- College of Life Sciences, Guangxi Normal University, Guilin 541006, China
| | - Qianwen Zhang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin 541006, China; (S.P.); (Q.Z.); (L.L.); (Y.Q.); (S.L.)
- College of Life Sciences, Guangxi Normal University, Guilin 541006, China
| | - Lili Liang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin 541006, China; (S.P.); (Q.Z.); (L.L.); (Y.Q.); (S.L.)
- College of Life Sciences, Guangxi Normal University, Guilin 541006, China
| | - Yanting Qin
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin 541006, China; (S.P.); (Q.Z.); (L.L.); (Y.Q.); (S.L.)
- College of Life Sciences, Guangxi Normal University, Guilin 541006, China
| | - Shan Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin 541006, China; (S.P.); (Q.Z.); (L.L.); (Y.Q.); (S.L.)
- College of Life Sciences, Guangxi Normal University, Guilin 541006, China
| | - Xun Bian
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin 541006, China; (S.P.); (Q.Z.); (L.L.); (Y.Q.); (S.L.)
- College of Life Sciences, Guangxi Normal University, Guilin 541006, China
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KARAKAŞ MÜŞERREFY, YAHYAOĞLU ÖZGÜL, ULUAR ONUR, BUDAK MAHIR, ÇIPLAK BATTAL. Mitochondrial genome of Poecilimon cretensis (Orthoptera: Tettigoniidae: Phaneropterinae): Strong phylogenetic signals in gene overlapping regions. Zootaxa 2023; 5263:141-147. [PMID: 37044993 DOI: 10.11646/zootaxa.5263.1.9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Indexed: 04/05/2023]
Abstract
We report the complete mitochondrial genome of the Cretan bush cricket Poecilimon cretensis. The mitogenome consists of 13 protein-coding regions, 22 tRNAs, two rRNAs, and one control region. The length of mitogenome in P. cretensis varies between15477 and 15631 bp, mainly due to variability in control region. The start and stop codons of protein coding genes exhibit the general pattern in Phaneropterinae. Phylogenetic tree constructed with the mitogenome obtained during this study and 12 mitogenomes of Phaneropterinae downloaded from GenBank, placed P. cretensis in Barbitistini as sister group to Poecilimon luschani. Data indicate that the gene overlapping pattern exhibit strong phylogenetic signals.
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Dan ZC, Guan DL, Jiang T, Wang H, Zhao L, Xu SQ. Evolution of Gene Arrangements in the Mitogenomes of Ensifera and Characterization of the Complete Mitogenome of Schizodactylus jimo. Int J Mol Sci 2022; 23:ijms232012094. [PMID: 36292953 PMCID: PMC9603354 DOI: 10.3390/ijms232012094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022] Open
Abstract
Gene arrangement (relative location of genes) is another evolutionary marker of the mitogenome that can provide extensive information on the evolutionary mechanism. To explore the evolution of gene arrangements in the mitogenome of diversified Ensifera, we sequenced the mitogenome of the unique dune cricket species found in China and used it for phylogenetic analysis, in combination with 84 known Ensiferan mitogenomes. The mitogenome of Schizodactylus jimo is a 16,428-bp circular molecule that contains 37 genes. We identified eight types of gene arrangement in the 85 ensiferan mitogenomes. The gene location changes (i.e., gene translocation and duplication) were in three gene blocks: I-Q-M-ND2, rrnl-rns-V, and ND3-A-R-N-S-E-F. From the phylogenetic tree, we found that Schizodactylus jimo and most other species share a typical and ancient gene arrangement type (Type I), while Grylloidea has two types (Types II and III), and the other five types are rare and scattered in the phylogenetic tree. We deduced that the tandem replication–random loss model is the evolutionary mechanism of gene arrangements in Ensifera. Selection pressure analysis revealed that purifying selection dominated the evolution of the ensiferan mitochondrial genome. This study suggests that most gene rearrangements in the ensiferan mitogenome are rare accidental events.
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Romanova EV, Bukin YS, Mikhailov KV, Logacheva MD, Aleoshin VV, Sherbakov DY. Hidden cases of tRNA gene duplication and remolding in mitochondrial genomes of amphipods. Mol Phylogenet Evol 2019; 144:106710. [PMID: 31846708 DOI: 10.1016/j.ympev.2019.106710] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 12/13/2019] [Accepted: 12/13/2019] [Indexed: 12/30/2022]
Abstract
The evolution of tRNA genes in mitochondrial (mt) genomes is a complex process that includes duplications, degenerations, and transpositions, as well as a specific process of identity change through mutations in the anticodon (tRNA gene remolding or tRNA gene recruitment). Using amphipod-specific tRNA models for annotation, we show that tRNA duplications are more common in the mt genomes of amphipods than what was revealed by previous annotations. Seventeen cases of tRNA gene duplications were detected in the mt genomes of amphipods, and ten of them were tRNA genes that underwent remolding. The additional tRNA gene findings were verified using phylogenetic analysis and genetic distance analysis. The majority of remolded tRNA genes (seven out of ten cases) were found in the mt genomes of endemic amphipod species from Lake Baikal. All additional mt tRNA genes arose independently in the Baikalian amphipods, indicating the unusual plasticity of tRNA gene evolution in these species assemblages. The possible reasons for the unusual abundance of additional tRNA genes in the mt genomes of Baikalian amphipods are discussed. The amphipod-specific tRNA models developed for MiTFi refine existing predictions of tRNA genes in amphipods and reveal additional cases of duplicated tRNA genes overlooked by using less specific Metazoa-wide models. The application of these models for mt tRNA gene prediction will be useful for the correct annotation of mt genomes of amphipods and probably other crustaceans.
