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Yan Z, Ye G, Werren JH. Evolutionary Rate Correlation between Mitochondrial-Encoded and Mitochondria-Associated Nuclear-Encoded Proteins in Insects. Mol Biol Evol 2019; 36:1022-1036. [PMID: 30785203 DOI: 10.1093/molbev/msz036] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The mitochondrion is a pivotal organelle for energy production, and includes components encoded by both the mitochondrial and nuclear genomes. Functional and evolutionary interactions are expected between the nuclear- and mitochondrial-encoded components. The topic is of broad interest in biology, with implications to genetics, evolution, and medicine. Here, we compare the evolutionary rates of mitochondrial proteins and ribosomal RNAs to rates of mitochondria-associated nuclear-encoded proteins, across the major orders of holometabolous insects. There are significant evolutionary rate correlations (ERCs) between mitochondrial-encoded and mitochondria-associated nuclear-encoded proteins, which are likely driven by different rates of mitochondrial sequence evolution and correlated changes in the interacting nuclear-encoded proteins. The pattern holds after correction for phylogenetic relationships and considering protein conservation levels. Correlations are stronger for both nuclear-encoded OXPHOS proteins that are in contact with mitochondrial OXPHOS proteins and for nuclear-encoded mitochondrial ribosomal amino acids directly contacting the mitochondrial rRNAs. We find that ERC between mitochondrial- and nuclear-encoded proteins is a strong predictor of nuclear-encoded proteins known to interact with mitochondria, and ERC shows promise for identifying new candidate proteins with mitochondrial function. Twenty-three additional candidate nuclear-encoded proteins warrant further study for mitochondrial function based on this approach, including proteins in the minichromosome maintenance helicase complex.
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Affiliation(s)
- Zhichao Yan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.,Department of Biology, University of Rochester, Rochester, NY
| | - Gongyin Ye
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY
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52
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Cao JJ, Wang Y, Huang YR, Li WH. Mitochondrial genomes of the stoneflies Mesonemourametafiligera and Mesonemouratritaenia (Plecoptera, Nemouridae), with a phylogenetic analysis of Nemouroidea. Zookeys 2019; 835:43-63. [PMID: 31043849 PMCID: PMC6477857 DOI: 10.3897/zookeys.835.32470] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/21/2019] [Indexed: 11/12/2022] Open
Abstract
In this study, two new mitochondrial genomes (mitogenomes) of Mesonemourametafiligera and Mesonemouratritaenia from the family Nemouridae (Insecta: Plecoptera) were sequenced. The Mesonemourametafiligera mitogenome was a 15,739 bp circular DNA molecule, which was smaller than that of M.tritaenia (15,778 bp) due to differences in the size of the A+T-rich region. Results show that gene content, gene arrangement, base composition, and codon usage were highly conserved in two species. Ka/Ks ratios analyses of protein-coding genes revealed that the highest and lowest rates were found in ND6 and COI and that all these genes were evolving under purifying selection. All tRNA genes in nemourid mitogenomes had a typical cloverleaf secondary structure, except for tRNASer(AGN) which appeared to lack the dihydrouridine arm. The multiple alignments of nemourid lrRNA and srRNA genes showed that sequences of three species were highly conserved. All the A+T-rich region included tandem repeats regions and stem-loop structures. The phylogenetic analyses using Bayesian inference (BI) and maximum likelihood methods (ML) generated identical results. Amphinemurinae and Nemourinae were sister-groups and the family Nemouridae was placed as sister to Capniidae and Taeniopterygidae.
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Affiliation(s)
- Jin-Jun Cao
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China Henan Institute of Science and Technology Xinxiang China.,Postdoctoral Research Base, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China Henan Institute of Science and Technology Xinxiang China
| | - Ying Wang
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China Henan Institute of Science and Technology Xinxiang China.,Postdoctoral Research Base, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China Henan Institute of Science and Technology Xinxiang China
| | - Yao-Rui Huang
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China Henan Institute of Science and Technology Xinxiang China
| | - Wei-Hai Li
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China Henan Institute of Science and Technology Xinxiang China
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53
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Arias-Robledo G, Stark T, Wall RL, Stevens JR. The toad fly Lucilia bufonivora: its evolutionary status and molecular identification. MEDICAL AND VETERINARY ENTOMOLOGY 2019; 33:131-139. [PMID: 30091469 DOI: 10.1111/mve.12328] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 06/07/2018] [Accepted: 06/19/2018] [Indexed: 06/08/2023]
Abstract
The blow fly genus Lucilia is composed largely of saprophages and facultative myasis agents, including the economically important species Lucilia cuprina (Wiedemann) (Diptera: Calliphoridae) and Lucilia sericata (Meigen). Only one species is generally recognized as an obligate agent of myiasis, Lucilia bufonivora Moniez, and this is an obligate parasite of toads. Lucilia silvarum (Meigen), a sister species, behaves mainly as a carrion breeder; however, it has also been reported as a facultative parasite of amphibians. Morphologically, these species are almost identical, and historically this has led to misidentification, taxonomic ambiguity and a paucity of studies of L. bufonivora. In this study, dipterous larvae were analysed from toad myiasis cases from the U.K., The Netherlands and Switzerland, together with adult specimens of fly species implicated in amphibian parasitism: L. bufonivora, L. silvarum and Lucilia elongata Shannon (from North America). Partial sequences of two genes, cox1 and ef1α, were amplified. Seven additional blow fly species were analysed as outgroups. Bayesian inference trees of cox1, ef1α and a combined-gene dataset were constructed. All larvae isolated from toads were identified as L. bufonivora and no specimens of L. silvarum were implicated in amphibian myiasis. This study confirms L. silvarum and L. bufonivora as distinct sister species and provides unambiguous molecular identification of L. bufonivora.
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Affiliation(s)
- G Arias-Robledo
- School of Biological Sciences, University of Bristol, Bristol, U.K
- Department of Biosciences, University of Exeter, Exeter, U.K
| | - T Stark
- Reptile, Amphibian and Fish Conservation the Netherlands (RAVON), Nijmegen, The Netherlands
| | - R L Wall
- School of Biological Sciences, University of Bristol, Bristol, U.K
| | - J R Stevens
- Department of Biosciences, University of Exeter, Exeter, U.K
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54
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Kumar V, Tyagi K, Kundu S, Chakraborty R, Singha D, Chandra K. The first complete mitochondrial genome of marigold pest thrips, Neohydatothrips samayunkur (Sericothripinae) and comparative analysis. Sci Rep 2019; 9:191. [PMID: 30655597 PMCID: PMC6336932 DOI: 10.1038/s41598-018-37889-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 12/10/2018] [Indexed: 11/16/2022] Open
Abstract
Complete mitogenomes from the order Thysanoptera are limited to representatives of the subfamily Thripinae. Therefore, in the present study, we sequenced the mitochondrial genome of Neohydatothrips samayunkur (15,295 bp), a member of subfamily Sericothripinae. The genome possesses the canonical 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs) as well as two putative control regions (CRs). The majority strand was 77.42% A + T content, and 22.58% G + C with weakly positive AT skew (0.04) and negative GC skew (-0.03). The majority of PCGs start with ATN codons as observed in other insect mitochondrial genomes. The GCG codon (Alanine) was not used in N. samayunkur. Most tRNAs have the typical cloverleaf secondary structure, however the DHU stem and loop were absent in trnV and trnS1, while the TΨC loop was absent in trnR and trnT. The two putative control regions (CR1 and CR2) show 99% sequence similarity indicated a possible duplication, and shared 57 bp repeats were identified. N. samayunkur showed extensive gene rearrangements, with 11 PCGs, 22 tRNAs, and two rRNAs translocated when compared to the ancestral insect. The gene trnL2 was separated from the 'trnL2-cox2' gene block, which is a conserved, ancestral gene order found in all previously sequenced thrips mitogenomes. Both maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees resulted in similar topologies. The phylogenetic position of N. samayunkur indicates that subfamily Sericothripinae is sister to subfamily Thripinae. More molecular data from different taxonomic groups is needed to understand thrips phylogeny and evolution.
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Affiliation(s)
- Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M- Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M- Block, New Alipore, Kolkata, 700 053, West Bengal, India.
| | - Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M- Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Rajasree Chakraborty
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M- Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Devkant Singha
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M- Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M- Block, New Alipore, Kolkata, 700 053, West Bengal, India
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55
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Zhu G, Xu H, Tang W, Yang S, Shi Q, Cheng Y, Wang Q, He T. The complete mitochondrial genome and phylogenetic analysis of Rhabdophis adleri (Squamata: Colubridae). MITOCHONDRIAL DNA PART B-RESOURCES 2019. [DOI: 10.1080/23802359.2018.1548916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Guangxiang Zhu
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Huaming Xu
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Wenjiao Tang
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Shijun Yang
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Qian Shi
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Yuqi Cheng
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Qin Wang
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Tao He
- College of Life Science, Sichuan Agricultural University, Ya'an, China
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56
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Wang G, Huang M. Characterization of the complete mitochondrial genome of Simulium (Byssodon) maculatum (Diptera: Simuliidae) and its phylogenetic implications. Int J Biol Macromol 2019; 121:152-160. [PMID: 30287375 DOI: 10.1016/j.ijbiomac.2018.09.205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/27/2018] [Accepted: 09/27/2018] [Indexed: 10/28/2022]
Abstract
The mitochondrial (mt) genome of the black fly Simulium (Byssodon) maculatum, a pest of great importance for both humans and livestock, is sequenced and annotated for the first time. The genome structure, gene order and codon usage are typical among Diptera mt genomes. The mt genome is circular and 15,799 bp in length with 13 protein coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a control region (CR), and with weakly positive AT-skew (0.02) and negative GC-skew (-0.12). Phylogenetic relationships of 16 species representing five families of Culicomorpha and two outgroups, based on mt genome data, were analyzed using both Maximum Likelihood and Bayesian methods. The monophyly of Culicomorpha is well supported, while Chironomoidea is indicated as a paraphyletic group. The well supported monophyletic Simuliidae is the sister group to Culicidae.
