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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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Pei W, Xu W, Li H, Yan L, Gai Y, Yang N, Yang J, Chen J, Peng H, Pape T, Zhang D, Zhang C. Unusual rearrangements of mitogenomes in Diptera revealed by comparative analysis of 135 tachinid species (Insecta, Diptera, Tachinidae). Int J Biol Macromol 2024; 258:128997. [PMID: 38154713 DOI: 10.1016/j.ijbiomac.2023.128997] [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: 05/25/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 12/30/2023]
Abstract
The Tachinidae is one of the most speciose families in Diptera, and the exclusively parasitoid species play an important role in regulating populations of many herbivorous insects in ecosystems, including many agricultural pests. To better comprehend the characteristics and evolution of the mitochondrial genome for the Tachinidae, we are adding a massive amount of new molecular data by assembling the mitogenomes for 71 genera and 135 species from all four tachinid subfamilies through next-generation sequencing, and we are presenting the most comprehensive mitogenomic phylogenetic analysis of this family so far. Extensive rearrangements observed in the mitogenome of Admontia podomyia (Exoristinae) are unique for the entire suborder Cyclorrhapha. The rearrangement pattern suggests that the process involved a tandem duplication of the complete mitogenome, followed by both random and nonrandom loss of one copy of each gene. Additionally, five minor mitogenome rearrangements are discovered and described in three subfamilies. We present the largest species-level phylogenetic hypothesis for Tachinidae to date, based on mitogenomes of 152 species of Tachinidae, representing all four subfamilies and with five non-tachinid outgroups. Our analyses support the monophyly of the Tachinidae and most tribes and genera were recovered with good support, but the higher-level phylogenetic relationships within Tachinidae were poorly resolved, indicating that mitogenome data alone are not enough to unambiguously resolve the deeper phylogenetic relationships within Tachinidae.
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Affiliation(s)
- Wenya Pei
- School of Ecology and Nature Conservation, Beijing Forestry University, Qinghua East Road 35, Beijing 10083, China
| | - Wentian Xu
- School of Ecology and Nature Conservation, Beijing Forestry University, Qinghua East Road 35, Beijing 10083, China
| | - Henan Li
- School of Ecology and Nature Conservation, Beijing Forestry University, Qinghua East Road 35, Beijing 10083, China
| | - Liping Yan
- School of Ecology and Nature Conservation, Beijing Forestry University, Qinghua East Road 35, Beijing 10083, China
| | - Yi Gai
- School of Ecology and Nature Conservation, Beijing Forestry University, Qinghua East Road 35, Beijing 10083, China
| | - Nan Yang
- Serving Officer in Administration Department of Baihua Mountain Reserve, Beijing 10083, China
| | - Jun Yang
- Serving Officer in Administration Department of Baihua Mountain Reserve, Beijing 10083, China
| | - Jinliang Chen
- Dalaoling Nature Reserve Administration of Yichang Three Gorges, Yichang 443000, China
| | - Honglin Peng
- Dalaoling Nature Reserve Administration of Yichang Three Gorges, Yichang 443000, China
| | - Thomas Pape
- Natural History Museum of Denmark, Science Faculty, University of Copenhagen, Copenhagen, Denmark
| | - Dong Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Qinghua East Road 35, Beijing 10083, China.
| | - Chuntian Zhang
- College of Life Science, Shenyang Normal University, Shenyang 110034, China.
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Fang X, Wang X, Mao B, Xiao Y, Shen M, Fu Y. Comparative mitogenome analyses of twelve non-biting flies and provide insights into the phylogeny of Chironomidae (Diptera: Culicomorpha). Sci Rep 2023; 13:9200. [PMID: 37280228 DOI: 10.1038/s41598-023-36227-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/31/2023] [Indexed: 06/08/2023] Open
Abstract
The family Chironomidae is represented by seven subfamilies in China, among which Chironominae and Orthocladiinae are the most diverse. To gain a better understanding of the architecture and evolution of the mitogenomes of Chironomidae, we sequenced mitogenomes of twelve species (including two published species) of the two subfamilies Chironominae and Orthocladiinae, and comparative mitogenomic analyses were performed. Thus, we identified highly conserved genome organization of twelve species with regard to genome content, nucleotide and amino acid composition, codon usage, and gene characteristics. The Ka/Ks values of most protein-coding genes were far smaller than 1, indicating that these genes were evolving under purifying selection. Phylogenetic relationships between the family Chironomidae were reconstructed using 23 species representing six subfamilies, based on protein-coding genes and rRNAs using Bayesian Inference and Maximum Likelihood. Our results suggested the following relationship within the Chironomidae: (Podonominae + Tanypodinae) + (Diamesinae + (Prodiamesinae + (Orthocladiinae + Chironominae))). This study contributes to the mitogenomic database of Chironomidae, which will be significant for studing the mitogenome evolution of Chironomidae.
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Affiliation(s)
- Xiangliang Fang
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, 438000, Hubei, People's Republic of China
| | - Xinhua Wang
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Bin Mao
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, 438000, Hubei, People's Republic of China
| | - Yunli Xiao
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, 438000, Hubei, People's Republic of China
| | - Mi Shen
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, 438000, Hubei, People's Republic of China
| | - Yue Fu
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, 438000, Hubei, People's Republic of China.
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Gopurenko D, Bellis G, Pengsakul T, Siriyasatien P, Thepparat A. DNA Barcoding of Culicoides Latreille (Diptera: Ceratopogonidae) From Thailand Reveals Taxonomic Inconsistencies and Novel Diversity Among Reported Sequences. JOURNAL OF MEDICAL ENTOMOLOGY 2022; 59:1960-1970. [PMID: 36189978 DOI: 10.1093/jme/tjac142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Indexed: 06/16/2023]
Abstract
Recent focus on Culicoides species diversity in Thailand was prompted by a need to identify vectors responsible for the transmission of African Horse Sickness in that country. To assist rapid genetic identification of species, we sampled mitochondrial cytochrome c oxidase subunit I (COI) DNA barcodes (N = 78) from 40 species of Culicoides biting midge from Thailand, including 17 species for which DNA barcodes were previously unavailable. The DNA barcodes were assigned to 39 Barcode Identification Numbers (BINs) representing terminal genetic clusters at the Barcode of Life Data systems (BOLD). BINs assisted with comparisons to published conspecific DNA barcodes and allowed partial barcodes obtained from seven specimens to be associated with BINs by their similarity. Some taxonomic issues were revealed and attributed to the possible misidentification of earlier reported specimens as well as a potential synonymy of C. elbeli Wirth & Hubert and C. menglaensis Chu & Liu. Comparison with published BINs also revealed genetic evidence of divergent population processes and or potentially cryptic species in 16 described taxa, flagged by their high levels of COI sequence difference among conspecifics. We recommend the BOLD BIN system to researchers preparing DNA barcodes of vouchered species for public release. This will alert them to taxonomic incongruencies between their records and publicly released DNA barcodes, and also flag genetically deep and potentially novel diversity in described species.
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Affiliation(s)
- David Gopurenko
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia
| | - Glenn Bellis
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
| | - Theerakamol Pengsakul
- Faculty of Medical Technology, Prince of Songkla University, Songkla 90110, Thailand
| | - Padet Siriyasatien
- Center of Excellence in Vector Biology and Vector Borne Diseases, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Arunrat Thepparat
- Department of Agricultural Technology, Ramkhamhaeng University, Bangkok, Thailand
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Huang YX, Xing ZP, Zhang H, Xu ZB, Tao LL, Hu HY, Kitching IJ, Wang X. Characterization of the Complete Mitochondrial Genome of Eight Diurnal Hawkmoths (Lepidoptera: Sphingidae): New Insights into the Origin and Evolution of Diurnalism in Sphingids. INSECTS 2022; 13:887. [PMID: 36292835 PMCID: PMC9604448 DOI: 10.3390/insects13100887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/20/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
In this study, the mitochondrial genomes of 22 species from three subfamilies in the Sphingidae were sequenced, assembled, and annotated. Eight diurnal hawkmoths were included, of which six were newly sequenced (Hemaris radians, Macroglossum bombylans, M. fritzei, M. pyrrhosticta, Neogurelca himachala, and Sataspes xylocoparis) and two were previously published (Cephonodes hylas and Macroglossum stellatarum). The mitochondrial genomes of these eight diurnal hawkmoths were comparatively analyzed in terms of sequence length, nucleotide composition, relative synonymous codon usage, non-synonymous/synonymous substitution ratio, gene spacing, and repeat sequences. The mitogenomes of the eight species, ranging in length from 15,201 to 15,461 bp, encode the complete set of 37 genes usually found in animal mitogenomes. The base composition of the mitochondrial genomes showed A+T bias. The most commonly used codons were UUA (Leu), AUU (Ile), UUU (Phe), AUA (Met), and AAU (Asn), whereas GCG (Ala) and CCG (Pro) were rarely used. A phylogenetic tree of Sphingidae was constructed based on both maximum likelihood and Bayesian methods. We verified the monophyly of the four current subfamilies of Sphingidae, all of which had high support. In addition, we performed divergence time estimation and ancestral character reconstruction analyses. Diurnal behavior in hawkmoths originated 29.19 million years ago (Mya). It may have been influenced by the combination of herbaceous flourishing, which occurred 26-28 Mya, the uplift of the Tibetan Plateau, and the large-scale evolution of bats in the Oligocene to Pre-Miocene. Moreover, diurnalism in hawkmoths had multiple independent origins in Sphingidae.
