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Amaya Romero JE, Chenal C, Ben Chehida Y, Miles A, Clarkson CS, Pedergnana V, Wertheim B, Fontaine MC. Mitochondrial Variation in Anopheles gambiae and Anopheles coluzzii: Phylogeographic Legacy and Mitonuclear Associations With Metabolic Resistance to Pathogens and Insecticides. Genome Biol Evol 2024; 16:evae172. [PMID: 39226386 PMCID: PMC11370803 DOI: 10.1093/gbe/evae172] [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] [Accepted: 07/22/2024] [Indexed: 09/05/2024] Open
Abstract
Mitochondrial DNA has been a popular marker in phylogeography, phylogeny, and molecular ecology, but its complex evolution is increasingly recognized. Here, we investigated mitochondrial DNA variation in Anopheles gambiae and Anopheles coluzzii, in relation to other species in the Anopheles gambiae complex, by assembling the mitogenomes of 1,219 mosquitoes across Africa. The mitochondrial DNA phylogeny of the Anopheles gambiae complex was consistent with previously reported highly reticulated evolutionary history, revealing important discordances with the species tree. The three most widespread species (An. gambiae, An. coluzzii, and Anopheles arabiensis), known for extensive historical introgression, could not be discriminated based on mitogenomes. Furthermore, a monophyletic clustering of the three saltwater-tolerant species (Anopheles merus, Anopheles melas, and Anopheles bwambae) in the Anopheles gambiae complex also suggested that introgression and possibly selection shaped mitochondrial DNA evolution. Mitochondrial DNA variation in An. gambiae and An. coluzzii across Africa revealed significant partitioning among populations and species. A peculiar mitochondrial DNA lineage found predominantly in An. coluzzii and in the hybrid taxon of the African "far-west" exhibited divergence comparable to the interspecies divergence in the Anopheles gambiae complex, with a geographic distribution matching closely An. coluzzii's geographic range. This phylogeographic relict of the An. coluzzii and An. gambiae split was associated with population and species structure, but not with the rare Wolbachia occurrence. The lineage was significantly associated with single nucleotide polymorphisms in the nuclear genome, particularly in genes associated with pathogen and insecticide resistance. These findings underline potential mitonuclear coevolution history and the role played by mitochondria in shaping metabolic responses to pathogens and insecticides in Anopheles.
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Affiliation(s)
- Jorge E Amaya Romero
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen 9747 AG, Netherlands
- MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Clothilde Chenal
- MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France
- Institut des Science de l’Évolution de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Yacine Ben Chehida
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen 9747 AG, Netherlands
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Alistair Miles
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | | | - Bregje Wertheim
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen 9747 AG, Netherlands
| | - Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen 9747 AG, Netherlands
- MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France
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Xiao ML, Yuan H, Li TJ, Chen B. Two New Mitogenomes of Bibionidae and Their Comparison within the Infraorder Bibionomorpha (Diptera). Genes (Basel) 2023; 14:1485. [PMID: 37510389 PMCID: PMC10378959 DOI: 10.3390/genes14071485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Despite the worldwide distribution and rich diversity of the infraorder Bibionomorpha in Diptera, the characteristics of mitochondrial genomes (mitogenomes) are still little-known, and the phylogenetics and evolution of the infraorder remains controversial. In the present study, we report complete and annotated mitogenome sequences of Penthetria simplioipes and Plecia hardyi representing Bibionidae. This is the first report of the complete mitogenomes for the superfamily Bibionoidea. There are 37 genes in each of the complete mitogenomes of all 20 studied species from eight families of four superfamilies within infraorder Bibionomorpha. The Ka/Ks analysis suggests that all 13 PCGs have undergone purifying selection. The gene rearrangement events exist in some families (Keroplatidae, Sciaridae, and Cecidomyiidae) but not in Mycetophilidae in Sciaroidea and also in Scatopsoidea, Anisopodoidea, and Bibionoidea, which suggests that these rearrangement events are derived in the late period in the evolution of the Bibionomorpha. The phylogenetic analysis suggests the phylogenetic relationships of Scatopsoidea + (Anisopodoidea + (Bibionoidea + Sciaroidea)) in Bibionomorpha. The divergence time analysis suggests that Bibionomorpha originated in the Triassic, Scatopsoidea and Anisopodoidea in the late Triassic, Bibionoidea in the Jurassic, and Sciaroidea in the Jurassic to the Cretaceous. The work lays a base for the study of mitogenomes in Bibionomorpha but further work and broader taxon sampling are necessary for a better understanding of the phylogenetics and evolution of the infraorder.