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Affiliation(s)
- Gang Wang
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Min Huang
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi 712100, China.
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57
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Su T, He B, Li K, Liang A. Comparative analysis of the mitochondrial genomes of oriental spittlebug trible Cosmoscartini: insights into the relationships among closely related taxa. BMC Genomics 2018; 19:961. [PMID: 30587118 PMCID: PMC6307326 DOI: 10.1186/s12864-018-5365-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 12/12/2018] [Indexed: 11/29/2022] Open
Abstract
Background Cosmoscartini (Hemiptera: Cercopoidea: Cercopidae) is a large and brightly colored Old World tropical tribe, currently containing over 310 phytophagous species (including some economically important pests of eucalyptus in China) in approximately 17 genera. However, very limited information of Cosmoscartini is available except for some scattered taxonomic studies. Even less is known about its phylogenetic relationship, especially among closely related genera or species. In this study, the detailed comparative genomic and phylogenetic analyses were performed on nine newly sequenced mitochondrial genomes (mitogenomes) of Cosmoscartini, with the purpose of exploring the taxonomic status of the previously defined genus Okiscarta and some closely related species within the genus Cosmoscarta. Results Mitogenomes of Cosmoscartini display similar genomic characters in terms of gene arrangement, nucleotide composition, codon usage and overlapping regions. However, there are also many differences in intergenic spacers, mismatches of tRNAs, and the control region. Additionally, the secondary structures of rRNAs within Cercopidae are inferred for the first time. Based on comparative genomic (especially for the substitution pattern of tRNA secondary structure) and phylogenetic analyses, the representative species of Okiscarta uchidae possesses similar structures with other Cosmoscarta species and is placed consistently in Cosmoscarta. Although Cosmoscarta bimacula is difficult to be distinguished from Cosmoscarta bispecularis by traditional morphological methods, evidence from mitogenomes highly support the relationships of (C. bimacula + Cosmoscarta rubroscutellata) + (C. bispecularis + Cosmoscarta sp.). Conclusions This study presents mitogenomes of nine Cosmoscartini species and represents the first detailed comparative genomic and phylogenetic analyses within Cercopidae. It is indicated that knowledge of mitogenomes can be effectively used to resolve phylogenetic relationships at low taxonomic levels. Sequencing more mitogenomes at various taxonomic levels will also improve our understanding of mitogenomic evolution and phylogeny in Cercopidae. Electronic supplementary material The online version of this article (10.1186/s12864-018-5365-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tianjuan Su
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bo He
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Kui Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Aiping Liang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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58
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Su T, Liang A. Comparative analysis of seven mitochondrial genomes of Phymatostetha (Hemiptera: Cercopidae) and phylogenetic implications. Int J Biol Macromol 2018; 125:1112-1117. [PMID: 30578900 DOI: 10.1016/j.ijbiomac.2018.12.174] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/18/2018] [Accepted: 12/19/2018] [Indexed: 11/25/2022]
Abstract
In this study, we present seven mitochondrial genomes (mitogenomes) of Phymatostetha. Each mitogenome contains the entire set of 37 genes, which arranged in the same order as the putative ancestral pattern of insects. The nucleotide composition of Phymatostetha mitogenomes is biased toward A/T, with rRNAs and PCG12 (i.e. the first and second codon positions of PCGs) exhibit the highest and lowest A + T content, respectively. Relative synonymous codon usage of PCGs also show that degenerate codons are biased to use more A/T than G/C. All tRNAs exhibit typical clover-leaf structure, with the exception of trnS1. Additionally, unpaired nucleotides are detected in trnS1 anticodon stem and trnR acceptor stem. Phylogenetic relationships, based on the dataset of 13 PCGs, 22tRNAs, and two rRNAs, are analyzed using both the Bayesian and maximum likelihood methods. Our results clearly revealed the systematic status of Phymatostetha species and robustly supported the monophyly of this genus, in which Phymatostetha semele is sister to other Phymatostetha species. It was demonstrated that mitogenome was an effective molecular marker to adequately resolve phylogeny at low taxonomic levels.
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Affiliation(s)
- Tianjuan Su
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Aiping Liang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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59
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Almeida EAB, Packer L, Melo GAR, Danforth BN, Cardinal SC, Quinteiro FB, Pie MR. The diversification of neopasiphaeine bees during the Cenozoic (Hymenoptera: Colletidae). ZOOL SCR 2018. [DOI: 10.1111/zsc.12333] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Eduardo A. B. Almeida
- Laboratório de Biologia Comparada e Abelhas (LBCA), Departamento de Biologia, Faculdade de Filosofia Ciências e Letras, Universidade de São Paulo Ribeirão Preto SP Brazil
| | | | - Gabriel A. R. Melo
- Departamento de Zoologia Universidade Federal do Paraná Curitiba PR Brazil
| | - Bryan N. Danforth
- Department of Entomology Comstock Hall, Cornell University. Ithaca New York
| | - Sophie C. Cardinal
- Agriculture and Agri‐Food Canada Canadian National Collection of Insects Ottawa Ontario Canada
| | - Fábio B. Quinteiro
- Laboratório de Biologia Comparada e Abelhas (LBCA), Departamento de Biologia, Faculdade de Filosofia Ciências e Letras, Universidade de São Paulo Ribeirão Preto SP Brazil
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia Universidade Federal de Pelotas Pelotas Rio Grande do Sul Brazil
| | - Marcio R. Pie
- Departamento de Zoologia Universidade Federal do Paraná Curitiba PR Brazil
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60
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Samstag CL, Hoekstra JG, Huang CH, Chaisson MJ, Youle RJ, Kennedy SR, Pallanck LJ. Deleterious mitochondrial DNA point mutations are overrepresented in Drosophila expressing a proofreading-defective DNA polymerase γ. PLoS Genet 2018; 14:e1007805. [PMID: 30452458 PMCID: PMC6289449 DOI: 10.1371/journal.pgen.1007805] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 12/11/2018] [Accepted: 11/01/2018] [Indexed: 01/08/2023] Open
Abstract
Mitochondrial DNA (mtDNA) mutations cause severe maternally inherited syndromes and the accumulation of somatic mtDNA mutations is implicated in aging and common diseases. However, the mechanisms that influence the frequency and pathogenicity of mtDNA mutations are poorly understood. To address this matter, we created a Drosophila mtDNA mutator strain expressing a proofreading-deficient form of the mitochondrial DNA polymerase. Mutator flies have a dramatically increased somatic mtDNA mutation frequency that correlates with the dosage of the proofreading-deficient polymerase. Mutator flies also exhibit mitochondrial dysfunction, shortened lifespan, a progressive locomotor deficit, and loss of dopaminergic neurons. Surprisingly, the frequency of nonsynonymous, pathogenic, and conserved-site mutations in mutator flies exceeded predictions of a neutral mutational model, indicating the existence of a positive selection mechanism that favors deleterious mtDNA variants. We propose from these findings that deleterious mtDNA mutations are overrepresented because they selectively evade quality control surveillance or because they are amplified through compensatory mitochondrial biogenesis. The energy needs of an animal cell are supplied by tiny organelles known as mitochondria. Each of the many mitochondria in a cell has a set of blueprints for making more mitochondria, known as mitochondrial DNA (mtDNA). As animals age, their mtDNA acquires irreversible defects called mutations, which accumulate and may cause aging. Cells can selectively destroy malfunctioning mitochondria, so we hypothesized that mitochondria with harmful mutations would be selectively destroyed. To test our theory, we created a fruit fly strain with a high mtDNA mutation rate. Our hypothesis predicts that, because mitochondria bearing harmful mtDNA mutations would be destroyed, we should detect primarily less harmful mutations in our strain. However, the mtDNA mutations we detected were more harmful than expected by chance. We suggest two possible explanations: First, mitochondria with harmful mtDNA mutations may be degraded less often because they generate little energy and are not damaged by toxic byproducts of energy production. Second, cells may compensate for harmful mtDNA mutations by stimulating mitochondria to multiply, creating more healthy mitochondria but also more mitochondria with harmful mtDNA mutations. Future studies will distinguish between these models and further advance our understanding of aging and aging related disease.
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Affiliation(s)
- Colby L. Samstag
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, United States of America
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Jake G. Hoekstra
- Department of Pathology, University of Washington, Seattle, WA, United States of America
| | - Chiu-Hui Huang
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States of America
| | - Mark J. Chaisson
- Computational Biology and Bioinformatics, University of Southern California, Los Angeles, CA, United States of America
| | - Richard J. Youle
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States of America
| | - Scott R. Kennedy
- Department of Pathology, University of Washington, Seattle, WA, United States of America
- * E-mail: (SRK); (LJP)
| | - Leo J. Pallanck
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
- * E-mail: (SRK); (LJP)
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61
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Wang Y, Cao JJ, Li N, Ma GY, Li WH. The first mitochondrial genome from Scopuridae (Insecta: Plecoptera) reveals structural features and phylogenetic implications. Int J Biol Macromol 2018; 122:893-902. [PMID: 30412754 DOI: 10.1016/j.ijbiomac.2018.11.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 09/04/2018] [Accepted: 11/04/2018] [Indexed: 01/10/2023]
Abstract
This study determined the first complete mitochondrial genome (mitogenome) of a stonefly, Scopura longa (Plecoptera: Scopuridae), and reconstructed a phylogeny based on two datasets of mitogenomes in eighteen available stoneflies to examine the relationships among Plecoptera. The complete mitogenome of S. longa is a circular molecule of 15,798bp in size. It contains 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a control region (CR). Most PCGs used standard ATN start codons and TAN stop codons. All tRNAs could be folded as typical cloverleaf secondary structures except tRNASer(AGN), with the dihydrouridine (DHU) arm missing. Tandem repeat regions, two potential stem-loop (SL) structures, Poly T structures and G+C-rich regions are detected in the control region. Finally, the phylogenetic relationships among the families within the Arctoperlaria were reconstructed. The topological structures of the two trees were almost identical. The present phylogenetic analysis shows that S. longa belongs to the infraorder Euholognatha. The monophyly of each family is generally well supported based on nucleotide sequences. The Pteronarcyidae is sister to ((Peltoperlidae+Styloperlidae)+(Perlidae+(Perlodidae+Chloroperlidae))).
