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Kapoor S, Yang YT, Hall RN, Gasser RB, Bowles VM, Perry T, Anstead CA. Complete Mitochondrial Genome for Lucilia cuprina dorsalis (Diptera: Calliphoridae) from the Northern Territory, Australia. Genes (Basel) 2024; 15:506. [PMID: 38674440 PMCID: PMC11050061 DOI: 10.3390/genes15040506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The Australian sheep blowfly, Lucilia cuprina dorsalis, is a major sheep ectoparasite causing subcutaneous myiasis (flystrike), which can lead to reduced livestock productivity and, in severe instances, death of the affected animals. It is also a primary colonizer of carrion, an efficient pollinator, and used in maggot debridement therapy and forensic investigations. In this study, we report the complete mitochondrial (mt) genome of L. c. dorsalis from the Northern Territory (NT), Australia, where sheep are prohibited animals, unlike the rest of Australia. The mt genome is 15,943 bp in length, comprising 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and a non-coding control region. The gene order of the current mt genome is consistent with the previously published L. cuprina mt genomes. Nucleotide composition revealed an AT bias, accounting for 77.5% of total mt genome nucleotides. Phylogenetic analyses of 56 species/taxa of dipterans indicated that L. c. dorsalis and L. sericata are the closest among all sibling species of the genus Lucilia, which helps to explain species evolution within the family Luciliinae. This study provides the first complete mt genome sequence for L. c. dorsalis derived from the NT, Australia to facilitate species identification and the examination of the evolutionary history of these blowflies.
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Affiliation(s)
- Shilpa Kapoor
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.T.Y.); (T.P.)
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia; (R.B.G.); (V.M.B.)
| | - Ying Ting Yang
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.T.Y.); (T.P.)
| | - Robyn N. Hall
- CSIRO Health & Biosecurity, Acton, ACT 2601, Australia;
- Ausvet Pty Ltd., Fremantle, WA 6160, Australia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia; (R.B.G.); (V.M.B.)
| | - Vernon M. Bowles
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia; (R.B.G.); (V.M.B.)
| | - Trent Perry
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.T.Y.); (T.P.)
| | - Clare A. Anstead
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia; (R.B.G.); (V.M.B.)
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Benito JB, Porter ML, Niemiller ML. Comparative mitogenomic analysis of subterranean and surface amphipods (Crustacea, Amphipoda) with special reference to the family Crangonyctidae. BMC Genomics 2024; 25:298. [PMID: 38509489 PMCID: PMC10956265 DOI: 10.1186/s12864-024-10111-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 02/09/2024] [Indexed: 03/22/2024] Open
Abstract
Mitochondrial genomes play important roles in studying genome evolution, phylogenetic analyses, and species identification. Amphipods (Class Malacostraca, Order Amphipoda) are one of the most ecologically diverse crustacean groups occurring in a diverse array of aquatic and terrestrial environments globally, from freshwater streams and lakes to groundwater aquifers and the deep sea, but we have a limited understanding of how habitat influences the molecular evolution of mitochondrial energy metabolism. Subterranean amphipods likely experience different evolutionary pressures on energy management compared to surface-dwelling taxa that generally encounter higher levels of predation and energy resources and live in more variable environments. In this study, we compared the mitogenomes, including the 13 protein-coding genes involved in the oxidative phosphorylation (OXPHOS) pathway, of surface and subterranean amphipods to uncover potentially different molecular signals of energy metabolism between surface and subterranean environments in this diverse crustacean group. We compared base composition, codon usage, gene order rearrangement, conducted comparative mitogenomic and phylogenomic analyses, and examined evolutionary signals of 35 amphipod mitogenomes representing 13 families, with an emphasis on Crangonyctidae. Mitogenome size, AT content, GC-skew, gene order, uncommon start codons, location of putative control region (CR), length of rrnL and intergenic spacers differed between surface and subterranean amphipods. Among crangonyctid amphipods, the spring-dwelling Crangonyx forbesi exhibited a unique gene order, a long nad5 locus, longer rrnL and rrnS loci, and unconventional start codons. Evidence of directional selection was detected in several protein-encoding genes of the OXPHOS pathway in the mitogenomes of surface amphipods, while a signal of purifying selection was more prominent in subterranean species, which is consistent with the hypothesis that the mitogenome of surface-adapted species has evolved in response to a more energy demanding environment compared to subterranean amphipods. Overall, gene order, locations of non-coding regions, and base-substitution rates points to habitat as an important factor influencing the evolution of amphipod mitogenomes.
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Affiliation(s)
- Joseph B Benito
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Megan L Porter
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, 35899, USA.
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Ma T, Zhang C, Huang J. Phylogenetic insights based on the first complete mitochondrial genome of Isomyia nebulosa (Diptera: Calliphoridae). Mitochondrial DNA B Resour 2023; 8:1320-1324. [PMID: 38196796 PMCID: PMC10776078 DOI: 10.1080/23802359.2023.2288916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/24/2023] [Indexed: 01/11/2024] Open
Abstract
To investigate the phylogenetic position of Isomyia Walker, 1860, a genus that suffered from frequent revisions of the taxonomic status following the subfamily Rhiniinae (Diptera, Calliphoridae), we sequenced, assembled, annotated, and analyzed the first complete mitochondrial genome (mitogenome) of Isomyia nebulosa (Townsend, 1917) in this study. This mitogenome is 16,438 bp in length, with a standard set of 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and an A + T riched non-coding region without genetic rearrangement as most dipteran mitogenomes, but long intergenic nucleotides (IGNs) between trnQ and trnM are found. The phylogeny yielded by both Bayesian inference and maximum-likelihood analysis for all mitochondrial PCGs and rRNAs of 23 mitogenomes supports the monophyly of the family Calliphoridae and the subfamilies Calliphorinae, Chrysomyinae, and Luciliinae. In addition, I. nebulosa diverged anterior to the above-mentioned three calliphorid subfamilies with high genetic distances.
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Affiliation(s)
- Ting Ma
- Police Experimental Training Center, Guangdong Police College, Guangzhou, Baiyun, China
| | - Caihong Zhang
- Department of Entomology, College of Plant Protection, South China Agricultural University, Tianhe, Guangzhou, China
| | - Jia Huang
- Department of Entomology, College of Plant Protection, South China Agricultural University, Tianhe, Guangzhou, China
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Shao S, Yang L, Hu G, Li L, Wang Y, Tao L. Application of omics techniques in forensic entomology research. Acta Trop 2023; 246:106985. [PMID: 37473953 DOI: 10.1016/j.actatropica.2023.106985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/22/2023]
Abstract
With the advent of the post-genome era, omics technologies have developed rapidly and are widely used, including in genomics, transcriptomics, proteomics, metabolomics, and microbiome research. These omics techniques are often based on comprehensive and systematic analysis of biological samples using high-throughput analysis methods and bioinformatics, to provide new insights into biological phenomena. Currently, omics techniques are gradually being applied to forensic entomology research and are useful in species identification, phylogenetics, screening for developmentally relevant differentially expressed genes, and the interpretation of behavioral characteristics of forensic-related species at the genetic level. These all provide valuable information for estimating the postmortem interval (PMI). This review mainly discusses the available omics techniques, summarizes the application of omics techniques in forensic entomology, and their future in the field.
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Affiliation(s)
- Shipeng Shao
- Department of Forensic Medicine, Soochow University, Ganjiang East Road, Suzhou, China
| | - Lijun Yang
- Criminal Police Branch, Suzhou Public Security Bureau, Renmin Road, Suzhou, China
| | - Gengwang Hu
- Department of Forensic Medicine, Soochow University, Ganjiang East Road, Suzhou, China
| | - Liangliang Li
- Department of Forensic Medicine, Soochow University, Ganjiang East Road, Suzhou, China
| | - Yu Wang
- Department of Forensic Medicine, Soochow University, Ganjiang East Road, Suzhou, China.
| | - Luyang Tao
- Department of Forensic Medicine, Soochow University, Ganjiang East Road, Suzhou, China
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Kapoor S, Young ND, Yang YT, Batterham P, Gasser RB, Bowles VM, Anstead CA, Perry T. Mitochondrial genomic investigation reveals a clear association between species and genotypes of Lucilia and geographic origin in Australia. Parasit Vectors 2023; 16:279. [PMID: 37573420 PMCID: PMC10423422 DOI: 10.1186/s13071-023-05902-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/27/2023] [Indexed: 08/14/2023] Open
Abstract
BACKGROUND Lucilia cuprina and L. sericata (family Calliphoridae) are globally significant ectoparasites of sheep. Current literature suggests that only one of these blowfly subspecies, L. cuprina dorsalis, is a primary parasite causing myiasis (flystrike) in sheep in Australia. These species and subspecies are difficult to distinguish using morphological features. Hence, being able to accurately identify blowflies is critical for diagnosis and for understanding their relationships with their hosts and environment. METHODS In this study, adult blowflies (5 pools of 17 flies; n = 85) were collected from five locations in different states [New South Wales (NSW), Queensland (QLD), Tasmania (TAS), Victoria (VIC) and Western Australia (WA)] of Australia and their mitochondrial (mt) genomes were assembled. RESULTS Each mt genome assembled was ~ 15 kb in size and encoded 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and a control region. The Lucilia species mt genomes were conserved in structure, and the genes retained the same order and direction. The overall nucleotide composition was heavily biased towards As and Ts-77.7% of the whole genomes. Pairwise nucleotide diversity suggested divergence between Lucilia cuprina cuprina, L. c. dorsalis and L. sericata. Comparative analyses of these mt genomes with published data demonstrated that the blowflies collected from sheep farm in TAS clustered within a clade with L. sericata. The flies collected from an urban location in QLD were more closely related to L. sericata and represented the subspecies L. c. cuprina, whereas the flies collected from sheep farms in NSW, VIC and WA represented the subspecies L. c. dorsalis. CONCLUSIONS Phylogenetic analyses of the mt genomes representing Lucilia from the five geographic locations in Australia supported the previously demonstrated paraphyly of L. cuprina with respect to L. sericata and revealed that L. c. cuprina is distinct from L. c. dorsalis and that L. c. cuprina is more closely related to L. sericata than L. c. dorsalis. The mt genomes reported here provide an important molecular resource to develop tools for species- and subspecies-level identification of Lucilia from different geographical regions across Australia.
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Affiliation(s)
- Shilpa Kapoor
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010 Australia
- Department of Veterinary Biosciences, Faculty of Science, Melbourne Veterinary School, The University of Melbourne, Building 400, Parkville, VIC 3010 Australia
| | - Neil D. Young
- Department of Veterinary Biosciences, Faculty of Science, Melbourne Veterinary School, The University of Melbourne, Building 400, Parkville, VIC 3010 Australia
| | - Ying Ting Yang
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Philip Batterham
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Faculty of Science, Melbourne Veterinary School, The University of Melbourne, Building 400, Parkville, VIC 3010 Australia
| | - Vernon M. Bowles
- Department of Veterinary Biosciences, Faculty of Science, Melbourne Veterinary School, The University of Melbourne, Building 400, Parkville, VIC 3010 Australia
| | - Clare A. Anstead
- Department of Veterinary Biosciences, Faculty of Science, Melbourne Veterinary School, The University of Melbourne, Building 400, Parkville, VIC 3010 Australia
| | - Trent Perry
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010 Australia
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The first complete mitochondrial genome sequences for Ulidiidae and phylogenetic analysis of Diptera. Mol Biol Rep 2023; 50:2501-2510. [PMID: 36609752 DOI: 10.1007/s11033-022-07869-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 01/09/2023]
Abstract
BACKGROUND Tetanops sintenisi is a pest that mainly damages the root of quinoa (Chenopodium quinoa) and it is first discovered in China in 2018. METHODS AND RESULTS Here, the complete mitochondrial genome (mitogenome) of T. sintenisi was sequenced and compared with the mitogenomes of other Diptera species. The results revealed that the mitogenome of T. sintenisi is 15,763 bp in length (GenBank accession number: MT795181) and is comprised of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA genes, and a non-coding A + T-rich region (959 bp). The highly conserved gene arrangement of the mitogenome of T. sintenisi was identical to that of other Diptera insects. Twelve PCGs contained the typical insect start codon ATN, while cox1 had CGA as the start codon. The genes cox2, nad4, and nad1 contained an incomplete termination codon T; nad3, nad5, and cob contained the complete termination codon TAG; and the remaining seven PCGs contained the termination codon TAA. All tRNA genes were predicted to fold into the typical cloverleaf secondary structure. Phylogenetic analysis of 48 species based on the mitogenome sequence revealed that T. sintenisi clustered with the Tephritidae family, indicating that T. sintenisi and Tephritidae have a close phylogenetic relationship. CONCLUSIONS The phylogenetic relationship of T. sintenisi based on the mitogenome is consistent with the traditional morphological taxonomy, according to which T. sintenisi belongs to the family Otitidae, which is closely related to the family Muscidae.
