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Castañeda-Osorio R, Belokobylskij SA, Jasso-Martínez JM, Samacá-Sáenz E, Kula RR, Zaldívar-Riverón A. Mitogenome architecture supports the non-monophyly of the cosmopolitan parasitoid wasp subfamily Doryctinae (Hymenoptera: Braconidae) recovered by nuclear and mitochondrial phylogenomics. INVERTEBR SYST 2024; 38:IS24029. [PMID: 38740060 DOI: 10.1071/is24029] [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: 03/17/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
Mitochondrial DNA gene organisation is an important source of phylogenetic information for various metazoan taxa at different evolutionary timescales, though this has not been broadly tested for all insect groups nor within a phylogenetic context. The cosmopolitan subfamily Doryctinae is a highly diverse group of braconid wasps mainly represented by ectoparasitoids of xylophagous beetle larvae. Previous molecular studies based on Sanger and genome-wide (ultraconserved elements, UCE; and mitochondrial genomes) sequence data have recovered a non-monophyletic Doryctinae, though the relationships involved have always been weakly supported. We characterised doryctine mitogenomes and conducted separate phylogenetic analyses based on mitogenome and UCE sequence data of ~100 representative doryctine genera to assess the monophyly and higher-level classification of the subfamily. We identified rearrangements of mitochondrial transfer RNAs (tRNAs) that support a non-monophyletic Doryctinae consisting of two separate non-related clades with strong geographic structure ('New World' and 'Old World' clades). This geographic structure was also consistently supported by the phylogenetic analyses preformed with mitogenome and UCE sequence data. These results highlight the utility of the mitogenome gene rearrangements as a potential source of phylogenetic information at different evolutionary timescales.
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Affiliation(s)
- Rubén Castañeda-Osorio
- Colección Nacional de Insectos, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, 3er circuito exterior s/n, Ciudad Universitaria, Coyoacán, Ciudad de México, México; and Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio A, 1er Piso, Circuito de Posgrados, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Sergey A Belokobylskij
- Zoological Institute of the Russian Academy of Sciences, Universitetskaya Naberezhnaya 1, Saint Petersburg, Russian Federation
| | - Jovana M Jasso-Martínez
- Colección Nacional de Insectos, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, 3er circuito exterior s/n, Ciudad Universitaria, Coyoacán, Ciudad de México, México; and Department of Entomology, Smithsonian Institution, National Museum of Natural History, 10th Street & Constitution Avenue NW, Washington, DC, USA
| | - Ernesto Samacá-Sáenz
- Instituto de Investigaciones Biomédicas, Departamento de Biología Celular y Fisiología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, Ciudad de México, México
| | - Robert R Kula
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, c/o Department of Entomology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Alejandro Zaldívar-Riverón
- Colección Nacional de Insectos, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, 3er circuito exterior s/n, Ciudad Universitaria, Coyoacán, Ciudad de México, México
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Zhang D, Chen X, Yang J, Yi W, Xie Q, Yang H, Sweet MH, Bu W, Li T. Phylogenetic placement and comparative analysis of the mitochondrial genomes of Idiostoloidea (Hemiptera: Heteroptera). Ecol Evol 2024; 14:e11328. [PMID: 38698924 PMCID: PMC11063732 DOI: 10.1002/ece3.11328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 04/06/2024] [Accepted: 04/10/2024] [Indexed: 05/05/2024] Open
Abstract
The classification system and the higher level phylogenetic relationships of Pentatomomorpha, the second largest infraorder of Heteroptera (Insecta: Hemiptera), have been debated and remain controversial over decades. In particular, the placement and phylogenetic relationship of Idiostoloidea are not well resolved, which hampers a better understanding of the evolutionary history of Pentatomomorpha. In this study, for the first time, we reported the complete mitochondrial genome for two narrowly distributed families of Idiostoloidea (including Idiostolidae and Henicocoridae), respectively. The length of the mitochondrial genome of Monteithocoris hirsutus and Henicocoris sp. is 16,632 and 16,013 bp, respectively. The content of AT is ranging from 75.15% to 80.48%. The mitogenomic structure of Idiostoloidea is highly conservative and there are no gene arrangements. By using the Bayesian inference, maximum likelihood, and Bayesian site-heterogeneous mixture model, we inferred the phylogenetic relationships within Pentatomomorpha and estimated their divergence times based on concatenated mitogenomes and nuclear ribosomal genes. Our results support the classification system of six superfamilies within Pentatomomorpha and confirm the monophyletic groups of each superfamily, with the following phylogenetic relationships: (Aradoidea + (Pentatomoidea + (Idiostoloidea + (Coreoidea + (Pyrrhocoroidea + Lygaeoidea))))). Furthermore, estimated divergence times revealed that most pentatomomorphan superfamilies and families diverged during the Late Jurassic to Early Cretaceous, which coincides with the explosive radiation of angiosperms.
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Affiliation(s)
- Danli Zhang
- College of Biological Sciences and TechnologyTaiyuan Normal UniversityJinzhongChina
| | - XiaoYan Chen
- College of Biological Sciences and TechnologyTaiyuan Normal UniversityJinzhongChina
| | - Jingjing Yang
- College of Biological Sciences and TechnologyTaiyuan Normal UniversityJinzhongChina
| | - Wenbo Yi
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Qiang Xie
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - HuanHuan Yang
- School of BioengineeringQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Merrill H. Sweet
- Department of Entomology, Plant Pathology, and Weed ScienceNew Mexico State UniversityLas CrucesNew MexicoUSA
| | - Wenjun Bu
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Teng Li
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
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Filée J, Merle M, Bastide H, Mougel F, Bérenger JM, Folly-Ramos E, Almeida CE, Harry M. Phylogenomics for Chagas Disease Vectors of the Rhodnius Genus (Hemiptera, Triatominae): What We Learn From Mito-Nuclear Conflicts and Recommendations. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.750317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We provide in this study a very large DNA dataset on Rhodnius species including 36 samples representing 16 valid species of the three Rhodnius groups, pictipes, prolixus and pallescens. Samples were sequenced at low-depth with whole-genome shotgun sequencing (Illumina technology). Using phylogenomics including 15 mitochondrial genes (13.3 kb), partial nuclear rDNA (5.2 kb) and 51 nuclear protein-coding genes (36.3 kb), we resolve sticking points in the Rhodnius phylogeny. At the species level, we confirmed the species-specific status of R. montenegrensis and R. marabaensis and we agree with the synonymy of R. taquarussuensis with R. neglectus. We also invite to revisit the species-specific status of R. milesi that is more likely R. nasutus. We proposed to define a robustus species complex that comprises the four close relative species: R. marabaensis, R. montenegrensis, R. prolixus and R. robustus. As Psammolestes tertius was included in the Rhodnius clade, we strongly recommend reclassifying this species as R. tertius. At the Rhodnius group level, molecular data consistently supports the clustering of the pictipes and pallescens groups, more related to each other than they are to the prolixus group. Moreover, comparing mitochondrial and nuclear tree topologies, our results demonstrated that various introgression events occurred in all the three Rhodnius groups, in laboratory strains but also in wild specimens. We demonstrated that introgressions occurred frequently in the prolixus group, involving the related species of the robustus complex but also the pairwise R. nasutus and R. neglectus. A genome wide analysis highlighted an introgression event in the pictipes group between R. stali and R. brethesi and suggested a complex gene flow between the three species of the pallescens group, R. colombiensis, R. pallescens and R. ecuadoriensis. The molecular data supports also a sylvatic distribution of R. prolixus in Brazil (Pará state) and the monophyly of R. robustus. As we detected extensive introgression events and selective pressure on mitochondrial genes, we strongly recommend performing separate mitochondrial and nuclear phylogenies and to take advantages of mito-nuclear conflicts in order to have a comprehensive evolutionary vision of this genus.
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Mu YL, Zhang CH, Zhang YJ, Yang L, Chen XS. Characterizing the Complete Mitochondrial Genome of Arma custos and Picromerus lewisi (Hemiptera: Pentatomidae: Asopinae) and Conducting Phylogenetic Analysis. JOURNAL OF INSECT SCIENCE (ONLINE) 2022; 22:6510058. [PMID: 35039857 PMCID: PMC8763613 DOI: 10.1093/jisesa/ieab105] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Indexed: 05/30/2023]
Abstract
We characterized the mitochondrial genome (mitogenome) and conducted phylogenetic analyses of 48 Hemiptera species by sequencing and analyzing the mitogenome of Arma custos (Fabricius) and Picromerus lewisi (Scott). The complete mitogenomes of the two predators were 16,024 bp and 19,587 bp in length, respectively, and it contained 37 classical genes, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs), and a control region. Most PCGs in these predators use ATN as the start codon. This research revealed that the genes of the two natural enemy species have an A + T content of 75.40% and all tRNAs have a typical cloverleaf structure, with the exception of trnS1, which lacks a dihydrouridine arm. This is the first study to compare the mitochondrial genetic structure of two predatory insects; the mitochondrial genetic structure of individual predatory insects has been sequenced in previous studies. Here, phylogenetic analysis on the basis of amino acid and nucleotide sequences of 13 mitochondrial PCGs using Bayesian inference and maximum likelihood methods were conducted to generate similar tree topologies, which suggested that the two predators with close genetic relationships belong to Asopinae subfamily. Furthermore, the monophyly of the Pentatomoidea superfamily is well accepted despite limited taxon and species sampling. Finally, their complete mitogenome provided data to establish a predator-prey food web, which is the foundation of effective pest management. Our results also enhanced the database of natural enemy insects.