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Affiliation(s)
- Elena V Romanova
- Laboratory of Molecular Systematics, Limnological Institute, Irkutsk, Russian Federation.
| | - Yurij S Bukin
- Laboratory of Molecular Systematics, Limnological Institute, Irkutsk, Russian Federation; Faculty of Biology and Soil Studies, Irkutsk State University, Irkutsk, Russian Federation
| | - Kirill V Mikhailov
- Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation; Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Maria D Logacheva
- Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation; Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir V Aleoshin
- Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation; Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Dmitry Yu Sherbakov
- Laboratory of Molecular Systematics, Limnological Institute, Irkutsk, Russian Federation; Faculty of Biology and Soil Studies, Irkutsk State University, Irkutsk, Russian Federation
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Öztürk PN, Çıplak B. Dummy. Int J Biol Macromol 2019; 132:1318-1326. [PMID: 30953723 DOI: 10.1016/j.ijbiomac.2019.04.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/02/2019] [Accepted: 04/02/2019] [Indexed: 11/19/2022]
Affiliation(s)
- Pembe Nur Öztürk
- Department of Biology, Faculty of Science, Akdeniz University 07058, Antalya, Turkey
| | - Battal Çıplak
- Department of Biology, Faculty of Science, Akdeniz University 07058, Antalya, Turkey.
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Zhu JC, Tang P, Zheng BY, Wu Q, Wei SJ, Chen XX. The first two mitochondrial genomes of the family Aphelinidae with novel gene orders and phylogenetic implications. Int J Biol Macromol 2018; 118:386-396. [PMID: 29932999 DOI: 10.1016/j.ijbiomac.2018.06.087] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/17/2018] [Accepted: 06/18/2018] [Indexed: 11/17/2022]
Abstract
Chalcidoidea is one of the most diverse group in Hymenoptera by possessing striking mitochondrial gene arrangement. By using next generation sequencing method, the first two nearly complete mitochondrial genomes in the family Aphelinidae (Insecta, Hymenopetra, Chalcidoidea) were obtained in this study. Almost all previously sequenced mitochondrial genome of Chalcidoidea species have a large inversion including six genes (atp6-atp8-trnD-trnK-cox2-trnL2-cox1) as compared with ancestral mitochondrial genome, but these two Encarsia mitochondrial genomes had a large inversion including nine genes (nad3-trnG-atp6-atp8-trnD-trnK-cox2-trnL2-cox1), which was only congruent with the species in the genus Nasonia. Moreover, we found that one shuffling changes (trnD and trnK) happened in the species E. obtusiclava but not in another species E. formosa within the same genus, of which such shuffling within the same genus at this region was only detected in Polisters within Insecta. Phylogenetic analysis displayed that different data matrix (13PCG+ 2 rRNA or 13 PCG) and inference methods (BI or ML) indicate the identical topology with high nodal supports that Aphelinidae formed a sister group with (Trichogrammatidae + Aganoidae) and the monophyly of Pteramalidae. Our results also indicated the validity of assembling and feasibility of next-generation technology to obtain the mitochondrial genomes of parasitic Hymenoptera.
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Affiliation(s)
- Jia-Chen Zhu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Plant Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Pu Tang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Plant Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Bo-Ying Zheng
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Plant Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qiong Wu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Plant Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xue-Xin Chen
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Plant Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.
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Zhang LP, Yu DN, Storey KB, Cheng HY, Zhang JY. Higher tRNA gene duplication in mitogenomes of praying mantises (Dictyoptera, Mantodea) and the phylogeny within Mantodea. Int J Biol Macromol 2018; 111:787-795. [DOI: 10.1016/j.ijbiomac.2018.01.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/30/2017] [Accepted: 01/03/2018] [Indexed: 12/21/2022]
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Qiu ZY, Yuan H, Wang X, Cui Y, Lian T, Mao S. Characterization of the mitochondrial genome of Phyllomimus sp. (Orthoptera: Pseudophyllidae). MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:900-901. [PMID: 33474028 PMCID: PMC7800922 DOI: 10.1080/23802359.2017.1413296] [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: 11/03/2022]
Abstract
The nearly complete mitochondrial genome (mitogenome) without tRNA-Met and with a partial A + T-rich region of phyllomimus sp. has been sequenced with the length of 15,543 bp. We found 140 bp-long intergenic spacers (IGSs) which located between tRNA-Gln and ND2, while this region should be tRNA-Met in most orthopteran mitogenomes. The content of As, Ts, Cs Gs and AT in the mitogenome is 37.3%, 32.5%, 20.6%, 9.5% and 69.8%, respectively. All protein-coding genes start with typical ATN codon except for ND1, which initiates with TTG codon instead, and end with either complete TAA/TAG codons or incomplete T(aa) codons. Phylogenetic analysis indicated that genetic distances of phyllomimus sp. and Orophyllus montanus was closer than other species.