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Affiliation(s)
- Yi-Xin Huang
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China
- Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Zhi-Ping Xing
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China
| | - Hao Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Zhen-Bang Xu
- Institute of Resource Plants, Yunnan University, Kunming 650500, China
| | - Li-Long Tao
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Hao-Yuan Hu
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China
| | | | - Xu Wang
- Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
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6
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Milián-García Y, Hempel CA, Janke LAA, Young RG, Furukawa-Stoffer T, Ambagala A, Steinke D, Hanner RH. Mitochondrial genome sequencing, mapping, and assembly benchmarking for Culicoides species (Diptera: Ceratopogonidae). BMC Genomics 2022; 23:584. [PMID: 35962326 PMCID: PMC9375341 DOI: 10.1186/s12864-022-08743-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 07/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondrial genomes are the most sequenced genomes after bacterial and fungal genomic DNA. However, little information on mitogenomes is available for multiple metazoan taxa, such as Culicoides, a globally distributed, megadiverse genus containing 1,347 species. AIM Generating novel mitogenomic information from single Culicoides sonorensis and C. biguttatus specimens, comparing available mitogenome mapping and de novo assembly tools, and identifying the best performing strategy and tools for Culicoides species. RESULTS We present two novel and fully annotated mitochondrial haplotypes for two Culicoides species, C. sonorensis and C. biguttatus. We also annotated or re-annotated the only available reference mitogenome for C. sonorensis and C. arakawae. All species present a high similarity in mitogenome organization. The general gene arrangement for all Culicoides species was identical to the ancestral insect mitochondrial genome. Only short spacers were found in C. sonorensis (up to 30 bp), contrary to C. biguttatus (up to 114 bp). The mitochondrial genes ATP8, NAD2, NAD6, and LSU rRNA exhibited the highest nucleotide diversity and pairwise interspecific p genetic distance, suggesting that these genes might be suitable and complementary molecular barcodes for Culicoides identification in addition to the commonly utilized COI gene. We observed performance differences between the compared mitogenome generation strategies. The mapping strategy outperformed the de novo assembly strategy, but mapping results were partially biased in the absence of species-specific reference mitogenome. Among the utilized tools, BWA performed best for C. sonorensis while SPAdes, MEGAHIT, and MitoZ were among the best for C. biguttatus. The best-performing mitogenome annotator was MITOS2. Additionally, we were able to recover exogenous mitochondrial DNA from Bos taurus (biting midges host) from a C. biguttatus blood meal sample. CONCLUSIONS Two novel annotated mitogenome haplotypes for C. sonorensis and C. biguttatus using High-Throughput Sequencing are presented. Current results are useful as the baseline for mitogenome reconstruction of the remaining Culicoides species from single specimens to HTS and genome annotation. Mapping to a species-specific reference mitogenome generated better results for Culicoides mitochondrial genome reconstruction than de novo assembly, while de novo assembly resulted better in the absence of a closely related reference mitogenome. These results have direct implications for molecular-based identification of these vectors of human and zoonotic diseases, setting the basis for using the whole mitochondrial genome as a marker in Culicoides identification.
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Affiliation(s)
- Yoamel Milián-García
- Department of Integrative Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada.
| | - Christopher A Hempel
- Department of Integrative Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
| | - Lauren A A Janke
- Department of Integrative Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada.,John H. Daniels Faculty of Architecture, Landscape, and Design, University of Toronto, 33 Willcocks Street, Toronto, ON, M5S 3B3, Canada
| | - Robert G Young
- Department of Integrative Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
| | - Tara Furukawa-Stoffer
- Canadian Food Inspection Agency, National Centre for Animal Disease, 225090 Township Road 9-1, Lethbridge LaboratoryLethbridge, AB, T1J 0P3, Canada
| | - Aruna Ambagala
- National Centre for Foreign Animal Disease, 1015, Arlington Street, Winnipeg, MB, R3E 3M4, Canada
| | - Dirk Steinke
- Department of Integrative Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
| | - Robert H Hanner
- Department of Integrative Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
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Zheng CG, Zhu XX, Yan LP, Yao Y, Bu WJ, Wang XH, Lin XL. First complete mitogenomes of Diamesinae, Orthocladiinae, Prodiamesinae, Tanypodinae (Diptera: Chironomidae) and their implication in phylogenetics. PeerJ 2021; 9:e11294. [PMID: 33996279 PMCID: PMC8106913 DOI: 10.7717/peerj.11294] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/27/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The mitochondrial genome (mitogenome) has been extensively used for phylogenetic and evolutionary analysis in Diptera, but the study of mitogenome is still scarce in the family Chironomidae. METHODS Here, the first complete mitochondrial genomes of four Chironomid species representing Diamesinae, Orthocladiinae, Prodiamesinae and Tanypodinae are presented. Coupled with published mitogenomes of two, a comparative mitochondrial genomic analysis between six subfamilies of Chironomidae was carried out. RESULTS Mitogenomes of Chironomidae are conserved in structure, each contains 37 typical genes and a control region, and all genes arrange the same gene order as the ancestral insect mitogenome. Nucleotide composition is highly biased, the control region displayed the highest A + T content. All protein coding genes are under purifying selection, and the ATP8 evolves at the fastest rate. In addition, the phylogenetic analysis covering six subfamilies within Chironomidae was conducted. The monophyly of Chironomidae is strongly supported. However, the topology of six subfamilies based on mitogenomes in this study is inconsistent with previous morphological and molecular studies. This may be due to the high mutation rate of the mitochondrial genetic markers within Chironomidae. Our results indicate that mitogenomes showed poor signals in phylogenetic reconstructions at the subfamily level of Chironomidae.
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Affiliation(s)
| | - Xiu-Xiu Zhu
- College of Life Sciences, Nankai University, Tianjin, China
| | - Li-Ping Yan
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yuan Yao
- College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Wen-Jun Bu
- College of Life Sciences, Nankai University, Tianjin, China
| | - Xin-Hua Wang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Xiao-Long Lin
- College of Life Sciences, Nankai University, Tianjin, China
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Zapelloni F, Jurado-Rivera JA, Jaume D, Juan C, Pons J. Comparative Mitogenomics in Hyalella (Amphipoda: Crustacea). Genes (Basel) 2021; 12:genes12020292. [PMID: 33669879 PMCID: PMC7923271 DOI: 10.3390/genes12020292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 02/02/2023] Open
Abstract
We present the sequencing and comparative analysis of 17 mitochondrial genomes of Nearctic and Neotropical amphipods of the genus Hyalella, most from the Andean Altiplano. The mitogenomes obtained comprised the usual 37 gene-set of the metazoan mitochondrial genome showing a gene rearrangement (a reverse transposition and a reversal) between the North and South American Hyalella mitogenomes. Hyalella mitochondrial genomes show the typical AT-richness and strong nucleotide bias among codon sites and strands of pancrustaceans. Protein-coding sequences are biased towards AT-rich codons, with a preference for leucine and serine amino acids. Numerous base changes (539) were found in tRNA stems, with 103 classified as fully compensatory, 253 hemi-compensatory and the remaining base mismatches and indels. Most compensatory Watson–Crick switches were AU -> GC linked in the same haplotype, whereas most hemi-compensatory changes resulted in wobble GU and a few AC pairs. These results suggest a pairing fitness increase in tRNAs after crossing low fitness valleys. Branch-site level models detected positive selection for several amino acid positions in up to eight mitochondrial genes, with atp6 and nad5 as the genes displaying more sites under selection.
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Affiliation(s)
- Francesco Zapelloni
- Department of Biology, University of the Balearic Islands, Ctra. Valldemossa km 7,5, 07122 Palma, Spain; (F.Z.); (J.A.J.-R.); (C.J.)
| | - José A. Jurado-Rivera
- Department of Biology, University of the Balearic Islands, Ctra. Valldemossa km 7,5, 07122 Palma, Spain; (F.Z.); (J.A.J.-R.); (C.J.)
| | - Damià Jaume
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/Miquel Marquès 21, 07190 Esporles, Spain;
| | - Carlos Juan
- Department of Biology, University of the Balearic Islands, Ctra. Valldemossa km 7,5, 07122 Palma, Spain; (F.Z.); (J.A.J.-R.); (C.J.)
