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Dial DT, Weglarz KM, Brunet BMT, Havill NP, von Dohlen CD, Burke GR. Whole-genome sequence of the Cooley spruce gall adelgid, Adelges cooleyi (Hemiptera: Sternorrhyncha: Adelgidae). G3 (BETHESDA, MD.) 2023; 14:jkad224. [PMID: 37766465 PMCID: PMC10755206 DOI: 10.1093/g3journal/jkad224] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
The adelgids (Adelgidae) are a small family of sap-feeding insects, which, together with true aphids (Aphididae) and phylloxerans (Phylloxeridae), make up the infraorder Aphidomorpha. Some adelgid species are highly destructive to forest ecosystems such as Adelges tsugae, Adelges piceae, Adelges laricis, Pineus pini, and Pineus boerneri. Despite this, there are no high-quality genomic resources for adelgids, hindering advanced genomic analyses within Adelgidae and among Aphidomorpha. Here, we used PacBio continuous long-read and Illumina RNA-sequencing to construct a high-quality draft genome assembly for the Cooley spruce gall adelgid, Adelges cooleyi (Gillette), a gall-forming species endemic to North America. The assembled genome is 270.2 Mb in total size and has scaffold and contig N50 statistics of 14.87 and 7.18 Mb, respectively. There are 24,967 predicted coding sequences, and the assembly completeness is estimated at 98.1 and 99.6% with core BUSCO gene sets of Arthropoda and Hemiptera, respectively. Phylogenomic analysis using the A. cooleyi genome, 3 publicly available adelgid transcriptomes, 4 phylloxera transcriptomes, the Daktulosphaira vitifoliae (grape phylloxera) genome, 4 aphid genomes, and 2 outgroup coccoid genomes fully resolves adelgids and phylloxerans as sister taxa. The mitochondrial genome is 24 kb, among the largest in insects sampled to date, with 39.4% composed of noncoding regions. This genome assembly is currently the only genome-scale, annotated assembly for adelgids and will be a valuable resource for understanding the ecology and evolution of Aphidomorpha.
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Affiliation(s)
- Dustin T Dial
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
| | | | - Bryan M T Brunet
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada K1A 0C6
| | - Nathan P Havill
- USDA Forest Service, Northern Research Station, Hamden, CT 06514, USA
| | | | - Gaelen R Burke
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
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Wang SH, Hu SY, Li M, Liu M, Sun H, Zhao JR, Chen WT, Yuan ML. Comparative Mitogenomic Analyses of Darkling Beetles (Coleoptera: Tenebrionidae) Provide Evolutionary Insights into tRNA-like Sequences. Genes (Basel) 2023; 14:1738. [PMID: 37761878 PMCID: PMC10530909 DOI: 10.3390/genes14091738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/25/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Tenebrionidae is widely recognized owing to its species diversity and economic importance. Here, we determined the mitochondrial genomes (mitogenomes) of three Tenebrionidae species (Melanesthes exilidentata, Anatolica potanini, and Myladina unguiculina) and performed a comparative mitogenomic analysis to characterize the evolutionary characteristics of the family. The tenebrionid mitogenomes were highly conserved with respect to genome size, gene arrangement, base composition, and codon usage. All protein-coding genes evolved under purifying selection. The largest non-coding region (i.e., control region) showed several unusual features, including several conserved repetitive fragments (e.g., A+T-rich regions, G+C-rich regions, Poly-T tracts, TATA repeat units, and longer repetitive fragments) and tRNA-like structures. These tRNA-like structures can bind to the appropriate anticodon to form a cloverleaf structure, although base-pairing is not complete. We summarized the quantity, types, and conservation of tRNA-like sequences and performed functional and evolutionary analyses of tRNA-like sequences with various anticodons. Phylogenetic analyses based on three mitogenomic datasets and two tree inference methods largely supported the monophyly of each of the three subfamilies (Stenochiinae, Pimeliinae, and Lagriinae), whereas both Tenebrioninae and Diaperinae were consistently recovered as polyphyletic. We obtained a tenebrionid mitogenomic phylogeny: (Lagriinae, (Pimeliinae, ((Tenebrioninae + Diaperinae), Stenochiinae))). Our results provide insights into the evolution and function of tRNA-like sequences in tenebrionid mitogenomes and contribute to our general understanding of the evolution of Tenebrionidae.
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Affiliation(s)
- Su-Hao Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Shi-Yun Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou 730020, China
| | - Min Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Min Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou 730020, China
| | - Hao Sun
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou 730020, China
| | - Jia-Rui Zhao
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Wen-Ting Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Ming-Long Yuan
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou 730020, China
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Chen WT, Li M, Hu SY, Wang SH, Yuan ML. Comparative mitogenomic and evolutionary analysis of Lycaenidae (Insecta: Lepidoptera): Potential association with high-altitude adaptation. Front Genet 2023; 14:1137588. [PMID: 37144132 PMCID: PMC10151513 DOI: 10.3389/fgene.2023.1137588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/03/2023] [Indexed: 05/06/2023] Open
Abstract
Harsh environments (e.g., hypoxia and cold temperatures) of the Qinghai-Tibetan Plateau have a substantial influence on adaptive evolution in various species. Some species in Lycaenidae, a large and widely distributed family of butterflies, are adapted to the Qinghai-Tibetan Plateau. Here, we sequenced four mitogenomes of two lycaenid species in the Qinghai-Tibetan Plateau and performed a detailed comparative mitogenomic analysis including nine other lycaenid mitogenomes (nine species) to explore the molecular basis of high-altitude adaptation. Based on mitogenomic data, Bayesian inference, and maximum likelihood methods, we recovered a lycaenid phylogeny of [Curetinae + (Aphnaeinae + (Lycaeninae + (Theclinae + Polyommatinae)))]. The gene content, gene arrangement, base composition, codon usage, and transfer RNA genes (sequence and structure) were highly conserved within Lycaenidae. TrnS1 not only lacked the dihydrouridine arm but also showed anticodon and copy number diversity. The ratios of non-synonymous substitutions to synonymous substitutions of 13 protein-coding genes (PCGs) were less than 1.0, indicating that all PCGs evolved under purifying selection. However, signals of positive selection were detected in cox1 in the two Qinghai-Tibetan Plateau lycaenid species, indicating that this gene may be associated with high-altitude adaptation. Three large non-coding regions, i.e., rrnS-trnM (control region), trnQ-nad2, and trnS2-nad1, were found in the mitogenomes of all lycaenid species. Conserved motifs in three non-coding regions (trnE-trnF, trnS1-trnE, and trnP-nad6) and long sequences in two non-coding regions (nad6-cob and cob-trnS2) were detected in the Qinghai-Tibetan Plateau lycaenid species, suggesting that these non-coding regions were involved in high-altitude adaptation. In addition to the characterization of Lycaenidae mitogenomes, this study highlights the importance of both PCGs and non-coding regions in high-altitude adaptation.
