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Liu Z, Zhou T. The effect of migration on transmission of Wolbachia in Nilaparvata lugens. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:20213-20244. [PMID: 38052643 DOI: 10.3934/mbe.2023895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Brown planthopper Nilaparvata lugens, which can transmit rice ragged stunt virus, is a serious and damaging pest to rice plants. Rice plants can protect themselves from the associated diseases of N.lugens by either suppressing or replacing N.lugens by releasing N.lugens infected by a special strain of Wolbachia wStri. The long-distance migration habit of N.lugens is one of the important precursors leading up to the large-scale occurrence of N.lugens. To study the effect of migration on the transmission of Wolbachia in N.lugens, a Wolbachia spreading dynamics model with migration of N.lugens between two patches is put forward. The existence and local stability conditions of equilibrium points of the system and its subsystems are obtained. Moreover, the effects of migration on the dynamic properties and the control of N.lugens are analyzed; the results show that the system can exhibit a bistable phenomenon, and the migration can change the stability of equilibrium infected with wStri from stable to unstable. The quantitative control methods for the migration of the insect N.lugens are proposed, which provide a theoretical guidance for future field experiments. Lastly, we use the Markov chain Monte Carlo (MCMC) method to estimate the parameters of the wild N.lugens migration model based on limited observational data; the numerical simulation results show that migration can increase the quantity of N.lugens, which is consistent with the relevant experimental results.
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Affiliation(s)
- Zhigang Liu
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, Hunan, China
- College of Mathematics and Statistics, Hengyang Normal University, Hengyang, 421008, Hunan, China
- Guangzhou Center for Applied Mathematics, Guangzhou University, Guangzhou, 510006, Guangdong, China
| | - Tiejun Zhou
- College of Information and Intelligence Science, Hunan Agricultural University, Changsha, 410128, Hunan, China
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Anand R, Singh SP, Sahu N, Singh YT, Mazumdar-Leighton S, Bentur JS, Nair S. Polymorphisms in the hypervariable control region of the mitochondrial DNA differentiate BPH populations. FRONTIERS IN INSECT SCIENCE 2022; 2:987718. [PMID: 38468808 PMCID: PMC10926497 DOI: 10.3389/finsc.2022.987718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/17/2022] [Indexed: 03/13/2024]
Abstract
The brown planthopper (BPH; Nilaparvata lugens) is one of India's most destructive pests of rice. BPH, a monophagous migratory insect, reported from all major rice-growing ecosystems of the country, is capable of traversing large distances and causing massive crop loss. A crucial step for developing viable management strategies is understanding its population dynamics. Very few reliable markers are currently available to screen BPH populations for their diversity. In the current investigation, we developed a combinatorial approach using the polymorphism present within the mitochondrial Control Region of BPH and in the nuclear genome (genomic simple sequence repeats; gSSRs) to unravel the diversity present in BPH populations collected from various rice-growing regions of India. Using two specific primer pairs, the complete Control Region (1112 to 2612 bp) was PCR amplified as two overlapping fragments, cloned and sequenced from BPH individuals representing nine different populations. Results revealed extensive polymorphism within this region due to a variable number of tandem repeats. The three selected gSSR markers also exhibited population-specific amplification patterns. Overall genetic diversity between the nine populations was high (>5%). Further, in silico double-digestion of the consensus sequences of the Control Region, with HpyCH4IV and Tsp45I restriction enzymes, revealed unique restriction fragment length polymorphisms (digital-RFLPs; dRFLPs) that differentiated all the nine BPH populations. To the best of our knowledge, this is the first report of markers developed from the Control Region of the BPH mitogenome that can differentiate populations. Eventually, such reliable and rapid marker-based identification of BPH populations will pave the way for an efficient pest management strategy.
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Affiliation(s)
- Rashi Anand
- Plant-Insect Interaction Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
- Plant Biotic Interaction Lab, Department of Botany, University of Delhi, Delhi, India
| | | | - Nihar Sahu
- Agri Biotech Foundation, Hyderabad, India
| | | | | | | | - Suresh Nair
- Plant-Insect Interaction Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
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Govindharaj GPP, Babu SB, Choudhary JS, Asad M, Chidambaranathan P, Gadratagi BG, Rath PC, Naaz N, Jaremko M, Qureshi KA, Kumar U. Genome Organization and Comparative Evolutionary Mitochondriomics of Brown Planthopper, Nilaparvata lugens Biotype 4 Using Next Generation Sequencing (NGS). Life (Basel) 2022; 12:life12091289. [PMID: 36143326 PMCID: PMC9506247 DOI: 10.3390/life12091289] [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] [Received: 07/17/2022] [Revised: 08/13/2022] [Accepted: 08/15/2022] [Indexed: 11/27/2022] Open
Abstract
Nilaparvata lugens is the main rice pest in India. Until now, the Indian N. lugens mitochondrial genome has not been sequenced, which is a very important basis for population genetics and phylogenetic evolution studies. An attempt was made to sequence two examples of the whole mitochondrial genome of N. lugens biotype 4 from the Indian population for the first time. The mitogenomes of N. lugens are 16,072 and 16,081 bp long with 77.50% and 77.45% A + T contents, respectively, for both of the samples. The mitochondrial genome of N. lugens contains 37 genes, including 13 protein-coding genes (PCGs) (cox1-3, atp6, atp8, nad1-6, nad4l, and cob), 22 transfer RNA genes, and two ribosomal RNA (rrnS and rrnL) subunits genes, which are typical of metazoan mitogenomes. However, both samples of N. lugens mitogenome in the present study retained one extra copy of the trnC gene. Additionally, we also found 93 bp lengths for the atp8 gene in both of the samples, which were 60–70 bp less than that of the other sequenced mitogenomes of hemipteran insects. The phylogenetic analysis of the 19 delphacids mitogenome dataset yielded two identical topologies when rooted with Ugyops sp. in one clade, and the remaining species formed another clade with P. maidis and M. muiri being sisters to the remaining species. Further, the genus Nilaparvata formed a separate subclade with the other genera (Sogatella, Laodelphax, Changeondelphax, and Unkanodes) of Delphacidae. Additionally, the relationship among the biotypes of N. lugens was recovered as the present study samples (biotype-4) were separated from the three biotypes reported earlier. The present study provides the reference mitogenome for N. lugens biotype 4 that may be utilized for biotype differentiation and molecular-aspect-based future studies of N. lugens.
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Affiliation(s)
- Guru-Pirasanna-Pandi Govindharaj
- Division of Crop Protection, ICAR-National Rice Research Institute, Cuttack 753006, India
- Correspondence: (G.-P.-P.G.); (J.S.C.); (U.K.)
| | - Soumya Bharti Babu
- Division of Crop Protection, ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Jaipal Singh Choudhary
- ICAR-Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi 834010, India
- Correspondence: (G.-P.-P.G.); (J.S.C.); (U.K.)
| | - Muhammad Asad
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | | | - Basana-Gowda Gadratagi
- Division of Crop Protection, ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Prakash Chandra Rath
- Division of Crop Protection, ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Naiyar Naaz
- ICAR-Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi 834010, India
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Kamal Ahmad Qureshi
- Department of Pharmaceutics, Unaizah College of Pharmacy, Qassim University, Unaizah 51911, Saudi Arabia
| | - Uttam Kumar
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (G.-P.-P.G.); (J.S.C.); (U.K.)
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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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Mu YL, Zhang CH, Zhang YJ, Yang L, Chen XS. Characterizing the Complete Mitochondrial Genome of Arma custos and Picromerus lewisi (Hemiptera: Pentatomidae: Asopinae) and Conducting Phylogenetic Analysis. JOURNAL OF INSECT SCIENCE (ONLINE) 2022; 22:6510058. [PMID: 35039857 PMCID: PMC8763613 DOI: 10.1093/jisesa/ieab105] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Indexed: 05/30/2023]
Abstract
We characterized the mitochondrial genome (mitogenome) and conducted phylogenetic analyses of 48 Hemiptera species by sequencing and analyzing the mitogenome of Arma custos (Fabricius) and Picromerus lewisi (Scott). The complete mitogenomes of the two predators were 16,024 bp and 19,587 bp in length, respectively, and it contained 37 classical genes, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs), and a control region. Most PCGs in these predators use ATN as the start codon. This research revealed that the genes of the two natural enemy species have an A + T content of 75.40% and all tRNAs have a typical cloverleaf structure, with the exception of trnS1, which lacks a dihydrouridine arm. This is the first study to compare the mitochondrial genetic structure of two predatory insects; the mitochondrial genetic structure of individual predatory insects has been sequenced in previous studies. Here, phylogenetic analysis on the basis of amino acid and nucleotide sequences of 13 mitochondrial PCGs using Bayesian inference and maximum likelihood methods were conducted to generate similar tree topologies, which suggested that the two predators with close genetic relationships belong to Asopinae subfamily. Furthermore, the monophyly of the Pentatomoidea superfamily is well accepted despite limited taxon and species sampling. Finally, their complete mitogenome provided data to establish a predator-prey food web, which is the foundation of effective pest management. Our results also enhanced the database of natural enemy insects.