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/Miquel Marquès 21, 07190 Esporles, Spain;
| | - Joan Pons
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/Miquel Marquès 21, 07190 Esporles, Spain;
- Correspondence: ; Tel.: +34-971-173-332
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Tsai CL, Chu IH, Chou MH, Chareonviriyaphap T, Chiang MY, Lin PA, Lu KH, Yeh WB. Rapid identification of the invasive fall armyworm Spodoptera frugiperda (Lepidoptera, Noctuidae) using species-specific primers in multiplex PCR. Sci Rep 2020; 10:16508. [PMID: 33020593 PMCID: PMC7536291 DOI: 10.1038/s41598-020-73786-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 09/02/2020] [Indexed: 12/25/2022] Open
Abstract
The fall armyworm (FAW), Spodoptera frugiperda (Smith), is a major pest native to the Americas. A recent invasion of FAWs from Africa eastward to South Asia, the Indochina Peninsula, and mainland China has received much attention due to the considerable economic losses in agriculture. FAWs can rapidly colonise a new area, likely due to the wide range of host plants, good flying capability, and high egg production. Therefore, a convenient, quick, and accurate tool for FAW identification is urgently required to establish a FAW invasion management strategy. In this study, FAW-specific primers were designed to recognise FAWs on the basis of internal transcribed spacer 1 (ITS1). The results revealed the accurate FAW recognition of the three congeneric species and eight common corn lepidopteran pests, especially at their larval stage. Furthermore, species-specific primers have confirmed their efficacy by using 69 FAW specimens from Taiwan, Thailand, and the United States, with a 96% success rate, excluding 3 decayed specimens. By using the simple, reliable, and convenient FAW-specific primers, a pest management programme can be developed not only to reduce sequencing costs and experimental time from 2 days to 4 h, but eradicate the FAW as soon as it enters a new area.
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Affiliation(s)
- Cheng-Lung Tsai
- Department of Entomology, National Chung Hsing University, 145 Xingda Rd., South District, Taichung City, 40227, Taiwan
| | - I-Hsuan Chu
- Department of Entomology, National Chung Hsing University, 145 Xingda Rd., South District, Taichung City, 40227, Taiwan
| | - Ming-Hsun Chou
- Department of Entomology, National Chung Hsing University, 145 Xingda Rd., South District, Taichung City, 40227, Taiwan
| | - Theeraphap Chareonviriyaphap
- Department of Entomology, Faculty of Agriculture, Kasetsart University, 50 Ngamwongwan Rd., Chatuchak, Bangkok, 10900, Thailand
| | - Ming-Yao Chiang
- Applied Zoology Division, Taiwan Agricultural Research Institute, Council of Agriculture, Executive Yuan, 189 Zhongzheng Rd., Wufeng District, Taichung, 41326, Taiwan
| | - Po-An Lin
- Department of Entomology, Penn State University, 201 Old Main, University Park, PA, 16802, USA
| | - Kuang-Hui Lu
- Department of Entomology, National Chung Hsing University, 145 Xingda Rd., South District, Taichung City, 40227, Taiwan
| | - Wen-Bin Yeh
- Department of Entomology, National Chung Hsing University, 145 Xingda Rd., South District, Taichung City, 40227, Taiwan.
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Mathieu B, Garros C, Balenghien T, Candolfi E, Delécolle JC, Cêtre-Sossah C. A phylogenetic analysis of the biting midges belonging to Culicoides Latreille (Diptera: Ceratopogonidae) subgenus Avaritia using molecular data. Parasit Vectors 2020; 13:243. [PMID: 32398143 PMCID: PMC7216621 DOI: 10.1186/s13071-020-04111-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 04/29/2020] [Indexed: 11/11/2022] Open
Abstract
Background Within the genus Culicoides (Diptera: Ceratopogonidae), the subgenus Avaritia is of particular interest as it contains a significant number of economically important vector species. Disagreements about the systematic classification of species within this subgenus have resulted in a taxonomic imbroglio. Methods A molecular phylogeny of the subgenus Avaritia was conducted to test the existing systematic classification, which is based on phenetic assessment of morphological characters. Three nuclear ribosomal markers, internal transcribed spacer 1 and 2 (ITS1, ITS2), 5.8S, and three mitochondrial markers, cytochrome c oxidase subunit 1 and 2, and cytochrome b (cox1, cox2 and cytb), were obtained for 37 species of the subgenus Avaritia from all six biogeographical regions. Phylogenetic reconstructions using these genes independently and in combination were implemented using Bayesian inference analysis and maximum likelihood methods. Results Phylogenetic reconstructions gave strong support to several monophyletic groups within the subgenus Avaritia. Both C. actoni and C. pusillus formed a single clade with C. grahamii so their respective groups, the Actoni and Pusillus groups, have been merged with the Grahamii group. Some support was provided for the Boophagus and Jacobsoni groups. A group of species currently placed into the Orientalis group clustered in a clade with poor support. The Obsoletus group was defined as a sister clade to all other Avaritia groups. The clade including the Imicola group was well supported based on phylogenetic criteria. Conclusions This phylogenetic study combining five distinct molecular markers has provided meaningful insights into the systematic relationships of Culicoides (Avaritia) and highlighted future directions to continue the study of this subgenus. While the cox2 marker appeared to be useful to investigate closely related species, the 5.8S marker was highly conserved and uninformative. Further investigations including species absent from this work are needed to confirm the proposed systematic scheme. However, this systematic scheme can now serve as a foundation to investigate cryptic species affiliation within the subgenus. We advocate that future studies employ a combination of morphological and molecular analyses.![]()
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Affiliation(s)
- Bruno Mathieu
- IPPTS, Université de Strasbourg, DIHP UR 7292, 67000, Strasbourg, France.
| | - Claire Garros
- ASTRE, Univ Montpellier, Cirad, INRA, Montpellier, France.,Cirad, UMR ASTRE, F-34398, Montpellier, France
| | - Thomas Balenghien
- Cirad, UMR ASTRE, F-34398, Montpellier, France.,CIRAD, UMR ASTRE, Rabat, Morocco.,Unité Microbiologie, Immunologie et Maladies Contagieuses, IAV Hassan II, Rabat, Morocco
| | - Ermanno Candolfi
- IPPTS, Université de Strasbourg, DIHP UR 7292, 67000, Strasbourg, France
| | | | - Catherine Cêtre-Sossah
- ASTRE, Univ Montpellier, Cirad, INRA, Montpellier, France.,CIRAD, UMR ASTRE, Sainte Clotilde, La Réunion, France
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11
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Yanase T, Hayama Y, Shirafuji H, Tsutsui T, Terada Y. Surveillance of Culicoides biting midges in northern Honshu, Japan, during the period of Akabane virus spread. J Vet Med Sci 2019; 81:1496-1503. [PMID: 31447461 PMCID: PMC6863720 DOI: 10.1292/jvms.19-0303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A surveillance of Culicoides biting midges with light suction traps was
conducted in the northern region of Honshu, main island of Japan, during the summers and
autumns of 2009 and 2010. A total of 106 trap collections across 37 cattle farms were
investigated for the structure and distribution of Culicoides species.
Forty-thousand and one hundred forty-nine specimens of Culicoides biting
midges were identified at the species level, and ≥19 species were included in the
specimens. Culicoides oxystoma, which is a known major vector of Akabane
virus (AKAV), appeared not to have expanded in northern Honshu during the surveillance. Of
the potential AKAV vectors suggested by a previous laboratory experiment, C.
tainanus and C. punctatus widely infested cowsheds across
northern Honshu. The AKAV circulation was confirmed by serological surveillance of
sentinel cattle in northern Honshu during the summer and autumn of 2010 and, consequently,
>200 calves affected by the virus were identified as of spring 2011. Our surveillance
demonstrated that C. tainanus and C. punctatus were
widely spread and often dominated at cattle farms in/around the seroconverted regions, and
our results thus suggest that these species played a critical role in the AKAV
transmission in 2010. Because the distribution ranges of C. tainanus and
C. punctatus cover almost all of mainland Japan, a potential risk of
AKAV transmission might be expected even in areas outside the range of C.
oxystoma.
