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Guo S, Chen J, Song N. Phylogenomic analysis of Syrphoidea (Diptera: Syrphidae, Pipunculidae) based on the expanded mitogenomic data. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 114:1-13. [PMID: 36597178 DOI: 10.1002/arch.21998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 09/27/2023]
Abstract
The mitochondrial genome has become the most widely used genomic resource in resolving the insect phylogenetic relationships. In this study, we assess the interrelationships among the syrphid and pipunculid members of Syrphoidea using mitochondrial genome sequences of 152 taxa, 9 of which are newly reported and three are assembled from the existing transcriptome data. The Pipunculidae was found to be deeply nested members of Schizophora, which resulted in a nonmonophyletic Syrphoidea. In the monophyletic Syrphidae, unequivocal robust support was found for Microdontinae as the sister group of all other Syrphidae. The subfamily Eristalinae was nonmonophyletic. The Pipizinae was recovered as the sister group to the Syrphinae, albeit with strong support. As a whole, our results are concord with previously established hypotheses on Syrphoidea from the genome scale data. The mitochondrial genomes were successful in producing a robustly supported phylogenetic framework for the Syrphoidea.
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Affiliation(s)
- Shibao Guo
- Department of Plant Protection, College of Agronomy,Xinyang Agriculture and Forestry University, Xinyang, Henan, China
| | - Junhua Chen
- Department of Plant Protection, College of Agronomy,Xinyang Agriculture and Forestry University, Xinyang, Henan, China
| | - Nan Song
- Department of Entomology, College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan, China
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Freitas L, Nery MF. Expansions and contractions in gene families of independently-evolved blood-feeding insects. BMC Evol Biol 2020; 20:87. [PMID: 32680460 PMCID: PMC7367253 DOI: 10.1186/s12862-020-01650-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/06/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The blood-feeding behavior evolved multiple times in Insecta lineages and it represents an excellent opportunity to study patterns of convergent molecular evolution regarding this habit. In insects the expansion of some gene families is linked with blood-feeding behavior, but a wide study comparing the evolution of these gene families among different lineages is still missing. Here we gathered genomic data from six independently-evolved hematophagous lineages, aiming to identify convergent expansions and/or contractions of gene families in hematophagous lineages of insects. RESULTS We found four rapidly evolving gene families shared by at least two hematophagous independently-evolved lineages, including a heat-shock and a chemosensory protein. On the expression of these four rapidly evolving gene families we found more genes expressed in mated individuals compared with virgin individuals in rapidly-expanded families and more genes expressed in non-blood-feeding individuals compared with blood-feeding individuals in rapidly-contracted families. CONCLUSION Our results reveal a new set of candidate genes to be explored in further analysis to help the development of new strategies to deal with blood-feeding vectors and also presents a new perspective to study the evolution of hematophagy identifying convergent molecular patterns.
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Affiliation(s)
- Lucas Freitas
- Laboratório de Genômica Evolutiva, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Rua Bertrand Russell, S/N, Cidade Universitária, IB, Bloco H, Campinas, SP, Brazil.
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
| | - Mariana F Nery
- Laboratório de Genômica Evolutiva, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Rua Bertrand Russell, S/N, Cidade Universitária, IB, Bloco H, Campinas, SP, Brazil
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Complete mitochondrial genomes from transcriptomes: assessing pros and cons of data mining for assembling new mitogenomes. Sci Rep 2019; 9:14806. [PMID: 31616005 PMCID: PMC6794255 DOI: 10.1038/s41598-019-51313-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 09/25/2019] [Indexed: 11/16/2022] Open
Abstract
Thousands of eukaryotes transcriptomes have been generated, mainly to investigate nuclear genes expression, and the amount of available data is constantly increasing. A neglected but promising use of this large amount of data is to assemble organelle genomes. To assess the reliability of this approach, we attempted to reconstruct complete mitochondrial genomes from RNA-Seq experiments of Reticulitermes termite species, for which transcriptomes and conspecific mitogenomes are available. We successfully assembled complete molecules, although a few gaps corresponding to tRNAs had to be filled manually. We also reconstructed, for the first time, the mitogenome of Reticulitermes banyulensis. The accuracy and completeness of mitogenomes reconstruction appeared independent from transcriptome size, read length and sequencing design (single/paired end), and using reference genomes from congeneric or intra-familial taxa did not significantly affect the assembly. Transcriptome-derived mitogenomes were found highly similar to the conspecific ones obtained from genome sequencing (nucleotide divergence ranging from 0% to 3.5%) and yielded a congruent phylogenetic tree. Reads from contaminants and nuclear transcripts, although slowing down the process, did not result in chimeric sequence reconstruction. We suggest that the described approach has the potential to increase the number of available mitogenomes by exploiting the rapidly increasing number of transcriptomes.