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Affiliation(s)
- Yin-Lin Mu
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang, Guizhou 550025, China
- The Provincial Special Key Laboratory for Development and Utilization of Insect Resources of Guizhou, Guizhou University, Guiyang, Guizhou 550025, China
| | - Chang-Hua Zhang
- Guizhou Tobacco Company Zunyi Branch, Zunyi, Guizhou 563000, China
| | - Yu-Jie Zhang
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, China
| | - Lin Yang
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang, Guizhou 550025, China
- The Provincial Special Key Laboratory for Development and Utilization of Insect Resources of Guizhou, Guizhou University, Guiyang, Guizhou 550025, China
| | - Xiang-Sheng Chen
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang, Guizhou 550025, China
- The Provincial Special Key Laboratory for Development and Utilization of Insect Resources of Guizhou, Guizhou University, Guiyang, Guizhou 550025, China
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A New Mitochondrial Genome of Sogatella furcifera (Horváth) (Hemiptera: Delphacidae) and Mitogenome-Wide Investigation on Polymorphisms. INSECTS 2021; 12:insects12121066. [PMID: 34940154 PMCID: PMC8706918 DOI: 10.3390/insects12121066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 11/16/2021] [Accepted: 11/25/2021] [Indexed: 01/23/2023]
Abstract
Simple Summary We completed one mitogenome of white-backed planthopper (WBPH), Sogatella furcifera (Horváth), with finding heteroplasmy phenomenon confirmed by PCR reaction and Sanger sequencing method. This heteroplasmy was not observed in WBPHs (n = 24) collected from the fields, suggesting that it may be uncommon in fields. We also analyzed single nucleotide polymorphisms, insertion and deletions, and simple sequence repeats among three currently available WBPH mitogenomes of Korea and China, suggesting that identified intraspecific variations could be potential candidates for developing markers to distinguish geographical populations of WBPH including Korean and Chinese. Phylogenetic analysis of 32 mitogenomes of Delphacidae including the three WBPH mitogenomes suggested that Delphacinae seems to be monophyletic and Sogatella species including WBPH are clearly formed as one clade. Abstract White-backed planthopper (WBPH), Sogatella furcifera (Horváth), is one of the major sap-sucking rice pests in East Asia. We have determined a new complete mitochondrial genome of WBPH collected in the Korean peninsula using NGS technology. Its length and GC percentages are 16,613 bp and 23.8%, respectively. We observed one polymorphic site, a non-synonymous change, in the COX3 gene with confirmation heteroplasmy phenomenon within individuals of WBPH by PCR amplification and Sanger sequencing, the first report in this species. In addition, this heteroplasmy was not observed in wild WBPH populations, suggesting that it may be uncommon in fields. We analyzed single nucleotide polymorphisms, insertion, and deletions, and simple sequence repeats among the three WBPH mitogenomes from Korea and China and found diverse intraspecific variations, which could be potential candidates for developing markers to distinguish geographical populations. Phylogenetic analysis of 32 mitogenomes of Delphacidae including the three WBPH mitogenomes suggested that Delphacinae seems to be monophyletic and Sogatella species including WBPH are clearly formed as one clade. In the future, it is expected that complete mitogenomes of individuals of geographically dispersed WBPH populations will be used for further population genetic studies to understand the migration pathway of WBPH.
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Gong N, Yang L, Chen X. Comparative analysis of twelve mitogenomes of Caliscelidae (Hemiptera: Fulgoromorpha) and their phylogenetic implications. PeerJ 2021; 9:e12465. [PMID: 34820192 PMCID: PMC8603831 DOI: 10.7717/peerj.12465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/19/2021] [Indexed: 12/03/2022] Open
Abstract
Here, the complete mitochondrial genomes (mitogenomes) of 12 Caliscelidae species, Augilina tetraina, Augilina triaina, Symplana brevistrata, Symplana lii, Neosymplana vittatum, Pseudosymplanella nigrifasciata, Symplanella brevicephala, Symplanella unipuncta, Augilodes binghami, Cylindratus longicephalus, Caliscelis shandongensis, and Peltonotellus sp., were determined and comparatively analyzed. The genomes varied from 15,424 to 16,746 bp in size, comprising 37 mitochondrial genes and an A+T-rich region. The typical gene content and arrangement were similar to those of most Fulgoroidea species. The nucleotide compositions of the mitogenomes were biased toward A/T. All protein-coding genes (PCGs) started with a canonical ATN or GTG codon and ended with TAN or an incomplete stop codon, single T. Among 13 PCGs in 16 reported Caliscelidae mitogenomes, cox1 and atp8 showed the lowest and highest nucleotide diversity, respectively. All PCGs evolved under purifying selection, with atp8 considered a comparatively fast-evolving gene. Phylogenetic relationships were reconstructed based on 13 PCGs in 16 Caliscelidae species and five outgroups using maximum likelihood and Bayesian inference analyses. All species of Caliscelidae formed a steadily monophyletic group with high support. Peltonotellini was present at the basal position of the phylogenetic tree. Augilini was the sister group to Caliscelini and Peltonotellini.
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Affiliation(s)
- Nian Gong
- Guizhou University, Institute of Entomology, Guiyang, Guizhou, China
- Guizhou University, The Provincial Special Key Laboratory for Development and Utilization of Insect Resources, Guiyang, Guizhou, China
- Guizhou University, The Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Guiyang, Guizhou, China
| | - Lin Yang
- Guizhou University, Institute of Entomology, Guiyang, Guizhou, China
- Guizhou University, The Provincial Special Key Laboratory for Development and Utilization of Insect Resources, Guiyang, Guizhou, China
- Guizhou University, The Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Guiyang, Guizhou, China
| | - Xiangsheng Chen
- Guizhou University, Institute of Entomology, Guiyang, Guizhou, China
- Guizhou University, The Provincial Special Key Laboratory for Development and Utilization of Insect Resources, Guiyang, Guizhou, China
- Guizhou University, The Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Guiyang, Guizhou, China
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Wang W, Zhang H, Constant J, Bartlett CR, Qin D. Characterization, Comparative Analysis and Phylogenetic Implications of Mitogenomes of Fulgoridae (Hemiptera: Fulgoromorpha). Genes (Basel) 2021; 12:genes12081185. [PMID: 34440359 PMCID: PMC8394797 DOI: 10.3390/genes12081185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023] Open
Abstract
The complete mitogenomes of nine fulgorid species were sequenced and annotated to explore their mitogenome diversity and the phylogenetics of Fulgoridae. All species are from China and belong to five genera: Dichoptera Spinola, 1839 (Dichoptera sp.); Neoalcathous Wang and Huang, 1989 (Neoalcathous huangshanana Wang and Huang, 1989); Limois Stål, 1863 (Limois sp.); Penthicodes Blanchard, 1840 (Penthicodes atomaria (Weber, 1801), Penthicodes caja (Walker, 1851), Penthicodes variegata (Guérin-Méneville, 1829)); Pyrops Spinola, 1839 (Pyrops clavatus (Westwood, 1839), Pyrops lathburii (Kirby, 1818), Pyrops spinolae (Westwood, 1842)). The nine mitogenomes were 15,803 to 16,510 bp in length with 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and a control region (A + T-rich region). Combined with previously reported fulgorid mitogenomes, all PCGs initiate with either the standard start codon of ATN or the nonstandard GTG. The TAA codon was used for termination more often than the TAG codon and the incomplete T codon. The nad1 and nad4 genes varied in length within the same genus. A high percentage of F residues were found in the nad4 and nad5 genes of all fulgorid mitogenomes. The DHU stem of trnV was absent in the mitogenomes of all fulgorids sequenced except Dichoptera sp. Moreover, in most fulgorid mitogenomes, the trnL2, trnR, and trnT genes had an unpaired base in the aminoacyl stem and trnS1 had an unpaired base in the anticodon stem. The similar tandem repeat regions of the control region were found in the same genus. Phylogenetic analyses were conducted based on 13 PCGs and two rRNA genes from 53 species of Fulgoroidea and seven outgroups. The Bayesian inference and maximum likelihood trees had a similar topological structure. The major results show that Fulgoroidea was divided into two groups: Delphacidae and ((Achilidae + (Lophopidae + (Issidae + (Flatidae + Ricaniidae)))) + Fulgoridae). Furthermore, the monophyly of Fulgoridae was robustly supported, and Aphaeninae was divided into Aphaenini and Pyropsini, which includes Neoalcathous, Pyrops, Datua Schmidt, 1911, and Saiva Distant, 1906. The genus Limois is recovered in the Aphaeninae, and the Limoisini needs further confirmation; Dichoptera sp. was the earliest branch in the Fulgoridae.