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Tandonnet S, Krsticevic F, Basika T, Papathanos PA, Torres TT, Scott MJ. A chromosomal-scale reference genome of the New World Screwworm, Cochliomyia hominivorax. DNA Res 2022; 30:6825375. [PMID: 36370138 PMCID: PMC9835758 DOI: 10.1093/dnares/dsac042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/23/2022] [Accepted: 11/10/2022] [Indexed: 11/13/2022] Open
Abstract
The New World Screwworm, Cochliomyia hominivorax (Calliphoridae), is the most important myiasis-causing species in America. Screwworm myiasis is a zoonosis that can cause severe lesions in livestock, domesticated and wild animals, and occasionally in people. Beyond the sanitary problems associated with this species, these infestations negatively impact economic sectors, such as the cattle industry. Here, we present a chromosome-scale assembly of C. hominivorax's genome, organized in 6 chromosome-length and 515 unplaced scaffolds spanning 534 Mb. There was a clear correspondence between the D. melanogaster linkage groups A-E and the chromosomal-scale scaffolds. Chromosome quotient (CQ) analysis identified a single scaffold from the X chromosome that contains most of the orthologs of genes that are on the D. melanogaster fourth chromosome (linkage group F or dot chromosome). CQ analysis also identified potential X and Y unplaced scaffolds and genes. Y-linkage for selected regions was confirmed by PCR with male and female DNA. Some of the long chromosome-scale scaffolds include Y-linked sequences, suggesting misassembly of these regions. These resources will provide a basis for future studies aiming at understanding the biology and evolution of this devastating obligate parasite.
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Affiliation(s)
- Sophie Tandonnet
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo (USP), São Paulo, SP 05508-090, Brazil
| | - Flavia Krsticevic
- Department of Entomology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Tatiana Basika
- Present address: Pasteur+INIA Joint Unit, Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo Uruguay
| | - Philippos A Papathanos
- Department of Entomology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Tatiana T Torres
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo (USP), São Paulo, SP 05508-090, Brazil
| | - Maxwell J Scott
- To whom correspondence should be addressed. Tel: +1 919 515 0275; Fax: +1 919 515 7716.
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Yang W, Dong R, Song X, Yu H. Complete mitochondrial genome analysis and molecular phylogenetic implications of Kennelia xylinana (Lepidoptera: Tortricidae). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2022; 111:e21912. [PMID: 35535464 DOI: 10.1002/arch.21912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 04/21/2022] [Accepted: 04/26/2022] [Indexed: 06/14/2023]
Abstract
Kennelia is a small genus in Tortricidae that is distributed in the Oriental and Palaearctic regions, and its taxonomic position within the subfamily Olethreutinae is controversial. For a comprehensive understanding of the genus, we sequenced the mitogenome of Kennelia xylinana, the type species of Kennelia, and Ancylis unculana, a species of Enarmoniini; analyzed the mitogenome characteristics of K. xylinana; and explored its phylogenetic position. Similar to other members of Lepidoptera, the mitogenome of K. xylinana is 15,762-bp long and consists of 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes, and a noncoding control region. In particular, we found a structure (TATAATTAATAA)11 in the middle of the AT-rich region. Based on the Bayesian inference and maximum likelihood analyses of the 13 PCGs of 40 tortricid species, representing 8 tribes of 2 subfamilies, K. xylinana was clustered with two members of Enarmoniini, A. unculana and Loboschiza koenigiana, and formed highly supported monophyly. The results indicate that Kennelia should be placed in the tribe Enarmoniini.
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Affiliation(s)
- Wenxu Yang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Ruiqin Dong
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Xueling Song
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Haili Yu
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi'an, China
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Govindharaj GPP, Babu SB, Choudhary JS, Asad M, Chidambaranathan P, Gadratagi BG, Rath PC, Naaz N, Jaremko M, Qureshi KA, Kumar U. Genome Organization and Comparative Evolutionary Mitochondriomics of Brown Planthopper, Nilaparvata lugens Biotype 4 Using Next Generation Sequencing (NGS). Life (Basel) 2022; 12:life12091289. [PMID: 36143326 PMCID: PMC9506247 DOI: 10.3390/life12091289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/13/2022] [Accepted: 08/15/2022] [Indexed: 11/27/2022] Open
Abstract
Nilaparvata lugens is the main rice pest in India. Until now, the Indian N. lugens mitochondrial genome has not been sequenced, which is a very important basis for population genetics and phylogenetic evolution studies. An attempt was made to sequence two examples of the whole mitochondrial genome of N. lugens biotype 4 from the Indian population for the first time. The mitogenomes of N. lugens are 16,072 and 16,081 bp long with 77.50% and 77.45% A + T contents, respectively, for both of the samples. The mitochondrial genome of N. lugens contains 37 genes, including 13 protein-coding genes (PCGs) (cox1-3, atp6, atp8, nad1-6, nad4l, and cob), 22 transfer RNA genes, and two ribosomal RNA (rrnS and rrnL) subunits genes, which are typical of metazoan mitogenomes. However, both samples of N. lugens mitogenome in the present study retained one extra copy of the trnC gene. Additionally, we also found 93 bp lengths for the atp8 gene in both of the samples, which were 60–70 bp less than that of the other sequenced mitogenomes of hemipteran insects. The phylogenetic analysis of the 19 delphacids mitogenome dataset yielded two identical topologies when rooted with Ugyops sp. in one clade, and the remaining species formed another clade with P. maidis and M. muiri being sisters to the remaining species. Further, the genus Nilaparvata formed a separate subclade with the other genera (Sogatella, Laodelphax, Changeondelphax, and Unkanodes) of Delphacidae. Additionally, the relationship among the biotypes of N. lugens was recovered as the present study samples (biotype-4) were separated from the three biotypes reported earlier. The present study provides the reference mitogenome for N. lugens biotype 4 that may be utilized for biotype differentiation and molecular-aspect-based future studies of N. lugens.
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Affiliation(s)
- Guru-Pirasanna-Pandi Govindharaj
- Division of Crop Protection, ICAR-National Rice Research Institute, Cuttack 753006, India
- Correspondence: (G.-P.-P.G.); (J.S.C.); (U.K.)
| | - Soumya Bharti Babu
- Division of Crop Protection, ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Jaipal Singh Choudhary
- ICAR-Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi 834010, India
- Correspondence: (G.-P.-P.G.); (J.S.C.); (U.K.)
| | - Muhammad Asad
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | | | - Basana-Gowda Gadratagi
- Division of Crop Protection, ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Prakash Chandra Rath
- Division of Crop Protection, ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Naiyar Naaz
- ICAR-Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi 834010, India
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Kamal Ahmad Qureshi
- Department of Pharmaceutics, Unaizah College of Pharmacy, Qassim University, Unaizah 51911, Saudi Arabia
| | - Uttam Kumar
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (G.-P.-P.G.); (J.S.C.); (U.K.)
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Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies. Sci Rep 2022; 12:7028. [PMID: 35487927 PMCID: PMC9054809 DOI: 10.1038/s41598-022-10547-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/21/2022] [Indexed: 11/08/2022] Open
Abstract
Uziflies (Family: Tachinidae) are dipteran endoparasites of sericigenous insects which cause major economic loss in the silk industry globally. Here, we are presenting the first full mitogenome of Blepharipa sp. (Acc: KY644698, 15,080 bp, A + T = 78.41%), a dipteran parasitoid of Muga silkworm (Antheraea assamensis) found in the Indian states of Assam and Meghalaya. This study has confirmed that Blepharipa sp. mitogenome gene content and arrangement is similar to other Tachinidae and Sarcophagidae flies of Oestroidea superfamily, typical of ancestral Diptera. Although, Calliphoridae and Oestridae flies have undergone tRNA translocation and insertion, forming unique intergenic spacers (IGS) and overlapping regions (OL) and a few of them (IGS, OL) have been conserved across Oestroidea flies. The Tachinidae mitogenomes exhibit more AT content and AT biased codons in their protein-coding genes (PCGs) than the Oestroidea counterpart. About 92.07% of all (3722) codons in PCGs of this new species have A/T in their 3rd codon position. The high proportion of AT and repeats in the control region (CR) affects sequence coverage, resulting in a short CR (Blepharipa sp.: 168 bp) and a smaller tachinid mitogenome. Our research unveils those genes with a high AT content had a reduced effective number of codons, leading to high codon usage bias. The neutrality test shows that natural selection has a stronger influence on codon usage bias than directed mutational pressure. This study also reveals that longer PCGs (e.g., nad5, cox1) have a higher codon usage bias than shorter PCGs (e.g., atp8, nad4l). The divergence rates increase nonlinearly as AT content at the 3rd codon position increases and higher rate of synonymous divergence than nonsynonymous divergence causes strong purifying selection. The phylogenetic analysis explains that Blepharipa sp. is well suited in the family of insectivorous tachinid maggots. It's possible that biased codon usage in the Tachinidae family reduces the effective number of codons, and purifying selection retains the core functions in their mitogenome, which could help with efficient metabolism in their endo-parasitic life style and survival strategy.
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Sarwar H, Zhao WT, Kibet CJ, Sitko J, Nie P. Morphological and complete mitogenomic characterisation of the acanthocephalan Polymorphus minutus infecting the duck Anas platyrhynchos. Folia Parasitol (Praha) 2021; 68. [PMID: 34152291 DOI: 10.14411/fp.2021.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 01/29/2021] [Indexed: 11/19/2022]
Abstract
Morphological characteristics of the acanthocephalan Polymorphus minutus (Goeze, 1782), which was collected from the duck Anas platyrhynchos Linnaeus in the Czech Republic, are described. The mitochondrial (mt) genome of P. minutus was sequenced, with a total length of 14,149 bp, comprising 36 genes including 12 protein coding genes (PCGs), 22 transfer RNA (tRNA) genes and two ribosomal RNA genes (rrnL and rrnS). This genome is similar to the mt genomes of other syndermatan species. All these genes were encoded on the same DNA strand and in the same orientation. The overall nucleotide composition of the P. minutus mt genome was 38.2% T, 27.3% G, 26.2% A, and 8.3% C. The amino acid sequences of 12 PCGs for mt genomes of 28 platyzoans, including P. minutus, were used for phylogenetic analysis, and the resulting topology recovers P. minutus as sister to Southwellina hispida (Van Cleave, 1925), and the two taxa form a sister clade to Centrorhynchus aluconis (Müller, 1780) and Plagiorhynchus transversus (Rudolphi, 1819), which are all species in the Palaeacanthocephala, thus supporting the monophyly of this class.
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Affiliation(s)
- Huda Sarwar
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Ting Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Caroline Jepkorir Kibet
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | | | - Pin Nie
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,School of Marine Science and Engineering, Qingdao Agriculture University, Qingdao, China
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12
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Costa-Júnior LM, Chaves DP, Brito DRB, Santos VAFD, Costa-Júnior HN, Barros ATM. A review on the occurrence of Cochliomyia hominivorax (Diptera: Calliphoridae) in Brazil. ACTA ACUST UNITED AC 2020; 28:548-562. [PMID: 31483031 DOI: 10.1590/s1984-29612019059] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/03/2019] [Indexed: 11/22/2022]
Abstract
Cochliomyia hominivorax (Coquerel, 1858), the New World screwworm, causes primary myiasis in wild and domestic animals in tropical and subtropical regions of Brazil. Although this species is considered to occur throughout the country, organized information about its recorded distribution has not been available until now. This article aimed to provide a comprehensive review of the historical and current data published on both immature (myiasis) and adult stages of C. hominivorax in Brazil. A total of 174 articles were found; of these, 141 articles reported myiasis cases in cattle (146 records), humans (68 records), and other mammalian hosts (40 records), and captures of adult flies were reported in 33 articles. C. hominivorax is widespread in Brazil, having been recorded in 208 municipalities in all major biomes of the country.