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Affiliation(s)
- Mei-Ling Xiao
- Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing 401331, China
| | - Huan Yuan
- Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing 401331, China
| | - Ting-Jing Li
- Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing 401331, China
| | - Bin Chen
- Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing 401331, China
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Volarić M, Despot-Slade E, Veseljak D, Meštrović N, Mravinac B. Reference-Guided De Novo Genome Assembly of the Flour Beetle Tribolium freemani. Int J Mol Sci 2022; 23:5869. [PMID: 35682551 PMCID: PMC9180572 DOI: 10.3390/ijms23115869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 02/06/2023] Open
Abstract
The flour beetle Tribolium freemani is a sibling species of the model organism and important pest Tribolium castaneum. The two species are so closely related that they can produce hybrid progeny, but the genetic basis of their differences has not been revealed. In this work, we sequenced the T. freemani genome by applying PacBio HiFi technology. Using the well-assembled T. castaneum genome as a reference, we assembled 262 Mb of the T. freemani genomic sequence and anchored it in 10 linkage groups corresponding to nine autosomes and sex chromosome X. The assembly showed 99.8% completeness of conserved insect genes, indicating a high-quality reference genome. Comparison with the T. castaneum assembly revealed that the main differences in genomic sequence between the two sibling species come from repetitive DNA, including interspersed and tandem repeats. In this work, we also provided the complete assembled mitochondrial genome of T. freemani. Although the genome assembly needs to be ameliorated in tandemly repeated regions, the first version of the T. freemani reference genome and the complete mitogenome presented here represent useful resources for comparative evolutionary studies of related species and for further basic and applied research on different biological aspects of economically important pests.
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Affiliation(s)
| | | | | | | | - Brankica Mravinac
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (M.V.); (E.D.-S.); (D.V.); (N.M.)
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Zhang C, Luo C, Yang R, Yang Y, Guo X, Deng Y, Zhou H, Zhang Y. Morphological and molecular identification reveals a high diversity of Anopheles species in the forest region of the Cambodia-Laos border. Parasit Vectors 2022; 15:94. [PMID: 35303948 PMCID: PMC8933986 DOI: 10.1186/s13071-022-05167-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/17/2022] [Indexed: 11/25/2022] Open
Abstract
Background To develop an effective malaria vector intervention method in forested international border regions within the Greater Mekong Subregion (GMS), more in-depth studies should be conducted on local Anopheles species composition and bionomic features. There is a paucity of comprehensive surveys of biodiversity integrating morphological and molecular species identification conducted within the border of Laos and Cambodia. Methods A total of 2394 adult mosquitoes were trapped in the Cambodia–Laos border region. We first performed morphological identification of Anopheles mosquitoes and subsequently performed molecular identification using 412 recombinant DNA–internal transcribed spacer 2 (rDNA-ITS2) and 391 mitochondrial DNA–cytochrome c oxidase subunit 2 (mtDNA-COII) sequences. The molecular and morphological identification results were compared, and phylogenetic analysis of rDNA-ITS2 and mtDNA-COII was conducted for the sequence divergence among species. Results Thirteen distinct species of Anopheles were molecularly identified in a 26,415 km2 border region in Siem Pang (Cambodia) and Pathoomphone (Laos). According to the comparisons of morphological and molecular identity, the interpretation of local species composition for dominant species in the Cambodia–Laos border (An. dirus, An. maculatus, An. philippinensis, An. kochi and An. sinensis) achieved the highest accuracy of morphological identification, from 98.37 to 100%. In contrast, the other species which were molecularly identified were less frequently identified correctly (0–58.3%) by morphological methods. The average rDNA-ITS2 and mtDNA-COII interspecific divergence was respectively 318 times and 15 times higher than their average intraspecific divergence. The barcoding gap ranged from 0.042 to 0.193 for rDNA-ITS2, and from 0.033 to 0.047 for mtDNA-COII. Conclusions The Cambodia–Laos border hosts a high diversity of Anopheles species. The morphological identification of Anopheles species provides higher accuracy for dominant species than for other species. Molecular methods combined with morphological analysis to determine species composition, population dynamics and bionomic characteristics can facilitate a better understanding of the factors driving malaria transmission and the effects of interventions, and can aid in achieving the goal of eliminating malaria. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05167-0.