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Affiliation(s)
- Zhong-Ying Qiu
- School of Basic Medical Sciences, Xi'an Medical University, Xi'an, China
| | - Hao Yuan
- School of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xiaolong Wang
- School of Basic Medical Sciences, Xi'an Medical University, Xi'an, China
| | - Yuanyuan Cui
- School of Basic Medical Sciences, Xi'an Medical University, Xi'an, China
| | - Ting Lian
- Research Center for Prevention and Treatment of Respiratory Disease, School of Clinical Medicine, Xi'an Medical University, Xi'an, China
| | - Shaoli Mao
- Xi'an Botanical Garden of Shaanxi Province, Xi'an, Shaanxi, China
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Sayadi A, Immonen E, Tellgren-Roth C, Arnqvist G. The Evolution of Dark Matter in the Mitogenome of Seed Beetles. Genome Biol Evol 2017; 9:2697-2706. [PMID: 29048527 PMCID: PMC5737749 DOI: 10.1093/gbe/evx205] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2017] [Indexed: 12/14/2022] Open
Abstract
Animal mitogenomes are generally thought of as being economic and optimized for rapid replication and transcription. We use long-read sequencing technology to assemble the remarkable mitogenomes of four species of seed beetles. These are the largest circular mitogenomes ever assembled in insects, ranging from 24,496 to 26,613 bp in total length, and are exceptional in that some 40% consists of non-coding DNA. The size expansion is due to two very long intergenic spacers (LIGSs), rich in tandem repeats. The two LIGSs are present in all species but vary greatly in length (114-10,408 bp), show very low sequence similarity, divergent tandem repeat motifs, a very high AT content and concerted length evolution. The LIGSs have been retained for at least some 45 my but must have undergone repeated reductions and expansions, despite strong purifying selection on protein coding mtDNA genes. The LIGSs are located in two intergenic sites where a few recent studies of insects have also reported shorter LIGSs (>200 bp). These sites may represent spaces that tolerate neutral repeat array expansions or, alternatively, the LIGSs may function to allow a more economic translational machinery. Mitochondrial respiration in adult seed beetles is based almost exclusively on fatty acids, which reduces the need for building complex I of the oxidative phosphorylation pathway (NADH dehydrogenase). One possibility is thus that the LIGSs may allow depressed transcription of NAD genes. RNA sequencing showed that LIGSs are partly transcribed and transcriptional profiling suggested that all seven mtDNA NAD genes indeed show low levels of transcription and co-regulation of transcription across sexes and tissues.
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Affiliation(s)
- Ahmed Sayadi
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Sweden
| | - Elina Immonen
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Sweden
| | - Christian Tellgren-Roth
- National Genomics Infrastructure, Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Göran Arnqvist
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Sweden
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Du C, Zhang L, Lu T, Ma J, Zeng C, Yue B, Zhang X. Mitochondrial genomes of blister beetles (Coleoptera, Meloidae) and two large intergenic spacers in Hycleus genera. BMC Genomics 2017; 18:698. [PMID: 28874137 PMCID: PMC5585954 DOI: 10.1186/s12864-017-4102-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 08/31/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Insect mitochondrial genomes (mitogenomes) exhibit high diversity in some lineages. The gene rearrangement and large intergenic spacer (IGS) have been reported in several Coleopteran species, although very little is known about mitogenomes of Meloidae. RESULTS We determined complete or nearly complete mitogenomes of seven meloid species. The circular genomes encode 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs) and two ribosomal RNAs (rRNAs), and contain a control region, with gene arrangement identical to the ancestral type for insects. The evolutionary rates of all PCGs indicate that their evolution is based on purifying selection. The comparison of tRNA secondary structures indicates diverse substitution patterns in Meloidae. Remarkably, all mitogenomes of the three studied Hycleus species contain two large intergenic spacers (IGSs). IGS1 is located between trnW and trnC, including a 9 bp consensus motif. IGS2 is located between trnS2 (UCN) and nad1, containing discontinuous repeats of a pentanucleotide motif and two 18-bp repeat units in both ends. To date, IGS2 is found only in genera Hycleus across all published Coleopteran mitogenomes. The duplication/random loss model and slipped-strand mispairing are proposed as evolutionary mechanisms for the two IGSs (IGS1, IGS2). The phylogenetic analyses using MrBayes, RAxML, and PhyloBayes methods based on nucleotide and amino acid datasets of 13 PCGs from all published mitogenomes of Tenebrionoids, consistently recover the monophylies of Meloidae and Tenebrionidae. Within Meloidae, the genus Lytta clusters with Epicauta rather than with Mylabris. Although data collected thus far could not resolve the phylogenetic relationships within Meloidae, this study will assist in future mapping of the Meloidae phylogeny. CONCLUSIONS This study presents mitogenomes of seven meloid beetles. New mitogenomes retain the genomic architecture of the Coleopteran ancestor, but contain two IGSs in the three studied Hycleus species. Comparative analyses of two IGSs suggest that their evolutionary mechanisms are duplication/random loss model and slipped-strand mispairing.