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Affiliation(s)
- Tohru Yanase
- Kyushu Research Station, National Institute of Animal Health, NARO, 2702, Chuzan, Kagoshima 891-0105, Japan
| | - Yoko Hayama
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, NARO, 3-1-5, Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Hiroaki Shirafuji
- Kyushu Research Station, National Institute of Animal Health, NARO, 2702, Chuzan, Kagoshima 891-0105, Japan
| | - Toshiyuki Tsutsui
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, NARO, 3-1-5, Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Yutaka Terada
- Bacterial and Parasitic Disease Research Division, National Institute of Animal Health, NARO, 3-1-5, Kannondai, Tsukuba, Ibaraki 305-0856, Japan
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12
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Wang X, Zhang Y, Zhang H, Qin G, Lin Q. Complete mitochondrial genomes of eight seahorses and pipefishes (Syngnathiformes: Syngnathidae): insight into the adaptive radiation of syngnathid fishes. BMC Evol Biol 2019; 19:119. [PMID: 31185889 PMCID: PMC6560779 DOI: 10.1186/s12862-019-1430-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/30/2019] [Indexed: 11/17/2022] Open
Abstract
Background The evolution of male pregnancy is the most distinctive characteristic of syngnathids, and their specialized life history traits make syngnathid species excellent model species for many issues in biological evolution. However, the origin of syngnathids and the evolutionary divergence time of different syngnathid species remain poorly resolved. Comprehensive phylogenetic studies of the Syngnathidae will provide critical evidence to elucidate their origin, evolution, and dispersal patterns. Results We sequenced the mitochondrial genomes of eight syngnathid species in this study, and the estimated divergence times suggested that syngnathids diverged from other teleosts approximately 48.8 Mya during the Eocene period. Selection analysis showed that many mitochondrial genes of syngnathids exhibited significantly lower Ka/Ks values than those of other teleosts. The two most frequently used codons in syngnathid fishes were different from those in other teleosts, and a greater proportion of the mitochondrial simple sequence repeats (SSRs) were distributed in non-coding sequences in syngnathids compared with other teleosts. Conclusions Our study indicated that syngnathid fishes experienced an adaptive radiation process during the early explosion of species. Syngnathid mitochondrial OXPHOS genes appear to exhibit depressed Ka/Ks ratios compared with those of other teleosts, and this may suggest that their mitogenomes have experienced strong selective constraints to eliminate deleterious mutations. Electronic supplementary material The online version of this article (10.1186/s12862-019-1430-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xin Wang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, People's Republic of China.,University of the Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yanhong Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
| | - Huixian Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
| | - Geng Qin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, People's Republic of China. .,University of the Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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13
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Yanase T, Kato T, Hayama Y, Shirafuji H, Yamakawa M, Tanaka S. Oral Susceptibility of Japanese Culicoides (Diptera: Ceratopogonidae) Species to Akabane Virus. JOURNAL OF MEDICAL ENTOMOLOGY 2019; 56:533-539. [PMID: 30418597 DOI: 10.1093/jme/tjy201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Indexed: 06/09/2023]
Abstract
To test their virus susceptibility and capacity as transmission vectors, Japanese Culicoides species were artificially fed a mixture of Akabane virus (AKAV) and bovine blood, and virus recovery was attempted from infected midges 9-11 d post-exposure. Culicoides tainanus, C. punctatus, C. humeralis, C. jacobsoni, C. oxystoma, and C. asiana were found to be orally susceptible to AKAV. Virus titers in single infected midges of C. tainanus, C. oxystoma, C. punctatus, and C. jacobsoni ranged from 100.75 to 104.0 TCID50 (tissue culture infectious dose). The titers in the infected C. oxystoma were significantly higher than those in the other infected species. Viral RNA was detected from both midges testing positive and those testing negative for infectious virus particles, but the viral RNA copies in the infectious virus-negative midges were significantly lower than those in the infectious virus-positive midges. Lower viral amplification, limited dissemination or both caused by tissue barriers might occur in infected midges from which infectious viruses were undetectable. A fully disseminated infection was developed in orally infected C. oxystoma and C. tainanus. This finding indicates their capacity to transmit AKAV, assuming that salivary gland barriers have limited effects on viral entry to and replication in salivary gland tissue. This result also suggests that the other orally susceptible species are potentially competent for AKAV transmission and would be considered active vectors of its spread.
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Affiliation(s)
- Tohru Yanase
- Kyushu Research Station, National Institute of Animal Health, NARO, Chuzan, Kagoshima, Japan
| | - Tomoko Kato
- Kyushu Research Station, National Institute of Animal Health, NARO, Chuzan, Kagoshima, Japan
| | - Yoko Hayama
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, NARO, Kannondai, Tsukuba, Ibaraki, Japan
| | - Hiroaki Shirafuji
- Kyushu Research Station, National Institute of Animal Health, NARO, Chuzan, Kagoshima, Japan
| | - Makoto Yamakawa
- Kyushu Research Station, National Institute of Animal Health, NARO, Chuzan, Kagoshima, Japan
| | - Shogo Tanaka
- Kyushu Research Station, National Institute of Animal Health, NARO, Chuzan, Kagoshima, Japan
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14
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Liu Y, Tao H, Yu Y, Yue L, Xia W, Zheng W, Ma H, Liu X, Chen H. Molecular differentiation and species composition of genus Culicoides biting midges (Diptera: Ceratopogonidae) in different habitats in southern China. Vet Parasitol 2018; 254:49-57. [PMID: 29657011 DOI: 10.1016/j.vetpar.2018.02.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 02/05/2018] [Accepted: 02/21/2018] [Indexed: 11/26/2022]
Abstract
Culicoides biting midges (Diptera:Ceratopogonidae) cause a significant biting nuisance to humans, livestock, which are the biological vectors of a range of risky pathogens. Accurate illustration of vector play a key role in arthropod borne diseases surveillance. However, few studies have focused on the Culicoides, which caused bluetongue disease in 29 provinces of China since 1979. In this study, we assessed cytochrome oxidase subunit I (COI) mtDNA molecular marker for identification of ten major vector species and analyzed the Culicoides species community and diversity in different habitats. A total of 20,795 Culicoides samples collected from 11 sample sites were identified as 23 species belonging to 7 subgenera. Sequences of COI gene worked well as barcodes for identifying all the determined specimen in this study and were comparable with the existing sequence data from GenBank. We first reported COI barcode sequences of C. morisitai, C. insignipennis and C. homotomus. Morphological identification of Culicoides spp. samples within southern China appears relatively robust and some unidentified species were required further study. Our study shows that the COI sequence data can be used as a tool to identify species of Culicoides in Jiangxi Province. In our sampled area, the most abundant species was C. arakawae (61.89%), followed by C. oxystoma (13.77%), C. punctatus (10.10%), C. nipponensis (8.82%), C. homotomus (3.19%) and C.morisitai (1.17%) in this study. C. punctatus was the dominant species of Park habitat (62.22%), C. arakawae was the predominant species of Chicken habitat (96.66%), Vegetable plot habitat (92.0%), and Peasant household habitat (83.21%), respectively. C. oxystoma was the abundant species of Residential area habitat (40.11%), Hospital habitat (56.65%), and Pig & Cow habitat (48.77%), respectively. Results also show that the potential Bluetongue virus vectors belong to the Obsoletus and Pulicaris groups, are also included and relatively abundant, notably: Culicoides punctatus. These findings expand the current knowledge of Culicoides population composition in the southern part of China.
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Affiliation(s)
- Yangqing Liu
- Nanchang Center for Disease Control and Prevention, Nanchang, 330038, PR China.
| | - Huiying Tao
- Nanchang Center for Disease Control and Prevention, Nanchang, 330038, PR China.
| | - Yixin Yu
- Institute of Microbiology and Epidemiology Academy of Military Medical Sciences, Beijing, 100071, PR China.
| | - Liangliang Yue
- National Plateau Wetland Research Center, Southwest Forestry University, Kunming, 650224, PR China.
| | - Wen Xia
- Nanchang Center for Disease Control and Prevention, Nanchang, 330038, PR China.
| | - Weiqing Zheng
- Nanchang Center for Disease Control and Prevention, Nanchang, 330038, PR China.
| | - Hongmei Ma
- Nanchang Center for Disease Control and Prevention, Nanchang, 330038, PR China.
| | - Xiaoqing Liu
- Nanchang Center for Disease Control and Prevention, Nanchang, 330038, PR China.
| | - Haiying Chen
- Nanchang Center for Disease Control and Prevention, Nanchang, 330038, PR China.
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15
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Augot D, Mathieu B, Hadj-Henni L, Barriel V, Zapata Mena S, Smolis S, Slama D, Randrianambinintsoa FJ, Trueba G, Kaltenbach M, Rahola N, Depaquit J. Molecular phylogeny of 42 species of Culicoides (Diptera, Ceratopogonidae) from three continents. ACTA ACUST UNITED AC 2017. [PMID: 28643630 PMCID: PMC5482051 DOI: 10.1051/parasite/2017020] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The genus Culicoides includes vectors of important animal diseases such as bluetongue and Schmallenberg virus (BTV and SBV). This genus includes 1300 species classified in 32 subgenera and 38 unclassified species. However, the phylogenetic relationships between different subgenera of Culicoides have never been studied. Phylogenetic analyses of 42 species belonging to 12 subgenera and 8 ungrouped species of genus Culicoides from Ecuador, France, Gabon, Madagascar and Tunisia were carried out using two molecular markers (28S rDNA D1 and D2 domains and COI mtDNA). Sequences were subjected to non-probabilistic (maximum parsimony) and probabilistic (Bayesian inference (BI)) approaches. The subgenera Monoculicoides, Culicoides, Haematomyidium, Hoffmania, Remmia and Avaritia (including the main vectors of bluetongue disease) were monophyletic, whereas the subgenus Oecacta was paraphyletic. Our study validates the subgenus Remmia (= Schultzei group) as a valid subgenus, outside of the subgenus Oecacta. In Europe, Culicoides obsoletus, Culicoides scoticus and Culicoides chiopterus should be part of the Obsoletus complex whereas Culicoides dewulfi should be excluded from this complex. Our study suggests that the current Culicoides classification needs to be revisited with modern tools.
