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Yang H, Zhang C, Zhang Y, Li J. The complete mitochondrial genome of Vibrissina turrita (Meigen, 1824) (Diptera, Tachinidae). Mitochondrial DNA B Resour 2024; 9:762-765. [PMID: 38895508 PMCID: PMC11185082 DOI: 10.1080/23802359.2024.2363344] [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: 12/17/2023] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
In this study, the mitogenome of Vibrissina turrita (Meigen, 1824) (Diptera, Tachinidae) was sequenced based on the next-generation sequencing approach and analyzed here for the first time. The 17,387 bp genome has a high A + T content and consists of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one noncoding control region. The phylogenetic analysis results support that Exoristinae is monophyletic and V. turrita belongs to the subfamily. This study reveals the systematic classification status of V. turrita and will enrich the genetic data on Tachinidae.
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Affiliation(s)
- Hui Yang
- College of Life Sciences, Shenyang Normal University, Shenyang, China
| | - Chuntian Zhang
- College of Life Sciences, Shenyang Normal University, Shenyang, China
| | - Yahui Zhang
- College of Life Sciences, Shenyang Normal University, Shenyang, China
| | - Junjian Li
- College of Life Sciences, Shenyang Normal University, Shenyang, 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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Zhang P, Zhi Y, Guo C, Zhang C, Liu J. The complete mitochondrial genome of Peleteria iavana (Diptera, Tachinidae) in Guizhou, China, and its phylogenetic placement. MITOCHONDRIAL DNA PART B 2023; 8:466-470. [PMID: 37006954 PMCID: PMC10062221 DOI: 10.1080/23802359.2023.2194457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
The mitochondrial genome of the tachinid fly Peleteria iavana (Wiedemann, 1819), which belongs to the family Tachinidae, was obtained for the first time using high-throughput sequencing techniques. The complete mitochondrial genome is 15,697 bp in size and consists of 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNAs and a non-coding control region. The nucleotide composition biases A and T, the overall A + T percentage is up to 78.9% of the entire mitogenome. A phylogenetic analysis of 30 species within the family Tachinidae suggested that P. iavana is most closely related to (Janthinomyia sp.+Lydina aenea). The P. iavana mitochondrial genome will be a fundamental resource for understanding the molecular phylogenetic relationships of the species-rich subfamily Tachininae of Tachinidae.
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Wang R, Zhi Y, Yao Q, Zhang C, Liu J. Characterization of the complete mitochondrial genome of Gymnosoma dolycoridis (Diptera, Tachinidae) and phylogenetic analysis. Mitochondrial DNA B Resour 2022; 7:1435-1437. [PMID: 35958060 PMCID: PMC9359177 DOI: 10.1080/23802359.2022.2107449] [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: 12/02/2022] Open
Abstract
The complete mitogenome of Gymnosoma dolycoridis Dupuis, 1960 was determined in this study. It is 15,185 bp in length, consisting of 13 protein-coding genes (PCG), 22 transfer RNA genes, two ribosomal RNA genes and one non-coding control region. The A + T content of the mitogenome is 78.5%. A maximum-likelihood phylogenetic tree built on 13 PCGs of 15 tachinid species indicated that Gymnosoma dolycoridis is clustered with other members of the subfamily Phasiinae as conventional taxonomy predicted.
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Affiliation(s)
- Rong Wang
- Key Laboratory of Medical Insects, Guizhou Medical University, Guiyang, China
- School of Basic Medical Science, Guizhou Medical University, Guiyang, China
| | - Yan Zhi
- Laboratory Animal Center, Guizhou Medical University, Guiyang, China
| | - Qiuyu Yao
- Key Laboratory of Medical Insects, Guizhou Medical University, Guiyang, China
- School of Basic Medical Science, Guizhou Medical University, Guiyang, China
| | - Chuntian Zhang
- College of Life Sciences, Shenyang Normal University, Shenyang, China
| | - Jiayu Liu
- Key Laboratory of Medical Insects, Guizhou Medical University, Guiyang, China
- School of Basic Medical Science, Guizhou Medical University, Guiyang, China
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5
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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: 3] [Impact Index Per Article: 1.5] [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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Shang Y, Ren L, Zhang X, Li Y, Zhang C, Guo Y. Characterization and Comparative Analysis of Mitochondrial Genomes Among the Calliphoridae (Insecta: Diptera: Oestroidea) and Phylogenetic Implications. Front Genet 2022; 13:799203. [PMID: 35251125 PMCID: PMC8891575 DOI: 10.3389/fgene.2022.799203] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/27/2022] [Indexed: 11/21/2022] Open
Abstract
The Calliphoridae (blowflies) are significant for forensic science, veterinary management, medical science, and economic issues. However, the phylogenetic relationships within this family are poorly understood and controversial, and the status of the Calliphoridae has been a crucial problem for understanding the evolutionary relationships of the Oestroidea these years. In the present study, seven mitochondrial genomes (mitogenomes), including six calliphorid species and one Polleniidae species, were sequenced and annotated. Then a comparative mitochondrial genomic analysis among the Calliphoridae is presented. Additionally, the phylogenetic relationship of the Calliphoridae within the larger context of the other Oestroidea was reconstructed based on the mitogenomic datasets using maximum likelihood (ML) and Bayesian methods (BI). The results suggest that the gene arrangement, codon usage, and base composition are conserved within the calliphorid species. The phylogenetic analysis based on the mitogenomic dataset recovered the Calliphoridae as monophyletic and inferred the following topology within Oestroidea: (Oestridae (Sarcophagidae (Calliphoridae + (Polleniidae + (Mesembrinellidae + Tachinidae))))). Although the number of exemplar species is limited, further studies are required. Within the Calliphoridae, the Chrysomyinae were recovered as sister taxon to Luciliinae + Calliphorinae. Our analyses indicated that mitogenomic data have the potential for illuminating the phylogenetic relationships in the Oestroidea as well as for the classification of the Calliphoridae.