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Affiliation(s)
- Wen-Ting Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Min Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Shi-Yun Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou, Gansu, China
| | - Su-Hao Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Ming-Long Yuan
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou, Gansu, China
- *Correspondence: Ming-Long Yuan,
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Zhang H, Lu C, Liu Q, Zou T, Qiao G, Huang X. Insights into the Evolution of Aphid Mitogenome Features from New Data and Comparative Analysis. Animals (Basel) 2022; 12:ani12151970. [PMID: 35953959 PMCID: PMC9367533 DOI: 10.3390/ani12151970] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022] Open
Abstract
The complete mitochondrial genomes and their rearrangement patterns can provide useful information for inferring evolutionary history of organisms. Aphids are one of the insect groups with some unique mitogenome features. In this study, to examine whether some features in aphid mitogenomes are independent species-specific evolutionary events or clade-specific events at certain taxonomic levels, we sequenced three new aphid mitogenomes (Hormaphidinae: Ceratovacuna keduensis, Pseudoregma panicola; Lachninae: Nippolachnus piri) and compared them with all known aphid mitogenomes. The three mitogenomes are 16,059–17,033 bp in length, with a set of 37 typical mitochondrial genes, a non-coding control region and a tandem repeat region. The gene orders of them are all highly rearranged. Within the subfamily Hormaphidinae, the presence of repeat region and mitogenome rearrangement in Cerataphidini species but not in the other two tribes indicate that these may be Cerataphidini-specific features. The same gene rearrangement pattern in the two Lachninae species, N. piri (Tuberolachnini) and Stomaphis sinisalicis (Stomaphidini), supports that this feature should be at least derived from the common ancestor of two tribes. Overall, our data and analyses provide new insights into the evolutionary patterns of gene rearrangement and repeat region in aphid mitogenomes, and further corroborate the potential role of gene rearrangement in elucidating the evolutionary history of different insect lineages.
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Affiliation(s)
- Hui Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.L.); (Q.L.); (T.Z.)
| | - Congcong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.L.); (Q.L.); (T.Z.)
| | - Qian Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.L.); (Q.L.); (T.Z.)
| | - Tianmin Zou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.L.); (Q.L.); (T.Z.)
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;
- Correspondence: (G.Q.); (X.H.)
| | - Xiaolei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.L.); (Q.L.); (T.Z.)
- Correspondence: (G.Q.); (X.H.)
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Ge XY, Liu T, Kang Y, Liu HY, Yang YX. First complete mitochondrial genomes of Ototretinae (Coleoptera, Lampyridae) with evolutionary insights into the gene rearrangement. Genomics 2022; 114:110305. [DOI: 10.1016/j.ygeno.2022.110305] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 01/09/2022] [Accepted: 02/01/2022] [Indexed: 11/26/2022]
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Acosta M, Alcantar D, Alier-Reyes I, Alvarez C, Arroyo CB, Calderon D, Cardenas D, Castro AR, Companion JK, Constante C, Diaz Telles ES, Fletes G, Gama FC, Garcia Perez C, Garcia A, Garcia B, Gutierrez BS, Guzman KL, Hernandez C, Hughey JR, Flores MI, Jacobo AI, Lopez B, Lopez-De Leon NC, Martinez JD, Mendoza N, Perez K, Perez LJ, Perez-Moreno M, Pineda CD, Pinedo E, Portillo JG, Rico A, Ruiz LV, Serrano GM, Sheldon KM, Terada H, Trujillo VA, Vazquez-Ramos C, Wang F, Flora D, Zavala FG. The complete mitochondrial genome of the strawberry aphid Chaetosiphon fragaefolii Cockerell, 1901 (Hemiptera: Aphididae) from California, USA. Mitochondrial DNA B Resour 2021; 6:2373-2375. [PMID: 34350347 PMCID: PMC8291070 DOI: 10.1080/23802359.2021.1915206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The aphid Chaetosiphon fragaefolii Cockerell, 1901 is an agricultural pest and known vector of strawberry viruses. To better understand its biology and systematics, we performed a genomic analysis on C. fragaefolii collected from Quinalt strawberry plants from Pacific Grove, Monterey county, California, USA using Oxford Nanopore and Illumina sequencing. The resulting data were used to assemble the aphids complete mitogenome. The mitogenome of C. fragaefolii is 16,108 bp in length and contains 2 rRNA, 13 protein-coding, and 22 tRNA genes (GenBank accession number LC590896). The mitogenome is similar in content and organization to other Aphididae. Phylogenetic analysis of the C. fragaefolii mitogenome resolved it in a fully supported clade in the tribe Macrosiphini. Analysis of the cox1 barcode sequence of C. fragaefolii from California found exact and nearly identical sequences to C. fragaefolii and Chaetosiphon thomasi Hille Ris Lambers, 1953, suggesting the two species are conspecific.