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Affiliation(s)
- Ying Wang
- Department of Plant Protection, Henan Institute of Science and Technology, Henan 453003, China
| | - Jin-Jun Cao
- Department of Plant Protection, Henan Institute of Science and Technology, Henan 453003, China
| | - Ni Li
- Department of Plant Protection, Henan Institute of Science and Technology, Henan 453003, China
| | - Gao-Yan Ma
- Department of Plant Protection, Henan Institute of Science and Technology, Henan 453003, China
| | - Wei-Hai Li
- Department of Plant Protection, Henan Institute of Science and Technology, Henan 453003, China.
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62
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Su T, Liang A. Characterization of the complete mitochondrial genome of Phymatostetha huangshanensis (Hemiptera: Cercopidae) and phylogenetic analysis. Int J Biol Macromol 2018; 119:60-69. [DOI: 10.1016/j.ijbiomac.2018.07.135] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 07/17/2018] [Accepted: 07/20/2018] [Indexed: 11/25/2022]
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63
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Kaewkrajang N, Grootaert P, Boonrotpong S. Genetic Variation of the Long-Legged Flies Phacaspis mitis Complex (Diptera: Dolichopodidae) in Peninsular Thailand Inferred From Three Mitochondrial Genes. JOURNAL OF INSECT SCIENCE (ONLINE) 2018; 18:5181162. [PMID: 30423176 PMCID: PMC6232956 DOI: 10.1093/jisesa/iey024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Indexed: 06/09/2023]
Abstract
Phacaspis (Meuffels and Grootaert 1988) is a true marine dolichopodid fly genus. They are common on the mud flats in the front of mangroves where they deal with extreme conditions. The genus is represented in southern Thailand by Phacaspis mitis (Grootaert and Meuffels 2001) (Diptera: Dolichopodidae). Previous studies have focused on both taxonomy and classification of this genus, but there are a few studies focusing on this species in terms of molecular genetics. The objective of the present study was to investigate genetic variation and phylogenetic relationships of P. mitis using ribosomal DNA subunit 12S, ribosomal DNA subunit 16S, and cytochrome oxidase subunit I of mitochondrial genes. The specimens were collected in six coastal provinces from the Andaman Sea and the Gulf of Thailand. The phylogenetic relationship of combined mitochondrial genes revealed that P. mitis in peninsular Thailand is a monophyletic group that can be divided into two distinct clades. According to the haplotype network, 16 haplotype patterns were observed in P. mitis, but P. mitis was separated into two major haplotype networks. In addition, a positive correlation between genetic distance (FST) and geographical distance (km) was found among the populations of peninsular Thailand. The level of genetic differentiation between populations is influenced by geographic isolation. Moreover, P. mitis arose in late Eocene (35.5 Mya) and it diversified during the Plio-Pleistocene (3.14 Mya). Although, P. mitis is divided into two populations in this study, it is a well-supported monophyletic group.
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Affiliation(s)
- Natcha Kaewkrajang
- Department of Biology, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Patrick Grootaert
- Entomology, Royal Belgian Institute of Natural Sciences, Vautierstraat, Brussels, Belgium
| | - Singtoe Boonrotpong
- Department of Biology, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
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Yang M, Song L, Shi Y, Yin Y, Wang Y, Zhang P, Chen J, Lou L, Liu X. The complete mitochondrial genome of a medicinal insect, Hydrillodes repugnalis (Lepidoptera: Noctuoidea: Erebidae), and related phylogenetic analysis. Int J Biol Macromol 2018; 123:485-493. [PMID: 30359659 DOI: 10.1016/j.ijbiomac.2018.10.149] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/21/2018] [Accepted: 10/21/2018] [Indexed: 02/08/2023]
Abstract
The complete mitochondrial genome (mitogenome) of an important medicinal insect Hydrillodes repugnalis (Lepidoptera: Noctuoidea) was sequenced and analyzed. The mitogenome is circular with 15,570 bp long, and shows typical gene content and arrangement. Nucleotide composition is highly biased toward A + T nucleotides (81.1%). All protein-coding genes (PCGs) initiate with canonical start codon ATN, except for cox1 being CGA. The typical stop codon TAA is used for most PCGs, while the nad4l uses the TAG, and cox1 and cox2 use incomplete termination codon T. All tRNAs have a typical clover-leaf structure, except for trnS1 (AGN) lacking the dihydrouridine arm. Comparative mitogenome analysis showed that the motif "ATGATAA" between atp8 and atp6, and the motif "ATACTAA" between trnS2 and nad1 are commonly present in noctuoid mitogenomes. In A + T-rich regions, the motif "ATAGA" and subsequent poly-T structure, the motif "ATTTA" and followed macrosatellite (AT)n element and an "A"-rich 3' end upstream of the trnM gene can be recognized across noctuoid mitogenomes. Phylogenetic analyses showed that H. repugnalis is nested into the Erebidae clade, consistently being sister to the Aganainae. Within Noctuoidea, the (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))) was consistently recovered firstly based on multiple mitochondrial datasets.
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Affiliation(s)
- Mingsheng Yang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan 466000, China
| | - Lu Song
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan 466000, China
| | - Yuxia Shi
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan 466000, China
| | - Yanjun Yin
- Yongqiao District Plant Protection Station, Suzhou, Anhui 234000, China
| | - Yueying Wang
- Suzhou Academy of Agricultural Sciences, Suzhou, Anhui 234000, China
| | - Peipei Zhang
- Suzhou Academy of Agricultural Sciences, Suzhou, Anhui 234000, China
| | - Jiaqin Chen
- Oil Crops Research Institute of Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou 550000, China
| | - Lijiao Lou
- Oil Crops Research Institute of Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou 550000, China
| | - Xiaomeng Liu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan 466000, China.
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Huang Y, Liu Y, Zhu XY, Xin ZZ, Zhang HB, Zhang DZ, Wang JL, Tang BP, Zhou CL, Liu QN, Dai LS. Comparative mitochondrial genome analysis of Grammodes geometrica and other noctuid insects reveals conserved mitochondrial genome organization and phylogeny. Int J Biol Macromol 2018; 125:1257-1265. [PMID: 30240711 DOI: 10.1016/j.ijbiomac.2018.09.104] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 09/16/2018] [Accepted: 09/17/2018] [Indexed: 12/01/2022]
Abstract
The mitochondrial genome (mitogenome) plays an important role in revealing molecular evolution. In this study, the complete mitogenome of Grammodes geometrica (G. geometrica) (Lepidoptera: Erebidae) was sequenced and characterized. The nucleotide composition of the genome is highly A + T biased, accounting for 80.49%. Most protein-coding genes (PCGs) are initiated by ATN codons except for the cytochrome oxidase subunit 1 (cox1) gene, which was initiated by CGA. The order and orientation of genes with the order trnM-trnI-trnQ-nad2 is a typical rearrangement compared with those ancestral insects in which trnM is located between trnQ and nad2. Most tRNA genes were folded into the typical cloverleaf structure except for trnS1 (AGN). The A + T-rich region contains the conserved motif "ATAGA" followed by a 19 bp poly-T stretch, which was also observed in other Noctuoidea species. In addition, we reconstructed phylogenetic trees among the nucleotide alignments of five families of Noctuoidea species except the Oenosandridae. Finally, we achieved a well-supported tree, which showed that G. geometrica belongs to the Erebidae family. Moreover, the relationships at the family-level can be displayed as follows: (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))).
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Affiliation(s)
- Yan Huang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224007, People's Republic of China; School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, People's Republic of China; Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, People's Republic of China
| | - Yu Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224007, People's Republic of China; College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing 210009, People's Republic of China
| | - Xiao-Yu Zhu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224007, People's Republic of China
| | - Zhao-Zhe Xin
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224007, People's Republic of China; College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing 210009, People's Republic of China
| | - Hua-Bin Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224007, People's Republic of China.
| | - Dai-Zhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224007, People's Republic of China
| | - Jia-Lian Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224007, People's Republic of China
| | - Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224007, People's Republic of China
| | - Chun-Lin Zhou
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224007, People's Republic of China
| | - Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224007, People's Republic of China.
| | - Li-Shang Dai
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, People's Republic of China.
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Zhu XY, Xin ZZ, Liu Y, Wang Y, Huang Y, Yang ZH, Chu XH, Zhang DZ, Zhang HB, Zhou CL, Wang JL, Tang BP, Liu QN. The complete mitochondrial genome of Clostera anastomosis (Lepidoptera: Notodontidae) and implication for the phylogenetic relationships of Noctuoidea species. Int J Biol Macromol 2018; 118:1574-1583. [PMID: 29981329 DOI: 10.1016/j.ijbiomac.2018.06.188] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/29/2018] [Accepted: 06/30/2018] [Indexed: 10/28/2022]
Abstract
In the present study, the complete mitochondrial genome (mitogenome) of Clostera anastomosis (C. anastomosis) has been determined for the first time. The mitogenome is 15,390 base pairs (bp) in length, comprised of 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and one non-coding control region (CR). The gene order shows a typical trnM rearrangement (trnM-trnI-trnQ) compared to ancestral insects (trnI-trnQ-trnM). Almost all the PCGs have the same start codon (ATN) except for cox1 (CGA), and almost all tRNAs have a typical cloverleaf secondary structure except for trnS1. At the beginning of the CR, we found a conserved motif "ATAGA + poly-T" as found in other lepidopteran insects. There are 20 intergenic regions and 11 overlapping regions, ranging from 1 to 53 bp and 1 to 9 bp, respectively. The A + T content is relatively high across the whole mitogenome. The optimal tree topologies of Noctuoidea were given by the dataset consisting of all 13 PCGs from five families (exclude Oenosandridae). Our trees suggested a topology of (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))) and identified that C. anastomosis belongs to Notodontidae.