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Affiliation(s)
- Livio Martins Costa-Júnior
- Laboratório de Controle de Parasitos, Centro de Ciências Biológicas e da Saúde, Universidade Federal do Maranhão - UFMA, São Luís, MA, Brasil
| | - Daniel Praseres Chaves
- Departamento de Patologia, Centro de Ciências Agrárias, Universidade Federal do Maranhão - UFMA, São Luís, MA, Brasil
| | | | - Vitor Augusto Ferreira Dos Santos
- Laboratório de Controle de Parasitos, Centro de Ciências Biológicas e da Saúde, Universidade Federal do Maranhão - UFMA, São Luís, MA, Brasil
| | - Henrique Nelson Costa-Júnior
- Laboratório de Controle de Parasitos, Centro de Ciências Biológicas e da Saúde, Universidade Federal do Maranhão - UFMA, São Luís, MA, Brasil
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13
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Five mitochondrial genomes of black fungus gnats (Sciaridae) and their phylogenetic implications. Int J Biol Macromol 2020; 150:200-205. [PMID: 32004603 DOI: 10.1016/j.ijbiomac.2020.01.271] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 01/26/2020] [Accepted: 01/27/2020] [Indexed: 11/21/2022]
Abstract
Sciaridae is a family of great species diversity, distributed worldwide, that includes important agricultural pests of cultivated mushrooms and plants produced in greenhouses. Here we sequenced five nearly complete mitochondrial genomes representing three subfamilies of Sciaridae. The lengths of these mitogenomes range from 13,849 bp to 16,923 bp with 13 protein-coding genes (PCGs), 20-22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region (CR). Compared with other dipteran species, rearrangements in Sciaridae are more common. Inversion or transition is observed frequently of trnL2, and in the tRNA clusters trnI-trnQ-trnM, trnW-trnC-trnY, and trnA-trnR-trnN-trnS1-trnE-trnF. Phylogenetic relationships within the family were reconstructed based on these newly sequenced species, combined with the published mitogenomes of related families, and recovered the topology within Sciaroidea as Cecidomyiidae + (Sciaridae + Keroplatidae). Relationships recovered within Sciaridae were Sciarinae + ('Pseudolycoriella group' + Megalosphyinae).
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Gemmellaro MD, Hamilton GC, Ware JL. Review of Molecular Identification Techniques for Forensically Important Diptera. JOURNAL OF MEDICAL ENTOMOLOGY 2019; 56:887-902. [PMID: 31173634 DOI: 10.1093/jme/tjz040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Indexed: 06/09/2023]
Abstract
The medico-legal section of forensic entomology focuses on the analysis of insects associated with a corpse. Such insects are identified, and their life history characteristics are evaluated to provide information related to the corpse, such as postmortem interval and time of colonization. Forensically important insects are commonly identified using dichotomous keys, which rely on morphological characteristics. Morphological identifications can pose a challenge as local keys are not always available and can be difficult to use, especially when identifying juvenile stages. If a specimen is damaged, certain keys cannot be used for identification. In contrast, molecular identification can be a better instrument to identify forensically important insects, regardless of life stage or specimen completeness. Despite more than 20 yr since the first use of molecular data for the identification of forensic insects, there is little overlap in gene selection or phylogenetic methodology among studies, and this inconsistency reduces efficiency. Several methods such as genetic distance, reciprocal monophyly, or character-based methods have been implemented in forensic identification studies. It can be difficult to compare the results of studies that employ these different methods. Here we present a comprehensive review of the published results for the molecular identification of Diptera of forensic interest, with an emphasis on evaluating variation among studies in gene selection and phylogenetic methodology.
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Affiliation(s)
| | | | - Jessica L Ware
- Department of Entomology, Rutgers University, New Brunswick, NJ
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15
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Li XD, Jiang GF, Yan LY, Li R, Mu Y, Deng WA. Positive Selection Drove the Adaptation of Mitochondrial Genes to the Demands of Flight and High-Altitude Environments in Grasshoppers. Front Genet 2018; 9:605. [PMID: 30568672 PMCID: PMC6290170 DOI: 10.3389/fgene.2018.00605] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 11/19/2018] [Indexed: 01/23/2023] Open
Abstract
The molecular evolution of mitochondrial genes responds to changes in energy requirements and to high altitude adaptation in animals, but this has not been fully explored in invertebrates. The evolution of atmospheric oxygen content from high to low necessarily affects the energy requirements of insect movement. We examined 13 mitochondrial protein-coding genes (PCGs) of grasshoppers to test whether the adaptive evolution of genes involved in energy metabolism occurs in changes in atmospheric oxygen content and high altitude adaptation. Our molecular evolutionary analysis of the 13 PCGs in 15 species of flying grasshoppers and 13 related flightless grasshoppers indicated that, similar to previous studies, flightless grasshoppers have experienced relaxed selection. We found evidence of significant positive selection in the genes ATP8, COX3, ND2, ND4, ND4L, ND5, and ND6 in flying lineages. This results suggested that episodic positive selection allowed the mitochondrial genes of flying grasshoppers to adapt to increased energy demands during the continuous reduction of atmospheric oxygen content. Our analysis of five grasshopper endemic to the Tibetan Plateau and 13 non-Tibetan grasshoppers indicated that, due to positive selection, more non-synonymous nucleotide substitutions accumulated in Tibetan grasshoppers than in non-Tibetan grasshoppers. We also found evidence for significant positive selection in the genes ATP6, ND2, ND3, ND4, and ND5 in Tibetan lineages. Our results thus strongly suggest that, in grasshoppers, positive selection drives mitochondrial genes to better adapt both to the energy requirements of flight and to the high altitude of the Tibetan Plateau.
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Affiliation(s)
- Xiao-Dong Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
- School of Chemistry and Bioengineering, Hechi University, Yizhou, China
| | - Guo-Fang Jiang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
- College of Oceanology and Food Sciences, Quanzhou Normal University, Quanzhou, China
| | - Li-Yun Yan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ran Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yuan Mu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wei-An Deng
- School of Chemistry and Bioengineering, Hechi University, Yizhou, China
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16
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Schoofs KR, Krzeminska Ahmadzai U, Goodwin W. Analysis of the complete mitochondrial genomes of two forensically important blowfly species: Lucilia caesar and Lucilia illustris. Mitochondrial DNA B Resour 2018; 3:1114-1116. [PMID: 33644383 PMCID: PMC7871984 DOI: 10.1080/23802359.2018.1457991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Blowfly species of the family Calliphoridae can be used in forensic investigations to estimate the minimum post-mortem interval (PMImin). Lucilia caesar and Lucilia illustris (Diptera: Calliphoridae) are closely related and phenotypically similar, making reliable identification difficult. To identify potential genetic markers to distinguish these species, five complete mitochondrial genomes were sequenced: three for L. caesar (KM657111–KM657113) and two for L. illustris (KM657109, KM657110). The ND6 gene contained the most species-specific SNPs (1.71%), followed by the ND5 gene (1.68%) and the COI gene (1.56%), identifying ND6 and ND5 as valuable loci for differentiating L. caesar and L. illustris specimens.
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Affiliation(s)
- Kathleen R. Schoofs
- School of Forensic and Applied Sciences, University of Central Lancashire, Preston, UK
| | | | - William Goodwin
- School of Forensic and Applied Sciences, University of Central Lancashire, Preston, UK
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17
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Dupuis JR, Guerrero FD, Skoda SR, Phillips PL, Welch JB, Schlater JL, Azeredo-Espin AML, Pérez de León AA, Geib SM. Molecular Characterization of the 2016 New World Screwworm (Diptera: Calliphoridae) Outbreak in the Florida Keys. JOURNAL OF MEDICAL ENTOMOLOGY 2018; 55:938-946. [PMID: 29788142 DOI: 10.1093/jme/tjy078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Indexed: 06/08/2023]
Abstract
New World screwworm (NWS), Cochliomyia hominivorax (Coquerel 1858) (Diptera: Calliphoridae), is a myiasis-causing fly that can be a serious threat to the health of livestock, wildlife, and humans. Its progressive eradication from the southern United States, Mexico, and Central America from the 1950s to 2000s is an excellent example of successful pest management using sterile insect technique (SIT). In late 2016, autochthonous NWS were detected in the Florida Keys, representing this species' first invasion in the United States in >30 yr. Rapid use of quarantine and SIT was successful in eliminating the infestation by early 2017; however, the geographic source of this infestation remains unknown. Here, we use amplicon sequencing to generate mitochondrial and nuclear sequence data representing all confirmed cases of NWS from this infestation, and compare these sequences to preexisting data sets sampling the native distribution of NWS. We ask two questions regarding the FL Keys outbreak. First, is this infestation the result of a single invasion from one source, or multiple invasions from different sources? And second, what is the geographic origin of this invasion? We found virtually no sequence variation between specimens collected from the FL Keys outbreak, which is consistent with a single source of introduction. However, we also found very little geographic resolution in any of the data sets, which precludes identification of the source of this outbreak. Our lack of success in answering our second question speaks to the need for finer-scale genetic or genomic assessments of NWS population structure, which would facilitate source determination of potential future outbreaks.
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Affiliation(s)
- Julian R Dupuis
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, HI
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, HI
| | - Felix D Guerrero
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Kerrville, TX
| | - Steven R Skoda
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Kerrville, TX
| | - Pamela L Phillips
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Kerrville, TX
| | - John B Welch
- USDA-APHIS, International Services, Action Programs, College Station, TX
| | - Jack L Schlater
- USDA-APHIS, National Veterinary Services Laboratory, Ames, IA
| | - Ana Maria L Azeredo-Espin
- Centro de Biologia Molecular e Engenharia Genética and Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas Instituto de Biologia, São Paulo, Brazil
| | - Adalberto A Pérez de León
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Kerrville, TX
| | - Scott M Geib
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, HI
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18
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Stamper T, Wong ES, Timm A, DeBry RW. Validating sonication as a DNA extraction method for use with carrion flies. Forensic Sci Int 2017; 275:171-177. [DOI: 10.1016/j.forsciint.2017.02.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 01/27/2017] [Accepted: 02/15/2017] [Indexed: 11/28/2022]
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Anstead CA, Perry T, Richards S, Korhonen PK, Young ND, Bowles VM, Batterham P, Gasser RB. The Battle Against Flystrike - Past Research and New Prospects Through Genomics. ADVANCES IN PARASITOLOGY 2017; 98:227-281. [PMID: 28942770 DOI: 10.1016/bs.apar.2017.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Flystrike, or cutaneous myiasis, is caused by blow fly larvae of the genus Lucilia. This disease is a major problem in countries with large sheep populations. In Australia, Lucilia cuprina (Wiedemann, 1830) is the principal fly involved in flystrike. While much research has been conducted on L. cuprina, including physical, chemical, immunological, genetic and biological investigations, the molecular biology of this fly is still poorly understood. The recent sequencing, assembly and annotation of the draft genome and analyses of selected transcriptomes of L. cuprina have given a first global glimpse of its molecular biology and insights into host-fly interactions, insecticide resistance genes and intervention targets. The present article introduces L. cuprina, flystrike and associated issues, details past control efforts and research foci, reviews salient aspects of the L. cuprina genome project and discusses how the new genomic and transcriptomic resources for this fly might accelerate fundamental molecular research of L. cuprina towards developing new methods for the treatment and control of flystrike.
