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Iyyappan S, Rather MA, Ahmad I, Ahmad I. Comparative mitochondrial genomics analysis of selected species of Schizothoracinae sub family to explore the differences at mitochondrial DNA level. Comput Biol Chem 2024; 112:108165. [PMID: 39106606 DOI: 10.1016/j.compbiolchem.2024.108165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 08/09/2024]
Abstract
A comprehensive analysis of the whole mitochondrial genomes of the Schizothoracinae subfamily of the family Cyprinidae has been revealed for the first time. The species analyzed include Schizothorax niger, Schizothorax esocinus, Schizothorax labiatus and Schizothorax plagoistomus. The total mitochondrial DNA (mtDNA) length was determined to be 16585 bp, 16583 bp, 16582 bp and 16576 bp, respectively with 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 non-coding area genes. The combined mean base compositions of the four species were as follows: A: 29.91 % T: 25.47 % G: 17.65 % C 27.01 %. The range of the GC content is 45-44 %, respectively. All protein coding genes (PCGs) commenced with the typical ATG codon, except for the cytochrome c oxidase subunit 1 (COX1) gene with GTG. The analysis of vital amino acid biosynthesis genes (COX1, ATPase 6, ATPase 8) in four different species revealed no significant differences. All 13 PCGs had Ka/Ks ratios that were all lesser than one, demonstrating purifying selection on those molecules. These tRNA genes were predicted to fold into the typical cloverleaf secondary structures with normal base pairing and ranged in size from 66 to 75 nucleotides. Additionally, the phylogenetic tree analysis revealed that S. esocinus species that was most alike to S. labiatus. This study provides critical data for phylogenetic analysis of the Schizothoracinae subfamily, which will help to resolve taxonomic difficulties and identify evolutionary links. Detailed mtDNA data are an invaluable resource for studying genetic diversity, population structure, and gene flow. Understanding genetic makeup can help inform conservation plans, identify unique populations, and track genetic variation to ensure effective preservation.
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Affiliation(s)
- S Iyyappan
- Division of Fish Genetics and Biotechnology, Faculty of Fisheries, Rangil, Ganderbal, Sher-e-Kashmir University of Agricultural Science and Technology, Kashmir 190006, India
| | - Mohd Ashraf Rather
- Division of Fish Genetics and Biotechnology, Faculty of Fisheries, Rangil, Ganderbal, Sher-e-Kashmir University of Agricultural Science and Technology, Kashmir 190006, India.
| | - Ishtiyaq Ahmad
- Division of Fish Genetics and Biotechnology, Faculty of Fisheries, Rangil, Ganderbal, Sher-e-Kashmir University of Agricultural Science and Technology, Kashmir 190006, India
| | - Irfan Ahmad
- Division of Fish Genetics and Biotechnology, Faculty of Fisheries, Rangil, Ganderbal, Sher-e-Kashmir University of Agricultural Science and Technology, Kashmir 190006, India
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Wang SH, Hu SY, Li M, Liu M, Sun H, Zhao JR, Chen WT, Yuan ML. Comparative Mitogenomic Analyses of Darkling Beetles (Coleoptera: Tenebrionidae) Provide Evolutionary Insights into tRNA-like Sequences. Genes (Basel) 2023; 14:1738. [PMID: 37761878 PMCID: PMC10530909 DOI: 10.3390/genes14091738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/25/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Tenebrionidae is widely recognized owing to its species diversity and economic importance. Here, we determined the mitochondrial genomes (mitogenomes) of three Tenebrionidae species (Melanesthes exilidentata, Anatolica potanini, and Myladina unguiculina) and performed a comparative mitogenomic analysis to characterize the evolutionary characteristics of the family. The tenebrionid mitogenomes were highly conserved with respect to genome size, gene arrangement, base composition, and codon usage. All protein-coding genes evolved under purifying selection. The largest non-coding region (i.e., control region) showed several unusual features, including several conserved repetitive fragments (e.g., A+T-rich regions, G+C-rich regions, Poly-T tracts, TATA repeat units, and longer repetitive fragments) and tRNA-like structures. These tRNA-like structures can bind to the appropriate anticodon to form a cloverleaf structure, although base-pairing is not complete. We summarized the quantity, types, and conservation of tRNA-like sequences and performed functional and evolutionary analyses of tRNA-like sequences with various anticodons. Phylogenetic analyses based on three mitogenomic datasets and two tree inference methods largely supported the monophyly of each of the three subfamilies (Stenochiinae, Pimeliinae, and Lagriinae), whereas both Tenebrioninae and Diaperinae were consistently recovered as polyphyletic. We obtained a tenebrionid mitogenomic phylogeny: (Lagriinae, (Pimeliinae, ((Tenebrioninae + Diaperinae), Stenochiinae))). Our results provide insights into the evolution and function of tRNA-like sequences in tenebrionid mitogenomes and contribute to our general understanding of the evolution of Tenebrionidae.