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Affiliation(s)
- Xiao-Yu Zhu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224051, PR China
| | - Zhao-Zhe Xin
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224051, PR China
| | - Yu Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224051, PR China
| | - Ying Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224051, PR China
| | - Yan Huang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224051, PR China
| | - Zhi-Hui Yang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224051, PR China
| | - Xiao-Hua Chu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224051, PR China
| | - Dai-Zhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224051, PR China.
| | - Hua-Bin Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224051, PR China
| | - Chun-Lin Zhou
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224051, PR China
| | - Jia-Lian Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224051, PR China
| | - Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224051, PR China.
| | - Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224051, PR China.
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Smith ML, Ruffley M, Rankin AM, Espíndola A, Tank DC, Sullivan J, Carstens BC. Testing for the presence of cryptic diversity in tail-dropper slugs (Prophysaon) using molecular data. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly067] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Megan L Smith
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Aronoff Labs, Columbus, OH, USA
| | - Megan Ruffley
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Andrew M Rankin
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Anahí Espíndola
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, Moscow, ID, USA
| | - David C Tank
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Aronoff Labs, Columbus, OH, USA
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68
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Benabdelkrim Filali O, Kabine M, El Hamouchi A, Lemrani M, Debboun M, Sarih M. First Molecular Identification and Phylogeny of Moroccan Anopheles sergentii (Diptera: Culicidae) Based on Second Internal Transcribed Spencer (ITS2) and Cytochrome c Oxidase I (COI) Sequences. Vector Borne Zoonotic Dis 2018; 18:479-484. [PMID: 29870316 DOI: 10.1089/vbz.2018.2269] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Anopheles sergentii known as the "oasis vector" or the "desert malaria vector" is considered the main vector of malaria in the southern parts of Morocco. Its presence in Morocco is confirmed for the first time through sequencing of mitochondrial DNA (mDNA) cytochrome c oxidase subunit I (COI) barcodes and nuclear ribosomal DNA (rDNA) second internal transcribed spacer (ITS2) sequences and direct comparison with specimens of A. sergentii of other countries. The DNA barcodes (n = 39) obtained from A. sergentii collected in 2015 and 2016 showed more diversity with 10 haplotypes, compared with 3 haplotypes obtained from ITS2 sequences (n = 59). Moreover, the comparison using the ITS2 sequences showed closer evolutionary relationship between the Moroccan and Egyptian strains than the Iranian strain. Nevertheless, genetic differences due to geographical segregation were also observed. This study provides the first report on the sequence of rDNA-ITS2 and mtDNA COI, which could be used to better understand the biodiversity of A. sergentii.
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Affiliation(s)
- Oumama Benabdelkrim Filali
- 1 Laboratory of Vector-Borne-Diseases, Institut Pasteur du Maroc , Casablanca, Morocco .,2 Health and Environment Laboratory, Hassan II University of Casablanca , Aïn Chock Faculty of Sciences, Casablanca, Morocco
| | - Mostafa Kabine
- 2 Health and Environment Laboratory, Hassan II University of Casablanca , Aïn Chock Faculty of Sciences, Casablanca, Morocco
| | - Adil El Hamouchi
- 3 Laboratory of Parasitology and Vector-Borne-Diseases, Institut Pasteur du Maroc , Casablanca, Morocco
| | - Meryem Lemrani
- 3 Laboratory of Parasitology and Vector-Borne-Diseases, Institut Pasteur du Maroc , Casablanca, Morocco
| | - Mustapha Debboun
- 4 Division of Mosquito and Vector Control, Harris County Public Health , Houston, Texas
| | - M'hammed Sarih
- 1 Laboratory of Vector-Borne-Diseases, Institut Pasteur du Maroc , Casablanca, Morocco
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69
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Barnabé C, Brenière SF, Guégan JF, Blanchet D, Aznar C. Molecular characterization of Rhodnius robustus specimens, potential vectors for Chagas disease in French Guiana, South America. INFECTION GENETICS AND EVOLUTION 2018; 59:28-31. [DOI: 10.1016/j.meegid.2018.01.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 01/22/2018] [Accepted: 01/24/2018] [Indexed: 01/28/2023]
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70
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Sarvani RK, Parmar DR, Tabasum W, Thota N, Sreenivas A, Gaur A. Characterization of the complete mitogenome of Indian Mouse Deer, Moschiola indica (Artiodactyla: Tragulidae) and its evolutionary significance. Sci Rep 2018; 8:2697. [PMID: 29426945 PMCID: PMC5807545 DOI: 10.1038/s41598-018-20946-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 01/24/2018] [Indexed: 11/09/2022] Open
Abstract
The mitochondrial genome of Indian mouse deer (Moschiola indica) was sequenced, assembled and characterized for the first time using 22 pairs of polymerase chain reaction (PCR) primers. The mitogenome of M. indica which is 16,444 bp in size was found very similar to most vertebrates in organisation that harbours 13 protein-coding genes, 22 transfer RNA, 2 ribosomal RNA and 1A + T-rich region. Its comparison with over 52 mitogenomes of the order Artiodactyla, showed a conserved nature of gene organisation, codon usage, gene orientation and evolutionary rates of proteins except that M. indica possesses an extra copy of trnF. The complete mitogenome and protein-coding genes of M. indica were found to be highly A + T biased. Rate of protein evolution was highest in atp8 and lowest in cox3. Further, a higher purifying selection pressure was found to be acting on family Tragulidae compared to Bovidae and Cervidae. The phylogenetic analysis of M. indica placed the Tragulidae as sister-group of all other ruminants, similar to previous analyses. Moschiola forms the sister-group to the other two tragulid genera Tragulus (from Asia) and Hyemoschus (from Africa), which is unexpected as usually the Asian species are thought to form a monophyletic group.
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Affiliation(s)
- Rama K Sarvani
- Laboratory for Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology (CCMB) Annexe 1, Hyderguda, Attapur, Hyderabad, 500048, India
| | - Drashti R Parmar
- Laboratory for Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology (CCMB) Annexe 1, Hyderguda, Attapur, Hyderabad, 500048, India
| | - Wajeeda Tabasum
- Laboratory for Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology (CCMB) Annexe 1, Hyderguda, Attapur, Hyderabad, 500048, India
| | - Neelima Thota
- Laboratory for Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology (CCMB) Annexe 1, Hyderguda, Attapur, Hyderabad, 500048, India
| | - Ara Sreenivas
- Laboratory for Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology (CCMB) Annexe 1, Hyderguda, Attapur, Hyderabad, 500048, India
| | - Ajay Gaur
- Laboratory for Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology (CCMB) Annexe 1, Hyderguda, Attapur, Hyderabad, 500048, India.
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71
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Hsu Y, Cocroft RB, Snyder RL, Lin C. You stay, but I Hop: Host shifting near and far co-dominated the evolution of Enchenopa treehoppers. Ecol Evol 2018; 8:1954-1965. [PMID: 29468015 PMCID: PMC5817127 DOI: 10.1002/ece3.3815] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 11/24/2017] [Accepted: 12/06/2017] [Indexed: 12/11/2022] Open
Abstract
The importance and prevalence of phylogenetic tracking between hosts and dependent organisms caused by co-evolution and shifting between closely related host species have been debated for decades. Most studies of phylogenetic tracking among phytophagous insects and their host plants have been limited to insects feeding on a narrow range of host species. However, narrow host ranges can confound phylogenetic tracking (phylogenetic tracking hypothesis) with host shifting between hosts of intermediate relationship (intermediate hypothesis). Here, we investigated the evolutionary history of the Enchenopa binotata complex of treehoppers. Each species in this complex has high host fidelity, but the entire complex uses hosts across eight plant orders. The phylogenies of E. binotata were reconstructed to evaluate whether (1) tracking host phylogeny; or (2) shifting between intermediately related host plants better explains the evolutionary history of E. binotata. Our results suggest that E. binotata primarily shifted between both distant and intermediate host plants regardless of host phylogeny and less frequently tracked the phylogeny of their hosts. These findings indicate that phytophagous insects with high host fidelity, such as E. binotata, are capable of adaptation not only to closely related host plants but also to novel hosts, likely with diverse phenology and defense mechanisms.
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Affiliation(s)
- Yu‐Hsun Hsu
- Department of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
| | | | - Robert L. Snyder
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
- Present address:
Department of BiologyState University of New York College at PotsdamPotsdamNYUSA
| | - Chung‐Ping Lin
- Department of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
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72
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Martoni F, Bulman SR, Pitman A, Armstrong KF. Elongation Factor-1α Accurately Reconstructs Relationships Amongst Psyllid Families (Hemiptera: Psylloidea), with Possible Diagnostic Implications. JOURNAL OF ECONOMIC ENTOMOLOGY 2017; 110:2618-2622. [PMID: 29040629 DOI: 10.1093/jee/tox261] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 06/07/2023]
Abstract
The superfamily Psylloidea (Hemiptera: Sternorrhyncha) lacks a robust multigene phylogeny. This impedes our understanding of the evolution of this group of insects and, consequently, an accurate identification of individuals, of their plant host associations, and their roles as vectors of economically important plant pathogens. The conserved nuclear gene elongation factor-1 alpha (EF-1α) has been valuable as a higher-level phylogenetic marker in insects and it has also been widely used to investigate the evolution of intron/exon structure. To explore evolutionary relationships among Psylloidea, polymerase chain reaction amplification and nucleotide sequencing of a 250-bp EF-1α gene fragment was applied to psyllids belonging to five different families. Introns were detected in three individuals belonging to two families. The nine genera belonging to the family Aphalaridae all lacked introns, highlighting the possibility of using intron presence/absence as a diagnostic tool at a family level. When paired with cytochrome oxidase I gene sequences, the 250 bp EF-1α sequence appeared to be a very promising higher-level phylogenetic marker for psyllids.