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Affiliation(s)
| | - Trent Perry
- The University of Melbourne, Parkville, VIC, Australia
| | | | | | - Neil D Young
- The University of Melbourne, Parkville, VIC, Australia
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20
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Li X, Li W, Ding S, Cameron SL, Mao M, Shi L, Yang D. Mitochondrial Genomes Provide Insights into the Phylogeny of Lauxanioidea (Diptera: Cyclorrhapha). Int J Mol Sci 2017; 18:E773. [PMID: 28420076 PMCID: PMC5412357 DOI: 10.3390/ijms18040773] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/23/2017] [Accepted: 04/01/2017] [Indexed: 11/17/2022] Open
Abstract
The superfamily Lauxanioidea is a significant dipteran clade including over 2500 known species in three families: Lauxaniidae, Celyphidae and Chamaemyiidae. We sequenced the first five (three complete and two partial) lauxanioid mitochondrial (mt) genomes, and used them to reconstruct the phylogeny of this group. The lauxanioid mt genomes are typical of the Diptera, containing all 37 genes usually present in bilaterian animals. A total of three conserved intergenic sequences have been reported across the Cyclorrhapha. The inferred secondary structure of 22 tRNAs suggested five substitution patterns among the Cyclorrhapha. The control region in the Lauxanioidea has apparently evolved very fast, but four conserved structural elements were detected in all three complete mt genome sequences. Phylogenetic relationships based on the mt genome data were inferred by Maximum Likelihood and Bayesian methods. The traditional relationships between families within the Lauxanioidea, (Chamaemyiidae + (Lauxaniidae + Celyphidae)), were corroborated; however, the higher-level relationships between cyclorrhaphan superfamilies are mostly poorly supported.
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Affiliation(s)
- Xuankun Li
- Department of Entomology, China Agricultural University, Beijing 100193, China.
| | - Wenliang Li
- College of Forestry, Henan University of Science and Technology, Luoyang 471023, China.
| | - Shuangmei Ding
- Department of Entomology, China Agricultural University, Beijing 100193, China.
| | - Stephen L Cameron
- Department of Entomology, Purdue University, West Lafayette, IN 47907, USA.
| | - Meng Mao
- Department of Plant and Environmental Protection Science, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
| | - Li Shi
- College of Agronomy, Inner Mongolia Agricultural University, Hohhot 010018, China.
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing 100193, China.
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21
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Tandonnet S, Torres TT. Traditional versus 3' RNA-seq in a non-model species. GENOMICS DATA 2016; 11:9-16. [PMID: 27909684 PMCID: PMC5124356 DOI: 10.1016/j.gdata.2016.11.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/01/2016] [Accepted: 11/02/2016] [Indexed: 11/30/2022]
Abstract
One limitation of the widely used RNA-seq method is that long transcripts are represented by more reads than shorter transcripts, resulting in a biased estimation of expression levels. The 3′ RNA-seq method, which yields only one sequence per transcript, bypasses this limitation. Here, RNA was extracted from two samples, in which we expected to find differentially expressed genes. Each was processed by both traditional and 3′ RNA-seq protocols. Both methods yielded similar differentially expressed genes and estimated expression levels in a comparable way, confirming they both represent valid tools for RNA-seq analysis. Notably, however, we identified more differentially expressed transcripts with the 3′ RNA-seq method, suggesting a greater power to detect expression variation using this method. Hence, when little genomic information is available for the species studied, the standard RNA-seq presents a better cost-benefit compromise, whereas for model species, the 3′ RNA-seq method might more accurately detect differential expression.
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Affiliation(s)
- Sophie Tandonnet
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Tatiana Teixeira Torres
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil; Research Center on Biodiversity and Computing (BioComp-USP), Universidade de São Paulo (USP), São Paulo, SP, Brazil
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22
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Junqueira ACM, Azeredo-Espin AML, Paulo DF, Marinho MAT, Tomsho LP, Drautz-Moses DI, Purbojati RW, Ratan A, Schuster SC. Large-scale mitogenomics enables insights into Schizophora (Diptera) radiation and population diversity. Sci Rep 2016; 6:21762. [PMID: 26912394 PMCID: PMC4766414 DOI: 10.1038/srep21762] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/28/2016] [Indexed: 11/21/2022] Open
Abstract
True flies are insects of the order Diptera and encompass one of the most diverse groups of animals on Earth. Within dipterans, Schizophora represents a recent radiation of insects that was used as a model to develop a pipeline for generating complete mitogenomes using various sequencing platforms and strategies. 91 mitogenomes from 32 different species were sequenced and assembled with high fidelity, using amplicon, whole genome shotgun or single molecule sequencing approaches. Based on the novel mitogenomes, we estimate the origin of Schizophora within the Cretaceous-Paleogene (K-Pg) boundary, about 68.3 Ma. Detailed analyses of the blowfly family (Calliphoridae) place its origin at 22 Ma, concomitant with the radiation of grazing mammals. The emergence of ectoparasitism within calliphorids was dated 6.95 Ma for the screwworm fly and 2.3 Ma for the Australian sheep blowfly. Varying population histories were observed for the blowfly Chrysomya megacephala and the housefly Musca domestica samples in our dataset. Whereas blowflies (n = 50) appear to have undergone selective sweeps and/or severe bottlenecks in the New World, houseflies (n = 14) display variation among populations from different zoogeographical zones and low levels of gene flow. The reported high-throughput mitogenomics approach for insects enables new insights into schizophoran diversity and population history of flies.
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Affiliation(s)
- Ana Carolina M. Junqueira
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551
| | - Ana Maria L. Azeredo-Espin
- Centro de Biologia Molecular e Engenharia Genética and Departamento de Genética, Evolução e Bioagentes, Universidade Estadual de Campinas, Campinas, SP, 13083-875, Brazil
| | - Daniel F. Paulo
- Centro de Biologia Molecular e Engenharia Genética and Departamento de Genética, Evolução e Bioagentes, Universidade Estadual de Campinas, Campinas, SP, 13083-875, Brazil
| | - Marco Antonio T. Marinho
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Departamento de Biologia, Universidade de São Paulo, Ribeirão Preto, SP, 14040-901, Brazil
| | - Lynn P. Tomsho
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Daniela I. Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551
| | - Rikky W. Purbojati
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551
| | - Aakrosh Ratan
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Stephan C. Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551
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Zhang D, Yan L, Zhang M, Chu H, Cao J, Li K, Hu D, Pape T. Phylogenetic inference of calyptrates, with the first mitogenomes for Gasterophilinae (Diptera: Oestridae) and Paramacronychiinae (Diptera: Sarcophagidae). Int J Biol Sci 2016; 12:489-504. [PMID: 27019632 PMCID: PMC4807417 DOI: 10.7150/ijbs.12148] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 12/22/2015] [Indexed: 11/05/2022] Open
Abstract
The complete mitogenome of the horse stomach bot fly Gasterophilus pecorum (Fabricius) and a near-complete mitogenome of Wohlfahrt's wound myiasis fly Wohlfahrtia magnifica (Schiner) were sequenced. The mitogenomes contain the typical 37 mitogenes found in metazoans, organized in the same order and orientation as in other cyclorrhaphan Diptera. Phylogenetic analyses of mitogenomes from 38 calyptrate taxa with and without two non-calyptrate outgroups were performed using Bayesian Inference and Maximum Likelihood. Three sub-analyses were performed on the concatenated data: (1) not partitioned; (2) partitioned by gene; (3) 3rd codon positions of protein-coding genes omitted. We estimated the contribution of each of the mitochondrial genes for phylogenetic analysis, as well as the effect of some popular methodologies on calyptrate phylogeny reconstruction. In the favoured trees, the Oestroidea are nested within the muscoid grade. Relationships at the family level within Oestroidea are (remaining Calliphoridae (Sarcophagidae (Oestridae, Pollenia + Tachinidae))). Our mito-phylogenetic reconstruction of the Calyptratae presents the most extensive taxon coverage so far, and the risk of long-branch attraction is reduced by an appropriate selection of outgroups. We find that in the Calyptratae the ND2, ND5, ND1, COIII, and COI genes are more phylogenetically informative compared with other mitochondrial protein-coding genes. Our study provides evidence that data partitioning and the inclusion of conserved tRNA genes have little influence on calyptrate phylogeny reconstruction, and that the 3rd codon positions of protein-coding genes are not saturated and therefore should be included.
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Affiliation(s)
- Dong Zhang
- 1. School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Liping Yan
- 1. School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Ming Zhang
- 1. School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Hongjun Chu
- 3. Wildlife Conservation Office of Altay Prefecture, Altay, Xinjiang, China
| | - Jie Cao
- 4. Xinjiang Research Centre for Breeding Przewalski's Horse, Ürümqi, Xinjiang, China
| | - Kai Li
- 1. School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Defu Hu
- 1. School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Thomas Pape
- 2. Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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Ye F, Liu T, King SD, You P. Mitochondrial genomes of two phlebotomine sand flies, Phlebotomus chinensis and Phlebotomus papatasi (Diptera: Nematocera), the first representatives from the family Psychodidae. Parasit Vectors 2015; 8:472. [PMID: 26381614 PMCID: PMC4573934 DOI: 10.1186/s13071-015-1081-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 09/10/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Leishmaniasis is a worldwide but neglected disease of humans and animal transmitted by sand flies, vectors that also transmit other important diseases. Mitochondrial genomes contain abundant information for population genetic and phylogenetic studies, important in disease management. However, the available mitochondrial sequences of these crucial vectors are limited, emphasizing the need for developing more mitochondrial genetic markers. METHODS The complete mitochondrial genome of Phlebotomus chinensis was amplified in eight fragments and sequenced using primer walking. The mitochondrial genome of Phlebotomus papatasi was reconstructed from whole-genome sequencing data available on Genbank. The phylogenetic relationship of 24 selected representatives of Diptera was deduced from codon positions 1 and 2 for 13 protein coding genes, using Bayesian inference (BI) and maximum likelihood (ML) methods. RESULTS We provide the first Phlebotomus (P. chinensis and P. papatasi) mitochondrial genomes. Both genomes contain 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and an A + T-rich region. The gene order of Phlebotomus mitochondrial genomes is identical with the ancestral gene order of insect. Phylogenetic analyses demonstrated that Psychodidae and Tanyderidae are sister taxa. Potential markers for population genetic study of Phlebotomus species were also revealed. CONCLUSION The generated mitochondrial genomes of P. chinensis and P. papatasi represent a useful resource for comparative genomic studies and provide valuable future markers for the population genetic study of these important Leishmania vectors. Our results also preliminary demonstrate the phylogenetic placement of Psychodidae based on their mitochondrial genomes.
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Affiliation(s)
- Fei Ye
- Co-Innovation Center for Qinba regions' sustainable development, College of Life Science, Shaanxi Normal University, Xi'an, 710062, China.
| | - Ting Liu
- Co-Innovation Center for Qinba regions' sustainable development, College of Life Science, Shaanxi Normal University, Xi'an, 710062, China.
| | - Stanley D King
- Department of Biology, Dalhousie University, Halifax, NS, Canada, B3H 4J1.
| | - Ping You
- Co-Innovation Center for Qinba regions' sustainable development, College of Life Science, Shaanxi Normal University, Xi'an, 710062, China.
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Wang YZ, Jin GH, Zhu JY, Wei SJ. The mitochondrial genome of the garden pea leafminer Chromatomyia horticola (Goureau, 1851) (Diptera: Agromyzidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2653-5. [PMID: 26066024 DOI: 10.3109/19401736.2015.1043531] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Here we report the mitochondrial genome sequence of the garden pea leafminer Chromatomyia horticola (Goureau, 1851) (Diptera: Agromyzidae) (GenBank accession no. KR047789). This is the first species with sequenced mitochondrial genome from the genus Chromatomyia. The current length with partial A + T-rich region of this mitochondrial genome is 15,320 bp with an A + T content of 77.54%. All the 13 protein-coding, two rRNA, and 22 tRNA genes were sequenced, except for the A + T-rich region. As in most other sequenced mitochondrial genomes of Diptera, there is no rearrangement compared with the pupative ancestral arrangement of insects. All protein-coding genes start with the ATN start codon except for the gene cox1, which uses abnormal TTG. The A + T-rich region is located between rrnS and trnI with a sequenced length of 503 bp. Phylogenetic analysis using the Bayesian method based on the first and second codon positions of the 13 protein-coding genes recovered the monophyly of Agromyzidae with one species of Chromatomyia and four species of Liriomyza in our study. The superfamily Oestroidea (with Agromyzidae in analysis) is sister to the Opomyzoidea.