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Affiliation(s)
- Denis Augot
- USC Vecpar, ANSES-LSA, Université de Reims Champagne-Ardenne, SFR Cap Santé, Faculté de Pharmacie, 51 rue Cognacq-Jay, EA 4688, Reims 51096, France
| | - Bruno Mathieu
- Institut de Parasitologie et de Pathologie Tropicale de Strasbourg, Université de Strasbourg, Faculté de Médecine, 3 rue Koeberlé, EA7292, Strasbourg 67000, France
| | - Leila Hadj-Henni
- USC Vecpar, ANSES-LSA, Université de Reims Champagne-Ardenne, SFR Cap Santé, Faculté de Pharmacie, 51 rue Cognacq-Jay, EA 4688, Reims 51096, France
| | - Véronique Barriel
- Muséum National d'Histoire Naturelle, CR2P-UMR 7207 CNRS, MNHN, UPMC, 8 rue Buffon, CP 38, 75005 Paris, France
| | - Sonia Zapata Mena
- Instituto de Microbiologia, Colegio de Ciencias Biologicas y Ambientales, Universidad San Francisco de Quito, Cumbayá, EC170157 Quito, Pichincha, Ecuador
| | - Sylvia Smolis
- USC Vecpar, ANSES-LSA, Université de Reims Champagne-Ardenne, SFR Cap Santé, Faculté de Pharmacie, 51 rue Cognacq-Jay, EA 4688, Reims 51096, France
| | - Darine Slama
- Laboratory of Medical and Molecular Parasitology-Mycology, Faculty of Pharmacy, University of Monastir, 99UR/08-05, 5000 Monastir, Tunisia
| | | | - Gabriel Trueba
- Instituto de Microbiologia, Colegio de Ciencias Biologicas y Ambientales, Universidad San Francisco de Quito, Cumbayá, EC170157 Quito, Pichincha, Ecuador
| | - Matthieu Kaltenbach
- Laboratoire de Pharmacologie, Université de Reims Champagne-Ardenne, UFR Pharmacie, 51 rue Cognacq-Jay, 51100 Reims, France
| | - Nil Rahola
- Unité MIVEGEC, UMR 224-5290 IRD-CNRS-UM, Centre IRD de Montpellier, BP 64501, 911 avenue Agropolis, 34394 Montpellier, France - Centre International de Recherches Médicales de Franceville (CIRMF), BP 769, Franceville, Gabon
| | - Jérôme Depaquit
- USC Vecpar, ANSES-LSA, Université de Reims Champagne-Ardenne, SFR Cap Santé, Faculté de Pharmacie, 51 rue Cognacq-Jay, EA 4688, Reims 51096, France
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16
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Romanova EV, Aleoshin VV, Kamaltynov RM, Mikhailov KV, Logacheva MD, Sirotinina EA, Gornov AY, Anikin AS, Sherbakov DY. Evolution of mitochondrial genomes in Baikalian amphipods. BMC Genomics 2016; 17:1016. [PMID: 28105939 PMCID: PMC5249044 DOI: 10.1186/s12864-016-3357-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Amphipods (Crustacea) of Lake Baikal are a very numerous and diverse group of invertebrates generally believed to have originated by adaptive radiation. The evolutionary history and phylogenetic relationships in Baikalian amphipods still remain poorly understood. Sequencing of mitochondrial genomes is a relatively feasible way for obtaining a set of gene sequences suitable for robust phylogenetic inferences. The architecture of mitochondrial genomes also may provide additional information on the mechanisms of evolution of amphipods in Lake Baikal. RESULTS Three complete and four nearly complete mitochondrial genomes of Baikalian amphipods were obtained by high-throughput sequencing using the Illumina platform. A phylogenetic inference based on the nucleotide sequences of all mitochondrial protein coding genes revealed the Baikalian species to be a monophyletic group relative to the nearest non-Baikalian species with a completely sequenced mitochondrial genome - Gammarus duebeni. The phylogeny of Baikalian amphipods also suggests that the shallow-water species Eulimnogammarus has likely evolved from a deep-water ancestor, however many other species have to be added to the analysis to test this hypothesis. The gene order in all mitochondrial genomes of studied Baikalian amphipods differs from the pancrustacean ground pattern. Mitochondrial genomes of four species possess 23 tRNA genes, and in three genomes the extra tRNA gene copies have likely undergone remolding. Widely varying lengths of putative control regions and other intergenic spacers are typical for the mitochondrial genomes of Baikalian amphipods. CONCLUSIONS The mitochondrial genomes of Baikalian amphipods display varying organization suggesting an intense rearrangement process during their evolution. Comparison of complete mitochondrial genomes is a potent approach for studying the amphipod evolution in Lake Baikal.
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Affiliation(s)
- Elena V. Romanova
- Laboratory of Molecular Systematics, Limnological Institute, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033 Russian Federation
| | - Vladimir V. Aleoshin
- Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, 119991 Russian Federation
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127994 Russian Federation
| | - Ravil M. Kamaltynov
- Laboratory of Molecular Systematics, Limnological Institute, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033 Russian Federation
| | - Kirill V. Mikhailov
- Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, 119991 Russian Federation
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127994 Russian Federation
| | - Maria D. Logacheva
- Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, 119991 Russian Federation
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127994 Russian Federation
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420012 Russian Federation
| | - Elena A. Sirotinina
- Laboratory of Molecular Systematics, Limnological Institute, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033 Russian Federation
| | - Alexander Yu. Gornov
- Institute for System Dynamics and Control Theory, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033 Russian Federation
| | - Anton S. Anikin
- Institute for System Dynamics and Control Theory, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033 Russian Federation
| | - Dmitry Yu. Sherbakov
- Laboratory of Molecular Systematics, Limnological Institute, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033 Russian Federation
- Faculty of Biology and Soil Studies, Irkutsk State University, Irkutsk, 664003 Russian Federation
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17
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Harrup LE, Laban S, Purse BV, Reddy YK, Reddy YN, Byregowda SM, Kumar N, Purushotham KM, Kowalli S, Prasad M, Prasad G, Bettis AA, De Keyser R, Logan J, Garros C, Gopurenko D, Bellis G, Labuschagne K, Mathieu B, Carpenter S. DNA barcoding and surveillance sampling strategies for Culicoides biting midges (Diptera: Ceratopogonidae) in southern India. Parasit Vectors 2016; 9:461. [PMID: 27549137 PMCID: PMC4994320 DOI: 10.1186/s13071-016-1722-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 07/25/2016] [Indexed: 11/10/2022] Open
Abstract
Background Culicoides spp. biting midges transmit bluetongue virus (BTV), the aetiological agent of bluetongue (BT), an economically important disease of ruminants. In southern India, hyperendemic outbreaks of BT exert high cost to subsistence farmers in the region, impacting on sheep production. Effective Culicoides spp. monitoring methods coupled with accurate species identification can accelerate responses for minimising BT outbreaks. Here, we assessed the utility of sampling methods and DNA barcoding for detection and identification of Culicoides spp. in southern India, in order to provide an informed basis for future monitoring of their populations in the region. Methods Culicoides spp. collected from Tamil Nadu and Karnataka were used to construct a framework for future morphological identification in surveillance, based on sequence comparison of the DNA barcode region of the mitochondrial cytochrome c oxidase I (COI) gene and achieving quality standards defined by the Barcode of Life initiative. Pairwise catches of Culicoides spp. were compared in diversity and abundance between green (570 nm) and ultraviolet (UV) (390 nm) light emitting diode (LED) suction traps at a single site in Chennai, Tamil Nadu over 20 nights of sampling in November 2013. Results DNA barcode sequences of Culicoides spp. were mostly congruent both with existing DNA barcode data from other countries and with morphological identification of major vector species. However, sequence differences symptomatic of cryptic species diversity were present in some groups which require further investigation. While the diversity of species collected by the UV LED Center for Disease Control (CDC) trap did not significantly vary from that collected by the green LED CDC trap, the UV CDC significantly outperformed the green LED CDC trap with regard to the number of Culicoides individuals collected. Conclusions Morphological identification of the majority of potential vector species of Culicoides spp. samples within southern India appears relatively robust; however, potential cryptic species diversity was present in some groups requiring further investigation. The UV LED CDC trap is recommended for surveillance of Culicoides in southern India. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1722-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lara E Harrup
- Vector-borne Viral Diseases Programme, The Pirbright Institute, Ash Road, Woking, Surrey, GU24 0NF, UK.