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Affiliation(s)
- Miguel Acosta
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Diana Alcantar
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Ivan Alier-Reyes
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Carlos Alvarez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Crystal B. Arroyo
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - David Calderon
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - David Cardenas
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Alejandro R. Castro
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Janelle K. Companion
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Cristian Constante
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Evelyn S. Diaz Telles
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Gabriel Fletes
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Fatima C. Gama
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Celia Garcia Perez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Abigail Garcia
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Bailey Garcia
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Brandon S. Gutierrez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Karina L. Guzman
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Cecilia Hernandez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Jeffery R. Hughey
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Monica Ibarra Flores
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Adilene I. Jacobo
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Brianna Lopez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | | | - Jaden D. Martinez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Nayelli Mendoza
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Kimberly Perez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Lucio J. Perez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Milagros Perez-Moreno
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Caitlin D. Pineda
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Elizabeth Pinedo
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Julissa G. Portillo
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Anais Rico
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Laura V. Ruiz
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Genevie M. Serrano
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Kalia M. Sheldon
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Hiroki Terada
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Victoria A. Trujillo
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | | | - Frank Wang
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Dawn Flora
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Felipe G. Zavala
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
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Xu XD, Guan JY, Zhang ZY, Cao YR, Cai YY, Storey KB, Yu DN, Zhang JY. Insight into the Phylogenetic Relationships among Three Subfamilies within Heptageniidae (Insecta: Ephemeroptera) along with Low-Temperature Selection Pressure Analyses Using Mitogenomes. INSECTS 2021; 12:656. [PMID: 34357316 PMCID: PMC8307263 DOI: 10.3390/insects12070656] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022]
Abstract
We determined 15 complete and two nearly complete mitogenomes of Heptageniidae belonging to three subfamilies (Heptageniinae, Rhithrogeninae, and Ecdyonurinae) and six genera (Afronurus, Epeorus, Leucrocuta, Maccaffertium, Stenacron, and Stenonema). Species of Rhithrogeninae and Ecdyonurinae had the same gene rearrangement of CR-I-M-Q-M-ND2, whereas a novel gene rearrangement of CR-I-M-Q-NCR-ND2 was found in Heptageniinae. Non-coding regions (NCRs) of 25-47 bp located between trnA and trnR were observed in all mayflies of Heptageniidae, which may be a synapomorphy for Heptageniidae. Both the BI and ML phylogenetic analyses supported the monophyly of Heptageniidae and its subfamilies (Heptageniinae, Rhithrogeninae, and Ecdyonurinae). The phylogenetic results combined with gene rearrangements and NCR locations confirmed the relationship of the subfamilies as (Heptageniinae + (Rhithrogeninae + Ecdyonurinae)). To assess the effects of low-temperature stress on Heptageniidae species from Ottawa, Canada, we found 27 positive selection sites in eight protein-coding genes (PCGs) using the branch-site model. The selection pressure analyses suggested that mitochondrial PCGs underwent positive selection to meet the energy requirements under low-temperature stress.
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Affiliation(s)
- Xiao-Dong Xu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (X.-D.X.); (J.-Y.G.); (Z.-Y.Z.); (Y.-R.C.); (Y.-Y.C.)
| | - Jia-Yin Guan
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (X.-D.X.); (J.-Y.G.); (Z.-Y.Z.); (Y.-R.C.); (Y.-Y.C.)
| | - Zi-Yi Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (X.-D.X.); (J.-Y.G.); (Z.-Y.Z.); (Y.-R.C.); (Y.-Y.C.)
| | - Yu-Rou Cao
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (X.-D.X.); (J.-Y.G.); (Z.-Y.Z.); (Y.-R.C.); (Y.-Y.C.)
| | - Yin-Yin Cai
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (X.-D.X.); (J.-Y.G.); (Z.-Y.Z.); (Y.-R.C.); (Y.-Y.C.)
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Dan-Na Yu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (X.-D.X.); (J.-Y.G.); (Z.-Y.Z.); (Y.-R.C.); (Y.-Y.C.)
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Jia-Yong Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (X.-D.X.); (J.-Y.G.); (Z.-Y.Z.); (Y.-R.C.); (Y.-Y.C.)
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
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8
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Novel tRNA gene rearrangements in the mitochondrial genomes of praying mantises (Mantodea: Mantidae): Translocation, duplication and pseudogenization. Int J Biol Macromol 2021; 185:403-411. [PMID: 34166699 DOI: 10.1016/j.ijbiomac.2021.06.096] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 06/12/2021] [Accepted: 06/14/2021] [Indexed: 11/20/2022]
Abstract
Gene rearrangements have been found in several mitochondrial genomes of Mantodea, located in the gene blocks CR-I-Q-M-ND2, COX1-K-D-ATP8 and ND3-A-R-N-S-E-F-ND5. We have sequenced one mitogenome of Amelidae (Yersinia mexicana) and six mitogenomes of Mantidae to discuss the mitochondrial gene rearrangement and the phylogenetic relationship within Mantidae. These mitogenomes showed rearrangements of tRNA genes except for Asiadodis yunnanensis and Hierodula zhangi. These novel gene rearrangements of Mantidae were primarily concentrated in the region of CR-I-Q-M-ND2, including gene translocation, duplication and pseudogenization. For the occurrences of these rearrangements, the tandem duplication-random loss (TDRL) model and slipped-strand mispairing model were suitable to explain. Large non-coding regions (LNCRs) located in the region of CR-I-Q-M-ND2 were detected in most Mantidae species, whereas some LNCRs had high similarity to the control region (CR). Both BI and ML phylogenetic analyses supported the monophyly of Mantidae and the paraphyly of Mantinae. The phylogenetic results with the gene order and the location of NCRs acted as forceful evidence that specific gene rearrangements and special LNCRs may be synapomorphies for several groups of mantises.
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9
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Ge X, Yuan L, Kang Y, Liu T, Liu H, Yang Y. Characterization of the First Complete Mitochondrial Genome of Cyphonocerinae (Coleoptera: Lampyridae) with Implications for Phylogeny and Evolution of Fireflies. INSECTS 2021; 12:570. [PMID: 34206376 PMCID: PMC8307346 DOI: 10.3390/insects12070570] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/11/2021] [Accepted: 06/19/2021] [Indexed: 11/16/2022]
Abstract
Complete mitochondrial genomes are valuable resources for phylogenetics in insects. The Cyphonoceridae represents an important lineage of fireflies. However, no complete mitogenome is available until now. Here, the first complete mitochondrial genome from this subfamily was reported, with Cyphonocerus sanguineus klapperichi as a representative. The mitogenome of C. sanguineus klapperichi was conserved in the structure and comparable to that of others in size and A+T content. Nucleotide composition was A+T-biased, and all genes exhibited a positive AT-skew and negative GC-skew. Two types of tandem repeat sequence units were present in the control region (136 bp × 2; 171 bp × 2 + 9 bp). For reconstruction of Lampyridae's phylogeny, three different datasets were analyzed by both maximum likelihood (ML) and Bayesian inference (BI) methods. As a result, the same topology was produced by both ML analysis of 13 protein-coding genes and 2rRNA and BI analysis of 37 genes. The results indicated that Lampyridae, Lampyrinae, Luciolinae (excluding Emeia) were monophyletic, but Ototretinae was paraphyletic, of which Stenocladius was recovered as the sister taxon to all others, while Drilaster was more closely related to Cyphonocerinae; Phturinae + Emeia were included in a monophyletic clade, which comprised sister groups with Lampyridae. Vesta was deeply rooted in the Luciolinae.