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Affiliation(s)
- You-Zhu Wang
- a Key Laboratory of Forest Disaster Warning and Control of Yunnan Province , College of Forestry, Southwest Forestry University , Kunming , China and.,b Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences , Beijing , China
| | - Gui-Hua Jin
- b Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences , Beijing , China
| | - Jia-Ying Zhu
- a Key Laboratory of Forest Disaster Warning and Control of Yunnan Province , College of Forestry, Southwest Forestry University , Kunming , China and
| | - Shu-Jun Wei
- b Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences , Beijing , China
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Bergamo LW, Fresia P, Azeredo-Espin AML. Incongruent nuclear and mitochondrial genetic structure of new world screwworm fly populations due to positive selection of mutations associated with dimethyl- and diethyl-organophosphates resistance. PLoS One 2015; 10:e0128441. [PMID: 26030866 PMCID: PMC4451984 DOI: 10.1371/journal.pone.0128441] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 04/27/2015] [Indexed: 11/30/2022] Open
Abstract
Livestock production is an important economic activity in Brazil, which has been suffering significant losses due to the impact of parasites. The New World screwworm (NWS) fly, Cochliomyia hominivorax, is an ectoparasite and one of the most important myiasis-causing flies endemic to the Americas. The geographic distribution of NWS has been reduced after the implementation of the Sterile Insect Technique (SIT), being eradicated in North America and part of Central America. In South America, C. hominivorax is controlled by chemical insecticides, although indiscriminate use can cause selection of resistant individuals. Previous studies have associated the Gly137Asp and Trp251Leu mutations in the active site of carboxylesterase E3 to resistance of diethyl and dimethyl-organophosphates insecticides, respectively. Here, we have sequenced a fragment of the carboxylesterase E3 gene (ChαE7), comprising part of intron iII, exon eIII, intron iIII and part of exon eIV, and three mitochondrial gene sequences (CR, COI and COII), of NWS flies from 21 locations in South America. These markers were used for population structure analyses and the ChαE7 gene was also investigated to gain insight into the selective pressures that have shaped its evolution. Analysis of molecular variance (AMOVA) and pairwise FST analysis indicated an increased genetic structure between locations in the ChαE7 compared to the concatenated mitochondrial genes. Discriminant analysis of principal components (DAPC) and spatial analysis of molecular variance (SAMOVA) indicated different degrees of genetic structure for all markers, in agreement with the AMOVA results, but with low correlation to geographic data. The NWS fly is considered a panmitic species based on mitochondrial data, while it is structured into three groups considering the ChαE7 gene. A negative association between the two mutations related to organophosphate resistance and Fay & Wu’s H significant negative values for the exons, suggest that these mutations evolved under positive selection.
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Affiliation(s)
- Luana Walravens Bergamo
- Center for Molecular Biology and Genetic Engineering (CBMEG), Campinas State University (UNICAMP), Campinas, SP, Brazil
- Department of Genetics, Evolution and Bioagents (DGEB), Institute of Biology (IB), Campinas State University (UNICAMP), Campinas, SP, Brazil
- * E-mail:
| | - Pablo Fresia
- Center for Molecular Biology and Genetic Engineering (CBMEG), Campinas State University (UNICAMP), Campinas, SP, Brazil
| | - Ana Maria L. Azeredo-Espin
- Center for Molecular Biology and Genetic Engineering (CBMEG), Campinas State University (UNICAMP), Campinas, SP, Brazil
- Department of Genetics, Evolution and Bioagents (DGEB), Institute of Biology (IB), Campinas State University (UNICAMP), Campinas, SP, Brazil
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Choudhary JS, Naaz N, Prabhakar CS, Rao MS, Das B. The mitochondrial genome of the peach fruit fly, Bactrocera zonata (Saunders) (Diptera: Tephritidae): Complete DNA sequence, genome organization, and phylogenetic analysis with other tephritids using next generation DNA sequencing. Gene 2015; 569:191-202. [PMID: 26031235 DOI: 10.1016/j.gene.2015.05.066] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 05/13/2015] [Accepted: 05/27/2015] [Indexed: 02/01/2023]
Abstract
Mitochondrial genome can provide information for genomic structure as well as for phylogenetic analysis and evolutionary biology. The complete 15,935 bp mitochondrial genome of Bactrocera zonata (Diptera: Tephritidae), is assembled from Illumina MiSeq read data. The mitogenome information for B. zonata was compared to the homologous sequences of other tephritids. Annotation indicated that the structure and orientation of 13 protein coding genes (PCGs), 22 tRNA and 2 rRNA sequences were typical of, and similar to, the ten closely related tephritid species. The nucleotide composition shows heavily biased toward As and Ts accounting 73.34% and exhibits a slightly positive AT skew, which is similar to other known tephritid species. All PCGs are initiated by ATN codons, except for cox1 with TCG and atp8 with GTG. Nine PCGs use a common stop codon of TAA or TAG, whereas the remaining four use an incomplete termination codon T or TA likely to be completed by adenylation. All tRNAs have the typical clover-leaf structure, with an exception for trnS((AGN)). Four short intergenic spacers showed high degree of conservation among B. zonata and other ten tephritids. A poly(T) stretch at the 5' end followed by [TA(A)]n-like stretch and a tandem repeats of 39 bp has been observed in CR. The analysis of gene evolutionary rate revealed that the cox1 and atp6 exhibits lowest and highest gene substitution rates, respectively than other genes. The phylogenetic relationships based on Maximum Likelihood method using all protein-coding genes and two ribosomal RNA genes confirmed that B. zonata is closely related to Bactrocera correcta, Bactrocera carambolae, Bactrocera papayae, and Bactrocera philippinensis and Bactrocera dorsalis belonging to B. dorsalis species complex forms a monophyletic clade, which is in accordance with the traditional morphological classification and recent molecular works.
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Affiliation(s)
- Jaipal S Choudhary
- ICAR Research Complex for Eastern Region, Research Centre, Plandu, Ranchi 834 010, Jharkhand, India.
| | - Naiyar Naaz
- ICAR Research Complex for Eastern Region, Research Centre, Plandu, Ranchi 834 010, Jharkhand, India.
| | - Chandra S Prabhakar
- ICAR Research Complex for Eastern Region, Research Centre, Plandu, Ranchi 834 010, Jharkhand, India; Department of Entomology, Bihar Agricultural University, Sabour, Bhagalpur 813 210, Bihar, India.
| | - Mathukumalli Srinivasa Rao
- Central Research Institute for Dryland Agriculture (CRIDA), Santoshnagar, Saidabad PO, Hyderabad 500 059, India.
| | - Bikash Das
- ICAR Research Complex for Eastern Region, Research Centre, Plandu, Ranchi 834 010, Jharkhand, India.
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Li X, Ding S, Cameron SL, Kang Z, Wang Y, Yang D. The first mitochondrial genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997 (Diptera: Sciomyzoidea: Sepsidae), with mitochondrial genome phylogeny of cyclorrhapha. PLoS One 2015; 10:e0123594. [PMID: 25826648 PMCID: PMC4380458 DOI: 10.1371/journal.pone.0123594] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 02/20/2015] [Indexed: 11/18/2022] Open
Abstract
Sepsid flies (Diptera: Sepsidae) are important model insects for sexual selection research. In order to develop mitochondrial (mt) genome data for this significant group, we sequenced the first complete mt genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997. The circular 15,878 bp mt genome is typical of Diptera, containing all 37 genes usually present in bilaterian animals. We discovered inaccurate annotations of fly mt genomes previously deposited on GenBank and thus re-annotated all published mt genomes of Cyclorrhapha. These re-annotations were based on comparative analysis of homologous genes, and provide a statistical analysis of start and stop codon positions. We further detected two 18 bp of conserved intergenic sequences from tRNAGlu-tRNAPhe and ND1-tRNASer(UCN) across Cyclorrhapha, which are the mtTERM binding site motifs. Additionally, we compared automated annotation software MITOS with hand annotation method. Phylogenetic trees based on the mt genome data from Cyclorrhapha were inferred by Maximum-likelihood and Bayesian methods, strongly supported a close relationship between Sepsidae and the Tephritoidea.
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Affiliation(s)
- Xuankun Li
- Department of Entomology, China Agricultural University, Beijing, China
| | - Shuangmei Ding
- Department of Entomology, China Agricultural University, Beijing, China
| | - Stephen L Cameron
- Earth, Environmental & Biological Sciences School, Science & Engineering Faculty, Queensland University of Technology, Brisbane, Australia
| | - Zehui Kang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Yuyu Wang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing, China
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Zhao X, Liang AP. Complete DNA sequence of the mitochondrial genome of the treehopper Leptobelus gazella (Membracoidea: Hemiptera). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3318-9. [DOI: 10.3109/19401736.2015.1018202] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Xing Zhao
- Institute of Zoology, Chinese Academy of Sciences, Beijing, P.R. China and
- University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Ai-Ping Liang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, P.R. China and
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30
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A 454 sequencing approach to dipteran mitochondrial genome research. Genomics 2015; 105:53-60. [DOI: 10.1016/j.ygeno.2014.10.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Revised: 10/29/2014] [Accepted: 10/31/2014] [Indexed: 01/14/2023]
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Zhang B, Nardi F, Hull-Sanders H, Wan X, Liu Y. The complete nucleotide sequence of the mitochondrial genome of Bactrocera minax (Diptera: Tephritidae). PLoS One 2014; 9:e100558. [PMID: 24964138 PMCID: PMC4070923 DOI: 10.1371/journal.pone.0100558] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Accepted: 05/29/2014] [Indexed: 11/18/2022] Open
Abstract
The complete 16,043 bp mitochondrial genome (mitogenome) of Bactrocera minax (Diptera: Tephritidae) has been sequenced. The genome encodes 37 genes usually found in insect mitogenomes. The mitogenome information for B. minax was compared to the homologous sequences of Bactrocera oleae, Bactrocera tryoni, Bactrocera philippinensis, Bactrocera carambolae, Bactrocera papayae, Bactrocera dorsalis, Bactrocera correcta, Bactrocera cucurbitae and Ceratitis capitata. The analysis indicated the structure and organization are typical of, and similar to, the nine closely related species mentioned above, although it contains the lowest genome-wide A+T content (67.3%). Four short intergenic spacers with a high degree of conservation among the nine tephritid species mentioned above and B. minax were observed, which also have clear counterparts in the control regions (CRs). Correlation analysis among these ten tephritid species revealed close positive correlation between the A+T content of zero-fold degenerate sites (P0FD), the ratio of nucleotide substitution frequency at P0FD sites to all degenerate sites (zero-fold degenerate sites, two-fold degenerate sites and four-fold degenerate sites) and amino acid sequence distance (ASD) were found. Further, significant positive correlation was observed between the A+T content of four-fold degenerate sites (P4FD) and the ratio of nucleotide substitution frequency at P4FD sites to all degenerate sites; however, we found significant negative correlation between ASD and the A+T content of P4FD, and the ratio of nucleotide substitution frequency at P4FD sites to all degenerate sites. A higher nucleotide substitution frequency at non-synonymous sites compared to synonymous sites was observed in nad4, the first time that has been observed in an insect mitogenome. A poly(T) stretch at the 5' end of the CR followed by a [TA(A)]n-like stretch was also found. In addition, a highly conserved G+A-rich sequence block was observed in front of the poly(T) stretch among the ten tephritid species and two tandem repeats were present in the CR.
