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Hao C, Liu Y, Wei N, Arken K, Shi C, Yue C. The complete mitochondrial genomes of the Leuciscus baicalensis and Rutilus rutilus: a detailed genomic comparison among closely related species of the Leuciscinae subfamily. Gene 2023:147535. [PMID: 37328078 DOI: 10.1016/j.gene.2023.147535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/04/2023] [Accepted: 05/31/2023] [Indexed: 06/18/2023]
Abstract
Cyprinidae is the largest family in the order of freshwater fish Cypriniformes. Increased subfamily members of Cyprinidae have been suggested to be re-classified for decades. In this study, we sequenced the mitochondrial genomes (mitogenomes) of Leuciscus baicalensis and Rutilus rutilus collected from northwest China and compared with other closely related species to determine their associated family or subfamily. We used Illumina NovaSeq to sequence the entire mitochondrial genomes of Leuciscus baicalensis and Rutilus rutilus and characterized the mitogenomes by the gene structure, gene order, and the secondary structures of the 22 tRNA genes. We compared mitogenome features of Leuciscinae with other subfamilies in Cyprinidae. We used the analytic Bayesian Information and Maximum Likelihood methods to determine phylogenetic trees of 13 PCGs. The mitogenomes of Leuciscus baicalensis and Rutilus rutilus were 16,607 bp and 16,606 bp, respectively. Organization and location of these genes were consistent with already studied Leuciscinae fishes. Synonymous codon usage was conservative in Leuciscinae as compared with other subfamilies in Cyprinidae. Phylogenetic analysis indicated that Leuciscinae was a monophyletic group, and genus Leuciscus was a paraphyletic group. Our approach, for the first time, of studying comparative mitochondrial genomics and phylogenetics together provided a supportive platform to the analysis of population genetics and phylogeny for Leuciscinae. Our results indicated a promising potential of comparative mitochondrial genomics in the manifestation of phylogenetic relationships between fishes, leading us to a suggestion that mitogenomes should be routinely considered in clarifying phylogenetics of family and subfamily members of fish.
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Affiliation(s)
- Cuilan Hao
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China.
| | - Yanjun Liu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Nianwen Wei
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Kadirden Arken
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Caixia Shi
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Cheng Yue
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
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2
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Huang Y, Yang Y, Qi L, Hu H, Rasplus JY, Wang X. Novel Gene Rearrangement Pattern in Pachycrepoideus vindemmiae Mitochondrial Genome: New Gene Order in Pteromalidae (Hymenoptera: Chalcidoidea). Animals (Basel) 2023; 13:1985. [PMID: 37370495 DOI: 10.3390/ani13121985] [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: 04/18/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
The mitochondrial genomes of Muscidifurax similadanacus, M. sinesensilla, Nasonia vitripennis, and Pachycrepoideus vindemmiae were sequenced to better understand the structural evolution of Pteromalidae mitogenomes. These newly sequenced mitogenomes all contained 37 genes. Nucleotide composition was AT-biased and the majority of the protein-coding genes exhibited a negative AT skew. All 13 protein-coding genes (PCGs) initiated with the standard start codon of ATN, excepted for nad1 of N. vitripennis, which started with TTG, and terminated with a typical stop codon TAA/TAG or an incomplete stop codon T. All transfer RNA (tRNA) genes were predicted to fold into the typical clover-leaf secondary structures, except for trnS1, which lacks the DHU arm in all species. In P. vindemmiae, trnR and trnQ lack the DHU arm and TΨC arm, respectively. Although most genes evolved under a strong purifying selection, the Ka/Ks value of the atp8 gene of P. vindemmiae was greater than 1, indicating putative positive selection. A novel transposition of trnR in P. vindemmiae was revealed, which was the first of this kind to be reported in Pteromalidae. Two kinds of datasets (PCG12 and AA) and two inference methods (maximum likelihood and Bayesian inference) were used to reconstruct a phylogenetic hypothesis for the newly sequenced mitogenomes of Pteromalidae and those deposited in GenBank. The topologies obtained recovered the monophyly of the three subfamilies included. Pachyneurinae and Pteromalinae were recovered as sister families, and both appeared sister to Sycophaginae. The pairwise breakpoint distances of mitogenome rearrangements were estimated to infer phylogeny among pteromalid species. The topology obtained was not totally congruent with those reconstructed using the ML and BI methods.