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Affiliation(s)
- Xueying Ge
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (X.G.); (L.Y.); (Y.K.); (T.L.)
| | - Lilan Yuan
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (X.G.); (L.Y.); (Y.K.); (T.L.)
- College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Ya Kang
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (X.G.); (L.Y.); (Y.K.); (T.L.)
| | - Tong Liu
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (X.G.); (L.Y.); (Y.K.); (T.L.)
| | - Haoyu Liu
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (X.G.); (L.Y.); (Y.K.); (T.L.)
| | - Yuxia Yang
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (X.G.); (L.Y.); (Y.K.); (T.L.)
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10
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Zhang H, Liu Q, Lu C, Deng J, Huang X. The First Complete Mitochondrial Genome of Lachninae Species and Comparative Genomics Provide New Insights into the Evolution of Gene Rearrangement and the Repeat Region. INSECTS 2021; 12:55. [PMID: 33440807 PMCID: PMC7828084 DOI: 10.3390/insects12010055] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/08/2021] [Accepted: 01/08/2021] [Indexed: 12/14/2022]
Abstract
Complete mitochondrial genomes are valuable resources for different research fields such as genomics, molecular evolution and phylogenetics. The subfamily Lachninae represents one of the most ancient evolutionary lineages of aphids. To date, however, no complete Lachninae mitogenome is available in public databases. Here we report the Stomaphis sinisalicis mitogenome, representing the first complete mitogenome of Lachninae. The S. sinisalicis mitogenome is consist of 13 protein-coding genes (PCGs), two rRNA genes (rRNAs), 22 tRNA genes (tRNAs), a control region and a large tandem repeat region. Strikingly, the mitogenome exhibits a novel, highly rearranged gene order between trnE and nad1 compared with that of other aphids. The presence of repeat region in the basal Lachninae may further indicate it is probably an ancestral feature of aphid mitogenomes. Collectively, this study provides new insights on mitogenome evolution and valuable data for future comparative studies across different insect lineages.
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Affiliation(s)
| | | | | | | | - Xiaolei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Z.); (Q.L.); (C.L.); (J.D.)
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11
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Yeh HT, Ko CC, Wu LW. The first complete mitochondrial genome of Adelges tsugae Annand (Hemiptera: Adelgidae). Mitochondrial DNA B Resour 2020; 5:2288-2290. [PMID: 33367011 PMCID: PMC7510656 DOI: 10.1080/23802359.2020.1772682] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/16/2020] [Indexed: 11/05/2022] Open
Abstract
Hemlock wooly adelgid (HWA), Adelgests ugae Annand (Hemiptera: Adelgidae), is a species native to Asia but later ravages Endangered hemlock forests (Tsuga spp.) in eastern North America. In this study, we obtained the first complete mitochondrial genome of HWA (16,509 bp in length) using meta-genomic sequencing method. The HWA mitogenome has a general gene annotation as other aphids, comprising 13 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs. Our phylogenetic result showed Aphidoidea is sister to Coccoidea and the newly sequenced mitogenome is put on the correct position, sister to Adelgeslaricis.
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Affiliation(s)
- Hsin-Ting Yeh
- The Experimental Forest, National Taiwan University, Nantou County, Taiwan
| | - Chiun-Cheng Ko
- Department of Entomology, National Taiwan University, Taipei, Taiwan
| | - Li-Wei Wu
- The Experimental Forest, National Taiwan University, Nantou County, Taiwan
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12
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Xu XD, Jia YY, Cao SS, Zhang ZY, Storey KB, Yu DN, Zhang JY. Six complete mitochondrial genomes of mayflies from three genera of Ephemerellidae (Insecta: Ephemeroptera) with inversion and translocation of trnI rearrangement and their phylogenetic relationships. PeerJ 2020; 8:e9740. [PMID: 32879803 PMCID: PMC7443110 DOI: 10.7717/peerj.9740] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/26/2020] [Indexed: 11/26/2022] Open
Abstract
As a small order of Pterygota (Insecta), Ephemeroptera has almost 3,500 species around the world. Ephemerellidae is a widely distributed common group of Ephemeroptera. However, the relationship among Ephemerellidae, Vietnamellidae and Teloganellidae is still in dispute. In this study, we sequenced six complete mitogenomes of three genera from Ephemerellidae (Insecta: Ephemeroptera): Ephemerella sp. Yunnan-2018, Serratella zapekinae, Serratella sp. Yunnan-2018, Serratella sp. Liaoning-2019, Torleya grandipennis and T. tumiforceps. These mitogenomes were employed to reveal controversial phylogenetic relationships among the Ephemeroptera, with emphasis on the phylogenetic relationships among Ephemerellidae. The lengths of the six mayfly mitogenomes ranged from 15,134 bp to 15,703 bp. Four mitogenomes of Ephemerella sp. Yunnan-2018, Serratella zapekinae, Serratella sp. Yunnan-2018 and Serratella sp. Liaoning-2019 had 22 tRNAs including an inversion and translocation of trnI. By contrast, the mitogenomes of T. tumiforceps and T. grandipennis had 24 tRNAs due to an extra two copies of inversion and translocation of trnI. Within the family Ephemerellidae, disparate gene rearrangement occurred in the mitogenomes of different genera: one copy of inversion and translocation trnI in the genera Ephemerella and Serratella, and three repeat copies of inversion and translocation of trnI in the genus Torleya. A large non-coding region (≥200 bp) between trnS1 (AGN) and trnE was detected in T. grandipennis and T. tumiforceps. Among the phylogenetic relationship of the Ephemeroptera, the monophyly of almost all families except Siphlonuridae was supported by BI and ML analyses. The phylogenetic results indicated that Ephemerellidae was the sister clade to Vietnamellidae whereas Teloganellidae was not a sister clade of Ephemerellidae and Vietnamellidae.
