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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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Johnson KP. Genomic Approaches to Uncovering the Coevolutionary History of Parasitic Lice. Life (Basel) 2022; 12:life12091442. [PMID: 36143478 PMCID: PMC9501036 DOI: 10.3390/life12091442] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/09/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary New sequencing technologies have now made it possible to sequence entire genomes for a diversity of life on earth. Parasites comprise nearly half of all species. Lice are one important group of parasites of birds and mammals, including humans. Genome sequencing approaches have been applied to this group of parasites to uncover patterns of diversification. These patterns can be compared to the patterns of diversification in their hosts. Key findings from these studies have revealed that parasitic lice likely originated on birds and then switched to mammals multiple times. Within groups of birds and mammals, the evolutionary trees of lice match those for mammal hosts more than those for birds. Genomic approaches have also revealed that individual birds and mammals harbor distinct populations of lice. Thus, these new techniques allow for the study of patterns of diversification at a wide variety of scales. Abstract Next-generation sequencing technologies are revolutionizing the fields of genomics, phylogenetics, and population genetics. These new genomic approaches have been extensively applied to a major group of parasites, the lice (Insecta: Phthiraptera) of birds and mammals. Two louse genomes have been assembled and annotated to date, and these have opened up new resources for the study of louse biology. Whole genome sequencing has been used to assemble large phylogenomic datasets for lice, incorporating sequences of thousands of genes. These datasets have provided highly supported trees at all taxonomic levels, ranging from relationships among the major groups of lice to those among closely related species. Such approaches have also been applied at the population scale in lice, revealing patterns of population subdivision and inbreeding. Finally, whole genome sequence datasets can also be used for additional study beyond that of the louse nuclear genome, such as in the study of mitochondrial genome fragmentation or endosymbiont function.
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Affiliation(s)
- Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA
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Liu Q, He J, Song F, Tian L, Cai W, Li H. Positive Correlation of the Gene Rearrangements and Evolutionary Rates in the Mitochondrial Genomes of Thrips (Insecta: Thysanoptera). INSECTS 2022; 13:insects13070585. [PMID: 35886761 PMCID: PMC9321049 DOI: 10.3390/insects13070585] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 01/04/2023]
Abstract
Simple Summary Aeolothrips, commonly known as banded thrips, is the largest genus of the family Aeolothripidae (predatory thrips). In the current study, we sequenced the mitochondrial genome (mitogenome) of the banded thrip species Aeolothrips xinjiangensis. We found a novel gene arrangement in this mitogenome that has not been reported in Thysanoptera. By comparing the gene order and rearrangement patterns, we found seven identical gene blocks and three identical rearrangement events in two mitogenomes of banded thrips. There was marked variation in the mitochondrial gene order across thrip species, with only two conserved gene blocks shared by all 14 thrips. In addition, we found a positive correlation between the degree of gene rearrangement and evolutionary rate. Our results suggested that the mitogenomes of thrips have tended to be stable since their massive rearrangement. Abstract Extensive gene rearrangement is characteristic in the mitogenomes of thrips (Thysanoptera), but the historical process giving rise to the contemporary gene rearrangement pattern remains unclear. To better understand the evolutionary processes of gene rearrangement in the mitogenomes of thrips, we sequenced the mitogenome of the banded thrip species Aeolothrips xinjiangensis. First, we found a novel mitochondrial gene order in this species. This mitogenome is 16,947 bp in length and encodes the typical 37 coding genes (13 protein-coding genes, 22 tRNA genes, and two rRNA genes) of insects. The gene arrangement was dramatically different from the putative ancestral mitogenome, with 26 genes being translocated, eight of which were inverted. Moreover, we found a novel, conserved gene block, trnC-trnY, which has not been previously reported in the mitogenomes of thrips. With this newly assembled mitogenome, we compared mitogenome sequences across Thysanoptera to assess the evolutionary processes giving rise to the current gene rearrangement pattern in thrips. Seven identical gene blocks were shared by two sequenced banded thrip mitogenomes, while the reversal of ND2 combined with TDRL events resulted in the different gene orders of these two species. In phylogenetic analysis, the monophyly of the suborders and families of Thysanoptera was well supported. Across the gene orders of 14 thrips, only two conserved gene blocks, ATP8-ATP6 and ND4-ND4L, could be found. Correlation analysis showed that the degree of gene rearrangement was positively correlated with the non-synonymous substitution rate in thrips. Our study suggests that the mitogenomes of thrips remain stable over long evolutionary timescales after massive rearrangement during early diversification.
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Affiliation(s)
- Qiaoqiao Liu
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (Q.L.); (J.H.); (F.S.); (L.T.); (W.C.)
| | - Jia He
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (Q.L.); (J.H.); (F.S.); (L.T.); (W.C.)
- Institute of Plant Protection, Academy of Ningxia Agriculture and Forestry Science, Yinchuan 750002, China
| | - Fan Song
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (Q.L.); (J.H.); (F.S.); (L.T.); (W.C.)
| | - Li Tian
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (Q.L.); (J.H.); (F.S.); (L.T.); (W.C.)
| | - Wanzhi Cai
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (Q.L.); (J.H.); (F.S.); (L.T.); (W.C.)
| | - Hu Li
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (Q.L.); (J.H.); (F.S.); (L.T.); (W.C.)
- Correspondence:
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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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Gong S, Xu Y, Xu S, Liang Y, Tian L, Cai W, Li H, Song F. The Complete Mitochondrial Genome of the Chicken Body Louse, Menacanthus cornutus, and Evolutionary Patterns of Extensive Gene Rearrangements in the Mitochondrial Genomes of Amblycera (Psocodea: Phthiraptera). Genes (Basel) 2022; 13:genes13030522. [PMID: 35328076 PMCID: PMC8950984 DOI: 10.3390/genes13030522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/11/2022] [Accepted: 03/12/2022] [Indexed: 02/04/2023] Open
Abstract
Animal mitochondrial (mt) genomes are typically double-strand circular DNA molecules, but diverse structural variations have been widely found in multiple groups. In parasitic lice (Phthiraptera), the structure of mt genomes varies remarkably across all five suborders. In this study, we reported the complete mt genome of a chicken body louse, Menacanthus cornutus, which has a typical single circular mt chromosome and drastic mt gene rearrangements. This mt genome is 15,693 bp in length, consisting of 13 protein-coding genes, 23 tRNA genes, 2 rRNA genes, and a control region. A comparison with a typical insect mt genome suggested that two highly similar trnM are present in the mt genome of M. cornutus. Moreover, almost every single gene was rearranged, and over half of mt genes were inverted. Phylogenetic analyses inferred from the mt genome sequences supported the monophyly and position of Amblycera. Mapped over the phylogenetic relationships of Amblycera, we identified two inversion events for the conserved gene blocks in Boopidae and Menoponidae. The inverted ND4L-ND4 was likely a synapomorphic rearrangement in Menoponidae. Our study demonstrated the importance of sequencing mt genomes for additional taxa to uncover the mechanism underlying the structural evolution of the mt genome in parasitic lice.
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Affiliation(s)
| | | | | | | | | | | | | | - Fan Song
- Correspondence: ; Tel.: +86-10-62734842
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