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Affiliation(s)
- Yin-Lin Mu
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang, Guizhou 550025, China
- The Provincial Special Key Laboratory for Development and Utilization of Insect Resources of Guizhou, Guizhou University, Guiyang, Guizhou 550025, China
| | - Chang-Hua Zhang
- Guizhou Tobacco Company Zunyi Branch, Zunyi, Guizhou 563000, China
| | - Yu-Jie Zhang
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, China
| | - Lin Yang
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang, Guizhou 550025, China
- The Provincial Special Key Laboratory for Development and Utilization of Insect Resources of Guizhou, Guizhou University, Guiyang, Guizhou 550025, China
| | - Xiang-Sheng Chen
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang, Guizhou 550025, China
- The Provincial Special Key Laboratory for Development and Utilization of Insect Resources of Guizhou, Guizhou University, Guiyang, Guizhou 550025, China
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A New Mitochondrial Genome of Sogatella furcifera (Horváth) (Hemiptera: Delphacidae) and Mitogenome-Wide Investigation on Polymorphisms. INSECTS 2021; 12:insects12121066. [PMID: 34940154 PMCID: PMC8706918 DOI: 10.3390/insects12121066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 11/16/2021] [Accepted: 11/25/2021] [Indexed: 01/23/2023]
Abstract
Simple Summary We completed one mitogenome of white-backed planthopper (WBPH), Sogatella furcifera (Horváth), with finding heteroplasmy phenomenon confirmed by PCR reaction and Sanger sequencing method. This heteroplasmy was not observed in WBPHs (n = 24) collected from the fields, suggesting that it may be uncommon in fields. We also analyzed single nucleotide polymorphisms, insertion and deletions, and simple sequence repeats among three currently available WBPH mitogenomes of Korea and China, suggesting that identified intraspecific variations could be potential candidates for developing markers to distinguish geographical populations of WBPH including Korean and Chinese. Phylogenetic analysis of 32 mitogenomes of Delphacidae including the three WBPH mitogenomes suggested that Delphacinae seems to be monophyletic and Sogatella species including WBPH are clearly formed as one clade. Abstract White-backed planthopper (WBPH), Sogatella furcifera (Horváth), is one of the major sap-sucking rice pests in East Asia. We have determined a new complete mitochondrial genome of WBPH collected in the Korean peninsula using NGS technology. Its length and GC percentages are 16,613 bp and 23.8%, respectively. We observed one polymorphic site, a non-synonymous change, in the COX3 gene with confirmation heteroplasmy phenomenon within individuals of WBPH by PCR amplification and Sanger sequencing, the first report in this species. In addition, this heteroplasmy was not observed in wild WBPH populations, suggesting that it may be uncommon in fields. We analyzed single nucleotide polymorphisms, insertion, and deletions, and simple sequence repeats among the three WBPH mitogenomes from Korea and China and found diverse intraspecific variations, which could be potential candidates for developing markers to distinguish geographical populations. Phylogenetic analysis of 32 mitogenomes of Delphacidae including the three WBPH mitogenomes suggested that Delphacinae seems to be monophyletic and Sogatella species including WBPH are clearly formed as one clade. In the future, it is expected that complete mitogenomes of individuals of geographically dispersed WBPH populations will be used for further population genetic studies to understand the migration pathway of WBPH.
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Zhao W, Liu D, Jia Q, Wu X, Zhang H. Characterization of the complete mitochondrial genome of Myrmuslateralis (Heteroptera, Rhopalidae) and its implication for phylogenetic analyses. Zookeys 2021; 1070:13-30. [PMID: 34819768 PMCID: PMC8599289 DOI: 10.3897/zookeys.1070.72742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/25/2021] [Indexed: 11/23/2022] Open
Abstract
Mitochondrial genomes (mitogenomes) are widely used in research studies on phylogenetic relationships and evolutionary history. Here, we sequenced and analyzed the mitogenome of the scentless plant bug Myrmuslateralis Hsiao, 1964 (Heteroptera, Rhopalidae). The complete 17,309 bp genome encoded 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region. The mitogenome revealed a high A+T content (75.8%), a positive AT-skew (0.092), and a negative GC-skew (-0.165). All 13 PCGs were found to start with ATN codons, except for cox1, in which TTG was the start codon. The Ka/Ks ratios of 13 PCGs were all lower than 1, indicating that purifying selection evolved in these genes. All tRNAs could be folded into the typical cloverleaf secondary structure, except for trnS1 and trnV, which lack dihydrouridine arms. Phylogenetic trees were constructed and analyzed based on the PCG+rRNA from 38 mitogenomes, using maximum likelihood and Bayesian inference methods, showed that M.lateralis and Chorosomamacilentum Stål, 1858 grouped together in the tribe Chorosomatini. In addition, Coreoidea and Pyrrhocoroidea were sister groups among the superfamilies of Trichophora, and Rhopalidae was a sister group to Alydidae + Coreidae.
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Affiliation(s)
- Wanqing Zhao
- Department of Biology, Xinzhou Teachers University, Xinzhou 034000, Shanxi, ChinaXinzhou Teachers UniversityXinzhouChina
| | - Dajun Liu
- Department of Biology, Xinzhou Teachers University, Xinzhou 034000, Shanxi, ChinaXinzhou Teachers UniversityXinzhouChina
| | - Qian Jia
- Department of Biology, Xinzhou Teachers University, Xinzhou 034000, Shanxi, ChinaXinzhou Teachers UniversityXinzhouChina
| | - Xin Wu
- Department of Biology, Xinzhou Teachers University, Xinzhou 034000, Shanxi, ChinaXinzhou Teachers UniversityXinzhouChina
| | - Hufang Zhang
- Department of Biology, Xinzhou Teachers University, Xinzhou 034000, Shanxi, ChinaXinzhou Teachers UniversityXinzhouChina
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Ye F, Li H, Xie Q. Mitochondrial Genomes from Two Specialized Subfamilies of Reduviidae (Insecta: Hemiptera) Reveal Novel Gene Rearrangements of True Bugs. Genes (Basel) 2021; 12:1134. [PMID: 34440308 PMCID: PMC8392325 DOI: 10.3390/genes12081134] [Citation(s) in RCA: 4] [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: 05/08/2021] [Revised: 07/11/2021] [Accepted: 07/22/2021] [Indexed: 11/16/2022] Open
Abstract
Reduviidae, a hyper-diverse family, comprise 25 subfamilies with nearly 7000 species and include many natural enemies of crop pests and vectors of human disease. To date, 75 mitochondrial genomes (mitogenomes) of assassin bugs from only 11 subfamilies have been reported. The limited sampling of mitogenome at higher categories hinders a deep understanding of mitogenome evolution and reduviid phylogeny. In this study, the first mitogenomes of Holoptilinae (Ptilocnemus lemur) and Emesinae (Ischnobaenella hainana) were sequenced. Two novel gene orders were detected in the newly sequenced mitogenomes. Combined 421 heteropteran mitogenomes, we identified 21 different gene orders and six gene rearrangement units located in three gene blocks. Comparative analyses of the diversity of gene order for each unit reveal that the tRNA gene cluster trnI-trnQ-trnM is the hotspot of heteropteran gene rearrangement. Furthermore, combined analyses of the gene rearrangement richness of each unit and the whole mitogenome among heteropteran lineages confirm Reduviidae as a 'hot-spot group' of gene rearrangement in Heteroptera. The phylogenetic analyses corroborate the current view of phylogenetic relationships between basal groups of Reduviidae with high support values. Our study provides deeper insights into the evolution of mitochondrial gene arrangement in Heteroptera and the early divergence of reduviids.