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Affiliation(s)
- Wenqian Wang
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Xianyang 712100, China; (W.W.); (H.Z.)
| | - Huan Zhang
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Xianyang 712100, China; (W.W.); (H.Z.)
| | - Jérôme Constant
- O.D. Phylogeny and Taxonomy, Entomology, Royal Belgian Institute of Natural Sciences, Vautier Street 29, 1000 Brussels, Belgium;
| | - Charles R. Bartlett
- Department of Entomology and Wildlife Ecology, University of Delaware, 250 Townsend Hall, 531 S. College Ave., Newark, DE 9716-2160, USA;
| | - Daozheng Qin
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Xianyang 712100, China; (W.W.); (H.Z.)
- Correspondence:
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Lin S, Huang M, Zhang Y. Structural Features and Phylogenetic Implications of 11 New Mitogenomes of Typhlocybinae (Hemiptera: Cicadellidae). INSECTS 2021; 12:678. [PMID: 34442244 PMCID: PMC8396557 DOI: 10.3390/insects12080678] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/18/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023]
Abstract
To explore the characteristics of mitogenomes and discuss the phylogenetic relationships and molecular evolution of the six tribes within Typhlocybinae, 11 complete mitogenomes are newly sequenced and comparatively analyzed. In all of these complete mitogenomes, the number and order of the genes are highly conserved in overall organization. The PCGs initiate with ATN/TTG/GTG and terminate with TAA/TAG/T. Almost all tRNAs are folded into the typical clover-leaf secondary structure. The control region is always variable in length and in numbers of multiple tandem repeat units. The atp8 and nad2 exhibits the highest evolution rate among all the PCGs. Phylogenetic analyses based on whole mitogenome sequences, with three different datasets, using both maximum likelihood and Bayesian methods, indicate the monophyly of Typhlocybinae and its inner tribes, respectively, except for Typhlocybini and Zyginellini that are paraphyletic. Finally, we confirm that Erythroneurini is a subtribe of Dikraneurini.
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Affiliation(s)
| | | | - Yalin Zhang
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Entomological Museum, College of Plant Protection, Northwest A&F University, Yangling 712100, China; (S.L.); (M.H.)
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Ye F, Li H, Xie Q. Mitochondrial Genomes from Two Specialized Subfamilies of Reduviidae (Insecta: Hemiptera) Reveal Novel Gene Rearrangements of True Bugs. Genes (Basel) 2021; 12:1134. [PMID: 34440308 PMCID: PMC8392325 DOI: 10.3390/genes12081134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/11/2021] [Accepted: 07/22/2021] [Indexed: 11/16/2022] Open
Abstract
Reduviidae, a hyper-diverse family, comprise 25 subfamilies with nearly 7000 species and include many natural enemies of crop pests and vectors of human disease. To date, 75 mitochondrial genomes (mitogenomes) of assassin bugs from only 11 subfamilies have been reported. The limited sampling of mitogenome at higher categories hinders a deep understanding of mitogenome evolution and reduviid phylogeny. In this study, the first mitogenomes of Holoptilinae (Ptilocnemus lemur) and Emesinae (Ischnobaenella hainana) were sequenced. Two novel gene orders were detected in the newly sequenced mitogenomes. Combined 421 heteropteran mitogenomes, we identified 21 different gene orders and six gene rearrangement units located in three gene blocks. Comparative analyses of the diversity of gene order for each unit reveal that the tRNA gene cluster trnI-trnQ-trnM is the hotspot of heteropteran gene rearrangement. Furthermore, combined analyses of the gene rearrangement richness of each unit and the whole mitogenome among heteropteran lineages confirm Reduviidae as a 'hot-spot group' of gene rearrangement in Heteroptera. The phylogenetic analyses corroborate the current view of phylogenetic relationships between basal groups of Reduviidae with high support values. Our study provides deeper insights into the evolution of mitochondrial gene arrangement in Heteroptera and the early divergence of reduviids.
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Affiliation(s)
- Fei Ye
- Department of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Qiang Xie
- Department of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
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11
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Lv SS, Zhang YJ, Gong N, Chen XS. Characterization and Phylogenetic Analysis of the Mitochondrial Genome Sequence of Nisia fuliginosa (Hemiptera: Fulgoroidea: Meenoplidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2021; 21:8. [PMID: 34327530 PMCID: PMC8322432 DOI: 10.1093/jisesa/ieab050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Indexed: 06/13/2023]
Abstract
We explored characterization of the mitochondrial genome (mitogenome or mtGenome) and phylogenetic analysis between 32 Fulgoroid species by sequencing and analyzing the mitogenome of Nisia fuliginosa Yang and Hu, 1985 (Hemiptera: Fulgoroidea: Meenoplidae), thereby making it the first determined mitogenome from the family Meenoplidae. The mitogenome was found to be 15,754 bp in length and contained 13 protein-coding genes (PCGs), 22 tRNA genes, two ribosomal RNA genes (rRNAs), and a control region. All PCGs started with typical ATN codons, except for nad1, which used GTG as the start codon. Canonical TAA termination codons were found in 10 PCGs and the remaining three genes (cox2, nad6, and nad1) had incomplete stop codons T. All tRNAs could fold into typical cloverleaf secondary structures, with the exception of trnC, trnV, and trnS1. Additionally, we compared the AT and GC skews of 13 PCGs of 32 Fulgoroidea mitogenomes, on the L-strand, the AT and GC skews were negative and positive, respectively. However, on the H-strand, the AT skew could be positive or negative and the GC skew was always negative. Phylogenetic results showed that the eight families of Fulgoroidea were divided into two large groups. Delphacidae formed a monophyletic group sister to a clade comprising Meenoplidae and other six families (Fulgoridae, Ricaniidae, Flatidae, Issidae, Caliscelidae, and Achilidae). Meenoplidae was located near the clade of Delphacidae, and Fulgoridae was located near the clade of Meenoplidae. Furthermore, Caliscelidae, Issidae, Ricaniidae, and Flatidae are closely related and they collectively formed a sister group to Achilidae.
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Affiliation(s)
| | - Yu-Jie Zhang
- Institute of Entomology and Special Key Laboratory for Development and Utilization of Insect Resources of Guizhou, Guizhou University, Guiyang 550025, China
| | - Nian Gong
- Institute of Entomology and Special Key Laboratory for Development and Utilization of Insect Resources of Guizhou, Guizhou University, Guiyang 550025, China
| | - Xiang-Sheng Chen
- Institute of Entomology and Special Key Laboratory for Development and Utilization of Insect Resources of Guizhou, Guizhou University, Guiyang 550025, China
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12
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Ai D, Peng L, Qin D, Zhang Y. Characterization of Three Complete Mitogenomes of Flatidae (Hemiptera: Fulgoroidea) and Compositional Heterogeneity Analysis in the Planthoppers' Mitochondrial Phylogenomics. Int J Mol Sci 2021; 22:ijms22115586. [PMID: 34070437 PMCID: PMC8197536 DOI: 10.3390/ijms22115586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
Although sequences of mitogenomes have been widely used for investigating phylogenetic relationship, population genetics, and biogeography in many members of Fulgoroidea, only one complete mitogenome of a member of Flatidae has been sequenced. Here, the complete mitogenomes of Cerynia lineola, Cromna sinensis, and Zecheuna tonkinensis are sequenced. The gene arrangements of the three new mitogenomes are consistent with ancestral insect mitogenomes. The strategy of using mitogenomes in phylogenetics remains in dispute due to the heterogeneity in base composition and the possible variation in evolutionary rates. In this study, we found compositional heterogeneity and variable evolutionary rates among planthopper mitogenomes. Phylogenetic analysis based on site-homogeneous models showed that the families (Delphacidae and Derbidae) with high values of Ka/Ks and A + T content tended to fall together at a basal position on the trees. Using a site-heterogeneous mixture CAT + GTR model implemented in PhyloBayes yielded almost the same topology. Our results recovered the monophyly of Fulgoroidea. In this study, we apply the heterogeneous mixture model to the planthoppers’ phylogenetic analysis for the first time. Our study is based on a large sample and provides a methodological reference for future phylogenetic studies of Fulgoroidea.