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Affiliation(s)
- Yixin Huang
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
| | - Yuanhan Yang
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China
| | - Liqing Qi
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China
| | - Haoyuan Hu
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China
| | - Jean-Yves Rasplus
- Centre de Biologie pour la Gestion des Populations (CBGP), INRAE, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, 34398 Montpellier, France
| | - Xu Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
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Moreno-Carmona M, Cameron SL, Prada Quiroga CF. How are the mitochondrial genomes reorganized in Hexapoda? Differential evolution and the first report of convergences within Hexapoda. Gene 2021; 791:145719. [PMID: 33991648 DOI: 10.1016/j.gene.2021.145719] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/13/2021] [Accepted: 05/10/2021] [Indexed: 11/28/2022]
Abstract
The evolution of the Hexapoda mitochondrial genome has been the focus of several genetic and evolutionary studies over the last decades. However, they have concentrated on certain taxonomic orders of economic or health importance. The recent increase of mitochondrial genomes sequencing of diverse taxonomic orders generates an important opportunity to clarify the evolution of this group of organisms. However, there is no comparative study that investigates the evolution of the Hexapoda mitochondrial genome. In order to verify the level of rearrangement and the mitochondrial genome evolution, we performed a comparative genomic analysis of the Hexapoda mitochondrial genome available in the NCBI database. Using a combination of bioinformatics methods to carefully examine the mitochondrial gene rearrangements in 1198 Hexapoda species belonging to 32 taxonomic orders, we determined that there is a great variation in the rate of rearrangement by gene and by taxonomic order. A higher rate of genetic reassortment is observed in Phthiraptera, Thysanoptera, Protura, and Hymenoptera; compared to other taxonomic orders. Twenty-four events of convergence in the genetic order between different taxonomic orders were determined, most of them not previously reported; which proves the great evolutionary dynamics within Hexapoda.
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Affiliation(s)
- Manuela Moreno-Carmona
- Grupo de investigación de Biología y ecología de artrópodos, Facultad de Ciencias, Universidad del Tolima, Colombia
| | - Stephen L Cameron
- Department of Entomology, Purdue University, 901 West State Street, West Lafayette, IN 47907, USA
| | - Carlos Fernando Prada Quiroga
- Grupo de investigación de Biología y ecología de artrópodos, Facultad de Ciencias, Universidad del Tolima, Colombia.
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Carapelli A, Bu Y, Chen WJ, Nardi F, Leo C, Frati F, Luan YX. Going Deeper into High and Low Phylogenetic Relationships of Protura. Genes (Basel) 2019; 10:E292. [PMID: 30974866 PMCID: PMC6523364 DOI: 10.3390/genes10040292] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 11/16/2022] Open
Abstract
Proturans are small, wingless, soil-dwelling arthropods, generally associated with the early diversification of Hexapoda. Their bizarre morphology, together with conflicting results of molecular studies, has nevertheless made their classification ambiguous. Furthermore, their limited dispersal capability (due to the primarily absence of wings) and their euedaphic lifestyle have greatly complicated species-level identification. Mitochondrial and nuclear markers have been applied herein to investigate and summarize proturan systematics at different hierarchical levels. Two new mitochondrial genomes are described and included in a phylum-level phylogenetic analysis, but the position of Protura could not be resolved with confidence due to an accelerated rate of substitution and extensive gene rearrangements. Mitochondrial and nuclear loci were also applied in order to revise the intra-class systematics, recovering three proturan orders and most of the families/subfamilies included as monophyletic, with the exception of the subfamily Acerentominae. At the species level, most morphologically described species were confirmed using molecular markers, with some exceptions, and the advantages of including nuclear, as well as mitochondrial, markers and morphology are discussed. At all levels, an enlarged taxon sampling and the integration of data from different sources may be of significant help in solving open questions that still persist on the evolutionary history of Protura.
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Affiliation(s)
- Antonio Carapelli
- Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Yun Bu
- Natural History Research Center, Shanghai Natural History Museum, Shanghai Science & Technology Museum, Shanghai 200041, China.
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Wan-Jun Chen
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Francesco Nardi
- Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Chiara Leo
- Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Francesco Frati
- Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Yun-Xia Luan
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
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Chen L, Chen PY, Xue XF, Hua HQ, Li YX, Zhang F, Wei SJ. Extensive gene rearrangements in the mitochondrial genomes of two egg parasitoids, Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae). Sci Rep 2018; 8:7034. [PMID: 29728615 PMCID: PMC5935716 DOI: 10.1038/s41598-018-25338-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/20/2018] [Indexed: 12/01/2022] Open
Abstract
Animal mitochondrial genomes usually exhibit conserved gene arrangement across major lineages, while those in the Hymenoptera are known to possess frequent rearrangements, as are those of several other orders of insects. Here, we sequenced two complete mitochondrial genomes of Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae). In total, 37 mitochondrial genes were identified in both species. The same gene arrangement pattern was found in the two species, with extensive gene rearrangement compared with the ancestral insect mitochondrial genome. Most tRNA genes and all protein-coding genes were encoded on the minority strand. In total, 15 tRNA genes and seven protein-coding genes were rearranged. The rearrangements of cox1 and nad2 as well as most tRNA genes were novel. Phylogenetic analysis based on nucleotide sequences of protein-coding genes and on gene arrangement patterns produced identical topologies that support the relationship of (Agaonidae + Pteromalidae) + Trichogrammatidae in Chalcidoidea. CREx analysis revealed eight rearrangement operations occurred from presumed ancestral gene order of Chalcidoidea to form the derived gene order of Trichogramma. Our study shows that gene rearrangement information in Chalcidoidea can potentially contribute to the phylogeny of Chalcidoidea when more mitochondrial genome sequences are available.