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Affiliation(s)
| | | | | | | | | | - Yadong Guo
- *Correspondence: Changquan Zhang, ; Yadong Guo,
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7
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Luo Y, Zhi Y, Zhang C, Yang M, Liu J. Complete mitochondrial genome of Compsilura concinnata (Meigen) (Diptera, Tachinidae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:905-906. [PMID: 33796675 PMCID: PMC7995883 DOI: 10.1080/23802359.2021.1886020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The complete mitochondrial genome of Compsilura concinnata (Meigen), was analyzed by next-generation sequencing approach. Its mitogenome is 15,841 bp totally, which consists of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one non-coding control region. The nucleotide composition biases toward A and T, the overall A + T% was up to 80.9% of the entire mitogenome. Phylogenetic analysis supported the sister relationship between Goniini and Blondeliini. The result also suggested that the monophyly of the Exoristinae.
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Affiliation(s)
- Yu Luo
- Key Laboratory of Medical Insects, Guizhou Medical University, Guiyang, China.,School of Basic Medical Science, Guizhou Medical University, Guiyang, China
| | - Yan Zhi
- Laboratory Animal Center, Guizhou Medical University, Guiyang, China
| | - Chuntian Zhang
- College of Life Sciences, Shenyang Normal University, Shenyang, China
| | - Ming Yang
- Key Laboratory of Medical Insects, Guizhou Medical University, Guiyang, China.,School of Basic Medical Science, Guizhou Medical University, Guiyang, China
| | - Jiayu Liu
- Key Laboratory of Medical Insects, Guizhou Medical University, Guiyang, China.,School of Basic Medical Science, Guizhou Medical University, Guiyang, China
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Seo BY, Cho J, Lee GS, Park J, Park J. The complete mitochondrial genome of Exorista japonica (Townsend, 1909) (Diptera:Tachinidae). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2244-2245. [PMID: 33365494 PMCID: PMC7687561 DOI: 10.1080/23802359.2019.1624648] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Exorista japonica (Townsend, 1909), a dipteran tachinid fly, is an endoparasitoid of lepidopteran larvae as a potential biological agent. We have determined a 17,663 bp mitogenome of E. japonica which includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 2,773 bp. The base composition was AT-biased (81.4%). Phylogenetic trees present monophyly of Tachinidae and Exoristinae, where two Exorista species are clustered in single clade, Exoristini. The E. japonica mitogenome will be a good resource for understanding phylogenetic relationship among species of Tachinidae presenting morphological and ecological complexities.
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Affiliation(s)
- Bo Yoon Seo
- Crop Protection Division, National Institute of Agricultural Sciences, RDA, Wanju, Republic of Korea
| | - Jumrae Cho
- Crop Protection Division, National Institute of Agricultural Sciences, RDA, Wanju, Republic of Korea
| | - Gwan-Seok Lee
- Crop Protection Division, National Institute of Agricultural Sciences, RDA, Wanju, Republic of Korea
| | - Jonghyun Park
- InfoBoss Co., Ltd., Gangnam-gu, Seoul, Republic of Korea.,InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Co., Ltd., Gangnam-gu, Seoul, Republic of Korea.,InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
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9
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Huang J, Ma T. Comparative analysis of two mitochondrial genomes of flesh flies (Sarcophaga antilope and Sarcophaga dux) with phylogeny and evolutionary timescale for Sarcophagidae. Int J Biol Macromol 2018; 120:1955-1964. [DOI: 10.1016/j.ijbiomac.2018.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/29/2018] [Accepted: 10/01/2018] [Indexed: 11/28/2022]
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10
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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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11
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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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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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13
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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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