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Affiliation(s)
- Bin Zhang
- Key Lab of Integrated Pest Management of Shandong Province, College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao, China
| | - Francesco Nardi
- Department of Evolutionary Biology, University of Siena, Siena, Italy
| | - Helen Hull-Sanders
- Department of Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Xuanwu Wan
- Sichuan Plant Protection Station, Chengdu, China
| | - Yinghong Liu
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
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Rodovalho CDM, Lyra ML, Ferro M, Bacci M. The mitochondrial genome of the leaf-cutter ant Atta laevigata: a mitogenome with a large number of intergenic spacers. PLoS One 2014; 9:e97117. [PMID: 24828084 PMCID: PMC4020775 DOI: 10.1371/journal.pone.0097117] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 04/02/2014] [Indexed: 01/28/2023] Open
Abstract
In this paper we describe the nearly complete mitochondrial genome of the leaf-cutter ant Atta laevigata, assembled using transcriptomic libraries from Sanger and Illumina next generation sequencing (NGS), and PCR products. This mitogenome was found to be very large (18,729 bp), given the presence of 30 non-coding intergenic spacers (IGS) spanning 3,808 bp. A portion of the putative control region remained unsequenced. The gene content and organization correspond to that inferred for the ancestral pancrustacea, except for two tRNA gene rearrangements that have been described previously in other ants. The IGS were highly variable in length and dispersed through the mitogenome. This pattern was also found for the other hymenopterans in particular for the monophyletic Apocrita. These spacers with unknown function may be valuable for characterizing genome evolution and distinguishing closely related species and individuals. NGS provided better coverage than Sanger sequencing, especially for tRNA and ribosomal subunit genes, thus facilitating efforts to fill in sequence gaps. The results obtained showed that data from transcriptomic libraries contain valuable information for assembling mitogenomes. The present data also provide a source of molecular markers that will be very important for improving our understanding of genomic evolutionary processes and phylogenetic relationships among hymenopterans.
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Affiliation(s)
- Cynara de Melo Rodovalho
- Centro de Estudos de Insetos Sociais, UNESP – Univ Estadual Paulista. Rio Claro, São Paulo, Brazil
- Instituto Oswaldo Cruz, FIOCRUZ – Fundação Oswaldo Cruz. Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mariana Lúcio Lyra
- Departamento de Zoologia, UNESP – Univ Estadual Paulista. Rio Claro, São Paulo, Brazil
| | - Milene Ferro
- Centro de Estudos de Insetos Sociais, UNESP – Univ Estadual Paulista. Rio Claro, São Paulo, Brazil
| | - Maurício Bacci
- Centro de Estudos de Insetos Sociais, UNESP – Univ Estadual Paulista. Rio Claro, São Paulo, Brazil
- Departamento de Bioquímica e Microbiologia, UNESP – Univ Estadual Paulista. Rio Claro, São Paulo, Brazil
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Wang P, Li H, Wang Y, Zhang JH, Dai X, Chang J, Hu BW, Cai WZ. The mitochondrial genome of the plant bug Apolygus lucorum (Hemiptera: Miridae): Presently known as the smallest in Heteroptera. INSECT SCIENCE 2014; 21:159-173. [PMID: 23956187 DOI: 10.1111/1744-7917.12029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/05/2013] [Indexed: 06/02/2023]
Abstract
The complete mitochondrial (mt) genome of the plant bug, Apolygus lucorum, an important cotton pest, has been sequenced and annotated in this study. The entire circular genome is 14 768 bp in size and represents the smallest in presently known heteropteran mt genomes. The mt genome is encoding for two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, 13 protein coding genes and a control region, and the order, content, codon usage and base organization show similarity to a great extent to the hypothetical ancestral model. All protein coding genes use standard initiation codons ATN. Conventional stop codons TAA and TAG have been assigned to the most protein coding genes; however, COIII, ND4 and ND5 genes show incomplete terminator signal (T). All tRNA genes possess the typical clover leaf structure, but the dihydrouridine arm of tRNA(Ser(AGN)) only forms a simple loop. Secondary structure models of rRNA genes are generally in accordance with the former models, although some differences exist in certain parts. Three intergenic spacers have never been found in sequenced mt genomes of Heteroptera. The phylogenetic study based on protein coding genes is largely congruent with previous phylogenetic work. Both Bayesian inference and maximum likelihood analyses highly support the sister relationship of A. lucorum and Lygus lineolaris, and Miridae presents a sister position to Anthocoridae.
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Affiliation(s)
- Pei Wang
- Department of Entomology, China Agricultural University, Beijing
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Simon S, Hadrys H. A comparative analysis of complete mitochondrial genomes among Hexapoda. Mol Phylogenet Evol 2013; 69:393-403. [DOI: 10.1016/j.ympev.2013.03.033] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 02/13/2013] [Accepted: 03/05/2013] [Indexed: 10/27/2022]
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Pan TS, Nie P. The complete mitochondrial genome of Pallisentis celatus (Acanthocephala) with phylogenetic analysis of acanthocephalans and rotifers. Folia Parasitol (Praha) 2013; 60:181-91. [DOI: 10.14411/fp.2013.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Wang S, Lei Z, Wen J, Wang H, Li X, Dong B, Ren B. The complete mitochondrial genome of Liriomyza huidobrensis and comparison with L. trifolii and L. sativae (Diptera: Agromyzidae). ACTA ACUST UNITED AC 2013; 25:104-5. [PMID: 23617371 DOI: 10.3109/19401736.2013.786706] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Liriomyza huidobrensis, L. trifolii and L. sativae (Diptera: Agromyzidae) are serious horticultural pests. The three species are very similar and difficult to discriminate from each other. In this study, we report the mitochondrial genome of L. huidobrensis and compare with L. trifolii and L. sativae. The mitochondrial genome of L. huidobrensis is 16,239 bp long, and it contains 37 genes and one A + T-rich region as do the sequenced liriomyza species. The sequence and structure of H51-H100 region in srRNA is significantly different from that of L. trifolii and L. sativae. The greatest sequence differences among the three leafminers are located in the region including ND2, ND3, ND6, ATP6, ATP8, CYTb and A+T region, which can be considered as candidate regions for molecular identification or SNP markers.
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Affiliation(s)
- Shuaiyu Wang
- State Key Laboratory of Biology for Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences , Beijing , China and
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37
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Zhao Z, Su TJ, Chesters D, Wang SD, Ho SYW, Zhu CD, Chen XL, Zhang CT. The mitochondrial genome of Elodia flavipalpis Aldrich (Diptera: Tachinidae) and the evolutionary timescale of Tachinid flies. PLoS One 2013; 8:e61814. [PMID: 23626734 PMCID: PMC3634017 DOI: 10.1371/journal.pone.0061814] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 03/18/2013] [Indexed: 01/21/2023] Open
Abstract
Tachinid flies are natural enemies of many lepidopteran and coleopteran pests of forests, crops, and fruit trees. In order to address the lack of genetic data in this economically important group, we sequenced the complete mitochondrial genome of the Palaearctic tachinid fly Elodia flavipalpis Aldrich, 1933. Usually found in Northern China and Japan, this species is one of the primary natural enemies of the leaf-roller moths (Tortricidae), which are major pests of various fruit trees. The 14,932-bp mitochondrial genome was typical of Diptera, with 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. However, its control region is only 105 bp in length, which is the shortest found so far in flies. In order to estimate dipteran evolutionary relationships, we conducted a phylogenetic analysis of 58 mitochondrial genomes from 23 families. Maximum-likelihood and Bayesian methods supported the monophyly of both Tachinidae and superfamily Oestroidea. Within the subsection Calyptratae, Muscidae was inferred as the sister group to Oestroidea. Within Oestroidea, Calliphoridae and Sarcophagidae formed a sister clade to Oestridae and Tachinidae. Using a Bayesian relaxed clock calibrated with fossil data, we estimated that Tachinidae originated in the middle Eocene.
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Affiliation(s)
- Zhe Zhao
- Liaoning Key Laboratory of Evolution and Biodiversity, Shenyang Normal University, Shenyang, Liaoning, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Tian-juan Su
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Douglas Chesters
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shi-di Wang
- Liaoning Key Laboratory of Evolution and Biodiversity, Shenyang Normal University, Shenyang, Liaoning, China
| | - Simon Y. W. Ho
- School of Biological Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Chao-dong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- * E-mail: (CDZ); (XLC); (CTZ)
| | - Xiao-lin Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- * E-mail: (CDZ); (XLC); (CTZ)
| | - Chun-tian Zhang
- Liaoning Key Laboratory of Evolution and Biodiversity, Shenyang Normal University, Shenyang, Liaoning, China
- * E-mail: (CDZ); (XLC); (CTZ)
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Li T, Gao C, Cui Y, Xie Q, Bu W. The complete mitochondrial genome of the stalk-eyed bug Chauliops fallax Scott, and the monophyly of Malcidae (Hemiptera: Heteroptera). PLoS One 2013; 8:e55381. [PMID: 23390534 PMCID: PMC3563593 DOI: 10.1371/journal.pone.0055381] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 12/21/2012] [Indexed: 11/19/2022] Open
Abstract
Chauliops fallax Scott, 1874 (Hemiptera: Heteroptera: Malcidae: Chauliopinae) is one of the most destructive insect pests of soybean and rice fields in Asia. Here we sequenced the complete mitochondrial genome of this pest. This genome is 15,739 bp long, with an A+T content of 73.7%, containing 37 typical animal mitochondrial genes and a control region. All genes were arranged in the same order as most of other Heteroptera. A remarkable strand bias was found for all nine protein coding genes (PCGs) encoded by the majority strand were positive AT-skew and negative GC-skew, whereas the reverse were found in the remaining four PCGs encoded by the minority strand and two rRNA genes. The models of secondary structures for the two rRNA genes of sequenced true bugs and Lygaeoidea were predicted. 16S rRNA consisted of six domains (domain III is absent as in other known arthropod mitochondrial genomes) and 45 helices, while three domains and 27 helices for 12S rRNA. The control region consists of five subregions: a microsatellite-like region, a tandem repeats region and other three motifs. The unusual intergenic spacer between tRNA-H and ND4 only found in the species of Lygaeoidea, not in other heteropteran species, may be the synapomorphy of this superfamily. Phylogenetic analyses were carried out based on all the 13 PCGs showed that Chauliopinae was the sister group of Malcinae and the monophyly of Lygaeoidea.
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MESH Headings
- Animals
- Base Composition
- Base Sequence
- DNA, Intergenic/genetics
- DNA, Mitochondrial/classification
- DNA, Mitochondrial/genetics
- Evolution, Molecular
- Gene Order
- Genes, Mitochondrial
- Genome, Insect
- Genome, Mitochondrial
- Heteroptera/classification
- Heteroptera/genetics
- Microsatellite Repeats
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phylogeny
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Transfer/genetics
- Sequence Analysis, DNA
- Species Specificity
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Affiliation(s)
- Teng Li
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Cuiqing Gao
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Ying Cui
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Qiang Xie
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
- * E-mail:
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Nelson LA, Lambkin CL, Batterham P, Wallman JF, Dowton M, Whiting MF, Yeates DK, Cameron SL. Beyond barcoding: a mitochondrial genomics approach to molecular phylogenetics and diagnostics of blowflies (Diptera: Calliphoridae). Gene 2012; 511:131-42. [PMID: 23043935 DOI: 10.1016/j.gene.2012.09.103] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 09/21/2012] [Accepted: 09/29/2012] [Indexed: 11/28/2022]
Abstract
Members of the Calliphoridae (blowflies) are significant for medical and veterinary management, due to the ability of some species to consume living flesh as larvae, and for forensic investigations due to the ability of others to develop in corpses. Due to the difficulty of accurately identifying larval blowflies to species there is a need for DNA-based diagnostics for this family, however the widely used DNA-barcoding marker, cox1, has been shown to fail for several groups within this family. Additionally, many phylogenetic relationships within the Calliphoridae are still unresolved, particularly deeper level relationships. Sequencing whole mt genomes has been demonstrated both as an effective method for identifying the most informative diagnostic markers and for resolving phylogenetic relationships. Twenty-seven complete, or nearly so, mt genomes were sequenced representing 13 species, seven genera and four calliphorid subfamilies and a member of the related family Tachinidae. PCR and sequencing primers developed for sequencing one calliphorid species could be reused to sequence related species within the same superfamily with success rates ranging from 61% to 100%, demonstrating the speed and efficiency with which an mt genome dataset can be assembled. Comparison of molecular divergences for each of the 13 protein-coding genes and 2 ribosomal RNA genes, at a range of taxonomic scales identified novel targets for developing as diagnostic markers which were 117-200% more variable than the markers which have been used previously in calliphorids. Phylogenetic analysis of whole mt genome sequences resulted in much stronger support for family and subfamily-level relationships. The Calliphoridae are polyphyletic, with the Polleninae more closely related to the Tachinidae, and the Sarcophagidae are the sister group of the remaining calliphorids. Within the Calliphoridae, there was strong support for the monophyly of the Chrysomyinae and Luciliinae and for the sister-grouping of Luciliinae with Calliphorinae. Relationships within Chrysomya were not well resolved. Whole mt genome data, supported the previously demonstrated paraphyly of Lucilia cuprina with respect to L. sericata and allowed us to conclude that it is due to hybrid introgression prior to the last common ancestor of modern sericata populations, rather than due to recent hybridisation, nuclear pseudogenes or incomplete lineage sorting.