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Song H, Donthu RK, Hall R, Hon L, Weber E, Badger JH, Giordano R. Description of soybean aphid (Aphis glycines Matsumura) mitochondrial genome and comparative mitogenomics of Aphididae (Hemiptera: Sternorrhyncha). INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 113:103208. [PMID: 31422150 DOI: 10.1016/j.ibmb.2019.103208] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 06/26/2019] [Accepted: 07/25/2019] [Indexed: 06/10/2023]
Abstract
The complete mitochondrial genome of the soybean aphid (Aphis glycines Matsumura), a major agricultural pest in the world, is described for the first time, which consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, as well as a large repeat region between tRNA-Glu and tRNA-Phe, and an AT-rich control region. The 17,954 bp mtgenome is the largest reported from the family Aphididae, and its gene order follows the ancestral insect mtgenome except for the repeat region, which contains a 195 bp unit repeated 11.9 times, representing the highest reported repeats among the known aphid mtgenomes to date. A new molecular phylogeny of Aphidae is reconstructed based on all available aphid mtgenomes, and it is shown that the mtgenome data can robustly resolve relationships at the subfamily level, but do not have sufficient phylogenetic information to resolve deep relationships. A phylogeny-based comparative analysis of mtgenomes has been performed to investigate the evolution of the repeat region between tRNA-Glu and tRNA-Phe. So far, among aphids, 13 species are known to have this repeat region of variable lengths, and a phylogenetic analysis of the repeat region shows that a large proportion of the sequences are conserved across the phylogeny, suggesting that the repeat region evolved in the most recent common ancestor of Aphidinae and Eriosomatinae, and that it has gone through numerous episodes of lineage-specific losses and expansions. Combined together, this study provides novel insights into how the repeat regions have evolved within aphids.
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Affiliation(s)
- Hojun Song
- Department of Entomology, Texas A&M University, College Station, TX, USA.
| | - Ravi Kiran Donthu
- Puerto Rico, Science, Technology & Research Trust, San Juan, PR, USA; Know Your Bee, Inc, San Juan, PR, USA
| | | | | | - Everett Weber
- Puerto Rico, Science, Technology & Research Trust, San Juan, PR, USA; Know Your Bee, Inc, San Juan, PR, USA
| | - Jonathan H Badger
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institute of Health, DHHS, Bethesda, MD, USA
| | - Rosanna Giordano
- Puerto Rico, Science, Technology & Research Trust, San Juan, PR, USA; Know Your Bee, Inc, San Juan, PR, USA
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Sun L, Li TJ, Fu WB, Yan ZT, Si FL, Zhang YJ, Mao QM, Demari-Silva B, Chen B. The complete mt genomes of Lutzia halifaxia, Lt. fuscanus and Culex pallidothorax (Diptera: Culicidae) and comparative analysis of 16 Culex and Lutzia mt genome sequences. Parasit Vectors 2019; 12:368. [PMID: 31349856 PMCID: PMC6660957 DOI: 10.1186/s13071-019-3625-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 07/19/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite the medical importance of the genus Culex, the mitochondrial genome (mt genome) characteristics of Culex spp. are not well understood. The phylogeny of the genus and particularly the generic status of the genus Lutzia and the subgenus Culiciomyia remain unclear. METHODS The present study sequenced and analyzed the complete mt genomes of Lutzia halifaxia, Lutzia fuscanus and Cx. (Culiciomyia) pallidothorax and assessed the general characteristics and phylogenetics of all known 16 mt genome sequences for species in the genera Culex and Lutzia. RESULTS The complete mt genomes of Lt. halifaxia, Lt. fuscanus and Cx. pallidothorax are 15,744, 15,803 and 15,578 bp long, respectively, including 13 PCGs, 22 tRNAs, two tRNAs and a control region (CR). Length variations in the Culex and Lutzia mt genomes involved mainly the CR, and gene arrangements are the same as in other mosquitoes. We identified four types of repeat units in the CR sequences, and the poly-T stretch exists in all of these mt genomes. The repeat units of CR are conserved to different extent and provide information on their evolution. Phylogenetic analyses demonstrated that the Coronator and Sitiens groups are each monophyletic, whereas the monophyletic status of the Pipiens Group was not supported; Cx. pallidothorax is more closely related to the Sitiens and Pipiens groups; and both phylogenetics analysis and repeat unit features in CR show that Lutzia is a characteristic monophyletic entity, which should be an independent genus. CONCLUSIONS To our knowledge, this is the first comprehensive review of the mt genome sequences and taxonomic discussion based on the mt genomes of Culex spp. and Lutzia spp. The research provides general information on the mt genome of these two genera, and the phylogenetic and taxonomic status of Lutzia and Culiciomyia.