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Affiliation(s)
- Long Chen
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng-Yan Chen
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.,Department of Entomology, South China Agricultural University, Guangzhou, 510640, China
| | - Xiao-Feng Xue
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hai-Qing Hua
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuan-Xi Li
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Fan Zhang
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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Dong Y, Zhu L, Bai Y, Ou Y, Wang C. Complete mitochondrial genomes of two flat-backed millipedes by next-generation sequencing (Diplopoda, Polydesmida). Zookeys 2017:1-20. [PMID: 28138271 PMCID: PMC5240118 DOI: 10.3897/zookeys.637.9909] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 11/17/2016] [Indexed: 11/30/2022] Open
Abstract
A lack of mitochondrial genome data from myriapods is hampering progress across genetic, systematic, phylogenetic and evolutionary studies. Here, the complete mitochondrial genomes of two millipedes, Asiomorphacoarctata Saussure, 1860 (Diplopoda: Polydesmida: Paradoxosomatidae) and Xystodesmus sp. (Diplopoda: Polydesmida: Xystodesmidae) were assembled with high coverage using Illumina sequencing data. The mitochondrial genomes of the two newly sequenced species are circular molecules of 15,644 bp and 15,791 bp, within which the typical mitochondrial genome complement of 13 protein-coding genes, 22 tRNAs and two ribosomal RNA genes could be identified. The mitochondrial genome of Asiomorphacoarctata is the first complete sequence in the family Paradoxosomatidae (Diplopoda: Polydesmida) and the gene order of the two flat-backed millipedes is novel among known myriapod mitochondrial genomes. Unique translocations have occurred, including inversion of one half of the two genomes with respect to other millipede genomes. Inversion of the entire side of a genome (trnF-nad5-trnH-nad4-nad4L, trnP, nad1-trnL2-trnL1-rrnL-trnV-rrnS, trnQ, trnC and trnY) could constitute a common event in the order Polydesmida. Last, our phylogenetic analyses recovered the monophyletic Progoneata, subphylum Myriapoda and four internal classes.
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Affiliation(s)
- Yan Dong
- College of Biology and Food Engineering, Chuzhou University, Chuzhou 239000, China
| | - Lixin Zhu
- College of Biology and Food Engineering, Chuzhou University, Chuzhou 239000, China
| | - Yu Bai
- College of Biology and Food Engineering, Chuzhou University, Chuzhou 239000, China
| | - Yongyue Ou
- College of Biology and Food Engineering, Chuzhou University, Chuzhou 239000, China
| | - Changbao Wang
- College of Biology and Food Engineering, Chuzhou University, Chuzhou 239000, China
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7
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Zhang L, Sechi P, Yuan M, Jiang J, Dong Y, Qiu J. Fifteen new earthworm mitogenomes shed new light on phylogeny within the Pheretima complex. Sci Rep 2016; 6:20096. [PMID: 26833286 PMCID: PMC4735579 DOI: 10.1038/srep20096] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/17/2015] [Indexed: 01/26/2023] Open
Abstract
The Pheretima complex within the Megascolecidae family is a major earthworm group. Recently, the systematic status of the Pheretima complex based on morphology was challenged by molecular studies. In this study, we carry out the first comparative mitogenomic study in oligochaetes. The mitogenomes of 15 earthworm species were sequenced and compared with other 9 available earthworm mitogenomes, with the main aim to explore their phylogenetic relationships and test different analytical approaches on phylogeny reconstruction. The general earthworm mitogenomic features revealed to be conservative: all genes encoded on the same strand, all the protein coding loci shared the same initiation codon (ATG), and tRNA genes showed conserved structures. The Drawida japonica mitogenome displayed the highest A + T content, reversed AT/GC-skews and the highest genetic diversity. Genetic distances among protein coding genes displayed their maximum and minimum interspecific values in the ATP8 and CO1 genes, respectively. The 22 tRNAs showed variable substitution patterns between the considered earthworm mitogenomes. The inclusion of rRNAs positively increased phylogenetic support. Furthermore, we tested different trimming tools for alignment improvement. Our analyses rejected reciprocal monophyly among Amynthas and Metaphire and indicated that the two genera should be systematically classified into one.
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Affiliation(s)
- Liangliang Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Pierfrancesco Sechi
- Institute of Ecosystem Study (ISE), Italian National Research Council, Sassari, Italy
| | - Minglong Yuan
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Gansu, China
| | - Jibao Jiang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Dong
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiangping Qiu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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Mitochondrial genome evolution and tRNA truncation in Acariformes mites: new evidence from eriophyoid mites. Sci Rep 2016; 6:18920. [PMID: 26732998 PMCID: PMC4702108 DOI: 10.1038/srep18920] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 11/30/2015] [Indexed: 11/08/2022] Open
Abstract
The subclass Acari (mites and ticks) comprises two super-orders: Acariformes and Parasitiformes. Most species of the Parasitiformes known retained the ancestral pattern of mitochondrial (mt) gene arrangement of arthropods, and their mt tRNAs have the typical cloverleaf structure. All of the species of the Acariformes known, however, have rearranged mt genomes and truncated mt tRNAs. We sequenced the mt genomes of two species of Eriophyoidea: Phyllocoptes taishanensis and Epitrimerus sabinae. The mt genomes of P. taishanensis and E. sabinae are 13,475 bp and 13,531 bp, respectively, are circular and contain the 37 genes typical of animals; most mt tRNAs are highly truncated in both mites. On the other hand, these two eriophyoid mites have the least rearranged mt genomes seen in the Acariformes. Comparison between eriophyoid mites and other Aacariformes mites showed that: 1) the most recent common ancestor of Acariformes mites retained the ancestral pattern of mt gene arrangement of arthropods with slight modifications; 2) truncation of tRNAs for cysteine, phenylalanine and histidine occurred once in the most recent common ancestor of Acariformes mites whereas truncation of other tRNAs occurred multiple times; and 3) the placement of eriophyoid mites in the order Trombidiformes needs to be reviewed.