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Affiliation(s)
- Francesco Martoni
- Bio-Protection Research Centre, Lincoln University, New Zealand
- Australian Plant Biosecurity Cooperative Research Centre, Australia
| | - Simon R Bulman
- Australian Plant Biosecurity Cooperative Research Centre, Australia
- The New Zealand Institute for Plant & Food Research Limited, New Zealand
- Better Border Biosecurity (B3), New Zealand
| | - Andrew Pitman
- Bio-Protection Research Centre, Lincoln University, New Zealand
- The New Zealand Institute for Plant & Food Research Limited, New Zealand
| | - Karen F Armstrong
- Bio-Protection Research Centre, Lincoln University, New Zealand
- Australian Plant Biosecurity Cooperative Research Centre, Australia
- The New Zealand Institute for Plant & Food Research Limited, New Zealand
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73
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Tabasum W, Parmar DR, Jayaraman A, Mitra S, Sreenivas A, Kunteepuram V, Gaur A. The complete mitochondrial genome of Eld's deer ( Rucervus eldii eldii ) and its phylogenetic implications. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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74
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Brown SDJ. Austromonticola, a new genus of broad-nosed weevil (Coleoptera, Curculionidae, Entiminae) from montane areas of New Zealand. Zookeys 2017; 707:73-130. [PMID: 29118629 PMCID: PMC5674147 DOI: 10.3897/zookeys.707.12649] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 08/20/2017] [Indexed: 11/16/2022] Open
Abstract
Austromonticolagen. n. is proposed for a group of eight New Zealand alpine broad-nosed weevil species, all of which are here described: A. atriariussp. n. (type locality: Umbrella Mountains, Central Otago), A. caelibatussp. n. (type locality: Ohau Range, Mackenzie), A. furcatussp. n. (type locality: Old Man Range, Central Otago), A. inflatussp. n. (type locality: Hawkdun Range, Central Otago), A. planulatussp. n. (type locality: St Marys Range, Central Otago), A. postinventussp. n. (type locality: Kirkliston Range, South Canterbury), A. mataurasp. n. (type locality: Mt Dick, Otago Lakes) and A. rotundussp. n. (type locality: Old Man Range, Central Otago). All species occur exclusively above 1000 m elevation in the mountains of Central Otago and South Canterbury in the South Island. A phylogeny of the genus, including six outgroups, was inferred from 33 morphological characters. It resolved the genus as monophyletic, and revealed two strongly supported clades within Austromonticola. DNA sequences of four gene regions were obtained from five species. Of these, the 3' end of COI proved to be the most suitable for the identification of specimens. Females of all species have diagnostic secondary sexual structures on the elytra and ventrites. These structures are hypothesised to have evolved to assist with oviposition in and beside cushion plants or by selection for structures to mitigate the costs to females of prolonged mating.
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Affiliation(s)
- Samuel D. J. Brown
- Bio-Protection Research Centre, PO Box 85084, Lincoln University 7647, Canterbury, New Zealand
- AgResearch, Gerald St, Lincoln, Canterbury, New Zealand
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75
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Guzmán NV, Pietrokovsky SM, Cigliano MM, Confalonieri VA. Unraveling the diversification history of grasshoppers belonging to the " Trimerotropis pallidipennis" (Oedipodinae: Acrididae) species group: a hotspot of biodiversity in the Central Andes. PeerJ 2017; 5:e3835. [PMID: 28975055 PMCID: PMC5624295 DOI: 10.7717/peerj.3835] [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: 06/29/2017] [Accepted: 08/30/2017] [Indexed: 11/24/2022] Open
Abstract
The Andean Mountain range has been recognized as one of the biodiversity hotspots of the world. The proposed mechanisms for such species diversification, among others, are due to the elevation processes occurring during the Miocene and the intensive glacial action during the Pleistocene. In this study we investigated the diversification history of the grasshopper Trimerotropis pallidipennis species complex which shows a particularly wide latitudinal and altitudinal distribution range across the northern, central and southern Andes in South America. Many genetic lineages of this complex have been so far discovered, making it an excellent model to investigate the role of the central Andes Mountains together with climatic fluctuations as drivers of speciation. Phylogenetics, biogeographic and molecular clock analyses using a multi-locus dataset revealed that in Peru there are at least two, and possibly four genetic lineages. Two different stocks originated from a common ancestor from North/Central America—would have dispersed toward southern latitudes favored by the closure of the Panama Isthmus giving rise to two lineages, the coastal and mountain lineages, which still coexist in Peru (i.e., T. pallidipennis and T. andeana). Subsequent vicariant and dispersal events continued the differentiation process, giving rise to three to six genetic lineages (i.e., clades) detected in this study, which were geographically restricted to locations dispersed over the central Andes Mountains in South America. Our results provide another interesting example of “island diversification” motored by the topography plus unstable climatic conditions during the Pleistocene, pointing out the presence of a hotspot of diversification in the Andean region of Peru.
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Affiliation(s)
- Noelia Verónica Guzmán
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Ecología, Genética y Evolución (IEGEBA), Buenos Aires, Argentina
| | - Silvia Mónica Pietrokovsky
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Ecología, Genética y Evolución (IEGEBA), Buenos Aires, Argentina
| | - Maria Marta Cigliano
- Consejo Nacional de Investigaciones Científicas y Tecnológicas, Museo de La Plata, Universidad Nacional de la Plata, Centro de Estudios Parasitológicos y de Vectores (CEPAVE), La Plata, Buenos Aires, Argentina
| | - Viviana Andrea Confalonieri
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Ecología, Genética y Evolución (IEGEBA), Buenos Aires, Argentina
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76
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Navarro-Sigüenza AG, Vázquez-Miranda H, Hernández-Alonso G, García-Trejo EA, Sánchez-González LA. Complex biogeographic scenarios revealed in the diversification of the largest woodpecker radiation in the New World. Mol Phylogenet Evol 2017; 112:53-67. [DOI: 10.1016/j.ympev.2017.04.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/08/2017] [Accepted: 04/10/2017] [Indexed: 01/05/2023]
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77
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Novel insights into mitochondrial gene rearrangement in thrips (Insecta: Thysanoptera) from the grass thrips, Anaphothrips obscurus. Sci Rep 2017; 7:4284. [PMID: 28655921 PMCID: PMC5487348 DOI: 10.1038/s41598-017-04617-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/17/2017] [Indexed: 11/29/2022] Open
Abstract
We sequenced the mitochondrial (mt) genome of the grass thrips, Anaphothrips obscurus, which is highly rearranged and differs from the four thrips species reported previously in the arrangement of both tRNA genes and a protein-coding gene, nad3, and in the copy number of the control region (CR). We reconstructed the phylogeny of the thrips with mt genome sequences, and used it as a framework to gain insights into mt genome evolution in thrips. It is evident that A. obscurus is less rearranged in mt genome organization than the other four known thrips. nad3 is in its ancestral location in A. obscurus but was translocated in other four thrips. Also, A. obscurus has one CR, which is ancestral to hexapods whereas other thrips have two or three CRs. All of the five thrips whose mt genomes have been sequenced to date are from the subfamily Thripinae, which represents about a quarter of the species richness in the order Thysanoptera. The high variation in mt genome organization observed in a subfamily challenges our knowledge about animal mt genomes. It remains to be investigated why mt genomes evolved so fast in the subfamily Thripinae and how mt genomes evolved in other lineages of thrips.
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78
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Dhar B, Ghosh SK. Mini-DNA barcode in identification of the ornamental fish: A case study from Northeast India. Gene 2017; 627:248-254. [PMID: 28652184 DOI: 10.1016/j.gene.2017.06.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 05/28/2017] [Accepted: 06/22/2017] [Indexed: 11/30/2022]
Abstract
The ornamental fishes were exported under the trade names or generic names, thus creating problems in species identification. In this regard, DNA barcoding could effectively elucidate the actual species status. However, the problem arises if the specimen is having taxonomic disputes, falsified by trade/generic names, etc., On the other hand, barcoding the archival museum specimens would be of greater benefit to address such issues as it would create firm, error-free reference database for rapid identification of any species. This can be achieved only by generating short sequences as DNA from chemically preserved are mostly degraded. Here we aimed to identify a short stretch of informative sites within the full-length barcode segment, capable of delineating diverse group of ornamental fish species, commonly traded from NE India. We analyzed 287 full-length barcode sequences from the major fish orders and compared the interspecific K2P distance with nucleotide substitutions patterns and found a strong correlation of interspecies distance with transversions (0.95, p<0.001). We, therefore, proposed a short stretch of 171bp (transversion rich) segment as mini-barcode. The proposed segment was compared with the full-length barcodes and found to delineate the species effectively. Successful PCR amplification and sequencing of the 171bp segment using designed primers for different orders validated it as mini-barcodes for ornamental fishes. Thus, our findings would be helpful in strengthening the global database with the sequence of archived fish species as well as an effective identification tool of the traded ornamental fish species, as a less time consuming, cost effective field-based application.
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Affiliation(s)
- Bishal Dhar
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Sankar Kumar Ghosh
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India; University of Kalyani, Kalyani 741235, West Bengal, India.
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79
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Complete mitochondrial genome of Clistocoeloma sinensis (Brachyura: Grapsoidea): Gene rearrangements and higher-level phylogeny of the Brachyura. Sci Rep 2017. [PMID: 28646134 PMCID: PMC5482888 DOI: 10.1038/s41598-017-04489-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Deciphering the animal mitochondrial genome (mitogenome) is very important to understand their molecular evolution and phylogenetic relationships. In this study, the complete mitogenome of Clistocoeloma sinensis was determined. The mitogenome of C. sinensis was 15,706 bp long, and its A+T content was 75.7%. The A+T skew of the mitogenome of C. sinensis was slightly negative (−0.020). All the transfer RNA genes had the typical cloverleaf structure, except for the trnS1 gene, which lacked a dihydroxyuridine arm. The two ribosomal RNA genes had 80.2% A+T content. The A+T-rich region spanned 684 bp. The gene order within the complete mitogenome of C. sinensis was identical to the pancrustacean ground pattern except for the translocation of trnH. Additionally, the gene order of trnI-trnQ-trnM in the pancrustacean ground pattern becomes trnQ-trnI-trnM in C. sinensis. Our phylogenetic analysis showed that C. sinensis and Sesarmops sinensis cluster together with high nodal support values, indicating that C. sinensis and S. sinensis have a sister group relationship. The results support that C. sinensis belongs to Grapsoidea, Sesarmidae. Our findings also indicate that Varunidae and Sesarmidae species share close relationships. Thus, mitogenomes are likely to be valuable tools for systematics in other groups of Crustacea.
