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Mukherjee A, Ghosh A, Tyagi K, Kumar V, Banerjee D, Naskar A. Characterization of complete mitochondrial genome of three Horse flies of the genus Tabanus (Diptera: Tabanidae): comparative analysis. Mol Biol Rep 2023; 50:9897-9908. [PMID: 37864662 DOI: 10.1007/s11033-023-08837-z] [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: 08/04/2023] [Accepted: 09/25/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Tabanidae (Horse-Flies or Deer-Flies) are one of the most economically important as well as medically significant haematophagous insect family within the order Diptera. Members of this group are also responsible for the mortality of substantial number of live-stock every year. Due to their pathogen transmission potential and vector competencies makes them an important insect group to study. Till now, mitochondrial genome of 18 species of tabanids were available. METHODS AND RESULTS The complete mitogenome of three species T. diversifrons (15,809 bp), T. rubidus (15,878 bp) and T. tenens (15,872 bp) were generated by Next generation sequencing method. They consist 37 genes, with a positive AT skew and a negative GC skew. The gene order of these three species is similar to the typical gene arrangement of infra-order Tabanomorpha. Most of the tRNAs showed typical clover-leaf secondary structure except trnS1, which lacks the DHU arm. The sliding window analysis showed that the nad4L is the most conserved while atp8, and nad6 are the most variable genes. Moreover, the ratios of non-synonymous to synonymous substitution rates indicated that all PCGs under the purifying selection. Phylogeny revealed Chrysops and Haematopota are monophyletic while species of Hybomitra are nested within the polyphyletic clade of Tabanus. T. diversifrons exhibits sister relationship with Atylotus miser. Two morphologically divergent species T. rubidus and T. tenens are found to be genetically similar and indistinguishable by mitochondrial genome. CONCLUSIONS The hypervariable genes like atp8 and nad6 can be used as molecular markers for the identification of recently diverged lineages of family Tabanidae. Further, to address uncertainties arising from the two morphological divergent species, it is imperative to obtain data from nuclear gene markers.
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Affiliation(s)
- Arka Mukherjee
- Diptera Section, Zoological Survey of India, Kolkata, West Bengal, India
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
| | - Abhishek Ghosh
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India.
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India.
| | - Dhriti Banerjee
- Diptera Section, Zoological Survey of India, Kolkata, West Bengal, India
| | - Atanu Naskar
- Diptera Section, Zoological Survey of India, Kolkata, West Bengal, India
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Chen B, Liu YF, Lu XY, Jiang DD, Wang X, Zhang QF, Yang GP, Yang X. Complete mitochondrial genome of Ctenophthalmus quadratus and Stenischia humilis in China provides insights into fleas phylogeny. Front Vet Sci 2023; 10:1255017. [PMID: 37771942 PMCID: PMC10526365 DOI: 10.3389/fvets.2023.1255017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 08/21/2023] [Indexed: 09/30/2023] Open
Abstract
Fleas (Order Siphonaptera) are common blood-feeding ectoparasites, which have important economic significance. Limited mitochondrial genome information has impeded the study of flea biology, population genetics and phylogenetics. The Ctenophthalmus quadratus and Stenischia humilis complete mt genomes are described in this study. The samples were collected from Jianchuan, Yunnan plague foci, China. The mt genomes of C. quadratus and S. humilis were 15,938 bp and 15,617 bp, respectively. The gene arrangement of mt genome was consistent with that of other fleas, which include 22 tRNA genes, 13 protein-coding genes, and two rRNA genes, with a total of 37 genes. The relationship between C. quadratus and S. humilis in fleas was inferred by phylogenetic analysis of mt genome sequence datasets. Phylogenetic analyzes showed that the C. quadratus and S. humilis belonged to different species in the same family, and were closely related to Hystrichopsylla weida qinlingensis in the same family; and revealed that the family Hystrichopsyllidae is paraphyletic, supporting the monophyly of the order Siphonaptera. This study decodes the complete mt genomes of the C. quadratus and S. humilis for the first time. The results demonstrate that the C. quadratus and S. humilis are distinct species, and fleas are monophyletic. Analysis of mt genome provides novel molecular data for further studying the phylogeny and evolution of fleas.