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Ambriz-Morales P, De La Rosa-Reyna XF, Sifuentes-Rincon AM, Parra-Bracamonte GM, Villa-Melchor A, Chassin-Noria O, Arellano-Vera W. The complete mitochondrial genomes of nine white-tailed deer subspecies and their genomic differences. J Mammal 2015. [DOI: 10.1093/jmammal/gyv172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
The white-tailed deer ( Odocoileus virginianus ) is an important, sustainable-use species in Mexico; 14 subspecies are widely distributed throughout the Mexican territory. The criteria for classifying subspecies is based on morphological features throughout their geographical range; however, the complete genetic characterization of Mexican subspecies has not been established. The objective of the present work is to report the mitogenomes of 9 of the 14 white-tailed deer subspecies from Mexico and identify their unique variations. Typical vertebrate mitogenomes structures (i.e., 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes) were observed in the studied subspecies. The greatest numbers of polymorphisms were identified in the D-loop, ND4, ND5, CYTB/COI, ATP6, and COIII genes. Phylogenetic analyses showed that the southern and southeastern subspecies were distinct from the central and northern subspecies; the greatest genetic distances were also observed between these 2 groups. These subspecies-specific variations could be useful for designing a strategy to genetically characterize the studied subspecies.
El venado cola blanca es una de las especies de mayor importancia dentro del aprovechamiento de la fauna silvestre de México, donde se distribuyen de manera natural 14 subespecies. Actualmente, estas subespecies se han clasificado de acuerdo a sus variaciones fenotípicas que presentan a lo largo de su rango de distribución, sin embargo no se ha establecido la caracterización genética completa de las mismas. Es por esto que el objetivo del presente estudio es reportar los mitogenomas de 9 de las 14 subespecies de venado cola blanca, así como identificar las variaciones únicas de cada subespecie. En las 9 subespecies se observó la estructura típica de los mitogenomas de vertebrados (13 genes que codifican para proteínas, 22 ARNt, 2 ARNr). Los genes con mayor polimorfismo fueron D-loop, ND4, ND5, CYTB/COI, ATP6 y COIII. El análisis filogenético mostró la separación de las subespecies del sur y sureste de las subespecies del centro y norte del país, a su vez las distancias genéticas entre estos dos grupos fueron las más altas. Estas variaciones subespecie-específicas podrían ser útiles para diseñar una estrategia para caracterizar genéticamente las subespecies estudiadas.
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Katz AD, Giordano R, Soto-Adames FN. Operational criteria for cryptic species delimitation when evidence is limited, as exemplified by North AmericanEntomobrya(Collembola: Entomobryidae). Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12220] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aron D. Katz
- Department of Entomology; University of Illinois; 320 Morrill Hall 505 South Goodwin Avenue Urbana IL 61801 USA
- Illinois Natural History Survey; University of Illinois; 1816 South Oak Street Champaign IL 61820 USA
| | - Rosanna Giordano
- Department of Entomology; University of Illinois; 320 Morrill Hall 505 South Goodwin Avenue Urbana IL 61801 USA
| | - Felipe N. Soto-Adames
- Illinois Natural History Survey; University of Illinois; 1816 South Oak Street Champaign IL 61820 USA
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Ma Y, He K, Yu P, Yu D, Cheng X, Zhang J. The complete mitochondrial genomes of three bristletails (Insecta: Archaeognatha): the paraphyly of Machilidae and insights into archaeognathan phylogeny. PLoS One 2015; 10:e0117669. [PMID: 25635855 PMCID: PMC4323385 DOI: 10.1371/journal.pone.0117669] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 12/29/2014] [Indexed: 11/18/2022] Open
Abstract
The order Archaeognatha was an ancient group of Hexapoda and was considered as the most primitive of living insects. Two extant families (Meinertellidae and Machilidae) consisted of approximately 500 species. This study determined 3 complete mitochondrial genomes and 2 nearly complete mitochondrial genome sequences of the bristletail. The size of the 5 mitochondrial genome sequences of bristletail were relatively modest, containing 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region. The gene orders were identical to that of Drosophila yakuba and most bristletail species suggesting a conserved genome evolution within the Archaeognatha. In order to estimate archaeognathan evolutionary relationships, phylogenetic analyses were conducted using concatenated nucleotide sequences of 13 protein-coding genes, with four different computational algorithms (NJ, MP, ML and BI). Based on the results, the monophyly of the family Machilidae was challenged by both datasets (W12 and G12 datasets). The relationships among archaeognathan subfamilies seemed to be tangled and the subfamily Machilinae was also believed to be a paraphyletic group in our study.