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Affiliation(s)
- Fei Ye
- Department of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Qiang Xie
- Department of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
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Nie Y, Fu YT, Zhang Y, Deng YP, Wang W, Tu Y, Liu GH. Highly rearranged mitochondrial genome in Falcolipeurus lice (Phthiraptera: Philopteridae) from endangered eagles. Parasit Vectors 2021; 14:269. [PMID: 34016171 PMCID: PMC8139141 DOI: 10.1186/s13071-021-04776-5] [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: 02/16/2021] [Accepted: 05/06/2021] [Indexed: 11/10/2022] Open
Abstract
Background Fragmented mitochondrial (mt) genomes and extensive mt gene rearrangements have been frequently reported from parasitic lice (Insecta: Phthiraptera). However, relatively little is known about the mt genomes from the family Philopteridae, the most species-rich family within the suborder Ischnocera. Methods Herein, we use next-generation sequencing to decode the mt genome of Falcolipeurus suturalis and compare it with the mt genome of F. quadripustulatus. Phylogenetic relationships within the family Philopteridae were inferred from the concatenated 13 protein-coding genes of the two Falcolipeurus lice and members of the family Philopteridae using Bayesian inference (BI) and maximum likelihood (ML) methods. Results The complete mt genome of F. suturalis is a circular, double-stranded DNA molecule 16,659bp in size that contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and three non-coding regions. The gene order of the F. suturalis mt genome is rearranged relative to that of F. quadripustulatus, and is radically different from both other louse species and the putative ancestral insect. Phylogenetic analyses revealed clear genetic distinctiveness between F. suturalis and F. quadripustulatus (Bayesian posterior probabilities=1.0 and bootstrapping frequencies=100), and that the genus Falcolipeurus is sister to the genus Ibidoecus (Bayesian posterior probabilities=1.0 and bootstrapping frequencies=100). Conclusions These datasets help to better understand gene rearrangements in lice and the phylogenetic position of Falcolipeurus and provide useful genetic markers for systematic studies of bird lice. Graphic abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-04776-5.
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Affiliation(s)
- Yu Nie
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yi-Tian Fu
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yu Zhang
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yuan-Ping Deng
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Wei Wang
- School of Science and Engineering, GeneCology Research Centre, Animal Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia
| | - Ya Tu
- Beijing Wildlife Rescue and Rehabilitation Center, Beijing, 101300, China.
| | - Guo-Hua Liu
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China.
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Chen Z, Liu Y, Wu Y, Song F, Cai W, Li H. Novel tRNA gene rearrangements in the mitochondrial genome of Camarochiloides weiweii (Hemiptera: Pachynomidae). Int J Biol Macromol 2020; 165:1738-1744. [PMID: 33069822 DOI: 10.1016/j.ijbiomac.2020.10.051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 09/19/2020] [Accepted: 10/07/2020] [Indexed: 12/13/2022]
Abstract
Pachynomidae is a poorly known heteropteran group currently considered as a distinct family closely related to Reduviidae. Taxonomic position of Pachynomidae has been debated for a long time. Knowledge about mitochondrial genome (mitogenome) of this family also remain limited. In the present study, we describe the complete mitogenome of Camarochiloides weiweii, the first mitogenome sequenced for this family. This mitogenome consists of 13 protein-coding genes, two rRNA genes and 21 tRNA genes. Two tRNA gene rearrangements in this genome, including the translocation of trnA and trnR as well as the transposition of trnH, were observed and could be explained by the tandem duplication-random loss (TDRL) model. Bayesian and maximum likelihood analyses based on sequences of three different mitogenomic datasets recovered the monophyly of Reduvioidea, and the sister relationship between Reduvioidea and the remaining Cimicomorpha lineages. This study enlightens the future application of mitogenomic data in the phylogenetic study of Cimicomorpha based on the large-scale sampling.
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Affiliation(s)
- Zhuo Chen
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yingqi Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yunfei Wu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
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Aguilera-Uribe M, Meza-Lázaro RN, Kieran TJ, Ibarra-Cerdeña CN, Zaldívar-Riverón A. Phylogeny of the North-Central American clade of blood-sucking reduviid bugs of the tribe Triatomini (Hemiptera: Triatominae) based on the mitochondrial genome. INFECTION GENETICS AND EVOLUTION 2020; 84:104373. [DOI: 10.1016/j.meegid.2020.104373] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/19/2022]
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Magro A, Lecompte E, Hemptinne J, Soares AO, Dutrillaux A, Murienne J, Fürsch H, Dutrillaux B. First case of parthenogenesis in ladybirds (Coleoptera: Coccinellidae) suggests new mechanisms for the evolution of asexual reproduction. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12339] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Alexandra Magro
- Laboratoire Evolution et Diversité biologique UMR EDB 5174 CNRS / UT3 / IRDToulouse France
- Ecole Nationale Supérieure de Formation de l'Enseignement Agricole Auzeville-Tolosane France
| | - Emilie Lecompte
- Laboratoire Evolution et Diversité biologique UMR EDB 5174 CNRS / UT3 / IRDToulouse France
- Université Toulouse III‐Paul Sabatier Toulouse France
| | - Jean‐Louis Hemptinne
- Laboratoire Evolution et Diversité biologique UMR EDB 5174 CNRS / UT3 / IRDToulouse France
- Ecole Nationale Supérieure de Formation de l'Enseignement Agricole Auzeville-Tolosane France
| | - Antonio O. Soares
- Centre for Ecology, Evolution and Environmental Changes Azorean Biodiversity Group University of the Azores Ponta Delgada, Azores Portugal
| | - Anne‐Marie Dutrillaux
- Institut de Systématique, Evolution, Biodiversité UMR ISYEB 7205 CNRS / MNHN / UPMC / EPHE Museum National d'Histoire Naturelle Paris France
| | - Jérôme Murienne
- Laboratoire Evolution et Diversité biologique UMR EDB 5174 CNRS / UT3 / IRDToulouse France
- Université Toulouse III‐Paul Sabatier Toulouse France
| | | | - Bernard Dutrillaux
- Institut de Systématique, Evolution, Biodiversité UMR ISYEB 7205 CNRS / MNHN / UPMC / EPHE Museum National d'Histoire Naturelle Paris France
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Zhao W, Zhao Q, Li M, Wei J, Zhang X, Zhang H. Comparative Mitogenomic Analysis of the Eurydema Genus in the Context of Representative Pentatomidae (Hemiptera: Heteroptera) Taxa. JOURNAL OF INSECT SCIENCE (ONLINE) 2019; 19:20. [PMID: 31841604 PMCID: PMC6913905 DOI: 10.1093/jisesa/iez122] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Indexed: 05/30/2023]
Abstract
The family Pentatomidae, the largest within the superfamily Pentatomoidae, comprises about 5,000 species; many of which are economically important pests. Although the phylogeny of Pentatomidae species has been studied using various molecular markers, their phylogenetic relationships remain controversial. Recently, mitochondrial genomes (mitogenomes) have been extensively employed to examine the phylogenetics and evolution of different insects, and in this study, we sequenced complete/near-complete mitochondrial genomes from five shield bug species of Eurydema to gain a better understanding of phylogenetic relationships in the Pentatomidae. The five mitogenomes ranged in length from 15,500 to 16,752 bp and comprised 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region. We compared mitogenomic characteristics of the Pentatomidae and constructed phylogenetic trees using Bayesian inference and maximum likelihood methods. Our results showed that gene arrangements, base composition, start/stop codons, gene overlaps, and RNA structures were conserved within the Pentatomidae and that congeneric species shared more characteristics. Saturation and heterogeneity analyses revealed that our PCGs and PCGRNA datasets were valid for phylogenetic analysis. Phylogenetic analyses showed consistent topologies based on BI and ML methods. These analyses strongly supported that Eurydema species belong to the tribe Strachiini, and formed a sister group with Pentatomini. The relationships among Eurydema species were shown to be consistent with their morphological features. (Strachiini + Pentatomini) was found to be a stable sibling of the clade comprising Cappaeini, Graphosomini, and Carpocorini. Furthermore, our results indicated that Graphosoma rubrolineatum (Heteroptera: Pentatomidae) belongs to the Pentatominae and not the Podopinae.