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Affiliation(s)
- Canglin Zhang
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu'er, 665099, People's Republic of China
| | - Chunhai Luo
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu'er, 665099, People's Republic of China
| | - Rui Yang
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu'er, 665099, People's Republic of China
| | - Yaming Yang
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu'er, 665099, People's Republic of China
| | - Xiaofang Guo
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu'er, 665099, People's Republic of China
| | - Yan Deng
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu'er, 665099, People's Republic of China
| | - Hongning Zhou
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu'er, 665099, People's Republic of China.
| | - Yilong Zhang
- Department of Tropical Diseases, Faculty of Naval Medicine, Naval Medical University, Shanghai, 200433, China.
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Shen RX, Wang YT, Wu JH, Zhang N, Zhang HD, Xing D, Chen Y, Li CX, Zhao TY. Deltamethrin interacts with Culex quinquefasciatus odorant-binding protein: a novel potential resistance mechanism. Parasit Vectors 2022; 15:2. [PMID: 34980219 PMCID: PMC8725534 DOI: 10.1186/s13071-021-05041-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/27/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Odorant-binding proteins (OBPs) play important roles in many physiological processes of mosquitoes. Previous high-throughput sequencing studies have revealed that some OBPs of Culex quinquefasciatus might be involved in the development of resistance to insecticides. METHODS Based on the results of sequencing analyses, the OBP28 gene was selected for evaluation in this study. Three laboratory strains of Cx. quinquefasciatus [susceptible strain (SS), deltamethrin-resistant strain 1 (HN) and deltamethrin-resistant strain 2 (RR)] were first examined by using the Centers for Disease Control and Prevention bottle bioassay, after which the expression level of the OBP28 gene in the susceptible and deltamethrin-resistant strains was determined by real-time quantitative polymerase chain reaction. The OBP28 gene in deltamethrin-resistant strain RR was silenced using RNA interference technology. The expression level of OBP28 and the resistance level were tested in the silenced strain and control strain after microinjection of double-stranded RNA for a 48-h interference period. Four field-collected strains (henceforth 'field strains') of Cx. quinquefasciatus were also examined for their resistance to deltamethrin and levels of OBP28 expression. Finally, a correlation analysis between deltamethrin resistance and gene expression was carried out for all seven strains, i.e. the four field strains and the three laboratory strains. RESULTS In the bioassay, the mortality of SS, HN and RR was 100%, 21.33% and 1.67%, respectively. The relative expression levels of OBP28 in strains HN and RR were 6.30- and 6.86-fold higher, respectively, than that of strain SS. After silencing of the OBP28 gene, the mortality of strain RR was 72.20% and that of the control strain 26.32%. The mortality of strain RR increased significantly after interference compared to that of the control strain. There was a negative correlation between OBP28 gene expression and mortality in adult mosquitoes after exposure to deltamethrin. CONCLUSIONS To our knowledge, this study shows for the first time a correlation between the expression of a gene coding for OBP and insecticide resistance in mosquitoes. The potential resistance mechanism that was elucidated provides a new target gene for the surveillance of resistance in mosquitoes.