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Affiliation(s)
- Yue Ma
- Institute of Ecology, Zhejiang Normal University, Jinhua, Zhejiang Province, China
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Kun He
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Panpan Yu
- Institute of Ecology, Zhejiang Normal University, Jinhua, Zhejiang Province, China
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Danna Yu
- Institute of Ecology, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Xuefang Cheng
- Institute of Ecology, Zhejiang Normal University, Jinhua, Zhejiang Province, China
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Jiayong Zhang
- Institute of Ecology, Zhejiang Normal University, Jinhua, Zhejiang Province, China
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
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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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Ye F, King SD, Cone DK, You P. The mitochondrial genome of Paragyrodactylus variegatus (Platyhelminthes: Monogenea): differences in major non-coding region and gene order compared to Gyrodactylus. Parasit Vectors 2014; 7:377. [PMID: 25130627 PMCID: PMC4150975 DOI: 10.1186/1756-3305-7-377] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 08/04/2014] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Paragyrodactylus Gvosdev and Martechov, 1953, a viviparous genus of ectoparasite within the Gyrodactylidae, contains three nominal species all of which infect Asian river loaches. The group is suspected to be a basal lineage within Gyrodactylus Nordmann, 1832 sensu lato although this remains unclear. Further molecular study, beyond characterization of the standard Internal Transcribed Spacer region, is needed to clarify the evolutionary relationships within the family and the placement of this genus. METHODS The mitochondrial genome of Paragyrodactylus variegatus You, King, Ye and Cone, 2014 was amplified in six parts from a single worm, sequenced using primer walking, annotated and analyzed using bioinformatic tools. RESULTS The mitochondrial genome of P. variegatus is 14,517 bp, containing 12 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a major non-coding region (NCR). The overall A + T content of the mitochondrial genome is 76.3%, which is higher than all reported mitochondrial genomes of monogeneans. All of the 22 tRNAs have the typical cloverleaf secondary structure, except tRNACys, tRNASer1 and tRNASer2 that lack the dihydrouridine (DHU) arm. There are six domains (domain III is absent) and three domains in the inferred secondary structures of the large ribosomal subunit (rrnL) and small ribosomal subunit (rrnS), respectively. The NCR includes six 40 bp tandem repeat units and has the double identical poly-T stretches, stem-loop structure and some surrounding structure elements. The gene order (tRNAGln, tRNAMet and NCR) differs in arrangement compared to the mitochondrial genomes reported from Gyrodactylus spp. CONCLUSION The Duplication and Random Loss Model and Recombination Model together are the most plausible explanations for the variation in gene order. Both morphological characters and characteristics of the mitochondrial genome support Paragyrodactylus as a distinct genus from Gyrodactylus. Considering their specific distribution and known hosts, we believe that Paragyrodactylus is a relict freshwater lineage of viviparous monogenean isolated in the high plateaus of central Asia on closely related river loaches.
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Affiliation(s)
- Fei Ye
- />Co-Innovation Center for Qinba regions’ sustainable development, College of Life Science, Shaanxi Normal University, Xi’an, 710062 China
| | - Stanley D King
- />Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4 J1 Canada
| | - David K Cone
- />Department of Biology, Saint Mary’s University, Halifax, Nova Scotia B3H 3C3 Canada
| | - Ping You
- />Co-Innovation Center for Qinba regions’ sustainable development, College of Life Science, Shaanxi Normal University, Xi’an, 710062 China
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14
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Wei SJ, Li Q, van Achterberg K, Chen XX. Two mitochondrial genomes from the families Bethylidae and Mutillidae: Independent rearrangement of protein-coding genes and higher-level phylogeny of the Hymenoptera. Mol Phylogenet Evol 2014; 77:1-10. [DOI: 10.1016/j.ympev.2014.03.023] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 02/27/2014] [Accepted: 03/24/2014] [Indexed: 10/25/2022]
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15
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Bu Y, Potapov MB, Yin WY. Systematic and biogeographical study of Protura (Hexapoda) in Russian Far East: new data on high endemism of the group. Zookeys 2014:19-57. [PMID: 25061395 PMCID: PMC4106100 DOI: 10.3897/zookeys.424.7388] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 06/04/2014] [Indexed: 11/22/2022] Open
Abstract
Proturan collections from Magadan Oblast, Khabarovsk Krai, Primorsky Krai, and Sakhalin Oblast are reported here. Twenty-five species are found of which 13 species are new records for Russian Far East which enrich the knowledge of Protura known for this area. Three new species Baculentulus krabbensissp. n., Fjellbergella lazovskiensissp. n. and Yichunentulus alpatovisp. n. are illustrated and described. The new materials of Imadateiella sharovi (Martynova, 1977) are studied and described in details. Two new combinations, Yichunentulus borealis (Nakamura, 2004), comb. n. and Fjellbergella jilinensis (Wu & Yin, 2007), comb. n. are proposed as a result of morphological examination. Keys to species of the genera Fjellbergella and Yichunentulus are given. An annotated list of all species of Protura from Russian Far East is provided and discussed. Widely distributed species were not recorded in this area. This may be because of the high sensitivity of Protura to anthropogenic impact and low dispersal ability of the group.