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Affiliation(s)
- Chao Du
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China.,Nanchong Vocational and Technical College, Nanchong, 637131, Sichuan, People's Republic of China
| | - Lifang Zhang
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Ting Lu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Jingnan Ma
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Chenjuan Zeng
- Sichuan Key Laboratory of Medicinal American Cockroach, Chengdu, 610041, People's Republic of China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Xiuyue Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China.
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Yang J, Lu C, Zhang ZB, Huang Y, Lin LL. Mitochondrial Genomes of Two Pygmy Grasshoppers (Orthoptera: Tetrigoidea) and a Comparative Analysis of Caelifera Mitogenomes. Zoolog Sci 2017; 34:287-294. [DOI: 10.2108/zs160217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Jie Yang
- Co-Innovation Center for Qinba Regions' Sustainable Development, College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
| | - Chao Lu
- Co-Innovation Center for Qinba Regions' Sustainable Development, College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
| | - Zhi-Bin Zhang
- Co-Innovation Center for Qinba Regions' Sustainable Development, College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
| | - Yuan Huang
- Co-Innovation Center for Qinba Regions' Sustainable Development, College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
| | - Li-Liang Lin
- Co-Innovation Center for Qinba Regions' Sustainable Development, College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
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Zhou Z, Zhao L, Liu N, Guo H, Guan B, Di J, Shi F. Towards a higher-level Ensifera phylogeny inferred from mitogenome sequences. Mol Phylogenet Evol 2017; 108:22-33. [PMID: 28188878 DOI: 10.1016/j.ympev.2017.01.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 01/24/2017] [Accepted: 01/31/2017] [Indexed: 11/15/2022]
Abstract
Although mitogenomes are useful tools for inferring evolutionary history, only a few representative ones can be used for most Ensifera lineages. Thirty-two ensiferan mitogenomes were determined using ABI Sanger sequencing and standard primer walking of 2-3 overlapping Long-PCR fragments, or Illumina® HiSeq2000 for "shotgun" sequenced long-PCR-amplified mitochondrial or total genomic DNA. Six patterns of gene arrangements, including the novel trnR-trnSAGN-trnA-trnN-trnG-nad3 in Lipotactes tripyrga (Lipotactinae), were identified from 59 ensiferan mitogenomes. The results suggest that trnM-trnI-trnQ and trnA-trnR-trnE-trnSAGN-trnN-trnF rearrangements might be a shared derived character in Pseudophyllinae and Gryllidae, respectively. We found base composition biases in our dataset, which potentially complicate the inference of higher-level ensiferan phylogeny. Site-heterogeneous Bayesian inference (BI) and site-homogeneous maximum likelihood (ML) analyses recovered all ensiferan superfamilies as monophyletic. The site-homogeneous BI analysis failed to recover the monophyly of Stenopelmatoidea. As Schizodactyloidea was only represented by Comicus campestris, its monophyly could not be tested. In the Triassic/Jurassic boundary, Ensifera diverged into grylloid and non-grylloid clades. All analyses confirmed Grylloidea and Gryllotalpoidea as sister groups. Site-heterogeneous BI analysis found Schizodactyloidea as the most basal lineage and sister to the clade formed by Grylloidea and Gryllotalpoidea, but the site-homogeneous analyses placed it basally to the non-grylloid clade and recovered a sister relationship between Tettigonioidea and (Hagloidea, Rhaphidophoroidea, Stenopelmatoidea), although this clade had a low support. The site-heterogeneous BI analysis found Tettigonioidea and Hagloidea were sister groups (posterior probability (PP)=0.99), Stenopelmatoidea was sister to (Tettigonioidea, Hagloidea) (PP>0.91), and Rhaphidophoroidea was basal to the non-grylloid clade. At a lower level, all analyses divided Tettigonioidea into Phaneropteridae and Tettigoniidae.
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Affiliation(s)
- Zhijun Zhou
- Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China.
| | - Ling Zhao
- College of Life Sciences and Biotechnology, Mianyang Normal University, Mianyang, Sichuan 621000, China
| | - Nian Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710062, China
| | - Huifang Guo
- Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Bei Guan
- Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Juanxia Di
- Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Fuming Shi
- Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China.