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Affiliation(s)
- Xiao-Dong Xu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Yi-Yang Jia
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Si-Si Cao
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Zi-Yi Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | | | - Dan-Na Yu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Jia-Yong Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang, China
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13
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Voronova NV, Levykina S, Warner D, Shulinski R, Bandarenka Y, Zhorov D. Characteristic and variability of five complete aphid mitochondrial genomes: Aphis fabae mordvilkoi, Aphis craccivora, Myzus persicae, Therioaphis tenera and Appendiseta robiniae (Hemiptera; Sternorrhyncha; Aphididae). Int J Biol Macromol 2020; 149:187-206. [PMID: 31917211 DOI: 10.1016/j.ijbiomac.2019.12.276] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/31/2019] [Accepted: 12/31/2019] [Indexed: 02/06/2023]
Abstract
The complete mitochondrial genomes of aphids Aphis fabae mordvilkoi, A. craccivora, Myzus persicae from Aphidinae as well as Therioaphis tenera and Appendiseta robiniae from Calaphidinae were sequenced and compared with the genomes of other aphid species. A. fabae mordvilkoi, Th. tenera and A. robiniae mitogenomes were sequenced and analyzed for the first time. The annotation of A. craccivora and M. persicae were corrected compared to what was previously published. According to our data there is no translocation of tRNA-Tyr gene in A. craccivora mitogenome and this aphid species has an ancestral type of mitochondrial gene order. A + T content in all 5 mitogenomes was higher than 80%. A + T content in the Th. tenera CR was 59.5% which is untypically low. CRs of all 5 studied mitogenomes had 2 conserved motifs at their ends and extended G + C rich region. A. craccivora, M. persicae and Th. tenera had large tandem repeats inside the CRs. Detailed molecular analysis of all 5 aphid mitochondrial genomes showed the importance of a deep understanding of the molecular organization of all the functional regions of the mitochondrial DNA, which helps to avoid mistakes during genome annotation.
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Affiliation(s)
- Nina V Voronova
- Zoology Department, Belarusian State University, Minsk, Belarus.
| | - Sofiya Levykina
- Zoology Department, Belarusian State University, Minsk, Belarus
| | - Derek Warner
- DNA Sequencing Core Facility, University of Utah, Salt Lake City, UT, United States of America
| | - Raman Shulinski
- Zoology Department, Belarusian State University, Minsk, Belarus
| | - Yury Bandarenka
- Zoology Department, Belarusian State University, Minsk, Belarus
| | - Dmitrii Zhorov
- Zoology Department, Belarusian State University, Minsk, Belarus
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14
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Wang JJ, Li DF, Li H, Yang MF, Dai RH. Structural and phylogenetic implications of the complete mitochondrial genome of Ledra auditura. Sci Rep 2019; 9:15746. [PMID: 31673057 PMCID: PMC6823449 DOI: 10.1038/s41598-019-52337-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/16/2019] [Indexed: 11/17/2022] Open
Abstract
We sequenced and annotated the first complete mitochondrial genome (mitogenome) of Ledra auditura (Hemiptera: Cicadellidae: Ledrinae) and reconstructed phylogenetic relationships among 47 species (including 2 outgroup species) on the basis of 3 datasets using maximum likelihood (ML) and Bayesian inference (BI) analyses. The complete L. auditura mitogenome (length, 16,094 bp) comprises 37 genes [13 protein-coding genes (PCGs), 22 tRNAs, and 2 rRNAs], 1 control region, and 2 long non-coding regions. The first long non-coding region (length, 211 bp) is located between tRNA-I and tRNA-Q and the second region (length, 994 bp) between tRNA-S2 and ND1. All PCGs show ATN (Met/Ile) as their start codon and TAR as their stop codon. Except tRNA-S1 (AGN), which lacks the dihydrouridine arm, all tRNAs can fold into the typical cloverleaf secondary structure. The complete L. auditura mitogenome shows a base composition bias of 76.3% A + T (A = 29.9%, T = 46.4%, G = 13.3%, and C = 10.5%), negative AT skew of -0.22, and positive GC skew of 0.12. In ML and BI analyses, L. auditura was clustered with Evacanthus heimianus (Hemiptera: Cicadellidae: Evacanthinae) with strong branch support.
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Affiliation(s)
- Jia-Jia Wang
- The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, Guizhou, 550025, P.R. China
| | - De-Fang Li
- The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, Guizhou, 550025, P.R. China
| | - Hu Li
- The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, Guizhou, 550025, P.R. China
- Shaanxi Key Laboratory of Bioresources, Shaanxi University of Technology, Hanzhong, Shaanxi, 723000, P.R. China
| | - Mao-Fa Yang
- The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, Guizhou, 550025, P.R. China
| | - Ren-Huai Dai
- The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, Guizhou, 550025, P.R. China.
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15
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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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16
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The mitochondrial genome of the brown citrus aphid Aphis (Toxoptera) citricidus: Insights into the repeat regions in aphids and phylogenetic implications. Int J Biol Macromol 2019; 136:531-539. [DOI: 10.1016/j.ijbiomac.2019.06.101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/11/2019] [Accepted: 06/14/2019] [Indexed: 01/13/2023]
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17
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Zhong LK, Li HX, Yu XF, Yang MF. Complete mitochondrial genome sequence of Cicadella viridis (Hemiptera: Cicadellidae: Cicadellinae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1591207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Li-Kun Zhong
- College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, China
| | - Hao-Xi Li
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, China
- College of Tobacco Science, Guizhou University, Guiyang, China
| | - Xiao-Fei Yu
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, China
- College of Tobacco Science, Guizhou University, Guiyang, China
| | - Mao-Fa Yang
- College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, China
- College of Tobacco Science, Guizhou University, Guiyang, China
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18
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He H, Li HX, Yang M. Complete mitochondrial genome sequence of Mileewa albovittata (Hemiptera: Cicadellidae: Mileewinae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1565930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Hongli He
- College of Agricultural Science, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, China
| | - Hao-Xi Li
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, China
- College of Tobacco Science, Guizhou University, Guiyang, China
| | - Maofa Yang
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, China
- College of Tobacco Science, Guizhou University, Guiyang, China
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19
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Chen J, Wang Y, Qin M, Jiang LY, Qiao GX. The mitochondrial genome of Greenidea psidii van der Goot (Hemiptera: Aphididae: Greenideinae) and comparisons with other Aphididae aphids. Int J Biol Macromol 2018; 122:824-832. [PMID: 30389524 DOI: 10.1016/j.ijbiomac.2018.10.209] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 11/26/2022]
Abstract
The complete mitochondrial genome of Greenidea psidii was sequenced and compared with the genomes of other aphid species. The G. psidii mitogenome is 16,202 bp long with an A + T content of 85.4%, comprising 37 genes arranged in the same order as the inferred insect ancestral arrangement, a control region and a special repeat region between trnE and trnF. G. psidii is the first representative possessing such a repeat region from the subfamily Greenideinae. These repeat motifs found in Aphidinae, Eriosomatinae and Greenideinae are species-specific, differing in nucleotide composition, length and copy number across different species. All reported complete aphid mitogenomes are A- and C-skewed in the whole genomes and show opposite skewness for C and G between the majority and minority strands. The ratios of nonsynonymous to synonymous substitution rates indicated that the evolution of the aphid mitogenomes has been dominated by purifying selection. Based on whole mitogenome sequences, the phylogenetic relationships among all aphid species with complete mitogenomes were investigated. G. psidii was robustly clustered with Cervaphis quercus, confirming its affiliation with the subfamily Greenideinae.