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Affiliation(s)
- Wanqing Zhao
- Department of Biology, Xinzhou Teachers University, Xinzhou, China
| | - Qing Zhao
- Department of Entomology, Shanxi Agricultural University, Taigu, China
| | - Min Li
- Department of Biology, Taiyuan Normal University, Taiyuan, China
| | - Jiufeng Wei
- Department of Entomology, Shanxi Agricultural University, Taigu, China
| | - Xianhong Zhang
- Department of Entomology, Shanxi Agricultural University, Taigu, China
| | - Hufang Zhang
- Department of Biology, Xinzhou Teachers University, Xinzhou, China
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13
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Trevisan B, Alcantara DM, Machado DJ, Marques FP, Lahr DJ. Genome skimming is a low-cost and robust strategy to assemble complete mitochondrial genomes from ethanol preserved specimens in biodiversity studies. PeerJ 2019; 7:e7543. [PMID: 31565556 PMCID: PMC6746217 DOI: 10.7717/peerj.7543] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 07/24/2019] [Indexed: 12/17/2022] Open
Abstract
Global loss of biodiversity is an ongoing process that concerns both local and global authorities. Studies of biodiversity mainly involve traditional methods using morphological characters and molecular protocols. However, conventional methods are a time consuming and resource demanding task. The development of high-throughput sequencing (HTS) techniques has reshaped the way we explore biodiversity and opened a path to new questions and novel empirical approaches. With the emergence of HTS, sequencing the complete mitochondrial genome became more accessible, and the number of genome sequences published has increased exponentially during the last decades. Despite the current state of knowledge about the potential of mitogenomics in phylogenetics, this is still a relatively under-explored area for a multitude of taxonomic groups, especially for those without commercial relevance, non-models organisms and with preserved DNA. Here we take the first step to assemble and annotate the genomes from HTS data using a new protocol of genome skimming which will offer an opportunity to extend the field of mitogenomics to under-studied organisms. We extracted genomic DNA from specimens preserved in ethanol. We used Nextera XT DNA to prepare indexed paired-end libraries since it is a powerful tool for working with diverse samples, requiring a low amount of input DNA. We sequenced the samples in two different Illumina platform (MiSeq or NextSeq 550). We trimmed raw reads, filtered and had their quality tested accordingly. We performed the assembly using a baiting and iterative mapping strategy, and the annotated the putative mitochondrion through a semi-automatic procedure. We applied the contiguity index to access the completeness of each new mitogenome. Our results reveal the efficiency of the proposed method to recover the whole mitogenomes of preserved DNA from non-model organisms even if there are gene rearrangement in the specimens. Our findings suggest the potential of combining the adequate platform and library to the genome skimming as an innovative approach, which opens a new range of possibilities of its use to obtain molecular data from organisms with different levels of preservation.
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Affiliation(s)
- Bruna Trevisan
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Daniel M.C. Alcantara
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Denis Jacob Machado
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
- Department of Bioinformatics and Genomics / College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC, United States of America
| | - Fernando P.L. Marques
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Daniel J.G. Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
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14
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Zhao Y, Jiang M, Wu Y, Song F, Cai W, Li H. Mitochondrial genomes of three kissing bugs (Reduviidae: Triatominae) and their phylogenetic implications. Int J Biol Macromol 2019; 134:36-42. [DOI: 10.1016/j.ijbiomac.2019.05.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/04/2019] [Accepted: 05/04/2019] [Indexed: 01/19/2023]
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15
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Sun Z, Liu Y, Wilson JJ, Chen Z, Song F, Cai W, Li H. Mitochondrial genome of Phalantus geniculatus (Hemiptera: Reduviidae): trnT duplication and phylogenetic implications. Int J Biol Macromol 2019; 129:110-115. [PMID: 30711565 DOI: 10.1016/j.ijbiomac.2019.01.205] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 01/30/2019] [Accepted: 01/30/2019] [Indexed: 01/05/2023]
Abstract
Reduviidae is the second largest family of Heteroptera and most of them are important natural enemies of agricultural and forest pests. Most of the sequenced mitochondrial (mt) genomes in this family have the typical gene arrangement of insects and encode 37 coding genes (13 protein-coding genes, 22 tRNA genes and two rRNA genes). In the present study, we sequenced the mt genome of Phalantus geniculatus from the subfamily Peiratinae through high-throughput sequencing and encountered the duplication of tRNA genes for the first time in this subfamily. We identified 23 tRNA genes, including 22 tRNAs commonly found in insect mt genomes and an extra trnT (trnT2), which has high sequence similarity (96.9%) to trnT1. The presence of a "pseudo-trnP" in the non-coding region between trnT1 and trnT2 supports the hypothesis that the presence of an extra trnT can be explained by the tandem duplication-random loss (TDRL) model. Phylogenetic results inferred from mt genome sequences supported a sister relationship between Phymatinae and the remaining sampled subfamilies, as well as a paraphyletic Reduviinae. The present study highlights the utility of mt genomes in the phylogenetic study of Reduviidae based on the large scale taxon sampling in the future.
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Affiliation(s)
- Ziqiang Sun
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yingqi Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - John-James Wilson
- Vertebrate Zoology at World Museum, National Museums Liverpool, Liverpool L3 8EN, United Kingdom; Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Zhuo Chen
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
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16
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Dong L, Ma X, Wang M, Zhu D, Feng Y, Zhang Y, Wang J. Complete Mitochondrial Genome of the Chagas Disease Vector, Triatoma rubrofasciata. THE KOREAN JOURNAL OF PARASITOLOGY 2018; 56:515-519. [PMID: 30419739 PMCID: PMC6243191 DOI: 10.3347/kjp.2018.56.5.515] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/30/2018] [Indexed: 11/23/2022]
Abstract
Triatoma rubrofasciata is a wide-spread vector of Chagas disease in Americas. In this study, we completed the mitochondrial genome sequencing of T. rubrofasciata. The total length of T. rubrofasciata mitochondrial genome was 17,150 bp with the base composition of 40.4% A, 11.6% G, 29.4% T and 18.6% C. It included 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region. We constructed a phylogenetic tree on the 13 protein-coding genes of T. rubrofasciata and other 13 closely related species to show their phylogenic relationship. The determination of T. rubrofasciata mitogenome would play an important role in understanding the genetic diversity and evolution of triatomine bugs.
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Affiliation(s)
- Li Dong
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, P. R. China
| | - Xiaoling Ma
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, P. R. China
| | - Mengfei Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, P. R. China
| | - Dan Zhu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology, Ministry of Health, WHO Collaborating Center for Tropical Diseases, Shanghai 200025, P.R. China
| | - Yuebiao Feng
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, P. R. China
| | - Yi Zhang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology, Ministry of Health, WHO Collaborating Center for Tropical Diseases, Shanghai 200025, P.R. China
| | - Jingwen Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, P. R. China
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17
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Mitochondrial DNA and their nuclear copies in the parasitic wasp Pteromalus puparum: A comparative analysis in Chalcidoidea. Int J Biol Macromol 2018; 121:572-579. [PMID: 30315882 DOI: 10.1016/j.ijbiomac.2018.10.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 11/22/2022]
Abstract
Chalcidoidea (chalcidoid wasps) are an abundant and megadiverse insect group with both ecological and economical importance. Here we report a complete mitochondrial genome in Chalcidoidea from Pteromalus puparum (Pteromalidae). Eight tandem repeats followed by 6 reversed repeats were detected in its 3308 bp control region. This long and complex control region may explain failures of amplifying and sequencing of complete mitochondrial genomes in some chalcidoids. In addition to 37 typical mitochondrial genes, an extra identical isoleucine tRNA (trnI) was detected at the opposite end of the control region. This recent mitochondrial gene duplication indicates that gene arrangements in chalcidoids are ongoing. A comparison among available chalcidoid mitochondrial genomes reveals rapid gene order rearrangements overall and high protein substitution rates in most chalcidoid taxa. In addition, we identified 24 nuclear sequences of mitochondrial origin (NUMTs) in P. puparum, summing up to 9989 bp, with 3617 bp of these NUMTs originating from mitochondrial coding regions. NUMTs abundance in P. puparum is only one-twelfth of that in its relative, Nasonia vitripennis. Based on phylogenetic analysis, we provide evidence that a faster nuclear degradation rate contributes to the reduced NUMT numbers in P. puparum. Overall, our study shows unusually high rates of mitochondrial evolution and considerable variation in NUMT accumulation in Chalcidoidea.
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18
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Zhang LP, Cai YY, Yu DN, Storey KB, Zhang JY. Gene characteristics of the complete mitochondrial genomes of Paratoxodera polyacantha and Toxodera hauseri (Mantodea: Toxoderidae). PeerJ 2018; 6:e4595. [PMID: 29686943 PMCID: PMC5911385 DOI: 10.7717/peerj.4595] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/20/2018] [Indexed: 11/29/2022] Open
Abstract
The family Toxoderidae (Mantodea) contains an ecologically diverse group of praying mantis species that have in common greatly elongated bodies. In this study, we sequenced and compared the complete mitochondrial genomes of two Toxoderidae species, Paratoxodera polyacantha and Toxodera hauseri, and compared their mitochondrial genome characteristics with another member of the Toxoderidae, Stenotoxodera porioni (KY689118). The lengths of the mitogenomes of T. hauseri and P. polyacantha were 15,616 bp and 15,999 bp, respectively, which is similar to that of S. porioni (15,846 bp). The size of each gene as well as the A+T-rich region and the A+T content of the whole genome were also very similar among the three species as were the protein-coding genes, the A+T content and the codon usages. The mitogenome of T. hauseri had the typical 22 tRNAs, whereas that of P. polyacantha had 26 tRNAs including an extra two copies of trnA-trnR. Intergenic regions of 67 bp and 76 bp were found in T. hauseri and P. polyacantha, respectively, between COX2 and trnK; these can be explained as residues of a tandem duplication/random loss of trnK and trnD. This non-coding region may be synapomorphic for Toxoderidae. In BI and ML analyses, the monophyly of Toxoderidae was supported and P. polyacantha was the sister clade to T. hauseri and S. porioni.