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Affiliation(s)
- Bin Chen
- Integrated Laboratory of Pathogenic Biology, College of Preclinical Medicine, Dali University, Dali, China
| | - Ya-fang Liu
- Integrated Laboratory of Pathogenic Biology, College of Preclinical Medicine, Dali University, Dali, China
| | - Xin-yan Lu
- Integrated Laboratory of Pathogenic Biology, College of Preclinical Medicine, Dali University, Dali, China
| | - Dan-dan Jiang
- School of Public Health, Dali University, Dali, China
| | - Xuan Wang
- Nanchang University Queen Mary School, Nanchang University, Nanchang, China
| | - Quan-fu Zhang
- Department of Gastroenterology, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Guo-ping Yang
- Integrated Laboratory of Pathogenic Biology, College of Preclinical Medicine, Dali University, Dali, China
| | - Xing Yang
- Integrated Laboratory of Pathogenic Biology, College of Preclinical Medicine, Dali University, Dali, China
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Li H, Yan Y, Li J. Eighteen mitochondrial genomes of Syrphidae (Insecta: Diptera: Brachycera) with a phylogenetic analysis of Muscomorpha. PLoS One 2023; 18:e0278032. [PMID: 36602958 DOI: 10.1371/journal.pone.0278032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 11/08/2022] [Indexed: 01/06/2023] Open
Abstract
In this study, 18 mitochondrial genomes (mitogenomes) of Syrphidae were sequenced. These mitogenomes ranged from 15,648 to 16,405 bp and contained 37 genes that were similar to those from other Syrphidae species. Most protein-coding genes (PCGs) started with a standard ATN codon and ended with TAA/G. All transfer RNAs (tRNAs) could be folded into the cloverleaf secondary structure except tRNA-Ser (AGN), which lacks a dihydrouridine arm. The secondary structures of ribosomal RNAs (rRNAs) were predicted. Six domains (III is absent in arthropods) and 44 helices were included in the 16S rRNA, and three domains and 24 helices were included in the 12S rRNA. We found three conserved fragments in all syrphid mitogenomes. Phylogenetic analyses were performed based on the nucleotide data of 13 PCGs and two rRNAs from 76 Muscomorpha and three outgroup species. In results the paraphyly of Aschiza and Schizophora were supported, the Acalyptratae was also paraphyletic but the relationships of its superfamilies were difficult to determine, the monophyly of Calyptratea was supported with the relationships of Oestroidea and Muscoidea need to be further reconsidered. Within Syrphidae the monophyly of family level was supported, the Syrphinae were clustered into one branch, while the paraphyly of Eristalinae was still well supported.
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Affiliation(s)
- Hu Li
- Shaanxi Key Laboratory of Bio-Resources, State Key Laboratory of Biological Resources and Ecological Environment of Qinling-Bashan, School of Biological Science & Engineering, Shaanxi University of Technology, Qinling-Bashan Mountains Bioresources Comprehensive Development C.I.C., Hanzhong, Shaanxi, China
| | - Yan Yan
- Shaanxi Key Laboratory of Bio-Resources, State Key Laboratory of Biological Resources and Ecological Environment of Qinling-Bashan, School of Biological Science & Engineering, Shaanxi University of Technology, Qinling-Bashan Mountains Bioresources Comprehensive Development C.I.C., Hanzhong, Shaanxi, China
| | - Juan Li
- Shaanxi Key Laboratory of Bio-Resources, State Key Laboratory of Biological Resources and Ecological Environment of Qinling-Bashan, School of Biological Science & Engineering, Shaanxi University of Technology, Qinling-Bashan Mountains Bioresources Comprehensive Development C.I.C., Hanzhong, Shaanxi, China
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Fu YT, Suleman, Yao C, Wang HM, Wang W, Liu GH. A Novel Mitochondrial Genome Fragmentation Pattern in the Buffalo Louse Haematopinus tuberculatus (Psocodea: Haematopinidae). Int J Mol Sci 2022; 23:13092. [PMID: 36361879 PMCID: PMC9658350 DOI: 10.3390/ijms232113092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/08/2022] [Accepted: 10/25/2022] [Indexed: 08/01/2023] Open
Abstract
Sucking lice are obligate ectoparasites of mammalian hosts, causing serious public health problems and economic losses worldwide. It is well known that sucking lice have fragmented mitochondrial (mt) genomes, but many remain undetermined. To better understand patterns of mt genome fragmentation in the sucking lice, we sequenced the mt genome of the buffalo louse Haematopinus tuberculatus using next-generation sequencing (NGS). The mt genome of H. tuberculatus has ten circular minichromosomes containing a total of 37 genes. Each minichromosome is 2.9-5.0 kb long and carries one to eight genes plus one large non-coding region. The number of mt minichromosomes of H. tuberculatus (ten) is different from those of congeneric species (horse louse H. asini, domestic pig louse H. suis and wild pig louse H. apri) and other sucking lice. Two events (gene translocation and merger of mt minichromosome) are observed in Haematopinus. Compared to other studies, our phylogeny generated from mt genome datasets showed a different topology, suggesting that inclusion of data other than mt genomes would be required to resolve phylogeny of sucking lice. To our knowledge, this is the first report of a ten mt minichromosomes genome in sucking lice, which opens a new outlook into unexplored mt genome fragmentation patterns in sucking lice.