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Affiliation(s)
- Yun Bu
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Mikhail B Potapov
- Moscow State Pedagogical University, Kibalchich str., 6, korp. 5, Moscow, 129278 Russia
| | - Wen Ying Yin
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
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Li T, Hua J, Wright AM, Cui Y, Xie Q, Bu W, Hillis DM. Long-branch attraction and the phylogeny of true water bugs (Hemiptera: Nepomorpha) as estimated from mitochondrial genomes. BMC Evol Biol 2014; 14:99. [PMID: 24884699 PMCID: PMC4101842 DOI: 10.1186/1471-2148-14-99] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 04/29/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most previous studies of morphological and molecular data have consistently supported the monophyly of the true water bugs (Hemiptera: Nepomorpha). An exception is a recent study by Hua et al. (BMC Evol Biol 9: 134, 2009) based on nine nepomorphan mitochondrial genomes. In the analysis of Hua et al. (BMC Evol Biol 9: 134, 2009), the water bugs in the group Pleoidea formed the sister group to a clade that consisted of Nepomorpha (the remaining true water bugs) + Leptopodomorpha (shore bugs) + Cimicomorpha (assassin bugs and relatives) + Pentatomomorpha (stink bugs and relatives), thereby suggesting that fully aquatic hemipterans evolved independently at least twice. Based on these results, Hua et al. (BMC Evol Biol 9: 134, 2009) elevated the Pleoidea to a new infraorder, the Plemorpha. RESULTS Our reanalysis suggests that the lack of support for the monophyly of the true water bugs (including Pleoidea) by Hua et al. (BMC Evol Biol 9: 134, 2009) likely resulted from inadequate taxon sampling. In particular, long-branch attraction (LBA) between the distant outgroup taxa and Pleoidea, as well as LBA among taxa in the ingroup, made Nepomorpha appear to be polyphyletic. We used three complementary strategies to test and alleviate the effects of LBA: (1) the removal of distant outgroups from the analysis; (2) the addition of closely related outgroups; and (3) the addition of a mitochondrial genome from a second family of Pleoidea. We also performed likelihood-ratio tests to examine the support for monophyly of Nepomorpha with different combinations of taxa included in the analysis. Furthermore, we found that specimens of Helotrephes sp. were misidentified as Paraplea frontalis (Fieber, 1844) by Hua et al. (BMC Evol Biol 9: 134, 2009). CONCLUSIONS All analyses that included the addition of more taxa significantly and consistently supported the placement of Pleoidea within the Nepomorpha (i.e., supported the monophyly of the traditional true water bugs). Our analyses further support a close relationship between Notonectoidea and Pleoidea within Nepomorpha, and the superfamilies Nepoidea, Ochteroidea, Naucoroidea, and Pleoidea are resolved as monophyletic in all trees with strong support. Our results also confirmed that monophyly of Nepomorpha clearly is not refuted by the mitochondrial genome data.
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Affiliation(s)
- Teng Li
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Jimeng Hua
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - April M Wright
- Department of Integrative Biology, University of Texas at Austin, Austin TX 78712, USA
| | - Ying Cui
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Qiang Xie
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - David M Hillis
- Department of Integrative Biology, University of Texas at Austin, Austin TX 78712, USA
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17
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Wu QL, Li Q, Gu Y, Shi BC, van Achterberg C, Wei SJ, Chen XX. The complete mitochondrial genome of Taeniogonalos taihorina (Bischoff) (Hymenoptera: Trigonalyidae) reveals a novel gene rearrangement pattern in the Hymenoptera. Gene 2014; 543:76-84. [PMID: 24709108 DOI: 10.1016/j.gene.2014.04.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 11/14/2013] [Accepted: 04/01/2014] [Indexed: 10/25/2022]
Abstract
The family Trigonalyidae is considered to be one of the most basal lineages in the suborder Apocrita of Hymenoptera. Here, we determine the first complete mitochondrial genome of the Trigonalyidae, from the species Taeniogonalos taihorina (Bischoff, 1914). This mitochondrial genome is 15,927bp long, with a high A+T-content of 84.60%. It contains all of the 37 typical animal mitochondrial genes and an A+T-rich region. The orders and directions of all genes are different from those of previously reported hymenopteran mitochondrial genomes. Eight tRNA genes, three protein-coding genes and the A+T-rich region were rearranged, with the dominant gene rearrangement events being translocation and local inversion. The arrangements of three tRNA clusters, trnY-trnM-trnI-trnQ, trnW-trnL2-trnC, and trnH-trnA-trnR-trnN-trnS-trnE-trnF, and the position of the cox1 gene, are novel to the Hymenoptera, even the insects. Six long intergenic spacers are present in the genome. The secondary structures of the RNA genes are normal, except for trnS2, in which the D-stem pairing is absent.
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Affiliation(s)
- Qiu-Ling Wu
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China
| | - Qian Li
- Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yun Gu
- College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China
| | - Bao-Cai Shi
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Cees van Achterberg
- Terrestrial Zoology, Naturalis Biodiversity Center, 2300 RA Leiden, Netherlands
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Xue-Xin Chen
- Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.