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Affiliation(s)
- Rui-Xin Shen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Key Laboratory of Vector Borne and Natural Focus Infectious Disease, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.,Guizhou Medical University, Guiyang, 550000, China
| | - Yi-Ting Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Key Laboratory of Vector Borne and Natural Focus Infectious Disease, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Jia-Hong Wu
- Guizhou Medical University, Guiyang, 550000, China
| | - Ning Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Key Laboratory of Vector Borne and Natural Focus Infectious Disease, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Heng-Duan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Key Laboratory of Vector Borne and Natural Focus Infectious Disease, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Dan Xing
- State Key Laboratory of Pathogen and Biosecurity, Beijing Key Laboratory of Vector Borne and Natural Focus Infectious Disease, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yan Chen
- Guizhou Medical University, Guiyang, 550000, China.
| | - Chun-Xiao Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Key Laboratory of Vector Borne and Natural Focus Infectious Disease, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
| | - Tong-Yan Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Key Laboratory of Vector Borne and Natural Focus Infectious Disease, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
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Sureshan SC, Tanavade RV, Ghosh S, Ghosh S, Sella RN, Mohideen HS. Complete mitochondrial genome sequencing of Oxycarenus laetus (Hemiptera: Lygaeidae) from two geographically distinct regions of India. Sci Rep 2021; 11:23738. [PMID: 34887433 PMCID: PMC8660866 DOI: 10.1038/s41598-021-02881-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 11/18/2021] [Indexed: 11/09/2022] Open
Abstract
Oxycarenus laetus is a seed-sap sucking pest affecting a variety of crops, including cotton plants. Rising incidence and pesticide resistance by O. laetus have been reported from India and neighbouring countries. In this study, O. laetus samples were collected from Bhatinda and Coimbatore (India). Pure mtDNA was isolated and sequenced using Illumina MiSeq. Both the samples were found to be identical species (99.9%), and the complete genome was circular (15,672 bp), consisting of 13 PCGs, 2 rRNA, 23 tRNA genes, and a 962 bp control region. The mitogenome is 74.1% AT-rich, 0.11 AT, and - 0.19 GC skewed. All the genes had ATN as the start codon except cox1 (TTG), and an additional trnT was predicted. Nearly all tRNAs folded into the clover-leaf structure, except trnS1 and trnV. The intergenic space between trnH and nad4, considered as a synapomorphy of Lygaeoidea, was displaced. Two 5 bp motifs AATGA and ACCTA, two tandem repeats, and a few microsatellite sequences, were also found. The phylogenetic tree was constructed using 36 mitogenomes from 7 super-families of Hemiptera by employing rigorous bootstrapping and ML. Ours is the first study to sequence the complete mitogenome of O. laetus or any Oxycarenus species. The findings from this study would further help in the evolutionary studies of Lygaeidae.
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Affiliation(s)
- Shruthi Chalil Sureshan
- grid.412742.60000 0004 0635 5080Bioinformatics and Entomoinformatics Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203 Tamil Nadu India
| | - Ruchi Vivekanand Tanavade
- grid.412742.60000 0004 0635 5080Bioinformatics and Entomoinformatics Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203 Tamil Nadu India
| | - Sewali Ghosh
- Department of Advanced Zoology and Biotechnology, Guru Nanak College, Chennai, 600042 Tamil Nadu India
| | - Saswati Ghosh
- grid.506009.aDepartment of Virology, King Institute of Preventive Medicine and Research, Chennai, 600032 Tamil Nadu India
| | - Raja Natesan Sella
- grid.412742.60000 0004 0635 5080Membrane Protein Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203 Tamil Nadu India
| | - Habeeb Shaik Mohideen
- Bioinformatics and Entomoinformatics Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Tamil Nadu, India.
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