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Affiliation(s)
- Le-Ping Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Zhejiang, China
| | - Yin-Yin Cai
- College of Chemistry and Life Science, Zhejiang Normal University, Zhejiang, China
| | - Dan-Na Yu
- College of Chemistry and Life Science, Zhejiang Normal University, Zhejiang, China.,Key lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Kenneth B Storey
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Jia-Yong Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Zhejiang, China.,Key lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang, China.,Department of Biology, Carleton University, Ottawa, Ontario, Canada
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19
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Tan MH, Gan HM, Dally G, Horner S, Moreno PAR, Rahman S, Austin CM. More limbs on the tree: mitogenome characterisation and systematic position of ‘living fossil’ species Neoglyphea inopinata and Laurentaeglyphea neocaledonica (Decapoda : Glypheidea : Glypheidae). INVERTEBR SYST 2018. [DOI: 10.1071/is17050] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Glypheids first appeared in the Lower Triassic period and were believed to be extinct until specimens of Neoglyphea inopinata Forest & Saint Laurent and Laurentaeglyphea neocaledonica Richer de Forges were described in 1975 and 2006, respectively. The finding of extant species has meant that molecular data can now be used to complement morphological and fossil-based studies to investigate the relationships of Glypheidea within the Decapoda. However, despite several molecular studies, the placement of this infraorder within the decapod phylogenetic tree is not resolved. One limitation is that molecular resources available for glypheids have been limited to a few nuclear and mitochondrial gene fragments. Many of the more recent large-scale studies of decapod phylogeny have used information from complete mitogenomes, but have excluded the infraorder Glypheidea due to the unavailability of complete mitogenome sequences. Using next-generation sequencing, we successfully sequenced and assembled complete mitogenome sequences from museum specimens of N. inopinata and L. neocaledonica, the only two extant species of glypheids. With these sequences, we constructed the first decapod phylogenetic tree based on whole mitogenome sequences that includes Glypheidea as one of 10 decapod infraorders positioned within the suborder Pleocyemata. From this, the Glypheidea appears to be a relatively derived lineage related to the Polychelida and Astacidea. Also in our study, we conducted a survey on currently available decapod mitogenome resources available on National Center for Biotechnology Information (NCBI) and identified infraorders that would benefit from more strategic and expanded taxonomic sampling.
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20
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Sun S, Hui M, Wang M, Sha Z. The complete mitochondrial genome of the alvinocaridid shrimp Shinkaicaris leurokolos (Decapoda, Caridea): Insight into the mitochondrial genetic basis of deep-sea hydrothermal vent adaptation in the shrimp. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2017; 25:42-52. [PMID: 29145028 DOI: 10.1016/j.cbd.2017.11.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/02/2017] [Accepted: 11/06/2017] [Indexed: 01/02/2023]
Abstract
Deep-sea hydrothermal vent is one of the most extreme environments on Earth with low oxygen and high levels of toxins. Decapod species from the family Alvinocarididae have colonized and successfully adapted to this extremely harsh environment. Mitochondria plays a vital role in oxygen usage and energy metabolism, thus it may be under selection in the adaptive evolution of the hydrothermal vent shrimps. In this study, the mitochondrial genome (mitogenome) of alvinocaridid shrimp Shinkaicaris leurokolos (Kikuchi & Hashimoto, 2000) was determined through Illumina sequencing. The mitogenome of S. leurokolos was 15,903bp in length, containing 13 protein-coding genes, 2 rRNAs, and 22 tRNAs. The gene order and orientation were identical to those of sequenced alvinocaridids. It has the longest concatenated sequences of protein-coding genes, tRNAs and shortest pooled rRNAs among the alvinocaridids. The control regions (CRs) of alvinocaridid were significantly longer (p<0.01) than those of the other caridaen. The alignment of the alvinocaridid CRs revealed two conserved sequence blocks (CSBs), and each of the CSBs included a noncanonical open reading frame (ORF), which may be involved in adjusting mitochondrial energy metabolism to adapt to the hydrothermal environment. Phylogenetic analysis supported that the deep-sea hydrothermal vent shrimps may have originated from those living in shallow area. Positive selection analysis reveals the evidence of adaptive change in the mitogenome of Alvinocarididae. Thirty potentially important adaptive residues were identified, which were located in atp6, cox1, cox3, cytb and nad1-5. This study explores the mitochondrial genetic basis of hydrothermal vent adaptation in alvinocaridid for the first time, and provides valuable clues regarding the adaptation.
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Affiliation(s)
- Shao'e Sun
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Science, China
| | - Ming Hui
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Science, China
| | - Minxiao Wang
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Science, China
| | - Zhongli Sha
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Science, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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21
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Liu Y, Song F, Jiang P, Wilson JJ, Cai W, Li H. Compositional heterogeneity in true bug mitochondrial phylogenomics. Mol Phylogenet Evol 2017; 118:135-144. [PMID: 28986237 DOI: 10.1016/j.ympev.2017.09.025] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 08/28/2017] [Accepted: 09/30/2017] [Indexed: 01/05/2023]
Abstract
Mitochondrial phylogenomics is often controversial, in particular for inferring deep relationships. The recent rapid increase of mitochondrial genome data provides opportunities for better phylogenetic estimates and assessment of potential biases resulting from heterogeneity in nucleotide composition and mutation rates. Here, we gathered 76 mitochondrial genome sequences for Heteroptera representing all seven infraorders, including 17 newly sequenced mitochondrial genomes. We found strong heterogeneity in base composition and contrasting evolutionary rates among heteropteran mitochondrial genomes, which affected analyses with various datasets and partitioning schemes under site-homogeneous models and produced false groupings of unrelated taxa exhibiting similar base composition and accelerated evolutionary rates. Bayesian analyses using a site-heterogeneous mixture CAT+GTR model showed high congruence of topologies with the currently accepted phylogeny of Heteroptera. The results confirm the monophyly of the six infraorders within Heteroptera, except for Cimicomorpha which was recovered as two paraphyletic clades. The monophyly of Terheteroptera (Cimicomorpha and Pentatomomorpha) and Panheteroptera (Nepomorpha, Leptopodomorpha and Terheteroptera) was recovered demonstrating a significant improvement over previous studies using mitochondrial genome data. Our study shows the power of the site-heterogeneous mixture models for resolving phylogenetic relationships with Heteroptera and provides one more case showing that model adequacy is critical for accurate tree reconstruction in mitochondrial phylogenomics.
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Affiliation(s)
- Yingqi Liu
- Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture, Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Fan Song
- Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture, Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Pei Jiang
- National Agro-Technical Extension and Service Centre, Ministry of Agriculture, Beijing 100125, China
| | - John-James Wilson
- International College Beijing, China Agricultural University, Beijing 100083, China
| | - Wanzhi Cai
- Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture, Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Hu Li
- Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture, Department of Entomology, China Agricultural University, Beijing 100193, China.
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22
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Valero MC, Ojo JA, Sun W, Tamò M, Coates BS, Pittendrigh BR. The complete mitochondrial genome of Anoplocnemis curvipes F. (Coreinea, Coreidae, Heteroptera), a pest of fresh cowpea pods. MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:421-423. [PMID: 33473847 PMCID: PMC7800686 DOI: 10.1080/23802359.2017.1347829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The complete 16,345-bp mitochondrial genome of the agriculturally destructive pod sucking pest, the giant coreid bug, Anoplocnemis curvipes (Hemiptera: Coreidae), was assembled from paired-end Illumina HiSeq 2500 reads. The A. curvipes mitochondrial genome consists of 13 protein coding genes (PCGs), 22 tRNAs, 2 rRNAs and a control region in the order and orientation typical among insects. PCG initiation codons (ATG, ATC, ATT and ATA) with termination codon (TAA) are used with the exception of TAG stop codons by Cytb and ND3. All tRNA genes fold into predicted cloverleaf secondary structures having requisite triplets on the anticodon loop, apart from tRNA-Ser1 (AGN) whose dihydrouridine (DHU) arm forms a simple loop. The phylogenetic analysis of hemipteran mitogenomes clusters to the family level and supports the monophyly of the five superfamilies in Pentatomomorpha of Hemiptera. The Coreoidea and Pyrrhocoroidea are sister groups, while Coreidae and Alydidae are sister groups to Rhopalidae. These analyses provide insight to mitogenomics and evolutionary relationships among pentatomoid insects.