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Romanova EV, Aleoshin VV, Kamaltynov RM, Mikhailov KV, Logacheva MD, Sirotinina EA, Gornov AY, Anikin AS, Sherbakov DY. Evolution of mitochondrial genomes in Baikalian amphipods. BMC Genomics 2016; 17:1016. [PMID: 28105939 PMCID: PMC5249044 DOI: 10.1186/s12864-016-3357-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Amphipods (Crustacea) of Lake Baikal are a very numerous and diverse group of invertebrates generally believed to have originated by adaptive radiation. The evolutionary history and phylogenetic relationships in Baikalian amphipods still remain poorly understood. Sequencing of mitochondrial genomes is a relatively feasible way for obtaining a set of gene sequences suitable for robust phylogenetic inferences. The architecture of mitochondrial genomes also may provide additional information on the mechanisms of evolution of amphipods in Lake Baikal. RESULTS Three complete and four nearly complete mitochondrial genomes of Baikalian amphipods were obtained by high-throughput sequencing using the Illumina platform. A phylogenetic inference based on the nucleotide sequences of all mitochondrial protein coding genes revealed the Baikalian species to be a monophyletic group relative to the nearest non-Baikalian species with a completely sequenced mitochondrial genome - Gammarus duebeni. The phylogeny of Baikalian amphipods also suggests that the shallow-water species Eulimnogammarus has likely evolved from a deep-water ancestor, however many other species have to be added to the analysis to test this hypothesis. The gene order in all mitochondrial genomes of studied Baikalian amphipods differs from the pancrustacean ground pattern. Mitochondrial genomes of four species possess 23 tRNA genes, and in three genomes the extra tRNA gene copies have likely undergone remolding. Widely varying lengths of putative control regions and other intergenic spacers are typical for the mitochondrial genomes of Baikalian amphipods. CONCLUSIONS The mitochondrial genomes of Baikalian amphipods display varying organization suggesting an intense rearrangement process during their evolution. Comparison of complete mitochondrial genomes is a potent approach for studying the amphipod evolution in Lake Baikal.
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Affiliation(s)
- Elena V. Romanova
- Laboratory of Molecular Systematics, Limnological Institute, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033 Russian Federation
| | - Vladimir V. Aleoshin
- Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, 119991 Russian Federation
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127994 Russian Federation
| | - Ravil M. Kamaltynov
- Laboratory of Molecular Systematics, Limnological Institute, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033 Russian Federation
| | - Kirill V. Mikhailov
- Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, 119991 Russian Federation
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127994 Russian Federation
| | - Maria D. Logacheva
- Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, 119991 Russian Federation
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127994 Russian Federation
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420012 Russian Federation
| | - Elena A. Sirotinina
- Laboratory of Molecular Systematics, Limnological Institute, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033 Russian Federation
| | - Alexander Yu. Gornov
- Institute for System Dynamics and Control Theory, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033 Russian Federation
| | - Anton S. Anikin
- Institute for System Dynamics and Control Theory, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033 Russian Federation
| | - Dmitry Yu. Sherbakov
- Laboratory of Molecular Systematics, Limnological Institute, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033 Russian Federation
- Faculty of Biology and Soil Studies, Irkutsk State University, Irkutsk, 664003 Russian Federation
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14
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Guan B, Guo H, Zhou Z. Illumina next-generation sequencing reveals the mitochondrial genome of Ducetia japonica (Orthoptera: Tettigoniidae). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:361-362. [PMID: 33473484 PMCID: PMC7799970 DOI: 10.1080/23802359.2016.1168717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Using Illumina next-generation sequencing (NGS), the complete mitochondrial genome (mitogenome) of Ducetia japonica was sequenced in the present study. The mitogenome of D. japonica (Genbank accession no. KU885974) is 16,276 bp in size, had the typical invertebrate mitochondrial gene arrangement and containing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA) and a control region. Except for the control region (868 bp), one novel larger intergenic (616 bp) was found between nad2 and trnW. Phylogenetic results unambiguously support the monophyly of Phaneropterinae, although the gene order of two Sinochlora species different with other Tettigoniidae species. Using Illumina NGS platforms for mitogenome sequencing will provide rather essential and important DNA molecular data for the further phylogenetic analysis across major ensiferan lineages.