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Affiliation(s)
- Deqiang Ai
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of
Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China;
| | - Lingfei Peng
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fujian
Ag-riculture and Forestry University, Fuzhou 350002, Fujian, China;
| | - Daozheng Qin
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of
Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China;
- Correspondence: (D.Q.); (Y.Z.)
| | - Yalin Zhang
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of
Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China;
- Correspondence: (D.Q.); (Y.Z.)
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13
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Tang J, Huang W, Zhang Y. The Complete Mitochondrial Genome of Four Hylicinae (Hemiptera: Cicadellidae): Structural Features and Phylogenetic Implications. INSECTS 2020; 11:E869. [PMID: 33297415 PMCID: PMC7762291 DOI: 10.3390/insects11120869] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/04/2020] [Accepted: 12/04/2020] [Indexed: 02/02/2023]
Abstract
To reveal mtgenome characterizations and reconstruct phylogenetic relationships of Hylicinae, the complete mtgenomes of four hylicine species, including Nacolus tuberculatus, Hylica paradoxa, Balala fujiana, and Kalasha nativa, were sequenced and comparatively analyzed for the first time. We also carried out the richest (11) subfamily sampling of Cicadellidae to date, and reconstructed phylogenetic relationships of Membracoidea among 61 species based on three datasets using maximum likelihood and Bayesian inference analyses. All new sequenced mtgenomes are molecules ranging from 14,918 to 16,221 bp in length and are double stranded, circular in shape. The gene composition and arrangement of these mtgenomes are consistent with members of Membracoidea. Among 13 protein-coding genes, most show typical ATN start codons and TAR (TAA/TAG) or an incomplete stop codon T-, and several genes start by TTG/GTG. Results of the analysis for sliding window, nucleotide diversity, and nonsynonymous substitution/synonymous substitution indicate cox1 is a comparatively slower-evolving gene while atp8 is the fastest gene. In line with previous researches, phylogenetic results indicate that treehopper families are paraphyletic with respect to family Cicadellidae and also support the monophyly of all involved subfamilies including Hylicinae. Relationships among the four hylicine genera were recovered as (Hylica + (Nacolus + (Balala + Kalasha))).
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Affiliation(s)
| | | | - Yalin Zhang
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Entomological Museum, College of Plant Protection, Northwest A&F University, Yangling 712100, China; (J.T.); (W.H.)
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14
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Zhou X, Dietrich CH, Huang M. Characterization of the Complete Mitochondrial Genomes of Two Species with Preliminary Investigation on Phylogenetic Status of Zyginellini (Hemiptera: Cicadellidae: Typhlocybinae). INSECTS 2020; 11:E684. [PMID: 33050478 PMCID: PMC7600600 DOI: 10.3390/insects11100684] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 09/28/2020] [Accepted: 10/06/2020] [Indexed: 11/16/2022]
Abstract
To explore the characteristics of mitogenomes and reveal phylogenetic relationships of the tribes of Zyginellini and Typhlocybini in Typhlocybinae, mitogenomes of two species of the Zyginellini, Parazyginella tiani and Limassolla sp., were sequenced. Mitogenomes of both species contain 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a large non-coding region (A + T-rich region). These characteristics are similar to other Membracoidea mitogenomes. All PCGs initiate with the standard start codon of ATN and terminate with the complete stop codon of TAA/G or with an incomplete T codon. All tRNAs have the typical clover-leaf structure, except trnS1 which has a reduced DHU arm and the acceptor stem of trnR is 5 or 6 bp in some species, an unusual feature here reported for the first time in Typhlocybinae. The A + T-rich region is highly variable in length and in numbers of tandem repeats present. Our analyses indicate that nad6 and atp6 exhibit higher evolutionary rates compared to other PCGs. Phylogenetic analyses by both maximum likelihood and Bayesian methods based on 13 protein-coding genes of 12 species of Typhlocybinae suggest that Zyginellini are paraphyletic with respect to Typhlocybini.
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Affiliation(s)
- Xian Zhou
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Entomological Museum, Northwest A&F University, Yangling 712100, Shaanxi, China;
| | - Christopher H. Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, 1816 S. Oak St., Champaign, IL 61820, USA;
| | - Min Huang
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Entomological Museum, Northwest A&F University, Yangling 712100, Shaanxi, China;
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15
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Stable Introduction of Plant-Virus-Inhibiting Wolbachia into Planthoppers for Rice Protection. Curr Biol 2020; 30:4837-4845.e5. [PMID: 33035486 DOI: 10.1016/j.cub.2020.09.033] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/19/2020] [Accepted: 09/09/2020] [Indexed: 01/15/2023]
Abstract
Progress has been made in developing the maternally inherited endosymbiotic bacterium Wolbachia as a tool for protecting humans from mosquito-borne diseases. In contrast, Wolbachia-based approaches have not yet been developed for the protection of plants from insect pests and their associated diseases, with a major challenge being the establishment of artificial Wolbachia infections expressing desired characteristics in the hemipterans that transmit the majority of plant viruses. Here, we report stable introduction of Wolbachia into the brown planthopper, Nilaparvata lugens, the most destructive rice pest that annually destroys millions of hectares of staple crops. The Wolbachia strain wStri from the small brown planthopper, Laodelphax striatellus, was transferred to this new host, where it showed high levels of cytoplasmic incompatibility, enabling rapid invasion of laboratory populations. Furthermore, wStri inhibited infection and transmission of Rice ragged stunt virus and mitigated virus-induced symptoms in rice plants, opening up the development of Wolbachia-based strategies against major agricultural pests and their transmitted pathogens. VIDEO ABSTRACT.
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16
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Lu C, Huang X, Deng J. The challenge of Coccidae (Hemiptera: Coccoidea) mitochondrial genomes: The case of Saissetia coffeae with novel truncated tRNAs and gene rearrangements. Int J Biol Macromol 2020; 158:854-864. [PMID: 32387610 DOI: 10.1016/j.ijbiomac.2020.04.257] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 04/26/2020] [Accepted: 04/27/2020] [Indexed: 11/23/2022]
Abstract
There have been few reports of complete mitochondrial genomes (mitogenomes) of scale insects, and it has been indicated that complex and novel structures in their mitogenomes may lead to difficulties in sequencing, assembly and annotation. Transfer RNAs (tRNAs) usually possess typical cloverleaf secondary structures, and truncated tRNAs are rarely found in insect mitogenomes. Here, we report a complete Saissetia coffeae mitogenome (15,389 bp) with high A+T content (84.7%) sequenced by next-generation sequencing (NGS) methods. Genes in the mitogenome were annotated, and nine tRNAs were not found using MITOS. Most of the detected tRNAs were significantly truncated without the dihydrouridine (DHU) arm or the TΨC (T) arm. In addition, the 9 "lost" tRNAs containing mismatched base pairs were retrieved based on the tRNA annotation workflow for Coccidae described in our study. The gene arrangement in the Saissetia coffeae mitogenome was significantly different from that in other hemipteran insects. Additionally, Bayesian and maximum likelihood trees based on the mitochondrial genes showed a long branch of the Saissetia lineage, indicating significant nonsynonymous substitutions or high evolutionary rates in the Saissetia lineage. We provide a reference mitogenome for the assembly and annotation of the Coccidae mitogenome and offer insights into the evolution of scale insects.
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Affiliation(s)
- 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
| | - 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
| | - Jun Deng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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17
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Yu X, Tan W, Zhang H, Jiang W, Gao H, Wang W, Liu Y, Wang Y, Tian X. Characterization of the Complete Mitochondrial Genome of Harpalus sinicus and Its Implications for Phylogenetic Analyses. Genes (Basel) 2019; 10:E724. [PMID: 31540431 PMCID: PMC6771156 DOI: 10.3390/genes10090724] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/12/2019] [Accepted: 09/13/2019] [Indexed: 01/13/2023] Open
Abstract
In this study, we report the complete mitochondrial genome of Harpalus sinicus (occasionally named as the Chinese ground beetle) which is the first mitochondrial genome for Harpalus. The mitogenome is 16,521 bp in length, comprising 37 genes, and a control region. The A + T content of the mitogenome is as high as 80.6%. A mitochondrial origins of light-strand replication (OL)-like region is found firstly in the insect mitogenome, which can form a stem-loop hairpin structure. Thirteen protein-coding genes (PCGs) share high homology, and all of them are under purifying selection. All tRNA genes (tRNAs) can be folded into the classic cloverleaf secondary structures except tRNA-Ser (GCU), which lacks a dihydrouridine (DHU) stem. The secondary structure of two ribosomal RNA genes (rRNAs) is predicted based on previous insect models. Twelve types of tandem repeats and two stem-loop structures are detected in the control region, and two stem-loop structures may be involved in the initiation of replication and transcription. Additionally, phylogenetic analyses based on mitogenomes suggest that Harpalus is an independent lineage in Carabidae, and is closely related to four genera (Abax, Amara, Stomis, and Pterostichus). In general, this study provides meaningful genetic information for Harpalus sinicus and new insights into the phylogenetic relationships within the Carabidae.