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Affiliation(s)
- Leigh A Nelson
- Australian National Insect Collection, CSIRO Ecosystem Sciences, Canberra, ACT, 2601, Australia
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40
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Complete mitogenome of the Lesser Purple Emperor Apatura ilia (Lepidoptera: Nymphalidae: Apaturinae) and comparison with other nymphalid butterflies. DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2012; 33:191-201. [PMID: 22467396 DOI: 10.3724/sp.j.1141.2012.02191] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The complete mitochondrial genome of Apatura ilia (GenBank accession no. JF437925) was determined as a circular DNA molecule of 15 242 bp, with common genes of 13 putative proteins, 2 rRNAs, and 22 tRNAs and of the same gene arrangement as in other sequenced lepidopterans. All protein-coding genes had the typical start codon ATN, except for the COI's using CGA as its start codon as previously demonstrated in other lepidopteran species. The comparison of the nucleotide sequences of the A. ilia mitogenome with ten other Nymphalidae species showed nearly identical gene orientation and arrangement, with only a few alterations in non-coding fragments. The nucleotide composition and codon frequency all fell into the range estimated for the order Lepidoptera. The A. ilia mitochondrial genome had the canonical set of 22 tRNA genes folded in the typical cloverleaf structure, with an unique exception of tRNA(Ser) (AGN). The mitochondrial genes from A. ilia were overlapped in a total of 33 bp at 9 locations, as well as interleaved with a total of 155 bp intergenic spacers, spread over 12 regions with the size ranging from 1 to 49 bp. Furthermore, the spacer between ND6 and Cyt b harbored a microsatellite-like repeat (TA)(23) not found in other completely sequenced nymphalid genomes. The 403 bp AT-rich region harbored two conserved motifs (ATAGA, ATTTA), a 21 bp polyT stretch, a 10 bp poly-A region, along with two microsatellite-like repeats ( (TA)(10) and (TA)(7)), as detected in other nymphalid butterflies.
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41
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Chai HN, Du YZ, Zhai BP. Characterization of the complete mitochondrial genomes of Cnaphalocrocis medinalis and Chilo suppressalis (Lepidoptera: Pyralidae). Int J Biol Sci 2012; 8:561-79. [PMID: 22532789 PMCID: PMC3334671 DOI: 10.7150/ijbs.3540] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 02/24/2012] [Indexed: 11/25/2022] Open
Abstract
The complete mitochondrial genomes (mitogenomes) of Cnaphalocrocis medinalis and Chilo suppressalis (Lepidoptera: Pyralidae) were determined and analyzed. The circular genomes were 15,388 bp long for C. medinalis and 15,395 bp long for C. suppressalis. Both mitogenomes contained 37 genes, with gene order similar to that of other lepidopterans. Notably, 12 protein-coding genes (PCGs) utilized the standard ATN, but the cox1 gene used CGA as the initiation codon; the cox1, cox2, and nad4 genes in the two mitogenomes had the truncated termination codons T, T, and TA, respectively, but the nad5 gene was found to use T as the termination codon only in the C. medinalis mitogenome. Additionally, the codon distribution and Relative Synonymous Codon Usage of the 13 PCGs in the C. medinalis mitogenome were very different from those in other pyralid moth mitogenomes. Most of the tRNA genes had typical cloverleaf secondary structures. However, the dihydrouridine (DHU) arm of the trnS1(AGN) gene did not form a stable stem-loop structure. Forty-nine helices in six domains, and 33 helices in three domains were present in the secondary structures of the rrnL and rrnS genes of the two mitogenomes, respectively. There were four major intergenic spacers, except for the A+T-rich region, spanning at least 12 bp in the two mitogenomes. The A+T-rich region contained an 'ATAGT(A)'-like motif followed by a poly-T stretch in the two mitogenomes. In addition, there were a potential stem-loop structure, a duplicated 25-bp repeat element, and a microsatellite '(TA)13' observed in the A+T-rich region of the C. medinalis mitogenome. A poly-T motif, a duplicated 31-bp repeat element, and a 19-bp triplication were found in the C. suppressalis mitogenome. However, there are many differences in the A+T-rich regions between the C. suppressalis mitogenome sequence in the present study and previous reports. Finally, the phylogenetic relationships of these insects were reconstructed based on amino acid sequences of mitochondrial 13 PCGs using Bayesian inference and maximum likelihood methods. These molecular-based phylogenies support the traditional morphologically based view of relationships within the Pyralidae.
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Affiliation(s)
- Huan-Na Chai
- Institute of Applied Entomology, Yangzhou University, Yangzhou 225009, China
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42
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Yin H, Zhi Y, Jiang H, Wang P, Yin X, Zhang D. The complete mitochondrial genome of Gomphocerus tibetanus Uvarov, 1935 (Orthoptera: Acrididae: Gomphocerinae). Gene 2012; 494:214-8. [DOI: 10.1016/j.gene.2011.12.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 12/10/2011] [Accepted: 12/10/2011] [Indexed: 10/14/2022]
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43
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Wu YP, Li J, Zhao JL, Su TJ, Luo AR, Fan RJ, Chen MC, Wu CS, Zhu CD. The complete mitochondrial genome of the rice moth, Corcyra cephalonica. JOURNAL OF INSECT SCIENCE (ONLINE) 2012; 12:72. [PMID: 23413968 PMCID: PMC3593705 DOI: 10.1673/031.012.7201] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 09/23/2011] [Indexed: 05/22/2023]
Abstract
The complete mitochondrial genome (mitogenome) of the rice moth, Corcyra cephalonica Stainton (Lepidoptera: Pyralidae) was determined as a circular molecular of 15,273 bp in size. The mitogenome composition (37 genes) and gene order are the same as the other lepidopterans. Nucleotide composition of the C. cephalonica mitogenome is highly A+T biased (80.43%) like other insects. Twelve protein-coding genes start with a typical ATN codon, with the exception of coxl gene, which uses CGA as the initial codon. Nine protein-coding genes have the common stop codon TAA, and the nad2, cox1, cox2, and nad4 have single T as the incomplete stop codon. 22 tRNA genes demonstrated cloverleaf secondary structure. The mitogenome has several large intergenic spacer regions, the spacer1 between trnQ gene and nad2 gene, which is common in Lepidoptera. The spacer 3 between trnE and trnF includes microsatellite-like repeat regions (AT)18 and (TTAT)(3). The spacer 4 (16 bp) between trnS2 gene and nad1 gene has a motif ATACTAT; another species, Sesamia inferens encodes ATCATAT at the same position, while other lepidopteran insects encode a similar ATACTAA motif. The spacer 6 is A+T rich region, include motif ATAGA and a 20-bp poly(T) stretch and two microsatellite (AT)(9), (AT)(8) elements.
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MESH Headings
- Animals
- Codon, Terminator/genetics
- Codon, Terminator/metabolism
- DNA, Intergenic/genetics
- DNA, Intergenic/metabolism
- Gene Order
- Genome, Insect
- Genome, Mitochondrial
- Microsatellite Repeats
- Molecular Sequence Data
- Moths/chemistry
- Moths/genetics
- Polymerase Chain Reaction
- Protein Structure, Secondary
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Analysis, Protein
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Affiliation(s)
- Yu-Peng Wu
- Institute of Loess Plateau, Shanxi University, Taiyuan 030006, China
- Key Laboratory of Zoological Systematics and Evolution (CAS), Institute of Zoology, Chinese Academy of
Sciences, Beijing 100101, China
- Plant Protection and Quarantine Station of Shanxi Province, Taiyuan 030001, China
| | - Jie Li
- Institute of Fruit Trees, Shanxi Academy of Agricultural Sciences, 030031
| | - Jin-Liang Zhao
- Key Laboratory of Zoological Systematics and Evolution (CAS), Institute of Zoology, Chinese Academy of
Sciences, Beijing 100101, China
| | - Tian-Juan Su
- Key Laboratory of Zoological Systematics and Evolution (CAS), Institute of Zoology, Chinese Academy of
Sciences, Beijing 100101, China
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - A-Rong Luo
- Key Laboratory of Zoological Systematics and Evolution (CAS), Institute of Zoology, Chinese Academy of
Sciences, Beijing 100101, China
| | - Ren-Jun Fan
- Institute of Plant Protection, Shanxi Academy of Agricultural Sciences, 030031
| | | | - Chun-Sheng Wu
- Key Laboratory of Zoological Systematics and Evolution (CAS), Institute of Zoology, Chinese Academy of
Sciences, Beijing 100101, China
| | - Chao-Dong Zhu
- Key Laboratory of Zoological Systematics and Evolution (CAS), Institute of Zoology, Chinese Academy of
Sciences, Beijing 100101, China
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Evaluation of the internal transcribed spacer 2 (ITS2) as a molecular marker for phylogenetic inference using sequence and secondary structure information in blow flies (Diptera: Calliphoridae). Genetica 2011; 139:1189-207. [PMID: 22198224 DOI: 10.1007/s10709-011-9621-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 12/02/2011] [Indexed: 10/14/2022]
Abstract
The internal transcribed spacer 2 (ITS2) is a small non-coding region located inside the nuclear ribosomal DNA cluster. ITS2 sequence variability is thought to be appropriate to differentiate species and for phylogenetic reconstructions analyses, which can be further improved if structural information is considered. We evaluated the potential of ITS2 as a molecular marker for phylogenetic inference in Calliphoridae (Diptera: Brachycera) using a broad range of inference methods and different substitution models, accounting or not for structural information. Sequence analyses revealed a hierarchically organized pattern of sequence variation and a small level of nucleotide substitution saturation. Intragenomic variation due to small sequence repeats was found mainly in the most variable domain (IV), but it has no significant impact on the phylogenetic signal at the species level. Inferred secondary structures revealed that GC pairs are more frequently found flanking bulges and loops regions in more conserved domains, thus ensuring structure stability. In the phylogenetic analyses, the use of substitution models accounting for structural information significantly improves phylogenetic inference in both neighbour-joining and Bayesian analyses, although the former provides limited resolution for dealing with highly divergent sequences. For Bayesian analyses, a significant improvement in likelihood was observed when considering structure information, although with small changes in topology and overall support, probably reflecting better evolutionary rates estimates. Based on these findings, ITS2 is a suitable molecular marker for phylogenetic analyses in Calliphoridae, at both species and generic level.
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45
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Gazi M, Sultana T, Min GS, Park YC, García-Varela M, Nadler SA, Park JK. The complete mitochondrial genome sequence of Oncicola luehei (Acanthocephala: Archiacanthocephala) and its phylogenetic position within Syndermata. Parasitol Int 2011; 61:307-16. [PMID: 22198415 DOI: 10.1016/j.parint.2011.12.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2011] [Revised: 12/02/2011] [Accepted: 12/07/2011] [Indexed: 11/29/2022]
Abstract
In the present study, we determined the complete mitochondrial genome sequence of Oncicola luehei (14,281bp), the first archiacanthocephalan representative and the second complete sequence from the phylum Acanthocephala. The complete genome contains 36 genes including 12 protein coding genes, 22 transfer RNA (tRNA) genes and 2 ribosomal RNA genes (rrnL and rrnS) as reported for other syndermatan species. All genes are encoded on the same strand. The overall nucleotide composition of O. luehei mtDNA is 37.7% T, 29.6% G, 22.5% A, and 10.2% C. The overall A+T content (60.2%) is much lower, compared to other syndermatan species reported so far, due to the high frequency (18.3%) of valine encoded by GTN in its protein-coding genes. Results from phylogenetic analyses of amino acid sequences for 10 protein-coding genes from 41 representatives of major metazoan groups including O. luehei supported monophyly of the phylum Acanthocephala and of the clade Syndermata (Acanthocephala+Rotifera), and the paraphyly of the clade Eurotatoria (classes Bdelloidea+Monogononta from phylum Rotifera). Considering the position of the acanthocephalan species within Syndermata, it is inferred that obligatory parasitism characteristic of acanthocephalans was acquired after the common ancestor of acanthocephalans diverged from its sister group, Bdelloidea. Additional comparison of complete mtDNA sequences from unsampled acanthocephalan lineages, especially classes Polyacanthocephala and Eoacanthocephala, is required to test if mtDNA provides reliable information for the evolutionary relationships and pattern of life history diversification found in the syndermatan groups.
