1
|
Fu YT, Xun Y, Peng YY, Zhang Y, Wu X. The complete mitochondrial genome of the rodent flea Nosopsyllus laeviceps: genome description, comparative analysis, and phylogenetic implications. Parasit Vectors 2024; 17:253. [PMID: 38863074 PMCID: PMC11165799 DOI: 10.1186/s13071-024-06329-y] [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: 02/08/2024] [Accepted: 05/22/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND Fleas are one of the most common and pervasive ectoparasites worldwide, comprising at least 2500 valid species. They are vectors of several disease-causing agents, such as Yersinia pestis. Despite their significance, however, the molecular genetics, biology, and phylogenetics of fleas remain poorly understood. METHODS We sequenced, assembled, and annotated the complete mitochondrial (mt) genome of the rodent flea Nosopsyllus laeviceps using next-generation sequencing technology. Then we combined the new mitogenome generated here with mt genomic data available for 23 other flea species to perform comparative mitogenomics, nucleotide diversity, and evolutionary rate analysis. Subsequently, the phylogenetic relationship within the order Siphonaptera was explored using the Bayesian inference (BI) and maximum likelihood (ML) methods based on concentrated data for 13 mt protein-coding genes. RESULTS The complete mt genome of the rodent flea N. laeviceps was 16,533 base pairs (bp) in a circular DNA molecule, containing 37 typical genes (13 protein-coding genes, 22 transfer RNA [tRNA] genes, and two ribosomal RNA [rRNA] genes) with one large non-coding region (NCR). Comparative analysis among the order Siphonaptera showed a stable gene order with no gene arrangement, and high AT content (76.71-83.21%) with an apparent negative AT and GC skew except in three fleas Aviostivalius klossi bispiniformis, Leptopsylla segnis, and Neopsylla specialis. Moreover, we found robust evidence that the cytochrome c oxidase subunit 1 (cox1) gene was the most conserved protein-coding gene (Pi = 0.15, non-synonymous/synonymous [Ka/Ks] ratio = 0.13) of fleas. Phylogenomic analysis conducted using two methods revealed different topologies, but both results strongly indicated that (i) the families Ceratophyllidae and Leptopsyllidae were paraphyletic and were the closest to each other, and (ii) the family Ctenophthalmidae was paraphyletic. CONCLUSIONS In this study, we obtained a high-quality mt genome of the rodent flea N. laeviceps and performed comparative mitogenomics and phylogeny of the order Siphonaptera using the mt database. The results will enrich the mt genome data for fleas, lay a foundation for the phylogenetic analysis of fleas, and promote the evolutionary analysis of Siphonaptera.
Collapse
Affiliation(s)
- Yi-Tian Fu
- Department of Parasitology, Xiangya School of Basic Medicine, Central South University, Changsha, 410013, Hunan, China.
| | - Ying Xun
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yan-Yan Peng
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yu Zhang
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Xiang Wu
- Department of Parasitology, Xiangya School of Basic Medicine, Central South University, Changsha, 410013, Hunan, China.
| |
Collapse
|
2
|
Zeng JL, Chen HX, Ni XF, Kang JY, Li L. Molecular phylogeny of the family Rhabdiasidae (Nematoda: Rhabditida), with morphology, genetic characterization and mitochondrial genomes of Rhabdias kafunata and R. bufonis. Parasit Vectors 2024; 17:100. [PMID: 38429838 PMCID: PMC10908064 DOI: 10.1186/s13071-024-06201-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: 12/16/2023] [Accepted: 02/15/2024] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND The family Rhabdiasidae (Nematoda: Rhabditida) is a globally distributed group of nematode parasites, with over 110 species parasitic mainly in amphibians and reptiles. However, the systematic position of the family Rhabdiasidae in the order Rhabditida remains unsolved, and the evolutionary relationships among its genera are still unclear. Moreover, the present knowledge of the mitochondrial genomes of rhabdiasids remains limited. METHODS Two rhabdiasid species: Rhabdias kafunata Sata, Takeuchi & Nakano, 2020 and R. bufonis (Schrank, 1788) collected from the Asiatic toad Bufo gargarizans Cantor (Amphibia: Anura) in China, were identified based on morphology (light and scanning electron microscopy) and molecular characterization (sequencing of the nuclear 28S and ITS regions and mitochondrial cox1 and 12S genes). The complete mitochondrial genomes of R. kafunata and R. bufonis were also sequenced and annotated for the first time. Moreover, phylogenetic analyses based on the amino acid sequences of 12 protein-coding genes (PCGs) of the mitochondrial genomes were performed to clarify the systematic position of the family Rhabdiasidae in the order Rhabditida using maximum likelihood (ML) and Bayesian inference (BI). The phylogenetic analyses based on the 28S + ITS sequences, were also inferred to assess the evolutionary relationships among the genera within