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80
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Chakraborty M, Dhar B, Ghosh SK. Design of character-based DNA barcode motif for species identification: A computational approach and its validation in fishes. Mol Ecol Resour 2017; 17:1359-1370. [PMID: 28332322 DOI: 10.1111/1755-0998.12671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 01/26/2017] [Accepted: 03/07/2017] [Indexed: 11/29/2022]
Abstract
The DNA barcodes are generally interpreted using distance-based and character-based methods. The former uses clustering of comparable groups, based on the relative genetic distance, while the latter is based on the presence or absence of discrete nucleotide substitutions. The distance-based approach has a limitation in defining a universal species boundary across the taxa as the rate of mtDNA evolution is not constant throughout the taxa. However, character-based approach more accurately defines this using a unique set of nucleotide characters. The character-based analysis of full-length barcode has some inherent limitations, like sequencing of the full-length barcode, use of a sparse-data matrix and lack of a uniform diagnostic position for each group. A short continuous stretch of a fragment can be used to resolve the limitations. Here, we observe that a 154-bp fragment, from the transversion-rich domain of 1367 COI barcode sequences can successfully delimit species in the three most diverse orders of freshwater fishes. This fragment is used to design species-specific barcode motifs for 109 species by the character-based method, which successfully identifies the correct species using a pattern-matching program. The motifs also correctly identify geographically isolated population of the Cypriniformes species. Further, this region is validated as a species-specific mini-barcode for freshwater fishes by successful PCR amplification and sequencing of the motif (154 bp) using the designed primers. We anticipate that use of such motifs will enhance the diagnostic power of DNA barcode, and the mini-barcode approach will greatly benefit the field-based system of rapid species identification.
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Affiliation(s)
- Mohua Chakraborty
- Department of Biotechnology, Assam University, Silchar, Assam, India
| | - Bishal Dhar
- Department of Biotechnology, Assam University, Silchar, Assam, India
| | - Sankar Kumar Ghosh
- Department of Biotechnology, Assam University, Silchar, Assam, India.,University of Kalyani, Kalyani, West Bengal, India
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81
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Batovska J, Lynch SE, Cogan NOI, Brown K, Darbro JM, Kho EA, Blacket MJ. Effective mosquito and arbovirus surveillance using metabarcoding. Mol Ecol Resour 2017; 18:32-40. [PMID: 28417591 PMCID: PMC5811807 DOI: 10.1111/1755-0998.12682] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 02/13/2017] [Accepted: 04/03/2017] [Indexed: 01/04/2023]
Abstract
Effective vector and arbovirus surveillance requires timely and accurate screening techniques that can be easily upscaled. Next-generation sequencing (NGS) is a high-throughput technology that has the potential to modernize vector surveillance. When combined with DNA barcoding, it is termed 'metabarcoding.' The aim of our study was to establish a metabarcoding protocol to characterize pools of mosquitoes and screen them for virus. Pools contained 100 morphologically identified individuals, including one Ross River virus (RRV) infected mosquito, with three species present at different proportions: 1, 5, 94%. Nucleic acid extracted from both crude homogenate and supernatant was used to amplify a 269-bp section of the mitochondrial cytochrome c oxidase subunit I (COI) locus. Additionally, a 67-bp region of the RRV E2 gene was amplified from synthesized cDNA to screen for RRV. Amplicon sequencing was performed using an Illumina MiSeq, and bioinformatic analysis was performed using a DNA barcode database of Victorian mosquitoes. Metabarcoding successfully detected all mosquito species and RRV in every positive sample tested. The limits of species detection were also examined by screening a pool of 1000 individuals, successfully identifying the species and RRV from a single mosquito. The primers used for amplification, number of PCR cycles and total number of individuals present all have effects on the quantification of species in mixed bulk samples. Based on the results, a number of recommendations for future metabarcoding studies are presented. Overall, metabarcoding shows great promise for providing a new alternative approach to screening large insect surveillance trap catches.
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Affiliation(s)
- J Batovska
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Vic, Australia
| | - S E Lynch
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Vic, Australia
| | - N O I Cogan
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Vic, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Vic, Australia
| | - K Brown
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Vic, Australia
| | - J M Darbro
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Qld, Australia
| | - E A Kho
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Qld, Australia
| | - M J Blacket
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Vic, Australia
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82
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Rach J, Bergmann T, Paknia O, DeSalle R, Schierwater B, Hadrys H. The marker choice: Unexpected resolving power of an unexplored CO1 region for layered DNA barcoding approaches. PLoS One 2017; 12:e0174842. [PMID: 28406914 PMCID: PMC5390999 DOI: 10.1371/journal.pone.0174842] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/16/2017] [Indexed: 01/13/2023] Open
Abstract
The potential of DNA barcoding approaches to identify single species and characterize species compositions strongly depends on the marker choice. The prominent “Folmer region”, a 648 basepair fragment at the 5’ end of the mitochondrial CO1 gene, has been traditionally applied as a universal DNA barcoding region for metazoans. In order to find a suitable marker for biomonitoring odonates (dragonflies and damselflies), we here explore a new region of the CO1 gene (CO1B) for DNA barcoding in 51 populations of 23 dragonfly and damselfly species. We compare the “Folmer region”, the mitochondrial ND1 gene (NADH dehydrogenase 1) and the new CO1 region with regard to (i) speed and reproducibility of sequence generation, (ii) levels of homoplasy and (iii) numbers of diagnostic characters for discriminating closely related sister taxa and populations. The performances of the gene regions regarding these criteria were quite different. Both, the amplification of CO1B and ND1 was highly reproducible and CO1B showed the highest potential for discriminating sister taxa at different taxonomic levels. In contrast, the amplification of the “Folmer region” using the universal primers was difficult and the third codon positions of this fragment have experienced nucleotide substitution saturation. Most important, exploring this new barcode region of the CO1 gene identified a higher discriminating power between closely related sister taxa. Together with the design of layered barcode approaches adapted to the specific taxonomic “environment”, this new marker will further enhance the discrimination power at the species level.
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Affiliation(s)
- Jessica Rach
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
| | - Tjard Bergmann
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
| | - Omid Paknia
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
| | - Rob DeSalle
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, United States of America
| | - Bernd Schierwater
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, United States of America
| | - Heike Hadrys
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, United States of America
- * E-mail:
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83
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Che LH, Zhang SQ, Li Y, Liang D, Pang H, Ślipiński A, Zhang P. Genome-wide survey of nuclear protein-coding markers for beetle phylogenetics and their application in resolving both deep and shallow-level divergences. Mol Ecol Resour 2017; 17:1342-1358. [DOI: 10.1111/1755-0998.12664] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/09/2017] [Accepted: 02/14/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Li-Heng Che
- State Key Laboratory of Biocontrol; College of Ecology and Evolution; School of Life Sciences; Sun Yat-Sen University; Guangzhou 510006; Guangdong Province China
| | - Shao-Qian Zhang
- State Key Laboratory of Biocontrol; College of Ecology and Evolution; School of Life Sciences; Sun Yat-Sen University; Guangzhou 510006; Guangdong Province China
| | - Yun Li
- State Key Laboratory of Biocontrol; College of Ecology and Evolution; School of Life Sciences; Sun Yat-Sen University; Guangzhou 510006; Guangdong Province China
| | - Dan Liang
- State Key Laboratory of Biocontrol; College of Ecology and Evolution; School of Life Sciences; Sun Yat-Sen University; Guangzhou 510006; Guangdong Province China
| | - Hong Pang
- State Key Laboratory of Biocontrol; College of Ecology and Evolution; School of Life Sciences; Sun Yat-Sen University; Guangzhou 510006; Guangdong Province China
| | - Adam Ślipiński
- Australian National Insect Collection; CSIRO; GPO Box 1700 Canberra ACT 2601 Australia
| | - Peng Zhang
- State Key Laboratory of Biocontrol; College of Ecology and Evolution; School of Life Sciences; Sun Yat-Sen University; Guangzhou 510006; Guangdong Province China
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84
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Phylogeographic structure of Canthon cyanellus (Coleoptera: Scarabaeidae), a Neotropical dung beetle in the Mexican Transition Zone: Insights on its origin and the impacts of Pleistocene climatic fluctuations on population dynamics. Mol Phylogenet Evol 2017; 109:180-190. [DOI: 10.1016/j.ympev.2017.01.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 12/16/2016] [Accepted: 01/06/2017] [Indexed: 11/22/2022]
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85
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Vamosi JC, Gong YB, Adamowicz SJ, Packer L. Forecasting pollination declines through DNA barcoding: the potential contributions of macroecological and macroevolutionary scales of inquiry. THE NEW PHYTOLOGIST 2017; 214:11-18. [PMID: 27901268 DOI: 10.1111/nph.14356] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
While pollinators are widely acknowledged as important contributors to seed production in plant communities, we do not yet have a good understanding of the importance of pollinator specialists for this ecosystem service. Determination of the prevalence of pollinator specialists is often hindered by the occurrence of cryptic species and the limitations of observational data on pollinator visitation rates, two areas where DNA barcoding of pollinators and pollen can be useful. Further, the demonstrated adequacy of pollen DNA barcoding from historical records offers opportunities to observe the effects of pollinator loss over longer timescales, and phylogenetic approaches can elucidate the historical rates of extinction of specialist lineages. In this Viewpoint article, we review how advances in DNA barcoding and metabarcoding of plants and pollinators have brought important developments to our understanding of specialization in plant-pollinator interactions. We then put forth several lines of inquiry that we feel are especially promising for providing insight on changes in plant-pollinator interactions over space and time. Obtaining estimates of the effects of reductions in specialists will contribute to forecasting the loss of ecosystem services that will accompany the erosion of plant and pollinator diversity.