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Affiliation(s)
- Xiaolei Yu
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Wei Tan
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Huanyu Zhang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Weiling Jiang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Han Gao
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Wenxiu Wang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yuxia Liu
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yu Wang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Xiaoxuan Tian
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
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18
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The complete mitochondrial genome of Eterusia aedea (Lepidoptera, Zygaenidae) and comparison with other zygaenid moths. Genomics 2019; 111:1043-1052. [DOI: 10.1016/j.ygeno.2018.06.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 06/23/2018] [Accepted: 06/27/2018] [Indexed: 11/22/2022]
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19
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Wang W, Huang Y, Bartlett CR, Zhou F, Meng R, Qin D. Characterization of the complete mitochondrial genomes of two species of the genus Aphaena Guérin-Méneville (Hemiptera: Fulgoridae) and its phylogenetic implications. Int J Biol Macromol 2019; 141:29-40. [PMID: 31470055 DOI: 10.1016/j.ijbiomac.2019.08.222] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/19/2019] [Accepted: 08/26/2019] [Indexed: 12/27/2022]
Abstract
The complete mitochondrial genomes (mitogenomes) of Aphaena (Callidepsa) amabilis and Aphaena (Aphaena) discolor nigrotibiata were sequenced. The mitogenomes of these two species are 16,237 bp and 16,116 bp in length with an A + T content of 77.9% and 77.0%, respectively. Each contains 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a control region (A + T-rich region). All PCGs initiate with the standard start codon of ATN and terminate with the complete stop codon of TAA or TAG except for atp6, where nad1 ends with an incomplete T codon. All tRNAs have the typical clover-leaf structure except for trnS1 and trnV which have a reduced DHU arm. Moreover, these two mitogenomes have trnL2, trnR and trnT with an unpaired base in the acceptor stem. The putative A + T-rich region includes multiple types of tandem repeat regions. These phylogenetic analyses are reconstructed based on 13 protein-coding genes of 25 auchenorrhynchan mitogenomes, with both maximum likelihood and Bayesian analyses yielding robust identical phylogenetic trees. These results support a monophyletic Auchenorrhyncha and the relationship (Pyrops + (Lycorma + Aphaena)) within Fulgoridae.
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Affiliation(s)
- Wenqian Wang
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yixin Huang
- Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Charles R Bartlett
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, DE 19716, USA
| | - Fanmei Zhou
- Wuzhishan National Nature Reserve, Zhou Fanmei Photographic Art Gallery, Wuzhishan, Hainan 572200, China
| | - Rui Meng
- Post-Entry Quarantine Station for Tropical Plant, Haikou Customs District, Haikou, Hainan 570105, China
| | - Daozheng Qin
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi 712100, China.
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20
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Huang YX, Ren FJ, Bartlett CR, Wei YS, Qin DZ. Contribution to the mitogenome diversity in Delphacinae: Phylogenetic and ecological implications. Genomics 2019; 112:1363-1370. [PMID: 31421209 DOI: 10.1016/j.ygeno.2019.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/20/2019] [Accepted: 08/10/2019] [Indexed: 11/26/2022]
Abstract
We document the complete (or nearly complete) mitogenomes of 20 Delphacidae taxa, and together with 17 other delphacid mitogenomes currently in GenBank, to reconstruct the phylogeny of the Delphacinae and to investigate mitogenome differences among members of Delphacini, Tropidocephalini and Saccharosydnini. The mitogenomes of the 20 species encode the complete set of 37 genes usually found in animal mitogenomes. The length of complete mitogenomes in Delphacinae ranges from 15,531 to 16,231 bp. The gene order of all newly sequenced mitogenomes are identical, and the mitogenome gene order of Stenocranus matsumurai Metcalf in Stenocraninae has a transposition of tRNAThr. The two-clade system in Tropidocephalini was supported with high value (PP = 1, BS = 100), and the monophyly of Bambusiphaga was recovered in this study. Finally, we found that the host shift from plants with a C3 to a C4 photosynthetic pathway appears to have occurred independently in several clades.
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Affiliation(s)
- Yi-Xin Huang
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Feng-Juan Ren
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Charles R Bartlett
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, DE 19716, USA.
| | - Yong-Sheng Wei
- College of Life Science, Northwest A&F University, Yangling 712100, China
| | - Dao-Zheng Qin
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi 712100, China.
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21
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Park J, Jung JK, Ho Koh Y, Park J, Seo BY. The complete mitochondrial genome of Laodelphax striatellus (Fallén, 1826) (Hemiptera: Delphacidae) collected in a mid-Western part of Korean peninsula. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2229-2230. [PMID: 33365487 PMCID: PMC7687552 DOI: 10.1080/23802359.2019.1623112] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Laodelphax striatellus (Fallén, 1826) is one of key rice pests in Northeast Asia. We have determined the mitochondrial genome of L. striatellus collected in a mid-western part of Korean peninsula. The circular mitogenome of L. striatellus is 16,359 bp long including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 1,972 bp. The base composition was AT-biased (77.3%). In comparison of the two Chinese L. striatellus mitogenomes with Korean mitogenome, total 140 and 40 single nucleotide polymorphisms and 166 and 118 insertions and deletions were identified, presenting intra-species variations based on geographical distribution.
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Affiliation(s)
- Jongsun Park
- Infoboss Co., Ltd., Seoul, Republic of Korea.,InfoBoss Research Center, Seoul, Republic of Korea
| | - Jin Kyo Jung
- Department of Central Area Crop Science, National Institute of Crop Science, Suwon, Republic of Korea
| | - Young Ho Koh
- Ilsong Institute of Life Science, Hallym University, Anyang, Republic of Korea
| | - Jonghyun Park
- Infoboss Co., Ltd., Seoul, Republic of Korea.,InfoBoss Research Center, Seoul, Republic of Korea
| | - Bo Yoon Seo
- Crop Protection Division, National Institute of Agricultural Sciences, RDA, Wanju, Republic of Korea
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22
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Seo BY, Jung JK, Ho Koh Y, Park J. The complete mitochondrial genome of Laodelphax striatellus (Fallén, 1826) (Hemiptera: Delphacidae) collected in a southern part of Korean peninsula. Mitochondrial DNA B Resour 2019; 4:2242-2243. [PMID: 33365493 PMCID: PMC7687393 DOI: 10.1080/23802359.2019.1624645] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 05/17/2019] [Indexed: 11/12/2022] Open
Abstract
A 16,359 bp mitochondrial genome of Laodelphax striatellus collected in a southern part of Korean peninsula was completed and their intraspecies variations were compared with Korean and Chinese L. striatellus mitogenomes. The circular mitogenome of L. striatellus contains 13 protein-coding genes, two rRNA genes, 22 tRNAs, and a single large non-coding region of 1,972 bp. The base composition was AT-biased (77.3%). It has only one single nucleotide polymorphism (SNP) in AT-rich region compared to other Korean mitogenome, but total 41 and 141 SNPs and 118 and 166 insertions and deletions, respectively, compared to two Chinese mitogenomes, suggesting the possibility of tracing migration based on geographic genetic diversity.
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Affiliation(s)
- Bo Yoon Seo
- Crop Protection Division, National Institute of Agricultural Sciences, RDA, Wanju, Republic of Korea
| | - Jin Kyo Jung
- Department of Central Area Crop Science, National Institute of Crop Science, Suwon, Republic of Korea
| | - Young Ho Koh
- Ilsong Institute of Life Science, Hallym University, Anyang, Republic of Korea
| | - Jongsun Park
- Infoboss Co., Ltd., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
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23
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Sun JT, Duan XZ, Hoffmann AA, Liu Y, Garvin MR, Chen L, Hu G, Zhou JC, Huang HJ, Xue XF, Hong XY. Mitochondrial variation in small brown planthoppers linked to multiple traits and probably reflecting a complex evolutionary trajectory. Mol Ecol 2019; 28:3306-3323. [PMID: 31183910 DOI: 10.1111/mec.15148] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 05/24/2019] [Accepted: 05/31/2019] [Indexed: 12/27/2022]
Abstract
While it has been proposed in several taxa that the mitochondrial genome is associated with adaptive evolution to different climatic conditions, making links between mitochondrial haplotypes and organismal phenotypes remains a challenge. Mitonuclear discordance occurs in the small brown planthopper (SBPH), Laodelphax striatellus, with one mitochondrial haplogroup (HGI) more common in the cold climate region of China relative to another form (HGII) despite strong nuclear gene flow, providing a promising model to investigate climatic adaptation of mitochondrial genomes. We hypothesized that cold adaptation through HGI may be involved, and considered mitogenome evolution, population genetic analyses, and bioassays to test this hypothesis. In contrast to our hypothesis, chill-coma recovery tests and population genetic tests of selection both pointed to HGII being involved in cold adaptation. Phylogenetic analyses revealed that HGII is nested within HGI, and has three nonsynonymous changes in ND2, ND5 and CYTB in comparison to HGI. These molecular changes likely increased mtDNA copy number, cold tolerance and fecundity of SBPH, particularly through a function-altering amino acid change involving M114T in ND2. Nuclear background also influenced fecundity and chill recovery (i.e., mitonuclear epistasis) and protein modelling indicates possible nuclear interactions for the two nonsynonymous changes in ND2 and CYTB. The high occurrence frequency of HGI in the cold climate region of China remains unexplained, but several possible reasons are discussed. Overall, our study points to a link between mtDNA variation and organismal-level evolution and suggests a possible role of mitonuclear interactions in maintaining mtDNA diversity.