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Affiliation(s)
- Bei Guan
- College of Life Sciences, Hebei University, Baoding, China
| | - Huifang Guo
- College of Life Sciences, Hebei University, Baoding, China
| | - Zhijun Zhou
- College of Life Sciences, Hebei University, Baoding, China
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15
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Wang Y, Zhao H, Zhang X, Ren B. The Complete Mitochondrial Genome and Song Evolution of the Monotypic Genus U. Tarbinsky, 1932 (Orthoptera: Tettigoniidae). ENVIRONMENTAL ENTOMOLOGY 2016; 45:737-746. [PMID: 27108414 DOI: 10.1093/ee/nvw031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 03/12/2016] [Indexed: 06/05/2023]
Abstract
The insect Uvarovites inflatus Uvarov is highly appreciated in China. It is known for its distinctive songs and horn-like forewings and is raised commercially for insect lovers. U. inflatus was previously categorized as part of the monotypic genus Uvarovites; however, there was little molecular evidence to support this taxonomic classification. This study obtained and investigated the mitogenome of U. inflatus, and its songs were characterized and compared with other Ensifera species whose mitogenomes are available. By performing the mitochondrial analysis, we were able to assess the phylogenetic relationships between these species and discuss the evolution of Ensifera calling songs. The mitogenome of U. inflatus is 15,956 bp in length and contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. The organization and orientation of the U. inflatus mitogenome are similar to those of other Tettigonioidea species. Phylogenetic analysis based on 13 protein-coding genes showed that the superfamily Tettigonioidea is monophyletic, as are the other six tested subfamilies from Tettigonioidea. Our results also indicated that Grylloidea is monophyletic. A Bayesian relaxed clock analysis showed that the differentiation of U. inflatus and Gampsocleis gratiosa Brunner occurred in the middle Miocene, suggesting that their speciation occurred over a long evolutionary period. The results provide significant support for the establishment of the monotypic genus Uvarovites. Calling song analysis showed that at least two discrete steps of independent evolution occurred during the change from pure tone to broadband noise, and that the ancestor of existing Ensifera was more likely to have emitted pure-tone songs than broadband signals. Together, the mitogenome, molecular clock, and acoustic data allowed us to clarify the taxonomic state of U. inflatus and propose a timeline for the evolution of Ensifera songs.
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Affiliation(s)
- Yinliang Wang
- 1Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China,10 Renmin St. 5268, Changchun, China CO130024 (; )
- 3These authors equally contributed to the research, and
| | - Hanbo Zhao
- 1Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China,10 Renmin St. 5268, Changchun, China CO130024 (; )
- 3These authors equally contributed to the research, and
| | - Xue Zhang
- 1Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China,10 Renmin St. 5268, Changchun, China CO130024 (; )
- 2Key Laboratory of Vegetation Ecology, MOE, Northeast Normal University, Changchun, China
| | - Bingzhong Ren
- 1Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China,10 Renmin St. 5268, Changchun, China CO130024 (; )
- 4Corresponding author, e-mail:
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16
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Wang ZL, Li C, Fang WY, Yu XP. Characterization of the complete mitogenomes of two Neoscona spiders (Araneae: Araneidae) and its phylogenetic implications. Gene 2016; 590:298-306. [PMID: 27259661 DOI: 10.1016/j.gene.2016.05.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 04/15/2016] [Accepted: 05/25/2016] [Indexed: 01/14/2023]
Abstract
The complete mitogenomes of two orb-weaving spiders Neoscona doenitzi and Neoscona nautica were determined and a comparative mitogenomic analysis was performed to depict evolutionary trends of spider mitogenomes. The circular mitogenomes are 14,161bp with A+T content of 74.6% in N. doenitzi and 14,049bp with A+T content of 78.8% in N. nautica, respectively. Both mitogenomes contain a standard set of 37 genes typically presented in metazoans. Gene content and orientation are identical to all previously sequenced spider mitogenomes, while gene order is rearranged by tRNAs translocation when compared with the putative ancestral gene arrangement pattern presented by Limulus polyphemus. A comparative mitogenomic analysis reveals that the nucleotide composition bias is obviously divergent between spiders in suborder Opisthothelae and Mesothelae. The loss of D-arm in the trnS(UCN) among all of Opisthothelae spiders highly suggested that this common feature is a synapomorphy for entire suborder Opisthothelae. Moreover, the trnS(AGN) in araneoids preferred to use TCT as an anticodon rather than the typical anticodon GCT. Phylogenetic analysis based on the 13 protein-coding gene sequences consistently yields trees that nest the two Neoscona spiders within Araneidae and recover superfamily Araneoidea as a monophyletic group. The molecular information acquired from the results of this study should be very useful for future research on mitogenomic evolution and genetic diversities in spiders.
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Affiliation(s)
- Zheng-Liang Wang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang 310018, People's Republic of China
| | - Chao Li
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang 310018, People's Republic of China
| | - Wen-Yuan Fang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang 310018, People's Republic of China
| | - Xiao-Ping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang 310018, People's Republic of China.