Rhabdiasidae. RESULTS The detailed morphology of the cephalic structures, vulva and eggs in R. kafunata and R. bufonis was revealed using scanning electron microscopy (SEM) for the first time. The characterization of 28S and ITS regions of R. kafunata was reported for the first time. The mitogenomes of R. kafunata and R. bufonis are 15,437 bp and 15,128 bp long, respectively, and both contain 36 genes, including 12 PCGs (missing atp8). Comparative mitogenomics revealed that the gene arrangement of R. kafunata and R. bufonis is different from all of the currently available mitogenomes of nematodes. Phylogenetic analyses based on the ITS + 28S data showed Neoentomelas and Kurilonema as sister lineages, and supported the monophyly of Entomelas, Pneumonema, Serpentirhabdias and Rhabdias. Mitochondrial phylogenomic results supported Rhabdiasidae as a member of the superfamily Rhabditoidea in the suborder Rhabditina, and its occurrance as sister to the family Rhabditidae. CONCLUSIONS The complete mitochondrial genome of R. kafunata and R. bufonis were reported for the first time, and two new gene arrangements of mitogenomes in Nematoda were revealed. Mitogenomic phylogenetic results indicated that the family Rhabdiasidae is a member of Rhabditoidea in Rhabditina, and is closely related to Rhabditidae. Molecular phylogenies based on the ITS + 28S sequence data supported the validity of Kurilonema, and showed that Kurilonema is sister to Neoentomelas. The present phylogenetic results also indicated that the ancestors of rhabdiasids seem to have initially infected reptiles, then spreading to amphibians.
Collapse
Affiliation(s)
- Jia-Lu Zeng
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology; Hebei Collaborative Innovation Center for Eco-Environment; College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China
- Hebei Research Center of the Basic Discipline Cell Biology; Ministry of Education Key Laboratory of Molecular and Cellular Biology, Shijiazhuang, 050024, Hebei, People's Republic of China
| | - Hui-Xia Chen
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology; Hebei Collaborative Innovation Center for Eco-Environment; College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China
| | - Xue-Feng Ni
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology; Hebei Collaborative Innovation Center for Eco-Environment; College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China
| | - Jia-Yi Kang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology; Hebei Collaborative Innovation Center for Eco-Environment; College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China
| | - Liang Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology; Hebei Collaborative Innovation Center for Eco-Environment; College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China.
- Hebei Research Center of the Basic Discipline Cell Biology; Ministry of Education Key Laboratory of Molecular and Cellular Biology, Shijiazhuang, 050024, Hebei, People's Republic of China.
| |
Collapse
|
3
|
Xiang R, Wang S, Wan H. The complete chloroplast genome of Holarrhena pubescens and its phylogenetic analysis. Mitochondrial DNA B Resour 2023; 8:266-269. [PMID: 36816055 PMCID: PMC9937002 DOI: 10.1080/23802359.2022.2162349] [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] [Indexed: 02/18/2023] Open
Abstract
Holarrhena pubescens Wall. ex G. Don, 1837 is an important medicinal plant belonging to the Holarrhena genus in the Apocynaceae family. In this study, the complete chloroplast (cp) genome sequence of H. pubescens was sequenced using the Illumina NovaSeq platform. The cp genome of H. pubescens was 160,108 bp in length with 37.21% overall GC content. The cp genome of H. pubescens containing a large single-copy region (LSC, 88,685 bp), a small single-copy region (SSC, 18,671 bp), and a pair of inverted repeat regions (SSC, 26,376 bp). The cp genome encoded 129 genes, including 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis based on complete protein coding genes sequences revealed that H. pubescens was closest to Beaumontia murtonii.
Collapse
Affiliation(s)
- Rushuang Xiang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China,College of Pharmaceutical, Dali University, Dali, China
| | - Sijia Wang
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Huihua Wan
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China,School of Landscape Architecture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China,CONTACT Huihua Wan Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing100070, China
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Gao JF, Mao RF, Li Y, Sun YY, Gao ZY, Zhang XG, Jin ZH, An Q, Zhang ZH, Zhang AH, Wei W, Lan Z, Wang CR. Characterization of the mitochondrial genome of Tetrameres grusi and insights into the phylogeny of Spirurina. Int J Parasitol Parasites Wildl 2022; 17:35-42. [PMID: 34976723 PMCID: PMC8688868 DOI: 10.1016/j.ijppaw.2021.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/04/2021] [Accepted: 12/04/2021] [Indexed: 10/25/2022]
|