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Affiliation(s)
- Jing Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuan Wang
- Shaanxi International Travel Healthcare Center, Shaanxi Entry-Exit Inspection and Quarantine Bureau, Xi'an 710068, China
| | - Man Qin
- 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
| | - 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; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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20
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Sun W, Huynh BL, Ojo JA, Coates BS, Kusi F, Roberts PA, Pittendrigh BR. Comparison of complete mitochondrial DNA sequences between old and new world strains of the cowpea aphid, Aphis craccivora (Hemiptera: Aphididae). ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.aggene.2017.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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21
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Chen J, Wang Y, Jiang L, Qiao G. Mitochondrial genome sequences effectively reveal deep branching events in aphids (Insecta: Hemiptera: Aphididae). ZOOL SCR 2017. [DOI: 10.1111/zsc.12241] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Jing Chen
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing China
| | - Yuan Wang
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing China
- Shaanxi International Travel Healthcare Center; Shaanxi Entry-Exit Inspection and Quarantine Bureau; Xi'an China
| | - Liyun Jiang
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing China
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing China
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22
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The complete mitochondrial genome of Diaphorina citri (Hemiptera: Psyllidae) and phylogenetic analysis. BIOCHEM SYST ECOL 2017. [DOI: 10.1016/j.bse.2016.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Song N, An S, Yin X, Cai W, Li H. Application of RNA-seq for mitogenome reconstruction, and reconsideration of long-branch artifacts in Hemiptera phylogeny. Sci Rep 2016; 6:33465. [PMID: 27633117 PMCID: PMC5025853 DOI: 10.1038/srep33465] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 08/31/2016] [Indexed: 11/15/2022] Open
Abstract
Hemiptera make up the largest nonholometabolan insect assemblage. Despite previous efforts to elucidate phylogeny within this group, relationships among the major sub-lineages remain uncertain. In particular, mitochondrial genome (mitogenome) data are still sparse for many important hemipteran insect groups. Recent mitogenomic analyses of Hemiptera have usually included no more than 50 species, with conflicting hypotheses presented. Here, we determined the nearly complete nucleotide sequence of the mitogenome for the aphid species of Rhopalosiphum padi using RNA-seq plus gap filling. The 15,205 bp mitogenome included all mitochondrial genes except for trnF. The mitogenome organization and size for R. padi are similar to previously reported aphid species. In addition, the phylogenetic relationships for Hemiptera were examined using a mitogenomic dataset which included sequences from 103 ingroup species and 19 outgroup species. Our results showed that the seven species representing the Aleyrodidae exhibit extremely long branches, and always cluster with long-branched outgroups. This lead to the failure of recovering a monophyletic Hemiptera in most analyses. The data treatment of Degen-coding for protein-coding genes and the site-heterogeneous CAT model show improved suppression of the long-branch effect. Under these conditions, the Sternorrhyncha was often recovered as the most basal clade in Hemiptera.
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Affiliation(s)
- Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Shiheng An
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Xinming Yin
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Wanzhi Cai
- Department of Entomology, China Agricultural University, Beijing, China
| | - Hu Li
- Department of Entomology, China Agricultural University, Beijing, China
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Song N, Zhang H, Li H, Cai W. All 37 Mitochondrial Genes of Aphid Aphis craccivora Obtained from Transcriptome Sequencing: Implications for the Evolution of Aphids. PLoS One 2016; 11:e0157857. [PMID: 27314587 PMCID: PMC4912114 DOI: 10.1371/journal.pone.0157857] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 06/06/2016] [Indexed: 11/19/2022] Open
Abstract
The availability of mitochondrial genome data for Aphididae, one of the economically important insect pest families, in public databases is limited. The advent of next generation sequencing technology provides the potential to generate mitochondrial genome data for many species timely and cost-effectively. In this report, we used transcriptome sequencing technology to determine all the 37 mitochondrial genes of the cowpea aphid, Aphis craccivora. This method avoids the necessity of finding suitable primers for long PCRs or primer-walking amplicons, and is proved to be effective in obtaining the whole set of mitochondrial gene data for insects with difficulty in sequencing mitochondrial genome by PCR-based strategies. Phylogenetic analyses of aphid mitochondrial genome data show clustering based on tribe level, and strongly support the monophyly of the family Aphididae. Within the monophyletic Aphidini, three samples from Aphis grouped together. In another major clade of Aphididae, Pterocomma pilosum was recovered as a potential sister-group of Cavariella salicicola, as part of Macrosiphini.
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Affiliation(s)
- Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Hao Zhang
- Henan Vocational and Technological College of Communication, Zhengzhou, 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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Li YQ, Chen J, Qiao GX. Complete mitochondrial genome of the aphid Hormaphis betulae (Mordvilko) (Hemiptera: Aphididae: Hormaphidinae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:265-266. [DOI: 10.3109/19401736.2015.1118071] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Ya-Qiong Li
- College of Life Sciences, Shaanxi Normal University, Xi’an, PR China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, PR China
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, PR China
| | - Ge-Xia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, PR China
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Wang Y, Chen J, Jiang LY, Qiao GX. The Complete Mitochondrial Genome of Mindarus keteleerifoliae (Insecta: Hemiptera: Aphididae) and Comparison with Other Aphididae Insects. Int J Mol Sci 2015; 16:30091-102. [PMID: 26694371 PMCID: PMC4691162 DOI: 10.3390/ijms161226219] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 12/08/2015] [Accepted: 12/08/2015] [Indexed: 11/16/2022] Open
Abstract
The mitogenome of Mindarus keteleerifoliae Zhang (Hemiptera: Aphididae) is a 15,199 bp circular molecule. The gene order and orientation of M. keteleerifoliae is similarly arranged to that of the ancestral insect of other aphid mitogenomes, and, a tRNA isomerism event maybe identified in the mitogenome of M. keteleerifoliae. The tRNA-Trp gene is coded in the J-strand and the same sequence in the N-strand codes for the tRNA-Ser gene. A similar phenomenon was also found in the mitogenome of Eriosoma lanigerum. However, whether tRNA isomers in aphids exist requires further study. Phylogenetic analyses, using all available protein-coding genes, support Mindarinae as the basal position of Aphididae. Two tribes of Aphidinae were recovered with high statistical significance. Characteristics of the M. keteleerifoliae mitogenome revealed distinct mitogenome structures and provided abundant phylogenetic signals, thus advancing our understanding of insect mitogenomic architecture and evolution. But, because only eight complete aphid mitogenomes, including M. keteleerifoliae, were published, future studies with larger taxon sampling sizes are necessary.