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Affiliation(s)
- Yi-Tian Fu
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Suleman
- Department of Zoology, University of Swabi, Swabi 23561, Pakistan
| | - Chaoqun Yao
- Department of Biomedical Sciences and One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
| | - Hui-Mei Wang
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Wei Wang
- The Centre for Bioinnovation, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
| | - Guo-Hua Liu
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
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Phylogenetic Analysis of Mitochondrial Genome of Tabanidae (Diptera: Tabanidae) Reveals the Present Status of Tabanidae Classification. INSECTS 2022; 13:insects13080695. [PMID: 36005320 PMCID: PMC9408937 DOI: 10.3390/insects13080695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 12/04/2022]
Abstract
Simple Summary Tabanidae suck the blood of humans and animals, are important biological vectors for the transmission of diseases, and are of considerable economic and medical significance. However, current knowledge about the mitochondrial genome of this family is limited. Therefore, six newly completed mitochondrial genomes of four genera of Tabanidae (Haematopota turkestanica, Chrysops vanderwulpi, Chrysops dissectus, Tabanus chrysurus, Tabanus pleskei, and Hybomitra sp. species) were sequenced and analyzed. The results show that the six newly mitochondrial genomes have quite similar structures and features. Phylogeny was inferred by analyzing the 13 amino acid sequences coded by mitochondrial genes of 22 mitogenomes (all available complete mitochondrial genomes of tabanidae). Bayesian inference, maximum likelihood trees, and maximum parsimony inference analyses all showed consistent results. This study supports the concept of monophyly of all groups, ratifies the current taxonomic classification, and provides useful genetic markers for studying the molecular ecology, systematics, and population genetics of Tabanidae. Abstract Tabanidae suck the blood of humans and animals, are important biological vectors for the transmission of diseases, and are of considerable economic and medical significance. However, current knowledge about the mitochondrial genome of this family is limited. More complete mitochondrial genomes of Tabanidae are essential for the identification and phylogeny. Therefore, this study sequenced and analyzed six complete mitochondrial (mt) genome sequences of four genera of Tabanidae for the first time. The complete mt genomes of the six new sequences are circular molecules ranging from 15,851 to 16,107 base pairs (bp) in size, with AT content ranging from 75.64 to 77.91%. The six complete mitochondrial genomes all consist of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (RRNA), 22 transfer RNA genes (tRNAs), and a control region, making a total of 37 functional subunits. ATT/ATG was the most common start codon, and the stop codon was TAA of all PCGS. All tRNA except tRNA Ser1 had a typical clover structure. Phylogeny was inferred by analyzing the 13 concatenated amino acid sequences of the 22 mt genomes. Bayesian inference, maximum-likelihood trees, and maximum-parsimony inference analyses all showed consistent results. This study supports the concept of monophyly of all genus, ratifies the current taxonomic classification, and provides effective genetic markers for molecular classification, systematics, and genetic studies of Tabanidae.
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Zhang Y, Fu YT, Yao C, Deng YP, Nie Y, Liu GH. Mitochondrial phylogenomics provides insights into the taxonomy and phylogeny of fleas. Parasit Vectors 2022; 15:223. [PMID: 35733168 PMCID: PMC9215091 DOI: 10.1186/s13071-022-05334-3] [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: 02/11/2022] [Accepted: 05/20/2022] [Indexed: 11/30/2022] Open
Abstract
Background Fleas (Insecta: Siphonaptera) are obligatory hematophagous ectoparasites of humans and animals and serve as vectors of many disease-causing agents. Despite past and current research efforts on fleas due to their medical and veterinary importance, correct identification and robust phylogenetic analysis of these ectoparasites have often proved challenging. Methods We decoded the complete mitochondrial (mt) genome of the human flea Pulex irritans and nearly complete mt genome of the dog flea Ctenocephalides canis, and subsequently used this information to reconstruct the phylogeny of fleas among Endopterygota insects. Results The complete mt genome of P. irritans was 20,337 bp, whereas the clearly sequenced coding region of the C. canis mt genome was 15,609 bp. Both mt genomes were found to contain 37 genes, including 13 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes. The coding region of the C. canis mt genome was only 93.5% identical to that of the cat flea C. felis, unequivocally confirming that they are distinct species. Our phylogenomic analyses of the mt genomes showed a sister relationship between the order Siphonaptera and orders Diptera + Mecoptera + Megaloptera + Neuroptera and positively support the hypothesis that the fleas in the order Siphonaptera are monophyletic. Conclusions Our results demonstrate that the mt genomes of P. irritans and C. canis are different. The phylogenetic tree shows that fleas are monophyletic and strongly support an order-level objective. These mt genomes provide novel molecular markers for studying the taxonomy and phylogeny of fleas in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05334-3.
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Affiliation(s)
- Yu Zhang
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan province, China
| | - Yi-Tian Fu
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan province, China
| | - Chaoqun Yao
- Department of Biomedical Sciences and One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, P.O. Box 334, Basseterre, St. Kitts and Nevis
| | - Yuan-Ping Deng
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan province, China
| | - Yu Nie
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan province, China
| | - Guo-Hua Liu
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan province, China.
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