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Affiliation(s)
- M Carmen Valero
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, IL, USA
| | - James Adebayo Ojo
- Department of Crop Production, Kwara State University, Ilorin, Nigeria
| | - Weilin Sun
- Department of Entomology, Michigan State University, East Lansing, MI, USA
| | - Manuele Tamò
- International Institute of Tropical Agriculture, Cotonou, Benin
| | - Brad S Coates
- United States Department of Agriculture - Agricultural Research Service, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, USA
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23
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Pita S, Panzera F, Vela J, Mora P, Palomeque T, Lorite P. Complete mitochondrial genome of Triatoma infestans (Hemiptera, Reduviidae, Triatominae), main vector of Chagas disease. INFECTION GENETICS AND EVOLUTION 2017; 54:158-163. [PMID: 28684375 DOI: 10.1016/j.meegid.2017.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 05/30/2017] [Accepted: 06/03/2017] [Indexed: 10/19/2022]
Abstract
The complete mitogenome of Triatoma infestans, the main vector of Chagas disease in South America, was obtained by combining Illumina and Sanger sequencing sequence data. The 17,301bp long genome contains 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a control region. The number, order and orientation of mitochondrial genes are the same as in T. dimidiata, the only Triatominae mt genome published so far. The main differences between both mitogenomes are found in the control region and in the intergenic spacer between the nd1 gene and the tRNA-Ser. Comparative analysis with other Reduviidae species shows high conservation in the mt genome organization. Molecular phylogeny using all available complete mt genomes from Reduviidae species confirms the close relationship between Triatominae and Stenopodainae.
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Affiliation(s)
- Sebastián Pita
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
| | - Francisco Panzera
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
| | - Jesús Vela
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071 Jaén, Spain.
| | - Pablo Mora
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071 Jaén, Spain.
| | - Teresa Palomeque
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071 Jaén, Spain.
| | - Pedro Lorite
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071 Jaén, Spain.
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24
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Grandjean F, Tan MH, Gan HM, Lee YP, Kawai T, Distefano RJ, Blaha M, Roles AJ, Austin CM. Rapid recovery of nuclear and mitochondrial genes by genome skimming from Northern Hemisphere freshwater crayfish. ZOOL SCR 2017. [DOI: 10.1111/zsc.12247] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Frederic Grandjean
- UMR CNRS 7267 Equipe Ecologie Evolution Symbiose; Laboratoire Ecologie et Biologie des Interactions; 5 rue Albert Turpin Poitiers Cedex France
| | - Mun Hua Tan
- School of Science; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- Genomics Facility; Tropical Medicine and Biology Platform; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- School of Life and Environmental Sciences; Deakin University; Geelong Victoria 3126 Australia
| | - Han Ming Gan
- School of Science; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- Genomics Facility; Tropical Medicine and Biology Platform; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- School of Life and Environmental Sciences; Deakin University; Geelong Victoria 3126 Australia
| | - Yin Peng Lee
- School of Science; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- Genomics Facility; Tropical Medicine and Biology Platform; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
| | - Tadashi Kawai
- Fisheries Research Department; Wakkanai Fisheries Research Institute; 4-5-15 Suehiro Wakkanai-shi 097-0001 Hokkaido Japan
| | - Robert J. Distefano
- Missouri Department of Conservation; East Gans Road Columbia Missouri 65201 USA
| | - Martin Blaha
- Faculty of Fisheries and Protection of Waters; South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses; University of South Bohemia in České Budějovice; Zátiší 728/II Vodňany Czech Republic
| | - Angela J. Roles
- Biology Department; Oberlin College, Oberlin; Ohio 44074 USA
| | - Christopher M. Austin
- School of Science; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- Genomics Facility; Tropical Medicine and Biology Platform; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- School of Life and Environmental Sciences; Deakin University; Geelong Victoria 3126 Australia
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25
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Hyde J, Cooper SJB, Munguia P, Humphreys WF, Austin AD. The first complete mitochondrial genomes of subterranean dytiscid diving beetles (Limbodessus and Paroster) from calcrete aquifers of Western Australia. AUST J ZOOL 2017. [DOI: 10.1071/zo17076] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Comparative analyses of mitochondrial (mt) genomes may provide insights into the genetic changes, associated with metabolism, that occur when surface species adapt to living in underground habitats. Such analyses require comparisons among multiple independently evolved subterranean species, with the dytiscid beetle fauna from the calcrete archipelago of central Western Australia providing an outstanding model system to do this. Here, we present the first whole mt genomes from four subterranean dytiscid beetle species of the genera Limbodessus (L. palmulaoides) and Paroster (P. macrosturtensis, P. mesosturtensis and P. microsturtensis) and compare genome sequences with those from surface dytiscid species. The mt genomes were sequenced using a next-generation sequencing approach employing the Illumina Miseq system and assembled de novo. All four mt genomes are circular, ranging in size from 16 504 to 16 868 bp, and encode 37 genes and a control region. The overall structure (gene number, orientation and order) of the mt genomes is the same as that found in eight sequenced surface species, but with genome size variation resulting from length variation of intergenic regions and the control region . Our results provide a basis for future investigations of adaptive evolutionary changes that may occur in mt genes when species move underground.
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26
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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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Zhang L, Song F, Li H, Cai W. First complete mitochondrial genome sequence from the tribelocephaline assassin bugs (Hemiptera: Reduviidae). Mitochondrial DNA A DNA Mapp Seq Anal 2016; 27:4203-4204. [DOI: 10.3109/19401736.2015.1022740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Lijuan Zhang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Fan Song
- Department of Entomology, China Agricultural University, Beijing, China
| | - Hu Li
- Department of Entomology, China Agricultural University, Beijing, China
| | - Wanzhi Cai
- Department of Entomology, China Agricultural University, Beijing, China
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28
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Duplication and Remolding of tRNA Genes in the Mitochondrial Genome of Reduvius tenebrosus (Hemiptera: Reduviidae). Int J Mol Sci 2016; 17:ijms17060951. [PMID: 27322247 PMCID: PMC4926484 DOI: 10.3390/ijms17060951] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/06/2016] [Accepted: 06/09/2016] [Indexed: 11/17/2022] Open
Abstract
Most assassin bugs are predators that act as important natural enemies of insect pests. Mitochondrial (mt) genomes of these insects are double-strand circular DNAs that encode 37 genes. In the present study, we explore the duplication and rearrangement of tRNA genes in the mt genome of Reduvius tenebrosus, the first mt genome from the subfamily Reduviinae. The gene order rearranges from CR (control region)-trnI-trnQ-trnM-ND2 to CR-trnQ-trnI2-trnI1-trnM-ND2. We identified 23 tRNA genes, including 22 tRNAs commonly found in insects and an additional trnI (trnI2), which has high sequence similarity to trnM. We found several pseudo genes, such as pseudo-trnI, pseudo-CR, and pseudo-ND2, in the hotspot region of gene rearrangement (between the control region and ND2). These features provided evidence that this novel gene order could be explained by the tandem duplication/random loss (TDRL) model. The tRNA duplication/anticodon mutation mechanism further explains the presence of trnI2, which is remolded from a duplicated trnM in the TDRL process (through an anticodon mutation of CAT to GAT). Our study also raises new questions as to whether the two events proceed simultaneously and if the remolded tRNA gene is fully functional. Significantly, the duplicated tRNA gene in the mitochondrial genome has evolved independently at least two times within assassin bugs.
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29
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Moreira DA, Magalhães MGP, de Andrade PCC, Furtado C, Val AL, Parente TE. An RNA-based approach to sequence the mitogenome of Hypoptopoma incognitum (Siluriformes: Loricariidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3784-6. [PMID: 26370305 DOI: 10.3109/19401736.2015.1079903] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Hypoptopoma incognitum is a fish of the fifth most species-rich family of vertebrates and abundant in rivers from the Brazilian Amazon. Only two species of Loricariidae fish have their complete mitogenomes sequence deposited in the Genbank. An innovative RNA-based approach was used to assemble the complete mitogenome of H. incognitum with an average coverage depth of 5292×. The typical vertebrate mitochondrial features were found; 22 tRNA genes, two rRNA genes, 13 protein-coding genes, and a non-coding control region. Moreover, the use of this approach allowed the measurement of mtRNA expression levels, the punctuation pattern of editing, and the detection of heteroplasmies.