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Affiliation(s)
- Mohiuddin Gazi
- Graduate Program in Cell Biology and Genetics and Department of Parasitology, College of Medicine, Chungbuk National University, Cheongju 361-763, Republic of Korea
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Beckenbach AT. Mitochondrial genome sequences of Nematocera (lower Diptera): evidence of rearrangement following a complete genome duplication in a winter crane fly. Genome Biol Evol 2011; 4:89-101. [PMID: 22155689 PMCID: PMC3269971 DOI: 10.1093/gbe/evr131] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The complete mitochondrial DNA sequences of eight representatives of lower Diptera, suborder Nematocera, along with nearly complete sequences from two other species, are presented. These taxa represent eight families not previously represented by complete mitochondrial DNA sequences. Most of the sequences retain the ancestral dipteran mitochondrial gene arrangement, while one sequence, that of the midge Arachnocampa flava (family Keroplatidae), has an inversion of the trnE gene. The most unusual result is the extensive rearrangement of the mitochondrial genome of a winter crane fly, Paracladura trichoptera (family Trichocera). The pattern of rearrangement indicates that the mechanism of rearrangement involved a tandem duplication of the entire mitochondrial genome, followed by random and nonrandom loss of one copy of each gene. Another winter crane fly retains the ancestral diperan gene arrangement. A preliminary mitochondrial phylogeny of the Diptera is also presented.
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Affiliation(s)
- Andrew T Beckenbach
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.
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Li H, Liu H, Cao L, Shi A, Yang H, Cai W. The complete mitochondrial genome of the damsel bug Alloeorhynchus bakeri (Hemiptera: Nabidae). Int J Biol Sci 2011; 8:93-107. [PMID: 22211108 PMCID: PMC3248651 DOI: 10.7150/ijbs.8.93] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Accepted: 11/10/2011] [Indexed: 11/05/2022] Open
Abstract
The complete sequence of the mitochondrial DNA (mtDNA) of the damsel bug, Alloeorhynchus bakeri, has been completed and annotated in this study. It represents the first sequenced mitochondrial genome of heteropteran family Nabidae. The circular genome is 15, 851 bp in length with an A+T content of 73.5%, contains the typical 37 genes that are arranged in the same order as that of the putative ancestor of hexapods. Nucleotide composition and codon usage are similar to other known heteropteran mitochondrial genomes. All protein-coding genes (PCGs) use standard initiation codons (methionine and isoleucine), except COI, which started with TTG. Canonical TAA and TAG termination codons are found in eight protein-coding genes, the remaining five (COI, COII, COIII, ND5, ND1) have incomplete termination codons (T or TA). PCGs of two strands present opposite CG skew which is also reflected by the nucleotide composition and codon usage. All tRNAs have the typical clover-leaf structure, except the dihydrouridine (DHU) arm of tRNA(Ser (AGN))which forms a simple loop as known in many other metazoa. Secondary structure models of the ribosomal RNA genes of A. bakeri are presented, similar to those proposed for other insect orders. There are six domains and 45 helices and three domains and 27 helices in the secondary structures of rrnL and rrnS, respectively. The major non-coding region (also called control region) between the small ribosomal subunit and the tRNA(Ile )gene includes two special regions. The first region includes four 133 bp tandem repeat units plus a partial copy of the repeat (28 bp of the beginning), and the second region at the end of control region contains 4 potential stem-loop structures. Finally, PCGs sequences were used to perform a phylogenetic study. Both maximum likelihood and Bayesian inference analyses highly support Nabidae as the sister group to Anthocoridae and Miridae.
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Affiliation(s)
- Hu Li
- Department of Entomology, China Agricultural University, Beijing 100193, China
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48
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Gong YJ, Shi BC, Kang ZJ, Zhang F, Wei SJ. The complete mitochondrial genome of the oriental fruit moth Grapholita molesta (Busck) (Lepidoptera: Tortricidae). Mol Biol Rep 2011; 39:2893-900. [PMID: 21670960 PMCID: PMC3271229 DOI: 10.1007/s11033-011-1049-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2010] [Accepted: 06/06/2011] [Indexed: 11/28/2022]
Abstract
The oriental fruit moth, Grapholita molesta (Busck) (Lepidoptera: Tortricidae) currently is one of the economically most destructive pest species of stone and pome fruits worldwide. Here we sequenced the complete mitochondrial genome of this pest. This genome is 15,776 bp long, with an A + T content of 81.24%, containing 37 typical animal mitochondrial genes and an A + T-rich region. All gene are arranged as hypothesized ancestral gene order of insects except for trnM, which was shuffled from 3′ downstream of trnQ to 5′ upstream of trnI. cox1 gene uses unusual CGA start codon, as that in all other sequenced lepidopteran mitochondrial genome. The secondary structures for the two rRNA genes were predicted. All helices typically present in insect mitochondrial rRNA genes are generated. A microsatellite sequence was inserted into the region of H2347 in rrnL in G. molesta and two other sequenced tortricid mitochondrial genomes, indicating that the insertion event in this helix might occurred anciently in family Tortricidae. All of the 22 typical animal tRNA genes have a typical cloverleaf structure except for trnS2, in which the D-stem pairings in the DHU arm are absent. An intergenic sequence is present between trnQ and nad2 as well as in other sequenced lepidopteran mitochondrial genomes, which was presumed to be a remnant of trnM gene and its boundary sequences after the duplication of trnM to the upstream of trnI in Lepidoptera. The A + T-rich region is 836 bp, containing six repeat sequences of “TTATTATTATTATTAAATA(G)TTT.”
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Affiliation(s)
- Ya-jun Gong
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing 100097, China
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The mitochondrial genome of the ascalaphid owlfly Libelloides macaronius and comparative evolutionary mitochondriomics of neuropterid insects. BMC Genomics 2011; 12:221. [PMID: 21569260 PMCID: PMC3115881 DOI: 10.1186/1471-2164-12-221] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Accepted: 05/10/2011] [Indexed: 11/18/2022] Open
Abstract
Background The insect order Neuroptera encompasses more than 5,700 described species. To date, only three neuropteran mitochondrial genomes have been fully and one partly sequenced. Current knowledge on neuropteran mitochondrial genomes is limited, and new data are strongly required. In the present work, the mitochondrial genome of the ascalaphid owlfly Libelloides macaronius is described and compared with the known neuropterid mitochondrial genomes: Megaloptera, Neuroptera and Raphidioptera. These analyses are further extended to other endopterygotan orders. Results The mitochondrial genome of L. macaronius is a circular molecule 15,890 bp long. It includes the entire set of 37 genes usually present in animal mitochondrial genomes. The gene order of this newly sequenced genome is unique among Neuroptera and differs from the ancestral type of insects in the translocation of trnC. The L. macaronius genome shows the lowest A+T content (74.50%) among known neuropterid genomes. Protein-coding genes possess the typical mitochondrial start codons, except for cox1, which has an unusual ACG. Comparisons among endopterygotan mitochondrial genomes showed that A+T content and AT/GC-skews exhibit a broad range of variation among 84 analyzed taxa. Comparative analyses showed that neuropterid mitochondrial protein-coding genes experienced complex evolutionary histories, involving features ranging from codon usage to rate of substitution, that make them potential markers for population genetics/phylogenetics studies at different taxonomic ranks. The 22 tRNAs show variable substitution patterns in Neuropterida, with higher sequence conservation in genes located on the α strand. Inferred secondary structures for neuropterid rrnS and rrnL genes largely agree with those known for other insects. For the first time, a model is provided for domain I of an insect rrnL. The control region in Neuropterida, as in other insects, is fast-evolving genomic region, characterized by AT-rich motifs. Conclusions The new genome shares many features with known neuropteran genomes but differs in its low A+T content. Comparative analysis of neuropterid mitochondrial genes showed that they experienced distinct evolutionary patterns. Both tRNA families and ribosomal RNAs show composite substitution pathways. The neuropterid mitochondrial genome is characterized by a complex evolutionary history.
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50
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Margam VM, Coates BS, Hellmich RL, Agunbiade T, Seufferheld MJ, Sun W, Ba MN, Sanon A, Binso-Dabire CL, Baoua I, Ishiyaku MF, Covas FG, Srinivasan R, Armstrong J, Murdock LL, Pittendrigh BR. Mitochondrial genome sequence and expression profiling for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae). PLoS One 2011; 6:e16444. [PMID: 21311752 PMCID: PMC3032770 DOI: 10.1371/journal.pone.0016444] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 12/20/2010] [Indexed: 11/18/2022] Open
Abstract
We report the assembly of the 14,054 bp near complete sequencing of the mitochondrial genome of the legume pod borer (LPB), Maruca vitrata (Lepidoptera: Crambidae), which we subsequently used to estimate divergence and relationships within the lepidopteran lineage. The arrangement and orientation of the 13 protein-coding, 2 rRNA, and 19 tRNA genes sequenced was typical of insect mitochondrial DNA sequences described to date. The sequence contained a high A+T content of 80.1% and a bias for the use of codons with A or T nucleotides in the 3rd position. Transcript mapping with midgut and salivary gland ESTs for mitochondrial genome annotation showed that translation from protein-coding genes initiates and terminates at standard mitochondrial codons, except for the coxI gene, which may start from an arginine CGA codon. The genomic copy of coxII terminates at a T nucleotide, and a proposed polyadenylation mechanism for completion of the TAA stop codon was confirmed by comparisons to EST data. EST contig data further showed that mature M. vitrata mitochondrial transcripts are monocistronic, except for bicistronic transcripts for overlapping genes nd4/nd4L and nd6/cytb, and a tricistronic transcript for atp8/atp6/coxIII. This processing of polycistronic mitochondrial transcripts adheres to the tRNA punctuated cleavage mechanism, whereby mature transcripts are cleaved only at intervening tRNA gene sequences. In contrast, the tricistronic atp8/atp6/coxIII in Drosophila is present as separate atp8/atp6 and coxIII transcripts despite the lack of an intervening tRNA. Our results indicate that mitochondrial processing mechanisms vary between arthropod species, and that it is crucial to use transcriptional information to obtain full annotation of mitochondrial genomes.
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Affiliation(s)
- Venu M. Margam
- Department of Entomology, Purdue University, West Lafayette, Indiana, United States of America
| | - Brad S. Coates
- United States Department of Agriculture – Agricultural Research Service, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, Iowa, United States of America
| | - Richard L. Hellmich
- United States Department of Agriculture – Agricultural Research Service, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, Iowa, United States of America
| | - Tolulope Agunbiade
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Manfredo J. Seufferheld
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Weilin Sun
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Malick N. Ba
- Station de Kamboinsé,Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Antoine Sanon
- Station de Kamboinsé,Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Clementine L. Binso-Dabire
- Station de Kamboinsé,Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Ibrahim Baoua
- Institut National de Recherche Agronomique du Niger, Maradi, Niger
| | - Mohammad F. Ishiyaku
- Department of Plant Science, Institute for Agricultural Research, Ahmadu Bello University, Zaria, Nigeria
| | - Fernando G. Covas
- University of Puerto Rico, Mayaguez, Puerto Rico, United States of America
| | | | - Joel Armstrong
- Entomology, The Commonweatlth of Scientific and Industrial Research Organization, Black Mountain, Australian Capital Territory, Australia
| | - Larry L. Murdock
- Department of Entomology, Purdue University, West Lafayette, Indiana, United States of America
| | - Barry R. Pittendrigh
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
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