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Resch MC, Shrubovych J, Bartel D, Szucsich NU, Timelthaler G, Bu Y, Walzl M, Pass G. Where taxonomy based on subtle morphological differences is perfectly mirrored by huge genetic distances: DNA barcoding in Protura (Hexapoda). PLoS One 2014; 9:e90653. [PMID: 24609003 PMCID: PMC3946556 DOI: 10.1371/journal.pone.0090653] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 02/04/2014] [Indexed: 11/18/2022] Open
Abstract
Background Protura is a group of tiny, primarily wingless hexapods living in soil habitats. Presently about 800 valid species are known. Diagnostic characters are very inconspicuous and difficult to recognize. Therefore taxonomic work constitutes an extraordinary challenge which requires special skills and experience. Aim of the present pilot project was to examine if DNA barcoding can be a useful additional approach for delimiting and determining proturan species. Methodology and Principal Findings The study was performed on 103 proturan specimens, collected primarily in Austria, with additional samples from China and Japan. The animals were examined with two markers, the DNA barcoding region of the mitochondrial COI gene and a fragment of the nuclear 28S rDNA (Divergent Domain 2 and 3). Due to the minuteness of Protura a modified non-destructive DNA-extraction method was used which enables subsequent species determination. Both markers separated the examined proturans into highly congruent well supported clusters. Species determination was performed without knowledge of the results of the molecular analyses. The investigated specimens comprise a total of 16 species belonging to 8 genera. Remarkably, morphological determination in all species exactly mirrors molecular clusters. The investigation revealed unusually huge genetic COI distances among the investigated proturans, both maximal intraspecific distances (0–21.3%), as well as maximal congeneric interspecifical distances (up to 44.7%). Conclusions The study clearly demonstrates that the tricky morphological taxonomy in Protura has a solid biological background and that accurate species delimitation is possible using both markers, COI and 28S rDNA. The fact that both molecular and morphological analyses can be performed on the same individual will be of great importance for the description of new species and offers a valuable new tool for biological and ecological studies, in which proturans have generally remained undetermined at species level.
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Affiliation(s)
- Monika Carol Resch
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | - Julia Shrubovych
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Krakow, Poland
| | - Daniela Bartel
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | - Nikolaus U. Szucsich
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
- * E-mail:
| | - Gerald Timelthaler
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | - Yun Bu
- Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Manfred Walzl
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | - Günther Pass
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
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Chen WJ, Koch M, Mallatt JM, Luan YX. Comparative analysis of mitochondrial genomes in Diplura (hexapoda, arthropoda): taxon sampling is crucial for phylogenetic inferences. Genome Biol Evol 2014; 6:105-20. [PMID: 24391151 PMCID: PMC3914688 DOI: 10.1093/gbe/evt207] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2013] [Indexed: 11/14/2022] Open
Abstract
Two-pronged bristletails (Diplura) are traditionally classified into three major superfamilies: Campodeoidea, Projapygoidea, and Japygoidea. The interrelationships of these three superfamilies and the monophyly of Diplura have been much debated. Few previous studies included Projapygoidea in their phylogenetic considerations, and its position within Diplura still is a puzzle from both morphological and molecular points of view. Until now, no mitochondrial genome has been sequenced for any projapygoid species. To fill in this gap, we determined and annotated the complete mitochondrial genome of Octostigma sinensis (Octostigmatidae, Projapygoidea), and of three more dipluran species, one each from the Campodeidae, Parajapygidae, and Japygidae. All four newly sequenced dipluran mtDNAs encode the same set of genes in the same gene order as shared by most crustaceans and hexapods. Secondary structure truncations have occurred in trnR, trnC, trnS1, and trnS2, and the reduction of transfer RNA D-arms was found to be taxonomically correlated, with Campodeoidea having experienced the most reduction. Partitioned phylogenetic analyses, based on both amino acids and nucleotides of the protein-coding genes plus the ribosomal RNA genes, retrieve significant support for a monophyletic Diplura within Pancrustacea, with Projapygoidea more closely related to Campodeoidea than to Japygoidea. Another key finding is that monophyly of Diplura cannot be recovered unless Projapygoidea is included in the phylogenetic analyses; this explains the dipluran polyphyly found by past mitogenomic studies. Including Projapygoidea increased the sampling density within Diplura and probably helped by breaking up a long-branch-attraction artifact. This finding provides an example of how proper sampling is significant for phylogenetic inference.