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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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Wu Y, Dai R, Zhan H, Qu L. Complete mitochondrial genome of Drabescoides nuchalis (Hemiptera: Cicadellidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3626-7. [PMID: 26436567 DOI: 10.3109/19401736.2015.1079827] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome (mitogenome) of Drabescoides nuchalis (Hemiptera: Cicadellidae) was sequenced. It is 15 309 bp in length with 75.62% (A + T) content and comprises 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNA genes, and a non-coding region (GenBank accession no. KR349344). Gene order is identical to that of the inferred ancestral insect genome. All PCGs start with an ATN codon and terminate with TAA except ND4, which has an incomplete stop codon (T). The anticodons are identical to those of Drosophila yakuba. The phylogenetic tree confirms D. nuchalis and two Cicadellidae species are clustered into a clade, and Cicadellidae is a monophyletic group and provides support for the sister relationship of leafhopper and treehopper.
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Affiliation(s)
- Yunfei Wu
- a Institute of Entomology, Guizhou University; The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region , Guizhou , PR China
| | - Renhuai Dai
- a Institute of Entomology, Guizhou University; The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region , Guizhou , PR China
| | - Hongping Zhan
- a Institute of Entomology, Guizhou University; The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region , Guizhou , PR China
| | - Ling Qu
- a Institute of Entomology, Guizhou University; The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region , Guizhou , PR China
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28
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Justice JL, Weese DA, Santos SR. Phylogenetic utility, and variability in structure and content, of complete mitochondrial genomes among genetic lineages of the Hawaiian anchialine shrimp Halocaridina rubra Holthuis 1963 (Atyidae:Decapoda). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2710-8. [PMID: 26061341 DOI: 10.3109/19401736.2015.1046161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Atyidae are caridean shrimp possessing hair-like setae on their claws and are important contributors to ecological services in tropical and temperate fresh and brackish water ecosystems. Complete mitochondrial genomes have only been reported from five of the 449 species in the family, thus limiting understanding of mitochondrial genome evolution and the phylogenetic utility of complete mitochondrial sequences in the Atyidae. Here, comparative analyses of complete mitochondrial genomes from eight genetic lineages of Halocaridina rubra, an atyid endemic to the anchialine ecosystem of the Hawaiian Archipelago, are presented. Although gene number, order, and orientation were syntenic among genomes, three regions were identified and further quantified where conservation was substantially lower: (1) high length and sequence variability in the tRNA-Lys and tRNA-Asp intergenic region; (2) a 317-bp insertion between the NAD6 and CytB genes confined to a single lineage and representing a partial duplication of CytB; and (3) the putative control region. Phylogenetic analyses utilizing complete mitochondrial sequences provided new insights into relationships among the H. rubra genetic lineages, with the topology of one clade correlating to the geologic sequence of the islands. However, deeper nodes in the phylogeny lacked bootstrap support. Overall, our results from H. rubra suggest intra-specific mitochondrial genomic diversity could be underestimated across the Metazoa since the vast majority of complete genomes are from just a single individual of a species.
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Affiliation(s)
- Joshua L Justice
- a Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies , Auburn University , Auburn , AL , USA .,b Department of Microbiology , University of Alabama at Birmingham , Birmingham , AL , USA , and
| | - David A Weese
- a Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies , Auburn University , Auburn , AL , USA .,c Department of Biological and Environmental Sciences , Georgia College and State University , Milledgeville , GA , USA
| | - Scott Ross Santos
- a Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies , Auburn University , Auburn , AL , USA
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Nicholson SJ, Nickerson ML, Dean M, Song Y, Hoyt PR, Rhee H, Kim C, Puterka GJ. The genome of Diuraphis noxia, a global aphid pest of small grains. BMC Genomics 2015; 16:429. [PMID: 26044338 PMCID: PMC4561433 DOI: 10.1186/s12864-015-1525-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 04/11/2015] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The Russian wheat aphid, Diuraphis noxia Kurdjumov, is one of the most important pests of small grains throughout the temperate regions of the world. This phytotoxic aphid causes severe systemic damage symptoms in wheat, barley, and other small grains as a direct result of the salivary proteins it injects into the plant while feeding. RESULTS We sequenced and de novo assembled the genome of D. noxia Biotype 2, the strain most virulent to resistance genes in wheat. The assembled genomic scaffolds span 393 MB, equivalent to 93% of its 421 MB genome, and contains 19,097 genes. D. noxia has the most AT-rich insect genome sequenced to date (70.9%), with a bimodal CpG(O/E) distribution and a complete set of methylation related genes. The D. noxia genome displays a widespread, extensive reduction in the number of genes per ortholog group, including defensive, detoxification, chemosensory, and sugar transporter groups in comparison to the Acyrthosiphon pisum genome, including a 65% reduction in chemoreceptor genes. Thirty of 34 known D. noxia salivary genes were found in this assembly. These genes exhibited less homology with those salivary genes commonly expressed in insect saliva, such as glucose dehydrogenase and trehalase, yet greater conservation among genes that are expressed in D. noxia saliva but not detected in the saliva of other insects. Genes involved in insecticide activity and endosymbiont-derived genes were also found, as well as genes involved in virus transmission, although D. noxia is not a viral vector. CONCLUSIONS This genome is the second sequenced aphid genome, and the first of a phytotoxic insect. D. noxia's reduced gene content of may reflect the influence of phytotoxic feeding in shaping the D. noxia genome, and in turn in broadening its host range. The presence of methylation-related genes, including cytosine methylation, is consistent with other parthenogenetic and polyphenic insects. The D. noxia genome will provide an important contrast to the A. pisum genome and advance functional and comparative genomics of insects and other organisms.
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Affiliation(s)
- Scott J Nicholson
- USDA Agricultural Research Service, Stillwater, OK, 74075, USA.