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Affiliation(s)
- Jing-Tao Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Xing-Zhi Duan
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Yan Liu
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Michael R Garvin
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Lei Chen
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Gao Hu
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Jin-Cheng Zhou
- Department of Entomology, Shengyang Agricultural University, Shenyang, China
| | - Hai-Jian Huang
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Xiao-Feng Xue
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
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Park J, Kwon W, Park J, Kim HJ, Lee BC, Kim Y, Choi NJ. The complete mitochondrial genome of Nilaparvata lugens (stål, 1854) captured in Korea (Hemiptera: Delphacidae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1606680] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Jongsun Park
- InfoBoss Co., Ltd, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Woochan Kwon
- InfoBoss Co., Ltd, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Jonghyun Park
- InfoBoss Co., Ltd, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Hyun-Ju Kim
- Crop Foundation Division, National Institute of Crop Science, Wanju, Republic of Korea
| | - Bong-Choon Lee
- Crop Foundation Division, National Institute of Crop Science, Wanju, Republic of Korea
| | - Yongsung Kim
- InfoBoss Co., Ltd, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Nak Jung Choi
- Crop Foundation Division, National Institute of Crop Science, Wanju, Republic of Korea
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25
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Choi NJ, Lee BC, Park J, Park J. The complete mitochondrial genome of Nilaparvata lugens (Stål, 1854) captured in China (Hemiptera: Delphacidae): investigation of intraspecies variations between countries. MITOCHONDRIAL DNA PART B 2019. [DOI: 10.1080/23802359.2019.1606686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Nak Jung Choi
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, Republic of Korea
| | - Bong-Choon Lee
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, Republic of Korea
| | - Jonghyun Park
- InfoBoss Co., Ltd., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Co., Ltd., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
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26
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Zhu JC, Tang P, Zheng BY, Wu Q, Wei SJ, Chen XX. The first two mitochondrial genomes of the family Aphelinidae with novel gene orders and phylogenetic implications. Int J Biol Macromol 2018; 118:386-396. [PMID: 29932999 DOI: 10.1016/j.ijbiomac.2018.06.087] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/17/2018] [Accepted: 06/18/2018] [Indexed: 11/17/2022]
Abstract
Chalcidoidea is one of the most diverse group in Hymenoptera by possessing striking mitochondrial gene arrangement. By using next generation sequencing method, the first two nearly complete mitochondrial genomes in the family Aphelinidae (Insecta, Hymenopetra, Chalcidoidea) were obtained in this study. Almost all previously sequenced mitochondrial genome of Chalcidoidea species have a large inversion including six genes (atp6-atp8-trnD-trnK-cox2-trnL2-cox1) as compared with ancestral mitochondrial genome, but these two Encarsia mitochondrial genomes had a large inversion including nine genes (nad3-trnG-atp6-atp8-trnD-trnK-cox2-trnL2-cox1), which was only congruent with the species in the genus Nasonia. Moreover, we found that one shuffling changes (trnD and trnK) happened in the species E. obtusiclava but not in another species E. formosa within the same genus, of which such shuffling within the same genus at this region was only detected in Polisters within Insecta. Phylogenetic analysis displayed that different data matrix (13PCG+ 2 rRNA or 13 PCG) and inference methods (BI or ML) indicate the identical topology with high nodal supports that Aphelinidae formed a sister group with (Trichogrammatidae + Aganoidae) and the monophyly of Pteramalidae. Our results also indicated the validity of assembling and feasibility of next-generation technology to obtain the mitochondrial genomes of parasitic Hymenoptera.
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Affiliation(s)
- Jia-Chen Zhu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Plant Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Pu Tang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Plant Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Bo-Ying Zheng
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Plant Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qiong Wu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Plant Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xue-Xin Chen
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Plant Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.
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27
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Yu F, Liang AP. The Complete Mitochondrial Genome of Ugyops sp. (Hemiptera: Delphacidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2018; 18:5040086. [PMID: 29924333 PMCID: PMC6007673 DOI: 10.1093/jisesa/iey063] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Indexed: 05/22/2023]
Abstract
The complete mitochondrial genome (mitogenome) of Ugyops sp. (Hemiptera: Delphacidae) was sequenced, making it the first determined mitogenome from the subfamily Asiracinae, the basal clade of the family Delphacidae. The mitogenome was 15,259 bp in length with A + T content of 77.65% and contained 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a control region. The gene order was identical with that of the ancestral insect. The nucleotide composition analysis indicated that the whole mitogenome was strongly A-skewed (0.288) and highly C-skewed (-0.270). For PCGs on the J-strand, the AT skew was positive, and the GC skew was negative. All PCGs started with canonical ATN codons, except for cox1 and nad5, which used CTG and GTG as start codon, respectively. All tRNAs could fold into typical cloverleaf secondary structures, with the exception of trnS1 (AGN), in which the dihydrouridine arm was reduced to a simple loop. The control region included a poly-T stretch downstream of the small rRNA gene (rrnS), a subregion of higher A + T content and tandemly repeated sequence near trnI. The mitogenome of Ugyops sp. could be very helpful in exploring the diversity and evolution of mitogenomes in Delphacidae.
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Affiliation(s)
- Fang Yu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ai-Ping Liang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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28
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Huang YX, Qin DZ. Sequencing and analysis of the complete mitochondrial genome of Changeondelphax velitchkovskyi (Hemiptera: Fulgoroidea). MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:90-91. [PMID: 33474077 PMCID: PMC7799898 DOI: 10.1080/23802359.2017.1422407] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
We determined the complete mitochondrial genome sequence of Changeondelphax velitchkovskyi (Melichar 1913). The complete mitogenome sequence of C. velitchkovskyi was observed to be a circular molecule 16,449 bp long and consists of 13 protein-coding genes (PCG), two ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes (GenBank accession no. MG049916). This nucleotide composition is biased toward adenine and thymine (75.7% A + T). The A + T-rich region is found between rrnS and trnI, and this entire region was 1781 bp long.
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Affiliation(s)
- Yi-Xin Huang
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education Entomological Museum, Northwest A&F University, Yangling, Shaanxi, China
| | - Dao-Zheng Qin
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education Entomological Museum, Northwest A&F University, Yangling, Shaanxi, China
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29
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Huang YX, Qin DZ. The complete mitochondrial genome sequence of the corn planthopper, Peregrinus maidis (Hemiptera: Fulgoroidea). MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:783-784. [PMID: 33473978 PMCID: PMC7800928 DOI: 10.1080/23802359.2017.1398605] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this study, we analyzed the complete mitochondrial genome sequence of the corn planthopper, Peregrinus maidis. The complete mitogenome sequence of P. maidis was observed to be a circular molecule 16,279 bp long and consisting of 13 protein-coding genes (PCG), 2 ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes (GenBank accession no. MG049917). The nucleotide composition is biased toward adenine and thymine (77.8% A + T). The A + T-rich region was found between rrnS and trnI, and this entire region was 1596 bp long.