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Affiliation(s)
- Daniel Andrade Moreira
- a Laboratório de Toxicologia Ambiental , Fundação Oswaldo Cruz (FIOCRUZ) , Rio de Janeiro , Brasil
| | - Maithê G P Magalhães
- a Laboratório de Toxicologia Ambiental , Fundação Oswaldo Cruz (FIOCRUZ) , Rio de Janeiro , Brasil
| | - Paula C C de Andrade
- a Laboratório de Toxicologia Ambiental , Fundação Oswaldo Cruz (FIOCRUZ) , Rio de Janeiro , Brasil
| | - Carolina Furtado
- b Divisão de Genética , Instituto Nacional do Cancer (INCA) , Rio de Janeiro , Brasil , and
| | - Adalberto L Val
- c Laboratório de Ecofisiologia e Evolução Molecular , Instituto Nacional de Pesquisas da Amazônia (INPA) , Manaus , Brasil
| | - Thiago Estevam Parente
- a Laboratório de Toxicologia Ambiental , Fundação Oswaldo Cruz (FIOCRUZ) , Rio de Janeiro , Brasil
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30
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Lecompte E, Crouau-Roy B, Aujard F, Holota H, Murienne J. Complete mitochondrial genome of the gray mouse lemur, Microcebus murinus (Primates, Cheirogaleidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3514-6. [PMID: 27158869 DOI: 10.3109/19401736.2015.1074196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We report the high-coverage complete mitochondrial genome sequence of the gray mouse lemur Microcebus murinus. The sequencing has been performed on an Illumina Hiseq 2500 platform, with a genome skimming strategy. The total length of this mitogenome is 16 963 bp, containing 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 non-coding region (D-loop region). The genome organization, nucleotide composition and codon usage are similar to those reported from other primate's mitochondrial genomes. The complete mitochondrial genome sequence reported here will be useful for comparative genomics studies in primates.
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Affiliation(s)
- Emilie Lecompte
- a Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, CNRS, Université Toulouse 3 Paul Sabatier , ENFA, Toulouse , France and
| | - Brigitte Crouau-Roy
- a Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, CNRS, Université Toulouse 3 Paul Sabatier , ENFA, Toulouse , France and
| | | | - Hélène Holota
- a Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, CNRS, Université Toulouse 3 Paul Sabatier , ENFA, Toulouse , France and
| | - Jérôme Murienne
- a Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, CNRS, Université Toulouse 3 Paul Sabatier , ENFA, Toulouse , France and
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Yuan ML, Zhang QL, Guo ZL, Wang J, Shen YY. Comparative mitogenomic analysis of the superfamily Pentatomoidea (Insecta: Hemiptera: Heteroptera) and phylogenetic implications. BMC Genomics 2015; 16:460. [PMID: 26076960 PMCID: PMC4469028 DOI: 10.1186/s12864-015-1679-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 06/01/2015] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Insect mitochondrial genomes (mitogenomes) are the most extensively used genetic marker for evolutionary and population genetics studies of insects. The Pentatomoidea superfamily is economically important and the largest superfamily within Pentatomomorpha with over 7,000 species. To better understand the diversity and evolution of pentatomoid species, we sequenced and annotated the mitogenomes of Eurydema gebleri and Rubiconia intermedia, and present the first comparative analysis of the 11 pentatomoid mitogenomes that have been sequenced to date. RESULTS We obtained the complete mitogenome of Eurydema gebleri (16,005 bp) and a nearly complete mitogenome of Rubiconia intermedia (14,967 bp). Our results show that gene content, gene arrangement, base composition, codon usage, and mitochondrial transcription termination factor sequences are highly conserved in pentatomoid species, especially for species in the same family. Evolutionary rate analyses of protein-coding genes reveal that the highest and lowest rates are found in atp8 and cox1 and distinctive evolutionary patterns are significantly correlated with the G + C content of genes. We inferred the secondary structures for two rRNA genes for eleven pentatomoid species, and identify some conserved motifs of RNA structures in Pentatomidea. All tRNA genes in pentatomoid mitogenomes have a canonical cloverleaf secondary structure, except for two tRNAs (trnS1 and trnV) which appear to lack the dihydrouridine arm. Regions that are A + T-rich have several distinct characteristics (e.g. size variation and abundant tandem repeats), and have potential as species or population level molecular markers. Phylogenetic analyses based on mitogenomic data strongly support the monophyly of Pentatomoidea, and the estimated phylogenetic relationships are: (Urostylididae + (Plataspidae + (Pentatomidae + (Cydnidae + (Dinidoridae + Tessaratomidae))))). CONCLUSIONS This comparative mitogenomic analysis sheds light on the architecture and evolution of mitogenomes in the superfamily Pentatomoidea. Mitogenomes can be effectively used to resolve phylogenetic relationships of pentatomomorphan insects at various taxonomic levels. Sequencing more mitogenomes at various taxonomic levels, particularly from closely related species, will improve the annotation accuracy of mitochondrial genes, as well as greatly enhance our understanding of mitogenomic evolution and phylogenetic relationships in pentatomoids.
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Affiliation(s)
- Ming-Long Yuan
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, 730020, People's Republic of China.
| | - Qi-Lin Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, 730020, People's Republic of China.
| | - Zhong-Long Guo
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, 730020, People's Republic of China.
| | - Juan Wang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, 730020, People's Republic of China.
| | - Yu-Ying Shen
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, 730020, People's Republic of China.
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The Complete Mitochondrial Genome of Corizus tetraspilus (Hemiptera: Rhopalidae) and Phylogenetic Analysis of Pentatomomorpha. PLoS One 2015; 10:e0129003. [PMID: 26042898 PMCID: PMC4456165 DOI: 10.1371/journal.pone.0129003] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 05/04/2015] [Indexed: 11/19/2022] Open
Abstract
Insect mitochondrial genome (mitogenome) are the most extensively used genetic information for molecular evolution, phylogenetics and population genetics. Pentatomomorpha (>14,000 species) is the second largest infraorder of Heteroptera and of great economic importance. To better understand the diversity and phylogeny within Pentatomomorpha, we sequenced and annotated the complete mitogenome of Corizus tetraspilus (Hemiptera: Rhopalidae), an important pest of alfalfa in China. We analyzed the main features of the C. tetraspilus mitogenome, and provided a comparative analysis with four other Coreoidea species. Our results reveal that gene content, gene arrangement, nucleotide composition, codon usage, rRNA structures and sequences of mitochondrial transcription termination factor are conserved in Coreoidea. Comparative analysis shows that different protein-coding genes have been subject to different evolutionary rates correlated with the G+C content. All the transfer RNA genes found in Coreoidea have the typical clover leaf secondary structure, except for trnS1 (AGN) which lacks the dihydrouridine (DHU) arm and possesses a unusual anticodon stem (9 bp vs. the normal 5 bp). The control regions (CRs) among Coreoidea are highly variable in size, of which the CR of C. tetraspilus is the smallest (440 bp), making the C. tetraspilus mitogenome the smallest (14,989 bp) within all completely sequenced Coreoidea mitogenomes. No conserved motifs are found in the CRs of Coreoidea. In addition, the A+T content (60.68%) of the CR of C. tetraspilus is much lower than that of the entire mitogenome (74.88%), and is lowest among Coreoidea. Phylogenetic analyses based on mitogenomic data support the monophyly of each superfamily within Pentatomomorpha, and recognize a phylogenetic relationship of (Aradoidea + (Pentatomoidea + (Lygaeoidea + (Pyrrhocoroidea + Coreoidea)))).
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33
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Wang Y, Chen J, Jiang LY, Qiao GX. Hemipteran mitochondrial genomes: features, structures and implications for phylogeny. Int J Mol Sci 2015; 16:12382-404. [PMID: 26039239 PMCID: PMC4490450 DOI: 10.3390/ijms160612382] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 04/30/2015] [Accepted: 05/26/2015] [Indexed: 11/29/2022] Open
Abstract
The study of Hemipteran mitochondrial genomes (mitogenomes) began with the Chagas disease vector, Triatoma dimidiata, in 2001. At present, 90 complete Hemipteran mitogenomes have been sequenced and annotated. This review examines the history of Hemipteran mitogenomes research and summarizes the main features of them including genome organization, nucleotide composition, protein-coding genes, tRNAs and rRNAs, and non-coding regions. Special attention is given to the comparative analysis of repeat regions. Gene rearrangements are an additional data type for a few families, and most mitogenomes are arranged in the same order to the proposed ancestral insect. We also discuss and provide insights on the phylogenetic analyses of a variety of taxonomic levels. This review is expected to further expand our understanding of research in this field and serve as a valuable reference resource.
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Affiliation(s)
- Yuan Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Li-Yun Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Ge-Xia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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34
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Kocher A, Gantier JC, Holota H, Jeziorski C, Coissac E, Bañuls AL, Girod R, Gaborit P, Murienne J. Complete mitochondrial genome of Lutzomyia (Nyssomyia) umbratilis (Diptera: Psychodidae), the main vector of Leishmania guyanensis. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4219-4221. [PMID: 26000939 DOI: 10.3109/19401736.2015.1022748] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The nearly complete mitochondrial genome of Lutzomyia umbratilis Ward & Fraiha, 1977 (Psychodidae: Phlebotominae), considered as the main vector of Leishmania guyanensis, is presented. The sequencing has been performed on an Illumina Hiseq 2500 platform, with a genome skimming strategy. The full nuclear ribosomal RNA segment was also assembled. The mitogenome of L. umbratilis was determined to be at least 15,717 bp-long and presents an architecture found in many mitogenomes of insect (13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and one non-coding region also referred as the control region). The control region contains a large repeated element of c. 370 bp and a poly-AT region of unknown length. This is the first mitogenome of Psychodidae to be described.