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Affiliation(s)
- Wan-Jun Chen
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Markus Koch
- Biocentre Grindel and Zoological Museum, University of Hamburg, Germany
| | - Jon M. Mallatt
- School of Biological Sciences, Washington State University
| | - Yun-Xia Luan
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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Simon S, Hadrys H. A comparative analysis of complete mitochondrial genomes among Hexapoda. Mol Phylogenet Evol 2013; 69:393-403. [DOI: 10.1016/j.ympev.2013.03.033] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 02/13/2013] [Accepted: 03/05/2013] [Indexed: 10/27/2022]
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21
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Brewer MS, Swafford L, Spruill CL, Bond JE. Arthropod phylogenetics in light of three novel millipede (myriapoda: diplopoda) mitochondrial genomes with comments on the appropriateness of mitochondrial genome sequence data for inferring deep level relationships. PLoS One 2013; 8:e68005. [PMID: 23869209 PMCID: PMC3712015 DOI: 10.1371/journal.pone.0068005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 05/27/2013] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Arthropods are the most diverse group of eukaryotic organisms, but their phylogenetic relationships are poorly understood. Herein, we describe three mitochondrial genomes representing orders of millipedes for which complete genomes had not been characterized. Newly sequenced genomes are combined with existing data to characterize the protein coding regions of myriapods and to attempt to reconstruct the evolutionary relationships within the Myriapoda and Arthropoda. RESULTS The newly sequenced genomes are similar to previously characterized millipede sequences in terms of synteny and length. Unique translocations occurred within the newly sequenced taxa, including one half of the Appalachioria falcifera genome, which is inverted with respect to other millipede genomes. Across myriapods, amino acid conservation levels are highly dependent on the gene region. Additionally, individual loci varied in the level of amino acid conservation. Overall, most gene regions showed low levels of conservation at many sites. Attempts to reconstruct the evolutionary relationships suffered from questionable relationships and low support values. Analyses of phylogenetic informativeness show the lack of signal deep in the trees (i.e., genes evolve too quickly). As a result, the myriapod tree resembles previously published results but lacks convincing support, and, within the arthropod tree, well established groups were recovered as polyphyletic. CONCLUSIONS The novel genome sequences described herein provide useful genomic information concerning millipede groups that had not been investigated. Taken together with existing sequences, the variety of compositions and evolution of myriapod mitochondrial genomes are shown to be more complex than previously thought. Unfortunately, the use of mitochondrial protein-coding regions in deep arthropod phylogenetics appears problematic, a result consistent with previously published studies. Lack of phylogenetic signal renders the resulting tree topologies as suspect. As such, these data are likely inappropriate for investigating such ancient relationships.
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Affiliation(s)
- Michael S Brewer
- Department of Biology, East Carolina University, Greenville, North Carolina, USA.
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Xia X. DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution. Mol Biol Evol 2013; 30:1720-8. [PMID: 23564938 PMCID: PMC3684854 DOI: 10.1093/molbev/mst064] [Citation(s) in RCA: 739] [Impact Index Per Article: 67.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Since its first release in 2001 as mainly a software package for phylogenetic analysis, data analysis for molecular biology and evolution (DAMBE) has gained many new functions that may be classified into six categories: 1) sequence retrieval, editing, manipulation, and conversion among more than 20 standard sequence formats including MEGA, NEXUS, PHYLIP, GenBank, and the new NeXML format for interoperability, 2) motif characterization and discovery functions such as position weight matrix and Gibbs sampler, 3) descriptive genomic analysis tools with improved versions of codon adaptation index, effective number of codons, protein isoelectric point profiling, RNA and protein secondary structure prediction and calculation of minimum folding energy, and genomic skew plots with optimized window size, 4) molecular phylogenetics including sequence alignment, testing substitution saturation, distance-based, maximum parsimony, and maximum-likelihood methods for tree reconstructions, testing the molecular clock hypothesis with either a phylogeny or with relative-rate tests, dating gene duplication and speciation events, choosing the best-fit substitution models, and estimating rate heterogeneity over sites, 5) phylogeny-based comparative methods for continuous and discrete variables, and 6) graphic functions including secondary structure display, optimized skew plot, hydrophobicity plot, and many other plots of amino acid properties along a protein sequence, tree display and drawing by dragging nodes to each other, and visual searching of the maximum parsimony tree. DAMBE features a graphic, user-friendly, and intuitive interface and is freely available from http://dambe.bio.uottawa.ca (last accessed April 16, 2013).
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Affiliation(s)
- Xuhua Xia
- Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Ontario, Canada
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Fanciulli PP, Gottardo M, Dallai R. The spermatogenesis and oogenesis of the springtail Podura aquatica Linné, 1758 (Hexapoda: Collembola). Tissue Cell 2013; 45:211-8. [PMID: 23515073 DOI: 10.1016/j.tice.2013.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 02/13/2013] [Accepted: 02/13/2013] [Indexed: 10/27/2022]
Abstract
Podura aquatica is a springtail of uncertain systematic position. Our study dealing with the ultrastructure of the spermatogenesis and oogenesis of this species is a contribution to a better knowledge of both the reproduction and the systematics of the taxon. In the male, the spermatogenesis proceeds in a similar way to that of other Collembola. Primary spermatocytes do not show synaptonemal complexes which, instead, are found in primary oocytes. Thus a genomic recombination seems to be present only in females, as it occurs in other springtails. Degeneration of secondary spermatocytes, as reported in some families of the Symphypleona, was not observed in P. aquatica. At the end of spermiogenesis, a rolled up sperm cell provided with an anterior long appendage adhering to the acrosome is produced. In the female, the oogenesis also proceeds in a conventional way with the production of eggs rich in yolk. A branched spermatheca is present at the end of the common oviduct, close to the genital opening. It contains many sperm in its lumen. Contrary to the globular appearance of sperm cells in the male genital ducts, in the spermatheca they are straight, elongated, and lack the long anterior appendage. P. aquatica shows a spermatogenesis, sperm structure, and oogenesis similar to those of other Collembola. In agreement with the results of recent phylogenetic studies, we confirm that P. aquatica is a member of Poduridae, and it does not belong to a group close to the Symphypleona.
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