| | - Swathi Laban
- Vaccine Research Centre-Viral Vaccines, Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Madhavaram Milk Colony, Chennai, 600 051, India
| | - Bethan V Purse
- Centre for Ecology and Hydrology, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB, UK
| | - Yarabolu Krishnamohan Reddy
- Vaccine Research Centre-Viral Vaccines, Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Madhavaram Milk Colony, Chennai, 600 051, India
| | - Yella Narasimha Reddy
- Department of Veterinary Microbiology, College of Veterinary Science, Rajendranagar, Hyderabad, 500030, Andhra Pradesh, India
| | | | - Naveen Kumar
- Institute of Animal Health and Veterinary Biologicals, Hebbal, 560024, Bengaluru, India
| | | | - Shrikant Kowalli
- Institute of Animal Health and Veterinary Biologicals, Hebbal, 560024, Bengaluru, India
| | - Minakshi Prasad
- Department of Animal Biotechnology, Lala Lajpat Rai University of Veterinary and Animal Sciences, College of Veterinary Science, Hisar, 125004, Haryana, India
| | - Gaya Prasad
- Department of Animal Biotechnology, Lala Lajpat Rai University of Veterinary and Animal Sciences, College of Veterinary Science, Hisar, 125004, Haryana, India.,Indian Council Agricultural Research, New Delhi, 110 001, India
| | - Alison A Bettis
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Rien De Keyser
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - James Logan
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Claire Garros
- Cirad, UMR15 CMAEE, F-34398, Montpellier, France.,INRA, UMR1309 CMAEE, F-34398, Montpellier, France
| | - David Gopurenko
- NSW Department of Primary Industries, PMB, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia.,Graham Centre for Agricultural Innovation, Locked Bag 588, Wagga Wagga, NSW, 2678, Australia
| | - Glenn Bellis
- Department of Agriculture, Fisheries and Forestry, Winnellie, Australia
| | - Karien Labuschagne
- Onderstepoort Veterinary Institute, Agricultural Research Council-Onderstepoort Veterinary Institute, PVVD, ZA-0110, Onderstepoort, South Africa.,Department of Zoology and Entomology, University of Pretoria, ZA-0002, Pretoria, South Africa
| | - Bruno Mathieu
- Institut de Parasitologie et de Pathologie tropicale de Strasbourg (IPPTS), EA7292, Faculté de Médecine, 3 rue Koeberlé, F-67000, Strasbourg, France
| | - Simon Carpenter
- Vector-borne Viral Diseases Programme, The Pirbright Institute, Ash Road, Woking, Surrey, GU24 0NF, UK
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Zhang X, Kang Z, Mao M, Li X, Cameron SL, de Jong H, Wang M, Yang D. Comparative Mt Genomics of the Tipuloidea (Diptera: Nematocera: Tipulomorpha) and Its Implications for the Phylogeny of the Tipulomorpha. PLoS One 2016; 11:e0158167. [PMID: 27341029 PMCID: PMC4920351 DOI: 10.1371/journal.pone.0158167] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/10/2016] [Indexed: 11/18/2022] Open
Abstract
A traditionally controversial taxon, the Tipulomorpha has been frequently discussed with respect to both its familial composition and relationships with other Nematocera. The interpretation of internal relationships within the Tipuloidea, which include the Tipulidae sensu stricto, Cylindrotomidae, Pediciidae and Limoniidae, is also problematic. We sequenced the first complete mitochondrial (mt) genome of Symplecta hybrida (Meigen, 1804), which belongs to the subfamily Chioneinae of family Limoniidae, and another five nearly complete mt genomes from the Tipuloidea. We did a comparative analysis of these mt genomics and used them, along with some other representatives of the Nematocera to construct phylogenetic trees. Trees inferred by Bayesian methods strongly support a sister-group relationship between Trichoceridae and Tipuloidea. Tipulomorpha are not supported as the earliest branch of the Diptera. Furthermore, phylogenetic trees indicate that the family Limoniidae is a paraphyletic group.
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Affiliation(s)
- Xiao Zhang
- Department of Entomology, China Agricultural University, Beijing, 100193, China
| | - Zehui Kang
- Department of Entomology, China Agricultural University, Beijing, 100193, China
| | - Meng Mao
- Centre for Medical Bioscience, School of Biological Sciences, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Xuankun Li
- Department of Entomology, China Agricultural University, Beijing, 100193, China
| | - Stephen L. Cameron
- Earth, Environmental & Biological Sciences School, Science & Engineering Faculty, Queensland University of Technology, Brisbane, Australia
| | - Herman de Jong
- Naturalis Biodiversity Center Darwinweg 2, 2333 CR, Leiden, The Netherlands
| | - Mengqing Wang
- Department of Entomology, China Agricultural University, Beijing, 100193, China
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing, 100193, China
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Wang K, Li X, Ding S, Wang N, Mao M, Wang M, Yang D. The complete mitochondrial genome of the Atylotus miser (Diptera: Tabanomorpha: Tabanidae), with mitochondrial genome phylogeny of lower Brachycera (Orthorrhapha). Gene 2016; 586:184-96. [PMID: 27063560 DOI: 10.1016/j.gene.2016.04.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/22/2016] [Accepted: 04/05/2016] [Indexed: 11/25/2022]
Abstract
Brachycera is a clade with over 80,000 described species and originated from the Mesozoic, and its larvae employ comprehensive feeding strategies. The phylogeny of the lower Brachycera has been studied intensively over the past decades. In order to supplement the lack of genetic data in this important group, we sequenced the complete mitochondrial (mt) genome of Atylotus miser as well as the nearly complete mt genomes of another 11 orthorrhaphous flies. The mt genome of A. miser is 15,858bp, which is typical of Diptera, with 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a 993bp control region. The rest of the orthorrhaphous mt genomes in our study have the similar structure with A. miser. Additionally, we conducted a phylogenetic analysis of 20 mt genomes using Maximum-likelihood and Bayesian methods in order to reconstruct the evolutionary relationship of Orthorrhapha. The results show that all infraorders of Brachycera are monophyletic, and a relationship of Tabanomorpha+((Xylophagomorpha+Stratiomyomorpha)+Muscomorpha) has been proposed. Within Xylophagomorpha, Nemestrinoidae forms the sister group of Xylophagidae.
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Affiliation(s)
- Kai Wang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Xuankun Li
- Department of Entomology, China Agricultural University, Beijing, China
| | - Shuangmei Ding
- Department of Entomology, China Agricultural University, Beijing, China
| | - Ning Wang
- Department of Entomology, China Agricultural University, Beijing, China; Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Meng Mao
- School of Biological Sciences, University of Wollongong, Wollongong, Australia
| | - Mengqing Wang
- Department of Entomology, China Agricultural University, Beijing, China; Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing, China.
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20
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Tay WT, Kerr PJ, Jermiin LS. Population Genetic Structure and Potential Incursion Pathways of the Bluetongue Virus Vector Culicoides brevitarsis (Diptera: Ceratopogonidae) in Australia. PLoS One 2016; 11:e0146699. [PMID: 26771743 PMCID: PMC4714883 DOI: 10.1371/journal.pone.0146699] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 12/20/2015] [Indexed: 11/18/2022] Open
Abstract
Culicoides brevitarsis is a vector of the bluetongue virus (BTV), which infects sheep and cattle. It is an invasive species in Australia with an assumed Asian/South East Asian origin. Using one mitochondrial marker (i.e., part of the cytochrome oxidase subunit I gene) and six nuclear markers, we inferred population genetic structure and possible incursion pathways for Australian C. brevitarsis. Nine mitochondrial haplotypes, with low nucleotide sequence diversity (0.0–0.7%) among these, were identified in a sample of 70 individuals from seven sites. Both sets of markers revealed a homogeneous population structure, albeit with evidence of isolation by distance and two genetically distinct clusters distributed along a north-to-south cline. No evidence of a cryptic species complex was found. The geographical distribution of the mitochondrial haplotypes is consistent with at least two incursion pathways into Australia since the arrival of suitable livestock hosts. By contrast, 15 mitochondrial haplotypes, with up to four times greater nucleotide sequence diversity (0.0–2.9%) among these, were identified in a sample of 16 individuals of the endemic C. marksi (sampled from a site in South Australia and another in New South Wales). A phylogenetic tree inferred using the mitochondrial marker revealed that the Australian and Japanese samples of C. brevitarsis are as evolutionarily different from one another as some of the other Australian species (e.g., C. marksi, C. henryi, C. pallidothorax) are. The phylogenetic tree placed four of the species endemic to Australia (C. pallidothorax, C. bundyensis, C. marksi, C. henryi) in a clade, with a fifth such species (C. bunrooensis) sharing a common ancestor with that clade and a clade comprising two Japanese species (C. verbosus, C. kibunensis).