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17
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Yang J, Ye F, Huang Y. Mitochondrial genomes of four katydids (Orthoptera: Phaneropteridae): New gene rearrangements and their phylogenetic implications. Gene 2015; 575:702-11. [PMID: 26410415 DOI: 10.1016/j.gene.2015.09.052] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 08/18/2015] [Accepted: 09/21/2015] [Indexed: 11/29/2022]
Abstract
Phaneropteridae is a family of Orthoptera that displays an amazing amount of diversity in terms of both forms and species. We sequenced the mitochondrial genomes (mitogenomes) of two bush katydids: Ruidocollaris obscura and Kuwayamaea brachyptera (Phaneropterinae), and two true katydids: Orophyllus montanus and Phyllomimus detersus (Pseudophyllinae), to obtain further insight into the characteristics of the katydid mitogenomes and to investigate the taxonomic status of subfamily Pseudophyllinae and the diversity of gene arrangements among Phaneropteridae. The following general genomic characteristics were observed in the four katydids: a longer length of the mitogenomes (16,007bp-16,667bp) compared with Caelifera, abundant intergenic spacers, and accepted atypical initiation codons (GTG and TTG, found in cox1, nad1 and nad2). A new orientation of the gene arrangement "trnM-trnI-trnQ" was identified in P. detersus, which is the first representative of Polyneoptera found to carry this gene cluster. Large identical fragments (492bp) were detected in control region 1 (CR1) and control region 2 (CR2) of R. obscura. The high similarity of the duplicated CRs is likely due to a recent gene duplication or concerted evolution. Analyses of the duplicated CRs revealed one conserved stem-loop (on the N-strand) located in the identical sequences of both CRs that might be linked to replication initiation. Phylogenetic analyses based on 13 protein-coding genes and 2 ribosomal RNA genes from 20 Ensiferan species yielded the identical topologies between two different methods (maximum likelihood and bayesian inference). The newly sequenced Pseudophyllinae species was placed as the sister group of Phaneropterinae, and Mecopodinae clustered with Pseudophyllinae+Phaneropterinae. Additionally, we speculate that the species in Ruidocollaris and Sinochlora, as well as their closely related genera, may have undergone numerous rearrangement events.
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Affiliation(s)
- Jing Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
| | - Fei Ye
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
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18
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Justice JL, Weese DA, Santos SR. Phylogenetic utility, and variability in structure and content, of complete mitochondrial genomes among genetic lineages of the Hawaiian anchialine shrimp Halocaridina rubra Holthuis 1963 (Atyidae:Decapoda). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2710-8. [PMID: 26061341 DOI: 10.3109/19401736.2015.1046161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Atyidae are caridean shrimp possessing hair-like setae on their claws and are important contributors to ecological services in tropical and temperate fresh and brackish water ecosystems. Complete mitochondrial genomes have only been reported from five of the 449 species in the family, thus limiting understanding of mitochondrial genome evolution and the phylogenetic utility of complete mitochondrial sequences in the Atyidae. Here, comparative analyses of complete mitochondrial genomes from eight genetic lineages of Halocaridina rubra, an atyid endemic to the anchialine ecosystem of the Hawaiian Archipelago, are presented. Although gene number, order, and orientation were syntenic among genomes, three regions were identified and further quantified where conservation was substantially lower: (1) high length and sequence variability in the tRNA-Lys and tRNA-Asp intergenic region; (2) a 317-bp insertion between the NAD6 and CytB genes confined to a single lineage and representing a partial duplication of CytB; and (3) the putative control region. Phylogenetic analyses utilizing complete mitochondrial sequences provided new insights into relationships among the H. rubra genetic lineages, with the topology of one clade correlating to the geologic sequence of the islands. However, deeper nodes in the phylogeny lacked bootstrap support. Overall, our results from H. rubra suggest intra-specific mitochondrial genomic diversity could be underestimated across the Metazoa since the vast majority of complete genomes are from just a single individual of a species.
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Affiliation(s)
- Joshua L Justice
- a Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies , Auburn University , Auburn , AL , USA .,b Department of Microbiology , University of Alabama at Birmingham , Birmingham , AL , USA , and
| | - David A Weese
- a Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies , Auburn University , Auburn , AL , USA .,c Department of Biological and Environmental Sciences , Georgia College and State University , Milledgeville , GA , USA
| | - Scott Ross Santos
- a Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies , Auburn University , Auburn , AL , USA
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19
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Dong JJ, Guan DL, Xu SQ. Complete mitogenome of the semi-aquatic grasshopper Oxya intricate (Stål.) (Insecta: Orthoptera: Catantopidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3233-4. [DOI: 10.3109/19401736.2015.1007361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Jia-Jia Dong
- College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, P. R. China
| | - De-Long Guan
- College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, P. R. China
| | - Sheng-Quan Xu
- College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, P. R. China
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20
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Song H, Amédégnato C, Cigliano MM, Desutter‐Grandcolas L, Heads SW, Huang Y, Otte D, Whiting MF. 300 million years of diversification: elucidating the patterns of orthopteran evolution based on comprehensive taxon and gene sampling. Cladistics 2015; 31:621-651. [DOI: 10.1111/cla.12116] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2015] [Indexed: 10/23/2022] Open