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Affiliation(s)
- Ling Sun
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331 P. R. China
| | - Ting-Jing Li
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331 P. R. China
| | - Wen-Bo Fu
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331 P. R. China
| | - Zhen-Tian Yan
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331 P. R. China
| | - Feng-Ling Si
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331 P. R. China
| | - Yu-Juan Zhang
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331 P. R. China
| | - Qi-Meng Mao
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331 P. R. China
| | - Bruna Demari-Silva
- Faculdade de Saúde Pública, Departamento de Epidemiologia, Universidade de São Paulo, Avenida Dr. Arnaldo, 715, São Paulo, Brazil
| | - Bin Chen
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331 P. R. China
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Plese B, Rossi ME, Kenny NJ, Taboada S, Koutsouveli V, Riesgo A. Trimitomics: An efficient pipeline for mitochondrial assembly from transcriptomic reads in nonmodel species. Mol Ecol Resour 2019; 19:1230-1239. [DOI: 10.1111/1755-0998.13033] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 04/15/2019] [Accepted: 04/19/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Bruna Plese
- Life Sciences Department The Natural History Museum London UK
- Division of Molecular Biology Ruđer Bošković Institute Zagreb Croatia
| | | | | | - Sergi Taboada
- Life Sciences Department The Natural History Museum London UK
| | | | - Ana Riesgo
- Life Sciences Department The Natural History Museum London UK
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Song N, Zhang H, Zhao T. Insights into the phylogeny of Hemiptera from increased mitogenomic taxon sampling. Mol Phylogenet Evol 2019; 137:236-249. [PMID: 31121308 DOI: 10.1016/j.ympev.2019.05.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/15/2019] [Accepted: 05/16/2019] [Indexed: 10/26/2022]
Abstract
Although reconstruction of the phylogeny of Hemiptera has progressed tremendously over the past two decades, some higher-level relationships remain poorly resolved. Here, we investigated the Hemiptera higher-level relationships using full mitochondrial genome data from 357 ingroup species, representing the most comprehensive sampling yet undertaken for reconstructing the phylogeny of this group. In this study, 92 mitochondrial genomes were newly determined. Various data treatment methods and substitution models were applied to tree reconstructions. Effects of compositional heterogeneity, rate heterogeneity, model adequacy and taxon sampling on support values and topological stability were explored. Phylogenetic analyses (1) confirmed the monophyly of Hemiptera under site-heterogeneous model, (2) placed Sternorrhyncha as sister to all other Hemiptera, (3) recovered Coccoidea as the sister taxon of Aphidoidea, followed successively by Aleyrodoidea and Psylloidea, and (4) indicated that the grouping of Coleorrhyncha and Fulgoromorpha was the result of long-branch attraction effect.
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Affiliation(s)
- Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China.
| | - Hao Zhang
- Henan Vocational and Technological College of Communication, Zhengzhou 450015, China
| | - Te Zhao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China.
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Wang YH, Wu HY, Rédei D, Xie Q, Chen Y, Chen PP, Dong ZE, Dang K, Damgaard J, Štys P, Wu YZ, Luo JY, Sun XY, Hartung V, Kuechler SM, Liu Y, Liu HX, Bu WJ. When did the ancestor of true bugs become stinky? Disentangling the phylogenomics of Hemiptera-Heteroptera. Cladistics 2017; 35:42-66. [DOI: 10.1111/cla.12232] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2017] [Indexed: 01/27/2023] Open
Affiliation(s)
- Yan-Hui Wang
- Department of Ecology and Evolution; College of Life Sciences; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- State Key Laboratory of Biocontrol; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Hao-Yang Wu
- Department of Ecology and Evolution; College of Life Sciences; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- State Key Laboratory of Biocontrol; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Dávid Rédei
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Qiang Xie
- Department of Ecology and Evolution; College of Life Sciences; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- State Key Laboratory of Biocontrol; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Yan Chen
- Chinese Academy of Inspection and Quarantine; No. A3, Gaobeidian Bei Lu Chaoyang District Beijing 100123 China
| | - Ping-Ping Chen
- Netherlands Centre of Biodiversity Naturalis; 2300 RA Leiden Netherlands
| | - Zhuo-Er Dong
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Kai Dang
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Jakob Damgaard
- Natural History Museum of Denmark; Universitetsparken 15 2100 Copenhagen Ø Denmark
| | - Pavel Štys
- Department of Zoology; Faculty of Science; Charles University in Prague; Viničná 7 CZ-128 44 Praha 2 Czech Republic
| | - Yan-Zhuo Wu
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Jiu-Yang Luo
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Xiao-Ya Sun
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Viktor Hartung
- Staatliches Museum für Naturkunde Karslruhe; Erbprinzenstrasse 13 76133 Karlsruhe Germany
- Museum für Naturkunde - Leibniz-Institute for Research on Evolution and Biodiversity; Invalidenstrasse 43 10115 Berlin Germany
| | - Stefan M. Kuechler
- Department of Animal Ecology II; University of Bayreuth; Universitaetsstrasse 30 95440 Bayreuth Germany
| | - Yang Liu
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Hua-Xi Liu
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Wen-Jun Bu
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
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