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Affiliation(s)
- W. T. Tay
- CSIRO, Black Mountain Laboratories, Canberra, ACT, 2601, Australia
- * E-mail:
| | - P. J. Kerr
- CSIRO, Black Mountain Laboratories, Canberra, ACT, 2601, Australia
- School of Biological Sciences, The University of Sydney, Sydney, 2006, Australia
| | - L. S. Jermiin
- CSIRO, Black Mountain Laboratories, Canberra, ACT, 2601, Australia
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21
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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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Stokkan M, Jurado-Rivera JA, Juan C, Jaume D, Pons J. Mitochondrial genome rearrangements at low taxonomic levels: three distinct mitogenome gene orders in the genus Pseudoniphargus (Crustacea: Amphipoda). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3579-89. [PMID: 26329687 DOI: 10.3109/19401736.2015.1079821] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A comparison of mitochondrial genomes of three species of the amphipod Pseudoniphargus revealed the occurrence of a surprisingly high level of gene rearrangement involving protein-coding genes that is a rare phenomenon at low taxonomic levels. The three Pseudoniphargus mitogenomes also display a unique gene arrangement with respect to either the presumed Pancrustacean order or those known for other amphipods. Relative long non-coding sequences appear adjacent to the putative breakage points involved in gene rearrangements of protein coding genes. Other details of the newly obtained mitochondrial genomes - e.g., gene content, nucleotide composition and codon usage - are similar to those found in the mitogenomes of other amphipod species studied. They all contain the typical mitochondrial genome set consisting of 13 protein-coding genes, 22 tRNAs, and two rRNAS, as well as a large control region. The secondary structures and characteristics of tRNA and ribosomal mitochondrial genes of these three species are also discussed.
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Affiliation(s)
- Morten Stokkan
- a Department of Biodiversity and Conservation , Instituto Mediterraneo de Estudios Avanzados (IMEDEA, CSIC-UIB) , Esporles , Spain and
| | - Jose A Jurado-Rivera
- a Department of Biodiversity and Conservation , Instituto Mediterraneo de Estudios Avanzados (IMEDEA, CSIC-UIB) , Esporles , Spain and.,b Departament de Biologia , Universitat de les Illes Balears , Palma , Spain
| | - Carlos Juan
- a Department of Biodiversity and Conservation , Instituto Mediterraneo de Estudios Avanzados (IMEDEA, CSIC-UIB) , Esporles , Spain and.,b Departament de Biologia , Universitat de les Illes Balears , Palma , Spain
| | - Damià Jaume
- a Department of Biodiversity and Conservation , Instituto Mediterraneo de Estudios Avanzados (IMEDEA, CSIC-UIB) , Esporles , Spain and
| | - Joan Pons
- a Department of Biodiversity and Conservation , Instituto Mediterraneo de Estudios Avanzados (IMEDEA, CSIC-UIB) , Esporles , Spain and
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Harrup LE, Bellis GA, Balenghien T, Garros C. Culicoides Latreille (Diptera: Ceratopogonidae) taxonomy: current challenges and future directions. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2015; 30:249-266. [PMID: 25535946 PMCID: PMC4330985 DOI: 10.1016/j.meegid.2014.12.018] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 12/12/2014] [Accepted: 12/13/2014] [Indexed: 11/23/2022]
Abstract
Culicoides Latreille biting midges (Diptera: Ceratopogonidae) cause a significant biting nuisance to humans, livestock and equines, and are the biological vectors of a range of internationally important pathogens of both veterinary and medical importance. Despite their economic significance, the delimitation and identification of species and evolutionary relationships between species within this genus remains at best problematic. To date no phylogenetic study has attempted to validate the subgeneric classification of the genus and the monophyly of many of the subgenera remains doubtful. Many informal species groupings are also known to exist but few are adequately described, further complicating accurate identification. Recent contributions to Culicoides taxonomy at the species level have revealed a high correlation between morphological and molecular analyses although molecular analyses are revealing the existence of cryptic species. This review considers the methods for studying the systematics of Culicoides using both morphological and genetic techniques, with a view to understanding the factors limiting our current understanding of Culicoides biology and hence arbovirus epidemiology. In addition, we examine the global status of Culicoides identification, highlighting areas that are poorly addressed, including the potential implementation of emerging technologies.
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Affiliation(s)
- L E Harrup
- Vector-borne Viral Diseases Programme, The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK.
| | - G A Bellis
- University of Queensland, St Lucia, Brisbane, Qld, Australia
| | - T Balenghien
- Cirad, UMR15 CMAEE, 34398 Montpellier, France; INRA, UMR1309 CMAEE, 34398 Montpellier, France
| | - C Garros
- Cirad, UMR15 CMAEE, 34398 Montpellier, France; INRA, UMR1309 CMAEE, 34398 Montpellier, France
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24
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Biting midges monitoring (Diptera: Ceratopogonidae: Culicoides Latreille) in the governate of Monastir (Tunisia): species composition and molecular investigations. Parasitol Res 2014; 113:2435-43. [PMID: 24825311 DOI: 10.1007/s00436-014-3873-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 03/24/2014] [Indexed: 10/25/2022]
Abstract
The results of entomological studies carried out in the governate of Monastir (Tunisia) in 2009-2010 (captures and emergences from muds) focusing on Culicoides species are presented in the present study. Identification of Culicoides at the species level is based on morphological characters, and a molecular study has been carried out based on mitochondrial DNA cytochrome C oxidase I gene (COI) and D1 and D2 domains of the 28S rDNA. The DNA sequences reported here are related to 10 species (on 25 known) of Culicoides described in Tunisia: Culicoides cataneii-gejgelensis, Culicoides circumscriptus, Culicoides imicola, Culicoides jumineri, Culicoides kingi, Culicoides langeroni, Culicoides newsteadi, Culicoides paolae, Culicoides puncticollis and Culicoides sahariensis. DNA sequencing of the COI gene and D1D2 domains discriminated all morphologically determined species. The choice of D1D2 domains considered as a conserved region is informative for Culicoides species identification. The molecular analyses of COI has grouped both C. circumscriptus, C. puncticollis within two clusters and C. newsteadi within five subclusters. However, C. newsteadi shows relatively deep intraspecific divergence using COI sequences.
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25
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Sim S, Ramirez JL, Dimopoulos G. Molecular discrimination of mosquito vectors and their pathogens. Expert Rev Mol Diagn 2014; 9:757-65. [DOI: 10.1586/erm.09.56] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Ander M, Troell K, Chirico J. Barcoding of biting midges in the genus Culicoides: a tool for species determination. MEDICAL AND VETERINARY ENTOMOLOGY 2013; 27:323-31. [PMID: 23106166 DOI: 10.1111/j.1365-2915.2012.01050.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Biting midges of the genus Culicoides (Diptera: Ceratopogonidae) are insect vectors of economically important veterinary diseases such as African horse sickness virus and bluetongue virus. However, the identification of Culicoides based on morphological features is difficult. The sequencing of mitochondrial cytochrome oxidase subunit I (COI), referred to as DNA barcoding, has been proposed as a tool for rapid identification to species. Hence, a study was undertaken to establish DNA barcodes for all morphologically determined Culicoides species in Swedish collections. In total, 237 specimens of Culicoides representing 37 morphologically distinct species were used. The barcoding generated 37 supported clusters, 31 of which were in agreement with the morphological determination. However, two pairs of closely related species could not be separated using the DNA barcode approach. Moreover, Culicoides obsoletus Meigen and Culicoides newsteadi Austen showed relatively deep intraspecific divergence (more than 10 times the average), which led to the creation of two cryptic species within each of C. obsoletus and C. newsteadi. The use of COI barcodes as a tool for the species identification of biting midges can differentiate 95% of species studied. Identification of some closely related species should employ a less conserved region, such as a ribosomal internal transcribed spacer.
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Affiliation(s)
- M Ander
- Department of Virology, Immunobiology and Parasitology, National Veterinary Institute, Uppsala, Sweden
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27
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Yanase T, Matsumoto Y, Matsumori Y, Aizawa M, Hirata M, Kato T, Shirafuji H, Yamakawa M, Tsuda T, Noda H. Molecular identification of field-collected Culicoides larvae in the southern part of Japan. JOURNAL OF MEDICAL ENTOMOLOGY 2013; 50:1105-1110. [PMID: 24180116 DOI: 10.1603/me11235] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Although Culicoides biting midges act as a vector of important human and domestic animal diseases, their ecology is poorly understood. The lack of proper identification systems of Culicoides larvae is one of the main obstacles to progress in research. Based on mitochondrial sequences of 19 Japanese Culicoides species, we designed a universal primer set to amplify the partial sequence of the mitochondrial cytochrome c oxidase I (cox 1). The polymerase chain reaction product amplified from extracted DNA of Culicoides larvae using the primer set was directly sequenced, and species identification based on the variation at cox1 was conducted. Using the molecular identification system, we sorted 243 specimens of field-collected larvae from the southern part of Japan into 10 species including Culicoides arakawae (Arakawa), Culicoides oxystoma Kieffer, and Culicoides brevitarsis Kieffer, which are regarded as vectors of important livestock animal diseases. Eight species of Culicoides larvae, including C. arakawae and C. oxystoma, were recovered from active paddy fields and an abandoned paddy field. The result suggests that paddy fields contribute to breeding a variety of Culicoides species and maintenance and spread of Culicoides-borne pathogens. In contrast, larvae of C. brevitarsis were collected from cattle dung in pastures. The molecular identification system described herein using nucleotide sequences successfully achieved larval identification and will be useful for a better understanding of larval habitats of Culicoides biting midges.
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Affiliation(s)
- Tohru Yanase
- Kyushu Research Station, National Institute of Animal Health, NARO, 2702, Chuzan, Kagoshima 891-0105, Japan.