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Affiliation(s)
- Yi-Xin Huang
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi, China
| | - Dao-Zheng Qin
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi, China
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30
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Velozo Timbó R, Coiti Togawa R, M. C. Costa M, A. Andow D, Paula DP. Mitogenome sequence accuracy using different elucidation methods. PLoS One 2017; 12:e0179971. [PMID: 28662089 PMCID: PMC5491103 DOI: 10.1371/journal.pone.0179971] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/07/2017] [Indexed: 12/03/2022] Open
Abstract
Mitogenome sequences are highly desired because they are used in several biological disciplines. Their elucidation has been facilitated through the development of massive parallel sequencing, accelerating their deposition in public databases. However, sequencing, assembly and annotation methods might induce variability in their quality, raising concerns about the accuracy of the sequences that have been deposited in public databases. In this work we show that different sequencing methods (number of species pooled in a library, insert size and platform) and assembly and annotation methods generated variable completeness and similarity of the resulting mitogenome sequences, using three species of predaceous ladybird beetles as models. The identity of the sequences varied considerably depending on the method used and ranged from 38.19 to 90.1% for Cycloneda sanguinea, 72.85 to 91.06% for Harmonia axyridis and 41.15 to 93.60% for Hippodamia convergens. Dissimilarities were frequently found in the non-coding A+T rich region, but were also common in coding regions, and were not associated with low coverage. Mitogenome completeness and sequence identity were affected by the sequencing and assembly/annotation methods, and high within-species variation was also found for other mitogenome depositions in GenBank. This indicates a need for methods to confirm sequence accuracy, and guidelines for verifying mitogenomes should be discussed and developed by the scientific community.
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Affiliation(s)
- Renata Velozo Timbó
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, W5 Norte, Brasília, DF, Brazil
- University of Brasília, Campus Universitário Darcy Ribeiro, Brasília, Distrito Federal, Brazil
| | - Roberto Coiti Togawa
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, W5 Norte, Brasília, DF, Brazil
| | - Marcos M. C. Costa
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, W5 Norte, Brasília, DF, Brazil
| | - David A. Andow
- Department of Entomology, University of Minnesota, 219 Hodson Hall, 1980 Folwell Ave., St. Paul, MN, United States of America
| | - Débora P. Paula
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, W5 Norte, Brasília, DF, Brazil
- * E-mail:
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31
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Aunins AW, Nelms DL, Hobson CS, King TL. Comparative mitogenomic analyses of three North American stygobiont amphipods of the genus Stygobromus (Crustacea: Amphipoda). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:560-563. [PMID: 33473556 PMCID: PMC7800481 DOI: 10.1080/23802359.2016.1174086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The mitochondrial genomes of three North American stygobiont amphipods Stygobromus tenuis potomacus, S. foliatus and S. indentatus collected from Caroline County, VA, were sequenced using a shotgun sequencing approach on an Illumina NextSeq500 (Illumina Inc., San Diego, CA). All three mitogenomes displayed 13 protein-coding genes, 22 tRNAs and two rRNAs typical of metazoans. While S. tenuis and S. indentatus displayed identical gene orders similar to the pancrustacean ground pattern, S. foliatus displayed a transposition of the trnL2-cox2 genes to after atp8-atp6. In addition, a short atp8 gene, longer rrnL gene and large inverted repeat within the Control Region distinguished S. foliatus from S. tenuis potomacus and S. indentatus. Overall, it appears that gene order varies considerably among amphipods, and the addition of these Stygobromus mitogenomes to the existing sequenced amphipod mitogenomes will prove useful for characterizing evolutionary relationships among various amphipod taxa, as well as investigations of the evolutionary dynamics of the mitogenome in general.
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Affiliation(s)
- Aaron William Aunins
- Leetown Science Center, Aquatic Ecology Branch, Natural Systems Analysts, Inc, Kearneysville, WV, USA
| | - David L Nelms
- United States Geological Survey, Virginia Water Science Center, Richmond, VA, USA
| | | | - Timothy L King
- United States Geological Survey, Leetown Science Center, Aquatic Ecology Branch, Kearneysville, WV, USA
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32
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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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33
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Ye F, Liu T, King SD, You P. Mitochondrial genomes of two phlebotomine sand flies, Phlebotomus chinensis and Phlebotomus papatasi (Diptera: Nematocera), the first representatives from the family Psychodidae. Parasit Vectors 2015; 8:472. [PMID: 26381614 PMCID: PMC4573934 DOI: 10.1186/s13071-015-1081-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 09/10/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Leishmaniasis is a worldwide but neglected disease of humans and animal transmitted by sand flies, vectors that also transmit other important diseases. Mitochondrial genomes contain abundant information for population genetic and phylogenetic studies, important in disease management. However, the available mitochondrial sequences of these crucial vectors are limited, emphasizing the need for developing more mitochondrial genetic markers. METHODS The complete mitochondrial genome of Phlebotomus chinensis was amplified in eight fragments and sequenced using primer walking. The mitochondrial genome of Phlebotomus papatasi was reconstructed from whole-genome sequencing data available on Genbank. The phylogenetic relationship of 24 selected representatives of Diptera was deduced from codon positions 1 and 2 for 13 protein coding genes, using Bayesian inference (BI) and maximum likelihood (ML) methods. RESULTS We provide the first Phlebotomus (P. chinensis and P. papatasi) mitochondrial genomes. Both genomes contain 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and an A + T-rich region. The gene order of Phlebotomus mitochondrial genomes is identical with the ancestral gene order of insect. Phylogenetic analyses demonstrated that Psychodidae and Tanyderidae are sister taxa. Potential markers for population genetic study of Phlebotomus species were also revealed. CONCLUSION The generated mitochondrial genomes of P. chinensis and P. papatasi represent a useful resource for comparative genomic studies and provide valuable future markers for the population genetic study of these important Leishmania vectors. Our results also preliminary demonstrate the phylogenetic placement of Psychodidae based on their mitochondrial genomes.
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Affiliation(s)
- Fei Ye
- Co-Innovation Center for Qinba regions' sustainable development, College of Life Science, Shaanxi Normal University, Xi'an, 710062, China.
| | - Ting Liu
- Co-Innovation Center for Qinba regions' sustainable development, College of Life Science, Shaanxi Normal University, Xi'an, 710062, China.
| | - Stanley D King
- Department of Biology, Dalhousie University, Halifax, NS, Canada, B3H 4J1.
| | - Ping You
- Co-Innovation Center for Qinba regions' sustainable development, College of Life Science, Shaanxi Normal University, Xi'an, 710062, China.
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Lv L, Peng X, Jing S, Liu B, Zhu L, He G. Intraspecific and Interspecific Variations in the Mitochondrial Genomes of Nilaparvata (Hemiptera: Delphacidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2015; 108:2021-2029. [PMID: 26470349 DOI: 10.1093/jee/tov122] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 04/23/2015] [Indexed: 06/05/2023]
Abstract
Planthoppers in the genus Nilaparvata Distant are serious pests of rice and many other crops in tropical and temperate Asia, and northern Australia. In this study, the mitochondrial genomes of four Nilaparvata planthoppers were sequenced, three in Nilaparvata lugens Stål and one in Nilaparvata muiri China. Mitochondrial genome of Nilaparvata contain the standard set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region. The nucleotide composition of Nilaparvata mitochondrial sequence is biased toward adenine and thymine, and the amino acid composition is affected to a similar degree by the bias to AT. We compare the four mitochondrial genomes and find intra- and interspecific variation in gene length, base composition, nucleotide and amino acid substitutions, intergenic spacer length, and gene overlap. The intra- and interspecific variations reveal that nucleotide and amino acid substitutions in mitochondrial protein-coding genes make a contribution to the formation of various insect biotypes in one species. Furthermore, the accumulation of nonsynonymous substitutions in the mitochondrial protein-coding genes, as well as differences in start codons, the length of intergenic spacers, and gene overlap regions contribute to differences between the two species investigated here. In addition, cox is the most conserved gene family and nad4-nad4l cluster is variable in Nilaparvata mitochondrial genes for the intra- and interspecific variation.
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Affiliation(s)
- Lu Lv
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China
| | - Xinxin Peng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China
| | - Shengli Jing
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China
| | - Bingfang Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China
| | - Lili Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China
| | - Guangcun He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China.
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35
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Nam HY, Coates B, Kim KS, Park M, Lee JH. Characterization of 12 Novel Microsatellite Markers of Sogatella furcifera (Hemiptera: Delphacidae) Identified From Next-Generation Sequence Data. JOURNAL OF INSECT SCIENCE (ONLINE) 2015; 15:iev069. [PMID: 26163593 PMCID: PMC4535569 DOI: 10.1093/jisesa/iev069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 06/10/2015] [Indexed: 06/04/2023]
Abstract
The white-backed planthopper, Sogatella furcifera (Horváth) (Hemiptera: Delphacidae), is a major pest of rice and has long-range migratory behavior in Asia. Microsatellite markers (simple sequence repeats) have been widely used to determine the origins and genetic diversity of insect pests. We identified novel microsatellite loci for S. furcifera samples collected from Laos, Vietnam, and three localities in Bangladesh from next-generation Roche 454 pyrosequencing data. Size polymorphism at 12 microsatellite loci was verified for 40 adult individuals collected from Shinan, South Korea. The average number of alleles per locus was 7.92. The mean values of observed (H(o)) and expected heterozygosities (H(E)) were 0.615 and 0.757, respectively. These new microsatellite markers will be a resource for future ecological genetic studies of S. furcifera samples across more broad geographic regions in Asia and may assist in estimations of genetic differentiation and gene flow among populations for implementation of more effective management strategies to control this serious rice pest.