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Affiliation(s)
- Jana C Vamosi
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
| | - Yan-Bing Gong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Sarah J Adamowicz
- Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Laurence Packer
- Department of Biology, York University, Toronto, ON, M3J 1P3, Canada
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86
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Pu DQ, Liu HL, Gong YY, Ji PC, Li YJ, Mou FS, Wei SJ. Mitochondrial genomes of the hoverflies Episyrphus balteatus and Eupeodes corollae (Diptera: Syrphidae), with a phylogenetic analysis of Muscomorpha. Sci Rep 2017; 7:44300. [PMID: 28276531 PMCID: PMC5343577 DOI: 10.1038/srep44300] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 02/06/2017] [Indexed: 12/11/2022] Open
Abstract
The hoverflies Episyrphus balteatus and Eupeodes corollae (Diptera: Muscomorpha: Syrphidae) are important natural aphid predators. We obtained mitochondrial genome sequences from these two species using methods of PCR amplification and sequencing. The complete Episyrphus mitochondrial genome is 16,175 bp long while the incomplete one of Eupeodes is 15,326 bp long. All 37 typical mitochondrial genes are present in both species and arranged in ancestral positions and directions. The two mitochondrial genomes showed a biased A/T usage versus G/C. The cox1, cox2, cox3, cob and nad1 showed relatively low level of nucleotide diversity among protein-coding genes, while the trnM was the most conserved one without any nucleotide variation in stem regions within Muscomorpha. Phylogenetic relationships among the major lineages of Muscomorpha were reconstructed using a complete set of mitochondrial genes. Bayesian and maximum likelihood analyses generated congruent topologies. Our results supported the monophyly of five species within the Syrphidae (Syrphoidea). The Platypezoidea was sister to all other species of Muscomorpha in our phylogeny. Our study demonstrated the power of the complete mitochondrial gene set for phylogenetic analysis in Muscomorpha.
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Affiliation(s)
- De-qiang Pu
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610300, China
| | - Hong-ling Liu
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Yi-yun Gong
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610300, China
| | - Pei-cheng Ji
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610300, China
| | - Yue-jian Li
- Institute of Horticulture Research, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Fang-sheng Mou
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610300, China
| | - Shu-jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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87
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The complete mitochondrial genome of Japanese sparrowhawk (Accipiter gularis) and the phylogenetic relationships among some predatory birds. BIOCHEM SYST ECOL 2017. [DOI: 10.1016/j.bse.2016.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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88
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Zhang X, Li X, Liu F, Yuan H, Huang Y. The complete mitochondrial genome of Tonkinacris sinensis(Orthoptera: Acrididae): A tRNA-like sequence and its implications for phylogeny. BIOCHEM SYST ECOL 2017. [DOI: 10.1016/j.bse.2016.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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89
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Delrieu-Trottin E, Mona S, Maynard J, Neglia V, Veuille M, Planes S. Population expansions dominate demographic histories of endemic and widespread Pacific reef fishes. Sci Rep 2017; 7:40519. [PMID: 28091580 PMCID: PMC5238389 DOI: 10.1038/srep40519] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 12/07/2016] [Indexed: 12/20/2022] Open
Abstract
Despite the unique nature of endemic species, their origin and population history remain poorly studied. We investigated the population history of 28 coral reef fish species, close related, from the Gambier and Marquesas Islands, from five families, with range size varying from widespread to small-range endemic. We analyzed both mitochondrial and nuclear sequence data using neutrality test and Bayesian analysis (EBSP and ABC). We found evidence for demographic expansions for most species (24 of 28), irrespective of range size, reproduction strategy or archipelago. The timing of the expansions varied greatly among species, from 8,000 to 2,000,000 years ago. The typical hypothesis for reef fish that links population expansions to the Last Glacial Maximum fit for 14 of the 24 demographic expansions. We propose two evolutionary processes that could lead to expansions older than the LGM: (a) we are retrieving the signature of an old colonization process for widespread, large-range endemic and paleoendemic species or (b) speciation; the expansion reflects the birth of the species for neoendemic species. We show for the first time that the demographic histories of endemic and widespread reef fish are not distinctly different and suggest that a number of processes drive endemism.
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Affiliation(s)
- Erwan Delrieu-Trottin
- Laboratoire d’Excellence «CORAIL», EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, F-66360 Perpignan, France
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Stefano Mona
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205 - CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, Paris Sorbonne Universités, Paris, France
- EPHE, PSL Research University, Paris, France
| | - Jeffrey Maynard
- Laboratoire d’Excellence «CORAIL», EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, F-66360 Perpignan, France
- SymbioSeas and Marine Applied Research Center, Wilmington NC 28411, United States of America
| | - Valentina Neglia
- Laboratoire d’Excellence «CORAIL», EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, F-66360 Perpignan, France
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Michel Veuille
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205 - CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, Paris Sorbonne Universités, Paris, France
- EPHE, PSL Research University, Paris, France
| | - Serge Planes
- Laboratoire d’Excellence «CORAIL», EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, F-66360 Perpignan, France
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90
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Using Next-Generation Sequencing for DNA Barcoding: Capturing Allelic Variation in ITS2. G3-GENES GENOMES GENETICS 2017; 7:19-29. [PMID: 27799340 PMCID: PMC5217108 DOI: 10.1534/g3.116.036145] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Internal Transcribed Spacer 2 (ITS2) is a popular DNA barcoding marker; however, in some animal species it is hypervariable and therefore difficult to sequence with traditional methods. With next-generation sequencing (NGS) it is possible to sequence all gene variants despite the presence of single nucleotide polymorphisms (SNPs), insertions/deletions (indels), homopolymeric regions, and microsatellites. Our aim was to compare the performance of Sanger sequencing and NGS amplicon sequencing in characterizing ITS2 in 26 mosquito species represented by 88 samples. The suitability of ITS2 as a DNA barcoding marker for mosquitoes, and its allelic diversity in individuals and species, was also assessed. Compared to Sanger sequencing, NGS was able to characterize the ITS2 region to a greater extent, with resolution within and between individuals and species that was previously not possible. A total of 382 unique sequences (alleles) were generated from the 88 mosquito specimens, demonstrating the diversity present that has been overlooked by traditional sequencing methods. Multiple indels and microsatellites were present in the ITS2 alleles, which were often specific to species or genera, causing variation in sequence length. As a barcoding marker, ITS2 was able to separate all of the species, apart from members of the Culex pipiens complex, providing the same resolution as the commonly used Cytochrome Oxidase I (COI). The ability to cost-effectively sequence hypervariable markers makes NGS an invaluable tool with many applications in the DNA barcoding field, and provides insights into the limitations of previous studies and techniques.
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91
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The Megadiverse Australian Ant Genus Melophorus: Using CO1 Barcoding to Assess Species Richness. DIVERSITY-BASEL 2016. [DOI: 10.3390/d8040030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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92
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Tan J, Chan ZY, Lim PE, Koh JKH, Yong HS. A multigene approach to determine the molecular phylogeography of Argiope mangal and Argiope dang (Araneae: Araneidae) and their genetic relationships with the Argiope aetherea species group. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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93
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Tarasov S, Dimitrov D. Multigene phylogenetic analysis redefines dung beetles relationships and classification (Coleoptera: Scarabaeidae: Scarabaeinae). BMC Evol Biol 2016; 16:257. [PMID: 27899070 PMCID: PMC5129633 DOI: 10.1186/s12862-016-0822-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 10/28/2016] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Dung beetles (subfamily Scarabaeinae) are popular model organisms in ecology and developmental biology, and for the last two decades they have experienced a systematics renaissance with the adoption of modern phylogenetic approaches. Within this period 16 key phylogenies and numerous additional studies with limited scope have been published, but higher-level relationships of this pivotal group of beetles remain contentious and current classifications contain many unnatural groupings. The present study provides a robust phylogenetic framework and a revised classification of dung beetles. RESULTS We assembled the so far largest molecular dataset for dung beetles using sequences of 8 gene regions and 547 terminals including the outgroup taxa. This dataset was analyzed using Bayesian, maximum likelihood and parsimony approaches. In order to test the sensitivity of results to different analytical treatments, we evaluated alternative partitioning schemes based on secondary structure, domains and codon position. We assessed substitution models adequacy using Bayesian framework and used these results to exclude partitions where substitution models did not adequately depict the processes that generated the data. We show that exclusion of partitions that failed the model adequacy evaluation has a potential to improve phylogenetic inference, but efficient implementation of this approach on large datasets is problematic and awaits development of new computationally advanced software. In the class Insecta it is uncommon for the results of molecular phylogenetic analysis to lead to substantial changes in classification. However, the results presented here are congruent with recent morphological studies and support the largest change in dung beetle systematics for the last 50 years. Here we propose the revision of the concepts for the tribes Deltochilini (Canthonini), Dichotomiini and Coprini; additionally, we redefine the tribe Sisyphini. We provide and illustrate synapomorphies and diagnostic characters supporting the new concepts to facilitate diagnosability of the redefined tribes. As a result of the proposed changes a large number of genera previously assigned to these tribes are now left outside the redefined tribes and are treated as incertae sedis. CONCLUSIONS The present study redefines dung beetles classification and gives new insight into their phylogeny. It has broad implications for the systematics as well as for various ecological and evolutionary analyses in dung beetles.