Affiliation(s)
- Hojun Song
- Department of Biology University of Central Florida Orlando FL USA
- Department of Entomology Texas A&M University College Station TX USA
| | - Christiane Amédégnato
- Département Systématique et Évolution Muséum National d ‘Histoire Naturelle’ ISYEB, UMR7205 CNRS MNHN UPMC EPHE Paris France
| | | | - Laure Desutter‐Grandcolas
- Département Systématique et Évolution Muséum National d ‘Histoire Naturelle’ ISYEB, UMR7205 CNRS MNHN UPMC EPHE Paris France
| | - Sam W. Heads
- Illinois Natural History Survey University of Illinois at Urbana‐Champaign Champaign IL USA
| | - Yuan Huang
- Institute of Zoology Shaanxi Normal University Xi'an China
| | - Daniel Otte
- Department of Biodiversity, Earth & Environmental Science Academy of Natural Sciences of Drexel University Philadelphia PA USA
| | - Michael F. Whiting
- Department of Biology and M. L. Bean Museum Brigham Young University Provo UT USA
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21
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Ma C, Wang Y, Wu C, Kang L, Liu C. The compact mitochondrial genome of Zorotypus medoensis provides insights into phylogenetic position of Zoraptera. BMC Genomics 2014; 15:1156. [PMID: 25529234 PMCID: PMC4367826 DOI: 10.1186/1471-2164-15-1156] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 12/12/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Zoraptera, generally regarded as a member of Polyneoptera, represents one of the most enigmatic insect orders. Although phylogenetic analyses based on a wide array of morphological and/or nuclear data have been performed, the position of Zoraptera is still under debate. Mitochondrial genome (mitogenome) information is commonly considered to be preferable to reconstruct phylogenetic relationships, but no efforts have been made to incorporate it in Zorapteran phylogeny. To characterize Zoraptera mitogenome features and provide insights into its phylogenetic placement, here we sequenced, for the first time, one complete mitogenome of Zoraptera and reconstructed the phylogeny of Polyneoptera. RESULTS The mitogenome of Zorotypus medoensis with an A+T content of 72.50% is composed of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a noncoding A+T-rich region. The gene content and arrangement are identical to those considered ancestral for insects. This mitogenome shows a number of very unusual features. First, it is very compact, comprising 14,572 bp, and is the smallest among all known polyneopteran mitogenomes. Second, both noncoding sequences and coding genes exhibit a significant decrease in size compared with those of other polyneopterans. Third, Z. medoensis mitogenome has experienced an accelerated substitution rate. Fourth, truncated secondary structures of tRNA genes occur with loss of dihydrouridine (DHU) arm in trnC, trnR, and trnS(AGN) and loss of TΨC arm in trnH and trnT. The phylogenetic analyses based on the mitogenome sequence information indicate that Zoraptera, represented by Z. medoensis, is recovered as sister to Embioptera. However, both Zoraptera and Embioptera exhibit very long branches in phylogenetic trees. CONCLUSIONS Characterization of Z. medoensis mitogenome contributes to our understanding of the enigmatic Zoraptera. Mitogenome data demonstrate an overall strong resolution of deep-level phylogenies of Polyneoptera but not Insecta. It is preferable to expand taxon sampling of Zoraptera and other poorly represented orders in future to break up long branches.
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Affiliation(s)
- Chuan Ma
- />State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
- />Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yeying Wang
- />State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Chao Wu
- />State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Le Kang
- />State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
- />Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101 China
| | - Chunxiang Liu
- />State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
- />Laboratory of Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
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22
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Zhou Z, Shi F, Zhao L. The first mitochondrial genome for the superfamily Hagloidea and implications for its systematic status in Ensifera. PLoS One 2014; 9:e86027. [PMID: 24465850 PMCID: PMC3897600 DOI: 10.1371/journal.pone.0086027] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Accepted: 12/06/2013] [Indexed: 11/18/2022] Open
Abstract
Hagloidea Handlirsch, 1906 was an ancient group of Ensifera, that was much more diverse in the past extending at least into the Triassic, apparently diminishing in diversity through the Cretaceous, and now only represented by a few extant species. In this paper, we report the complete mitochondrial genome (mitogenome) of Tarragoilus diuturnus Gorochov, 2001, representing the first mitogenome of the superfamily Hagloidea. The size of the entire mitogenome of T. diuturnus is 16144 bp, containing 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region. The order and orientation of the gene arrangement pattern is identical to that of D. yakuba and most ensiferans species. A phylogenomic analysis was carried out based on the concatenated dataset of 13 PCGs and 2 rRNA genes from mitogenome sequences of 15 ensiferan species, comprising four superfamilies Grylloidea, Tettigonioidae, Rhaphidophoroidea and Hagloidea. Both maximum likelihood and Bayesian inference analyses strongly support Hagloidea T. diuturnus and Rhaphidophoroidea Troglophilus neglectus as forming a monophyletic group, sister to the Tettigonioidea. The relationships among four superfamilies of Ensifera were (Grylloidea, (Tettigonioidea, (Hagloidea, Rhaphidophoroidea))).
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Affiliation(s)
- Zhijun Zhou
- College of Life Sciences, Hebei University, Baoding, Hebei Province, China
- * E-mail: (ZJZ); (FMS)
| | - Fuming Shi
- College of Life Sciences, Hebei University, Baoding, Hebei Province, China
- * E-mail: (ZJZ); (FMS)
| | - Ling Zhao
- College of Life Science and Biotechnology, Mianyang Normal University, Mianyang, Sichuan Province, China
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