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Affiliation(s)
- Hwa Yeun Nam
- Entomology Program, Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea
| | - Brad Coates
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, 113 Genetics Laboratory, Iowa State University, Ames, IA 50011
| | - Kyung Seok Kim
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, 113 Genetics Laboratory, Iowa State University, Ames, IA 50011
| | - Marana Park
- Entomology Program, Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea
| | - Joon-Ho Lee
- Entomology Program, Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
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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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37
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Two nearly complete mitogenomes of wheat stem borers, Cephus pygmeus (L.) and Cephus sareptanus Dovnar-Zapolskij (Hymenoptera: Cephidae): an unusual elongation of rrnS gene. Gene 2015; 558:254-64. [PMID: 25576223 DOI: 10.1016/j.gene.2014.12.069] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Revised: 12/24/2014] [Accepted: 12/31/2014] [Indexed: 11/23/2022]
Abstract
Two nearly complete mitochondrial genomes (mitogenomes) of wheat stem borers, Cephus pygmeus and Cephus sareptanus (Hymenoptera: Cephidae), were sequenced, characterised and compared with the previously known mitogenome of Cephus cinctus. The gene orders are mostly conserved, except for translocation of trnM and swapped position of trnI and trnQ. An A+T bias was found, but a deviation from strand asymmetry was also detected on the J strand. All protein coding genes (PCGs) are initiated by ATN codons, except for nad1, nad2 and atp8, and all are terminated with TAA, TA- or T- as a stop codon. The predicted secondary structures of rrnS and rrnL genes are mostly consistent with reported hymenopteran species. However, an unusual elongation in rrnS, not know elsewhere in the order, was discovered in Cephus species. Three autonomous sequences detected in domains I and II are mainly responsible for the length expansions.
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Babbucci M, Basso A, Scupola A, Patarnello T, Negrisolo E. Is it an ant or a butterfly? Convergent evolution in the mitochondrial gene order of Hymenoptera and Lepidoptera. Genome Biol Evol 2014; 6:3326-43. [PMID: 25480682 PMCID: PMC4466343 DOI: 10.1093/gbe/evu265] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2014] [Indexed: 11/18/2022] Open
Abstract
Insect mitochondrial genomes (mtDNA) are usually double helical and circular molecules containing 37 genes that are encoded on both strands. The arrangement of the genes is not constant for all species, and produces distinct gene orders (GOs) that have proven to be diagnostic in defining clades at different taxonomic levels. In general, it is believed that distinct taxa have a very low chance of sharing identically arranged GOs. However, examples of identical, homoplastic local rearrangements occurring in distinct taxa do exist. In this study, we sequenced the complete mtDNAs of the ants Formica fusca and Myrmica scabrinodis (Formicidae, Hymenoptera) and compared their GOs with those of other Insecta. The GO of F. fusca was found to be identical to the GO of Dytrisia (the largest clade of Lepidoptera). This finding is the first documented case of an identical GO shared by distinct groups of Insecta, and it is the oldest known event of GO convergent evolution in animals. Both Hymenoptera and Lepidoptera acquired this GO early in their evolution. Using a phylogenetic approach combined with new bioinformatic tools, the chronological order of the evolutionary events that produced the diversity of the hymenopteran GOs was determined. Additionally, new local homoplastic rearrangements shared by distinct groups of insects were identified. Our study showed that local and global homoplasies affecting the insect GOs are more widespread than previously thought. Homoplastic GOs can still be useful for characterizing the various clades, provided that they are appropriately considered in a phylogenetic and taxonomic context.
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Affiliation(s)
- Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Agripolis, Legnaro (PD), Italy
| | - Andrea Basso
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Agripolis, Legnaro (PD), Italy Department of Agronomy, Food, Natural Resources, Animal and Environment (DAFNE), University of Padova, Agripolis, Legnaro (PD), Italy Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Agripolis, Legnaro (PD), Italy
| | - Antonio Scupola
- Natural History Museum (Museo di Storia Naturale), Verona, Italy
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Agripolis, Legnaro (PD), Italy
| | - Enrico Negrisolo
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Agripolis, Legnaro (PD), Italy
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Zhou G, Wang T, Lou Y, Cheng J, Zhang H, Xu JH. Identification and characterization of microRNAs in small brown planthopper (Laodephax striatellus) by next-generation sequencing. PLoS One 2014; 9:e103041. [PMID: 25057821 PMCID: PMC4109989 DOI: 10.1371/journal.pone.0103041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 06/26/2014] [Indexed: 01/01/2023] Open
Abstract
MicroRNAs (miRNAs) are endogenous non-coding small RNAs that regulate gene expression at the post-transcriptional level and are thought to play critical roles in many metabolic activities in eukaryotes. The small brown planthopper (Laodephax striatellus Fallén), one of the most destructive agricultural pests, causes great damage to crops including rice, wheat, and maize. However, information about the genome of L. striatellus is limited. In this study, a small RNA library was constructed from a mixed L. striatellus population and sequenced by Solexa sequencing technology. A total of 501 mature miRNAs were identified, including 227 conserved and 274 novel miRNAs belonging to 125 and 250 families, respectively. Sixty-nine conserved miRNAs that are included in 38 families are predicted to have an RNA secondary structure typically found in miRNAs. Many miRNAs were validated by stem-loop RT-PCR. Comparison with the miRNAs in 84 animal species from miRBase showed that the conserved miRNA families we identified are highly conserved in the Arthropoda phylum. Furthermore, miRanda predicted 2701 target genes for 378 miRNAs, which could be categorized into 52 functional groups annotated by gene ontology. The function of miRNA target genes was found to be very similar between conserved and novel miRNAs. This study of miRNAs in L. striatellus will provide new information and enhance the understanding of the role of miRNAs in the regulation of L. striatellus metabolism and development.
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Affiliation(s)
- Guoyan Zhou
- College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, China
| | - Tingzhang Wang
- College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, China
| | - Yonggen Lou
- College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, China
| | - Jia'an Cheng
- College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, China
| | - Hengmu Zhang
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- * E-mail: (HZ); (JHX)
| | - Jian-Hong Xu
- College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, China
- * E-mail: (HZ); (JHX)
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Zhang KJ, Zhu WC, Rong X, Liu J, Ding XL, Hong XY. The complete mitochondrial genome sequence of Sogatella furcifera (Horváth) and a comparative mitogenomic analysis of three predominant rice planthoppers. Gene 2013; 533:100-9. [PMID: 24120898 DOI: 10.1016/j.gene.2013.09.117] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 09/25/2013] [Accepted: 09/27/2013] [Indexed: 11/30/2022]
Abstract
The white-backed planthopper (WBPH), Sogatella furcifera (Horváth), is one of the most destructive pests of rice crops in many Asian countries. Using long-PCR and shotgun library methods, we sequenced the entire mitochondrial genomes (mt-genomes) of two WBPH individuals. Total lengths of the mt-genome of the two WBPH individuals were 16,612 bp and 16,654 bp with an identical AT content of 76.19%. Among the 13 protein coding genes (PCGs), only nad5 used an atypical initiation codon GTG. Most of the tRNA genes had the typical cloverleaf secondary structure except that the dihydrouridine (DHU) arms in two trnS genes and the TΨC arm of trnG gene did not form a stable stem-loop structure. Similar to the brown planthopper (BPH), Nilaparvata lugens (Stål), and the small brown planthopper (SBPH), Laodelphax striatellus (Fallén), some extraordinary features were observed in the WBPH mt-genome. These include similar gene rearrangement pattern, unusually short length of the atp8 gene and variable numbers of tandem repeat (VNTR) structure in control region. Interestingly, the same tandem repeat unit with stable secondary structure appeared in two different planthoppers, WBPH and SBPH, which belong to two different genera of the Delphacidae. This peculiar feature provides a direct evidence for the close relationship between the two planthoppers and updates our understanding of the evolutionary characteristics of mitochondrial control region. Comparison with two other predominant rice planthoppers (BPH and SBPH) revealed that different PCGs of mitochondria exhibit different evolutionary patterns.
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Affiliation(s)
- Kai-Jun Zhang
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; College of Plant Protection, Southwest University, Chongqing 400715, China
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