- Department of Molecular Biology and Biochemistry, Oklahoma State University, Stillwater, OK, 74078, USA.
| | - Michael L Nickerson
- National Institutes of Health, National Cancer Institute, Bethesda, MD, 20892, USA.
| | - Michael Dean
- National Institutes of Health, National Cancer Institute, Bethesda, MD, 20892, USA.
| | - Yan Song
- Department of Molecular Biology and Biochemistry, Oklahoma State University, Stillwater, OK, 74078, USA.
| | - Peter R Hoyt
- Department of Molecular Biology and Biochemistry, Oklahoma State University, Stillwater, OK, 74078, USA.
| | | | | | - Gary J Puterka
- USDA Agricultural Research Service, Stillwater, OK, 74075, USA.
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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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Ma C, Wang Y, Wu C, Kang L, Liu C. The compact mitochondrial genome of Zorotypus medoensis provides insights into phylogenetic position of Zoraptera. BMC Genomics 2014; 15:1156. [PMID: 25529234 PMCID: PMC4367826 DOI: 10.1186/1471-2164-15-1156] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 12/12/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Zoraptera, generally regarded as a member of Polyneoptera, represents one of the most enigmatic insect orders. Although phylogenetic analyses based on a wide array of morphological and/or nuclear data have been performed, the position of Zoraptera is still under debate. Mitochondrial genome (mitogenome) information is commonly considered to be preferable to reconstruct phylogenetic relationships, but no efforts have been made to incorporate it in Zorapteran phylogeny. To characterize Zoraptera mitogenome features and provide insights into its phylogenetic placement, here we sequenced, for the first time, one complete mitogenome of Zoraptera and reconstructed the phylogeny of Polyneoptera. RESULTS The mitogenome of Zorotypus medoensis with an A+T content of 72.50% is composed of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a noncoding A+T-rich region. The gene content and arrangement are identical to those considered ancestral for insects. This mitogenome shows a number of very unusual features. First, it is very compact, comprising 14,572 bp, and is the smallest among all known polyneopteran mitogenomes. Second, both noncoding sequences and coding genes exhibit a significant decrease in size compared with those of other polyneopterans. Third, Z. medoensis mitogenome has experienced an accelerated substitution rate. Fourth, truncated secondary structures of tRNA genes occur with loss of dihydrouridine (DHU) arm in trnC, trnR, and trnS(AGN) and loss of TΨC arm in trnH and trnT. The phylogenetic analyses based on the mitogenome sequence information indicate that Zoraptera, represented by Z. medoensis, is recovered as sister to Embioptera. However, both Zoraptera and Embioptera exhibit very long branches in phylogenetic trees. CONCLUSIONS Characterization of Z. medoensis mitogenome contributes to our understanding of the enigmatic Zoraptera. Mitogenome data demonstrate an overall strong resolution of deep-level phylogenies of Polyneoptera but not Insecta. It is preferable to expand taxon sampling of Zoraptera and other poorly represented orders in future to break up long branches.
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Affiliation(s)
- Chuan Ma
- />State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
- />Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yeying Wang
- />State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Chao Wu
- />State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Le Kang
- />State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
- />Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101 China
| | - Chunxiang Liu
- />State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
- />Laboratory of Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
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Zhang B, Zheng J, Liang L, Fuller S, Ma CS. The complete mitochondrial genome ofSitobion avenae(Hemiptera: Aphididae). ACTA ACUST UNITED AC 2014; 27:945-6. [DOI: 10.3109/19401736.2014.926498] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Wang Y, Huang XL, Qiao GX. The complete mitochondrial genome of Cervaphis quercus (Insecta: Hemiptera: Aphididae: Greenideinae). INSECT SCIENCE 2014; 21:278-290. [PMID: 24482299 DOI: 10.1111/1744-7917.12112] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/24/2014] [Indexed: 06/03/2023]
Abstract
The mitochondrial genome of Cervaphis quercus has been sequenced and annotated. The entire genome of 15,272 bp encodes two ribosomal RNA genes (rrnL and rrnS), 22 transfer RNA (tRNA) genes, 13 protein-coding genes and a control region. The genome has the same gene order as that found in the inferred ancestral insect. Nucleotide composition is highly A+T biased. All protein-coding genes use standard mitochondrial initiation codons. Secondary structure models of the two ribosomal RNA genes of C. quercus are similar to those proposed for other insects. All tRNAs have the classic clover-leaf structure, except for the dihydrouridine (DHU) arm of trnS (AGN), which forms a simple loop. The presence of structural elements in the control region is also discussed, with an emphasis on the possible regulation of replication and/or transcription. Comparison with mitochondrial genomes of other aphid species shows their gene arrangements are conserved; however, the variety of repeat regions in species from a different aphid subfamily, Aphidinae, suggests that they resulted from independent evolutionary events.
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Affiliation(s)
- Yuan Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Beijing, China
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Huang XL, Qiao GX. Aphids as models for ecological and evolutionary studies. INSECT SCIENCE 2014; 21:247-250. [PMID: 24740744 DOI: 10.1111/1744-7917.12130] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/09/2014] [Indexed: 06/03/2023]
Affiliation(s)
- Xiao-Lei Huang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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35
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Zhang B, Edwards O, Kang L, Fuller S. A multi-genome analysis approach enables tracking of the invasion of a single Russian wheat aphid (Diuraphis noxia) clone throughout the New World. Mol Ecol 2014; 23:1940-51. [DOI: 10.1111/mec.12714] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 03/04/2014] [Accepted: 03/04/2014] [Indexed: 11/30/2022]
Affiliation(s)
- B. Zhang
- Science & Engineering Faculty; Queensland University of Technology; GPO Box 2434 Brisbane Qld 4001 Australia
- State Key Laboratory of Integrated Management of Pest Insects and Rodents; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests; Institute of Plant Protection; Chinese Academy of Agricultural Sciences; Beijing 100193 China
- Cooperative Research Centre for National Plant Biosecurity; LPO Box 5012 Bruce ACT 2617 Australia
| | - O. Edwards
- Cooperative Research Centre for National Plant Biosecurity; LPO Box 5012 Bruce ACT 2617 Australia
- CSIRO Ecosystem Sciences; Centre for Environment and Life Sciences; Underwood Avenue Floreat WA 6014 Australia
| | - L. Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - S. Fuller
- Science & Engineering Faculty; Queensland University of Technology; GPO Box 2434 Brisbane Qld 4001 Australia
- Cooperative Research Centre for National Plant Biosecurity; LPO Box 5012 Bruce ACT 2617 Australia
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