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28
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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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Molecular identification, phylogenetic status, and geographic distribution of Culicoides oxystoma (Diptera: Ceratopogonidae) in Israel. PLoS One 2012; 7:e33610. [PMID: 22438964 PMCID: PMC3306425 DOI: 10.1371/journal.pone.0033610] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 02/13/2012] [Indexed: 11/24/2022] Open
Abstract
Culicoides oxystoma (Diptera: Ceratopogonidae) is an important vector species, reported mainly from Asia, with high potential to transmit viral diseases affecting livestock. In Japan, many arboviruses have been isolated from C. oxystoma, suggesting it as a key player in the epidemiology of several Culicoides-borne diseases. Over the years, C. oxystoma has also been reported in the Middle East region, including Israel. In this region, however, C. oxystoma cannot be easily distinguished morphologically from its sibling species included in the Culicoides schultzei complex. We therefore used genomic data for species identification and phylogeny resolution. Phylogenetic analyses based on internal transcribed spacer 1 (ITS-1) of ribosomal DNA and the mitochondrial gene encoding cytochrome oxidase subunit I (COI) showed that C. oxystoma from Israel is closely related to C. oxystoma from Japan. Using differential probing PCR, we showed that C. oxystoma is distributed all over the country, especially in Mediterranean climate regions. Culicoides oxystoma is less common or even absent in arid regions, while the other genetic cluster of C. schultzei complex was found only in the east of the country (mostly arid and semiarid regions). The molecular finding of C. oxystoma in wide geographical regions, together with its high proportion in the general Culicoides population and its vectoring potential, imply that it may be an important vector species in the Middle East.
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Mao M, Valerio A, Austin AD, Dowton M, Johnson NF. The first mitochondrial genome for the wasp superfamily Platygastroidea: the egg parasitoid Trissolcus basalis. Genome 2012; 55:194-204. [PMID: 22360780 DOI: 10.1139/g2012-005] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The nearly complete mitochondrial (mt) genome of an egg parasitoid, Trissolcus basalis (Wollaston), was sequenced using both 454 and Illumina next-generation sequencing technologies. A portion of the noncoding region remained unsequenced, possibly owing to the presence of repeats. The sequenced portion of the genome is 15,768 bp and has a high A+T content (84.2%), as is typical for hymenopteran mt genomes. A total of 36 of the 37 genes normally present in animal mt genomes were located. The one exception was trnR; a truncated version of this gene is present between trnS(1) and nd5, but it is unclear whether this gene fragment could code for the entire trnR gene. The mt gene arrangement of T. basalis is different from other Proctotrupomorpha mt genomes, with a number of trn genes in different positions. However, no shared derived gene rearrangements were identified in the present study. Bayesian analyses of mt genomes from 29 hymenopteran taxa and seven other orders of holometabolous insects support some uncontroversial evolutionary relationships, but indicate that much higher levels of taxonomic sampling are necessary for the resolution of family and superfamily relationships.
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Affiliation(s)
- Meng Mao
- Centre for Medical Bioscience, School of Biological Sciences, Wollongong University, Northfields Avenue, Wollongong, NSW, 2522, Australia.
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The complete mitochondrial genome of the leafminer Liriomyza trifolii (Diptera: Agromyzidae). Mol Biol Rep 2010; 38:687-92. [DOI: 10.1007/s11033-010-0155-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Accepted: 03/26/2010] [Indexed: 10/19/2022]
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McMahon DP, Hayward A, Kathirithamby J. The mitochondrial genome of the 'twisted-wing parasite' Mengenilla australiensis (Insecta, Strepsiptera): a comparative study. BMC Genomics 2009; 10:603. [PMID: 20003419 PMCID: PMC2800125 DOI: 10.1186/1471-2164-10-603] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Accepted: 12/14/2009] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Strepsiptera are an unusual group of sexually dimorphic, entomophagous parasitoids whose evolutionary origins remain elusive. The lineage leading to Mengenilla australiensis (Family Mengenillidae) is the sister group to all remaining extant strepsipterans. It is unique in that members of this family have retained a less derived condition, where females are free-living from pupation onwards, and are structurally much less simplified. We sequenced almost the entire mitochondrial genome of M. australiensis as an important comparative data point to the already available genome of its distant relative Xenos vesparum (Family Xenidae). This study represents the first in-depth comparative mitochondrial genomic analysis of Strepsiptera. RESULTS The partial genome of M. australiensis is presented as a 13421 bp fragment, across which all 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes and 18 transfer RNA (tRNA) sequences are identified. Two tRNA translocations disrupt an otherwise ancestral insect mitochondrial genome order. A+T content is measured at 84.3%, C-content is also very skewed. Compared with M. australiensis, codon bias in X. vesparum is more balanced. Interestingly, the size of the protein coding genome is truncated in both strepsipterans, especially in X. vesparum which, uniquely, has 4.3% fewer amino acids than the average holometabolan complement. A revised assessment of mitochondrial rRNA secondary structure based on comparative structural considerations is presented for M. australiensis and X. vesparum. CONCLUSIONS The mitochondrial genome of X. vesparum has undergone a series of alterations which are probably related to an extremely derived lifestyle. Although M. australiensis shares some of these attributes; it has retained greater signal from the hypothetical most recent common ancestor (MRCA) of Strepsiptera, inviting the possibility that a shift in the mitochondrial selective environment might be related to the specialization accompanying the evolution of a small, morphologically simplified completely host-dependent lifestyle. These results provide useful insights into the nature of the evolutionary transitions that accompanied the emergence of Strepsiptera, but we emphasize the need for adequate sampling across the order in future investigations concerning the extraordinary developmental and evolutionary origins of this group.
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Affiliation(s)
- Dino P McMahon
- Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford, OX1 3PS, UK
| | - Alexander Hayward
- Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford, OX1 3PS, UK
| | - Jeyaraney Kathirithamby
- Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford, OX1 3PS, UK
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Prevalence of Cardinium bacteria in planthoppers and spider mites and taxonomic revision of "Candidatus Cardinium hertigii" based on detection of a new Cardinium group from biting midges. Appl Environ Microbiol 2009; 75:6757-63. [PMID: 19734338 DOI: 10.1128/aem.01583-09] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cardinium bacteria, members of the phylum Cytophaga-Flavobacterium-Bacteroides (CFB), are intracellular bacteria in arthropods that are capable of inducing reproductive abnormalities in their hosts, which include parasitic wasps, mites, and spiders. A high frequency of Cardinium infection was detected in planthoppers (27 out of 57 species were infected). A high frequency of Cardinium infection was also found in spider mites (9 out of 22 species were infected). Frequencies of double infection by Cardinium and Wolbachia bacteria (Alphaproteobacteria capable of manipulating reproduction of their hosts) were disproportionately high in planthoppers but not in spider mites. A new group of bacteria, phylogenetically closely related to but distinct from previously described Cardinium bacteria (based on 16S rRNA and gyrB genes) was found in 4 out of 25 species of Culicoides biting midges. These bacteria possessed a microfilament-like structure that is a morphological feature previously found in Cardinium and Paenicardinium. The bacteria close to the genus Cardinium consist of at least three groups, A, B, and C. Group A is present in various species of arthropods and was previously referred to as "Candidatus Cardinium hertigii," group B is present in plant parasitic nematodes and was previously referred to as "Candidatus Paenicardinium endonii," and group C is present in Culicoides biting midges. On the basis of morphological and molecular data, we propose that the nomenclature of these three groups be integrated into a single species, "Candidatus Cardinium hertigii."
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Matsumoto Y, Yanase T, Tsuda T, Noda H. Characterization of internal transcribed spacer (ITS1)-ITS2 region of ribosomal RNA gene from 25 species of Culicoides biting midges (Diptera: Ceratopogonidae) in Japan. JOURNAL OF MEDICAL ENTOMOLOGY 2009; 46:1099-1108. [PMID: 19769041 DOI: 10.1603/033.046.0517] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We determined nucleotide sequences of the nuclear rDNA internal transcribed spacer (ITS)1-5.8S-ITS2a-2S-ITS2 region in 103 individuals of 25 Culicoides species (Diptera: Ceratopogonidae) from 11 locations in Japan. Ribosomal RNA genes, 5.8S and 2S rDNA, were highly conserved among the species with few variations. The ITS2a region showed length variation among species. Both ITS1 and ITS2 showed highly varied sequences among species. The noticeable indel regions among ITS1 sequences are present in some Culicoides species, separating species into two types having long or short ITS1 region. However, Culicoides cylindratus Kitaoka possesses both types of ITS1 in each individual; these results seem to indicate that the ITS1-long type was the prototype and the short type was produced through deletion in many Culicoides species. One species, belonging to subgenus Avaritia, possessed an Avaritia-specific sequence in ITS1 and phylogenetically formed a monophyletic group. Geographical genotypes in a species were not clear. Species-specific sequence features were observed, enabling molecular identification of Culicoides species.
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Affiliation(s)
- Y Matsumoto
- National Institute of Agrobiological Sciences, Owashi, Tsukuba, Ibaraki 305-8634, Japan.
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