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Affiliation(s)
- Sergei Tarasov
- Department of Research and Collections, Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, NO-0318 Oslo Norway
| | - Dimitar Dimitrov
- Department of Research and Collections, Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, NO-0318 Oslo Norway
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94
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Characterization of complete mitochondrial genome of fives tripe wrasse (Thalassoma quinquevittatum, Lay & Bennett, 1839) and phylogenetic analysis. Gene 2016; 598:71-78. [PMID: 27816474 DOI: 10.1016/j.gene.2016.10.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/16/2016] [Accepted: 10/28/2016] [Indexed: 11/21/2022]
Abstract
To further supplement the genome-level features in related species, T. quinquevittatum complete mtDNA was firstly sequenced and de novo assembled by next-generation sequencing. The full-length mtDNA of T. quinquevittatum was a 16,896bp fragment, which was atypical of Labridae, with 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, and a major non-coding control region (D-loop region). Additionally, the mtDNA of T. quinquevittatum exhibited characteristics of A (27.1%), T (29.3%), G (17.8%), and C (25.8%) with a high A+T content (56.4%). Furthermore, the analysis of the average Ka/Ks in the 13 PCGs of three Labridae species indicated a strong purifying selection within this group. Additionally, the phylogenetic analysis based on 13 concatenated PCGs nucleotide and amino acid datasets, showed high value support for the following sister clade among the four genera (T. quinquevittatum, Halichoeres trimaculatus, Halichoeres melanurus, Parajulis poecilepterus). The complete mtDNA of the T. quinquevittatum provided important information for the study in population genetics and evolutionary theory.
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95
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Complete Mitochondrial Genome of the Citrus Spiny Whitefly Aleurocanthus spiniferus (Quaintance) (Hemiptera: Aleyrodidae): Implications for the Phylogeny of Whiteflies. PLoS One 2016; 11:e0161385. [PMID: 27551782 PMCID: PMC4995055 DOI: 10.1371/journal.pone.0161385] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 08/04/2016] [Indexed: 11/20/2022] Open
Abstract
In this study, we sequenced the complete mitochondrial genome (15,220 bp) of the citrus spiny whitefly, Aleurocanthus spiniferus (Quaintance), a well-known pest from the superfamily Aleyrodidae. The A. spiniferus mitogenome contains 36 genes, including 13 protein-coding genes (PCGs), 21 transfer RNAs (tRNA), two ribosomal RNAs (rRNA) and a large non-coding region (control region, CR). Like most whiteflies, the A. spiniferus mitogenome had a large degree of rearrangement due to translocation of the nad3-trnG-cox3 gene cluster. The 13 PCGs initiated with ATN and generally terminated with TAA, although some used TAG or T as stop codons; atp6 showed the highest evolutionary rate, whereas cox2 appeared to have the lowest rate. The A. spiniferus mitogenome had 21 tRNAs with a typical cloverleaf secondary structure composed of four arms. Modeling of the two rRNA genes indicated that their secondary structure was similar to that of other insects. The CR of A. spiniferus was 920 bp and mapped between the nad3-trnG-cox3 and trnI-trnM gene clusters. One potential stem-loop structure and five tandem repeats were identified in the CR. Phylogenetic relationships of 11 species from the Aleyrodidae were analyzed based on the deduced amino acid sequences of the 13 PCGs and evolutionary characteristics were explored. Species with more genetic rearrangements were generally more evolved within the Aleyrodidae.
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96
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Cheng XF, Zhang LP, Yu DN, Storey KB, Zhang JY. The complete mitochondrial genomes of four cockroaches (Insecta: Blattodea) and phylogenetic analyses within cockroaches. Gene 2016; 586:115-22. [DOI: 10.1016/j.gene.2016.03.057] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 03/28/2016] [Accepted: 03/30/2016] [Indexed: 11/17/2022]
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97
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Comparative Mitochondrial Genome Analysis of Eligma narcissus and other Lepidopteran Insects Reveals Conserved Mitochondrial Genome Organization and Phylogenetic Relationships. Sci Rep 2016; 6:26387. [PMID: 27222440 PMCID: PMC4879558 DOI: 10.1038/srep26387] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 04/29/2016] [Indexed: 11/08/2022] Open
Abstract
In this study, we sequenced the complete mitochondrial genome of Eligma narcissus and compared it with 18 other lepidopteran species. The mitochondrial genome (mitogenome) was a circular molecule of 15,376 bp containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and an adenine (A) + thymine (T) − rich region. The positive AT skew (0.007) indicated the occurrence of more As than Ts. The arrangement of 13 PCGs was similar to that of other sequenced lepidopterans. All PCGs were initiated by ATN codons, except for the cytochrome c oxidase subunit 1 (cox1) gene, which was initiated by the CGA sequence, as observed in other lepidopterans. The results of the codon usage analysis indicated that Asn, Ile, Leu, Tyr and Phe were the five most frequent amino acids. All tRNA genes were shown to be folded into the expected typical cloverleaf structure observed for mitochondrial tRNA genes. Phylogenetic relationships were analyzed based on the nucleotide sequences of 13 PCGs from other insect mitogenomes, which confirmed that E. narcissus is a member of the Noctuidae superfamily.
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98
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Klinth MJ, Martinsson S, Erséus C. Phylogeny and species delimitation of North EuropeanLumbricillus(Clitellata, Enchytraeidae). ZOOL SCR 2016. [DOI: 10.1111/zsc.12187] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mårten J. Klinth
- Department of Biological & Environmental Sciences; University of Gothenburg; P.O. Box 463 SE-405 30 Gothenburg Sweden
| | - Svante Martinsson
- Department of Biological & Environmental Sciences; University of Gothenburg; P.O. Box 463 SE-405 30 Gothenburg Sweden
| | - Christer Erséus
- Department of Biological & Environmental Sciences; University of Gothenburg; P.O. Box 463 SE-405 30 Gothenburg Sweden
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99
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Kittel RN, Austin AD, Klopfstein S. Molecular and morphological phylogenetics of chelonine parasitoid wasps (Hymenoptera: Braconidae), with a critical assessment of divergence time estimations. Mol Phylogenet Evol 2016; 101:224-241. [PMID: 27179700 DOI: 10.1016/j.ympev.2016.05.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 05/02/2016] [Accepted: 05/11/2016] [Indexed: 10/21/2022]
Abstract
Parasitoid wasps of the subfamily Cheloninae are both species rich and poorly known. Although the taxonomy of Cheloninae appears to be relatively stable, there is no clear understanding of relationships among higher-level taxa. We here applied molecular phylogenetic analyses using three markers (COI, EF1α, 28S) and 37 morphological characters to elucidate the evolution and systematics of these wasps. Analyses were based on 83 specimens representing 13 genera. All genera except Ascogaster, Phanerotoma, and Pseudophanerotoma formed monophyletic groups; Furcidentia (stat. rev.) is raised to generic rank. Neither Chelonus (Chelonus) nor Chelonus (Microchelonus) were recovered as monophyletic, but together formed a monophyletic lineage. The tribes Chelonini and Odontosphaeropygini formed monophyletic groups, but the Phanerotomini sensu Zettel and Pseudophanerotomini were retrieved as either para- or polyphyletic. The genera comprising the former subfamily Adeliinae were confirmed as being nested within the Cheloninae. To estimate the age of the subfamily, we used 16 fossil taxa. Three approaches were compared: fixed-rate dating, node dating, and total-evidence dating, with age estimates differing greatly between the three methods. Shortcomings of each approach in relation to our dataset are discussed, and none of the age estimates is deemed sufficiently reliable. Given that most dating studies use a single method only, in most cases without presenting analyses on the sensitivity to priors, it is likely that numerous age estimates in the literature suffer from a similar lack of robustness. We argue for a more rigorous approach to dating analyses and for a faithful presentation of uncertainties in divergence time estimates. Given the results of the phylogenetic analysis the following taxonomic changes are proposed: Furcidentia Zettel (stat. rev.), previously treated as a subgenus of Pseudophanerotoma Zettel is raised to generic rank; Microchelonus Szépligeti (syn. nov.), variously treated by previous authors, is proposed as a junior synonym of Chelonus Jurine; the following subgenera of Microchelonus - Baculonus Braet & van Achterberg (syn. nov.), Carinichelonus Tobias (syn. nov.) and Scabrichelonus He, Chen & van Achterberg (syn. nov.), are proposed as junior synonyms of Chelonus; a number of new species names are proposed due to homonyms resulting from the above changes and these are listed in the paper.
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Affiliation(s)
- Rebecca N Kittel
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia.
| | - Andrew D Austin
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Seraina Klopfstein
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; Naturhistorisches Museum der Burgergemeinde Bern, Bernastr. 15, CH-3005 Bern, Switzerland
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100
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Wang K, Li X, Ding S, Wang N, Mao M, Wang M, Yang D. The complete mitochondrial genome of the Atylotus miser (Diptera: Tabanomorpha: Tabanidae), with mitochondrial genome phylogeny of lower Brachycera (Orthorrhapha). Gene 2016; 586:184-96. [PMID: 27063560 DOI: 10.1016/j.gene.2016.04.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/22/2016] [Accepted: 04/05/2016] [Indexed: 11/25/2022]
Abstract
Brachycera is a clade with over 80,000 described species and originated from the Mesozoic, and its larvae employ comprehensive feeding strategies. The phylogeny of the lower Brachycera has been studied intensively over the past decades. In order to supplement the lack of genetic data in this important group, we sequenced the complete mitochondrial (mt) genome of Atylotus miser as well as the nearly complete mt genomes of another 11 orthorrhaphous flies. The mt genome of A. miser is 15,858bp, which is typical of Diptera, with 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a 993bp control region. The rest of the orthorrhaphous mt genomes in our study have the similar structure with A. miser. Additionally, we conducted a phylogenetic analysis of 20 mt genomes using Maximum-likelihood and Bayesian methods in order to reconstruct the evolutionary relationship of Orthorrhapha. The results show that all infraorders of Brachycera are monophyletic, and a relationship of Tabanomorpha+((Xylophagomorpha+Stratiomyomorpha)+Muscomorpha) has been proposed. Within Xylophagomorpha, Nemestrinoidae forms the sister group of Xylophagidae.
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Affiliation(s)
- Kai Wang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Xuankun Li
- Department of Entomology, China Agricultural University, Beijing, China
| | - Shuangmei Ding
- Department of Entomology, China Agricultural University, Beijing, China
| | - Ning Wang
- Department of Entomology, China Agricultural University, Beijing, China; Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Meng Mao
- School of Biological Sciences, University of Wollongong, Wollongong, Australia
| | - Mengqing Wang
- Department of Entomology, China Agricultural University, Beijing, China; Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing, China.
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