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Affiliation(s)
- Arthur Kocher
- a CNRS, Université Toulouse III Paul Sabatier, ENFA; UMR5174 EDB (Laboratoire Evolution et Diversité Biologique) , Toulouse , France
| | - Jean-Charles Gantier
- b Laboratoire des Identifications Fongiques et Entomo-parasitologiques , Mennecy , France
| | - Hélène Holota
- a CNRS, Université Toulouse III Paul Sabatier, ENFA; UMR5174 EDB (Laboratoire Evolution et Diversité Biologique) , Toulouse , France
| | - Céline Jeziorski
- c INRA, UAR 1209 Département de génétique animale , INRA Auzeville , Castanet-Tolosan , France.,d GeT-PlaGe, Genotoul, INRA Auzeville , Castanet-Tolosan , France
| | - Eric Coissac
- e Laboratoire d'Ecologie Alpine , CNRS UMR 5553, Université Joseph Fourier , Grenoble , France
| | - Anne-Laure Bañuls
- f UMR MIVEGEC (IRD 224 - CNRS 5290), Université de Montpellier) , Montpellier , France , and
| | - Romain Girod
- g Medical Entomology Unit , Institut Pasteur de la Guyane , Cayenne Cedex , French Guiana
| | - Pascal Gaborit
- g Medical Entomology Unit , Institut Pasteur de la Guyane , Cayenne Cedex , French Guiana
| | - Jérôme Murienne
- a CNRS, Université Toulouse III Paul Sabatier, ENFA; UMR5174 EDB (Laboratoire Evolution et Diversité Biologique) , Toulouse , France
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35
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Murienne J, Jeziorski C, Holota H, Coissac E, Blanchet S, Grenouillet G. PCR-free shotgun sequencing of the stone loach mitochondrial genome (Barbatula barbatula). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4211-4212. [PMID: 26000945 DOI: 10.3109/19401736.2015.1022744] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The complete mitochondrial genome of the stone loach Barbatula barbatula (Linnaeus, 1758) (Actinopterygii: Cypriniformes: Nemacheilidae) has been sequenced using a genome-skimming approach on an Illumina Hiseq 2500 platform. The mitochondrial genome of B. barbatula was determined to be 16,630 bp long and presents an organization typical of vertebrate mitogenomes. The mean coverage was 82× with a minimum coverage of 33× for the control region and 52× for the remaining part of the genome. A phylogenetic analysis of the Nemacheilidae family shows the monophyly of the Barbatula genus with strong support.
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Affiliation(s)
- Jérôme Murienne
- a CNRS, Université de Toulouse III Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique) , Toulouse , France
| | - Céline Jeziorski
- b INRA, UAR1209, Département de Génétique Animale , INRA Auzeville , Castanet-Tolosan , France.,c GeT-PlaGe, Genotoul, INRA Auzeville , Castanet-Tolosan , France
| | - Hélène Holota
- a CNRS, Université de Toulouse III Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique) , Toulouse , France
| | - Eric Coissac
- d Laboratoire d'Ecologie Alpine , CNRS UMR , Grenoble , France , and
| | - Simon Blanchet
- a CNRS, Université de Toulouse III Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique) , Toulouse , France.,e Station Expérimentale du CNRS à Moulis, U.S.R , Moulis , France
| | - Gaël Grenouillet
- a CNRS, Université de Toulouse III Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique) , Toulouse , France
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36
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Zedane L, Hong-Wa C, Murienne J, Jeziorski C, Baldwin BG, Besnard G. Museomics illuminate the history of an extinct, paleoendemic plant lineage (Hesperelaea, Oleaceae) known from an 1875 collection from Guadalupe Island, Mexico. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12509] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Loubab Zedane
- CNRS-UPS-ENFA; UMR5174; EDB (Laboratoire Evolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Cynthia Hong-Wa
- Missouri Botanical Garden; PO Box 299 St. Louis MO 63166-0299 USA
| | - Jérôme Murienne
- CNRS-UPS-ENFA; UMR5174; EDB (Laboratoire Evolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Céline Jeziorski
- INRA; UAR1209; département de Génétique Animale; INRA Auzeville 31326; Castanet-Tolosan France
- GeT-PlaGe; Genotoul; INRA Auzeville 31326; Castanet-Tolosan France
| | - Bruce G. Baldwin
- Jepson Herbarium and Department of Integrative Biology; University of California; Berkeley CA 94720-2465 USA
| | - Guillaume Besnard
- CNRS-UPS-ENFA; UMR5174; EDB (Laboratoire Evolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
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Besnard G, Bertrand JAM, Delahaie B, Bourgeois YXC, Lhuillier E, Thébaud C. Valuing museum specimens: high-throughput DNA sequencing on historical collections of New Guinea crowned pigeons (Goura). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12494] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Guillaume Besnard
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Joris A. M. Bertrand
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
- Institute of Oceanography; National Taiwan University; n°1, sec. 4, Roosevelt Road, Daan District Taipei 10617 Taiwan
| | - Boris Delahaie
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Yann X. C. Bourgeois
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
- Zoological Institute; Department of Evolutionary Biology; University of Basel; Vesalgasse 1 4051 Basel Switzerland
| | - Emeline Lhuillier
- INRA; GeT-PlaGe; UAR 1209 Département de Génétique Animale; INRA Auzeville; 31326 Castanet-Tolosan France
| | - Christophe Thébaud
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
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Zhao G, Li H, Zhao P, Cai W. Comparative mitogenomics of the assassin bug genus Peirates (Hemiptera: Reduviidae: Peiratinae) reveal conserved mitochondrial genome organization of P. atromaculatus, P. fulvescens and P. turpis. PLoS One 2015; 10:e0117862. [PMID: 25689825 PMCID: PMC4331094 DOI: 10.1371/journal.pone.0117862] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 01/01/2015] [Indexed: 11/19/2022] Open
Abstract
In this study, we sequenced four new mitochondrial genomes and presented comparative mitogenomic analyses of five species in the genus Peirates (Hemiptera: Reduviidae). Mitochondrial genomes of these five assassin bugs had a typical set of 37 genes and retained the ancestral gene arrangement of insects. The A+T content, AT- and GC-skews were similar to the common base composition biases of insect mtDNA. Genomic size ranges from 15,702 bp to 16,314 bp and most of the size variation was due to length and copy number of the repeat unit in the putative control region. All of the control region sequences included large tandem repeats present in two or more copies. Our result revealed similarity in mitochondrial genomes of P. atromaculatus, P. fulvescens and P. turpis, as well as the highly conserved genomic-level characteristics of these three species, e.g., the same start and stop codons of protein-coding genes, conserved secondary structure of tRNAs, identical location and length of non-coding and overlapping regions, and conservation of structural elements and tandem repeat unit in control region. Phylogenetic analyses also supported a close relationship between P. atromaculatus, P. fulvescens and P. turpis, which might be recently diverged species. The present study indicates that mitochondrial genome has important implications on phylogenetics, population genetics and speciation in the genus Peirates.
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Affiliation(s)
- Guangyu Zhao
- Department of Entomology, China Agricultural University, Beijing, China
- Daxing No.1 Middle School, Beijing, China
| | - Hu Li
- Department of Entomology, China Agricultural University, Beijing, China
- Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Ping Zhao
- College of Environment and Life Sciences, Kaili University, Kaili, Guizhou, China
| | - Wanzhi Cai
- Department of Entomology, China Agricultural University, Beijing, China
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Sequencing of the mitochondrial genome of the avocado lace bug Pseudacysta perseae (Heteroptera, Tingidae) using a genome skimming approach. C R Biol 2015; 338:149-60. [PMID: 25636225 DOI: 10.1016/j.crvi.2014.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 12/09/2014] [Accepted: 12/10/2014] [Indexed: 11/23/2022]
Abstract
Lace bugs (Tingidae) are a family of phytophagous heteropterans, some of which are important agricultural and forestry pests. They currently comprise around 2500 species distributed worldwide, for which only one mitochondrial genome has been described so far. We sequenced the complete mitochondrial genome and the nuclear ribosomal gene segment of the avocado lace bug Pseudacysta perseae using a genome skimming approach on an Illumina Hiseq 2000 platform. Fifty-four additional heteropteran mitogenomes, including the one of the sycamore lace bug Corythucha ciliata, were retrieved to allow for comparisons and phylogenetic analyses. P. perseae mitochondrial genome was determined to be 15,850 bp long, and presented the typical organisation of insect mitogenomes. The phylogenetic analysis placed P. perseae as a sister to C. ciliata but did not confirm the monophyly of Miroidae including Tingidae. Our results contradicted widely accepted phylogenetic hypothesis, which highlights the limits of analyses based on mitochondrial data only. Shotgun sequencing approaches should provide substantial improvements in harmonizing mitochondrial and nuclear databases.
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