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Affiliation(s)
- Su-Hao Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Shi-Yun Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou 730020, China
| | - Min Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Min Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou 730020, China
| | - Hao Sun
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou 730020, China
| | - Jia-Rui Zhao
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Wen-Ting Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Ming-Long Yuan
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou 730020, China
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Huang X, Gan Y, Wang L, Xu Y, Wei Z, Shi A. The larval, pupal and mitogenomic characteristics of Agrilusadelphinus Kerremans, 1895 (Coleoptera, Buprestidae) from China. Zookeys 2023; 1174:15-33. [PMID: 38318285 PMCID: PMC10843335 DOI: 10.3897/zookeys.1174.105479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/15/2023] [Indexed: 02/07/2024] Open
Abstract
In this study, the larva and pupa of Agrilusadelphinus are described and illustrated. DNA barcoding (COI gene) was used to associate the larval and pupal stages with adults based on the maximum-likelihood method. In the resulting phylogenetic tree, species from the same species-group were found to be clustered on a branch with high support value. To better understand A.adelphinus, the complete mitochondrial genome of this species was also sequenced and annotated. Comparing this genome to the known mitogenomes of Agrilus species, the newly sequenced genome is shorter, with 15,732 bp. However, its whole mitogenome composition and gene orientation were consistent with that of most species of Buprestidae. In the mitogenome of A.adelphinus, the ATGATAG sequence was observed between ATP8 and ATP6, which is ATGATAA in other insect mitogenomes. Leu2, Phe, Ile, Gly, and Ser2 were the five most frequently encoded amino acids. The results further prove that DNA barcoding can remove the limitation of traditional taxonomy which cannot identify to species all developmental stages. This study also provides valuable molecular and morphological data for species identification and phylogenetic analyses of the genus Agrilus.
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Affiliation(s)
- Xuyan Huang
- College of Life Sciences, China West Normal University, Nanchong 637009, ChinaChina West Normal UniversityNanchongChina
| | - Yujie Gan
- College of Life Sciences, China West Normal University, Nanchong 637009, ChinaChina West Normal UniversityNanchongChina
| | - Lei Wang
- College of Life Sciences, China West Normal University, Nanchong 637009, ChinaChina West Normal UniversityNanchongChina
| | - Yanying Xu
- College of Life Sciences, China West Normal University, Nanchong 637009, ChinaChina West Normal UniversityNanchongChina
| | - Zhonghua Wei
- College of Life Sciences, China West Normal University, Nanchong 637009, ChinaChina West Normal UniversityNanchongChina
| | - Aimin Shi
- College of Life Sciences, China West Normal University, Nanchong 637009, ChinaChina West Normal UniversityNanchongChina
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Wei Z, Huang X, Shi A. First mitochondrial genome of subfamily Julodinae (Coleoptera, Buprestidae) with its phylogenetic implications. Zookeys 2023; 1139:165-182. [PMID: 36761279 PMCID: PMC9860506 DOI: 10.3897/zookeys.1139.96216] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
Complete mitochondrial genomes of three species of the family Buprestidae were sequenced, annotated, and analyzed in this study. To explore the mitogenome features of the subfamily Julodinae and verify its phylogenetic position, the complete mitogenome of Julodisvariolaris was sequenced and annotated. The complete mitogenomes of Ptosimachinensis and Chalcophorajaponica were also provided for the phylogenetic analyses within Buprestidae. Compared to the known mitogenomes of Buprestidae species varied from 15,499 bp to 16,771 bp in length, three newly sequenced mitogenomes were medium length (15,759-16,227 bp). These mitogenomes were encoded 37 typical mitochondrial genes. Among the three studied mitogenomes, Leu2 (L2), Ser2 (S2), and Pro (P) were the three most frequently encoded amino acids. Within the Buprestidae, the heterogeneity in sequence divergences of Agrilinae was highest, whereas the sequence homogeneity of Chrysochroinae was highest. Moreover, phylogenetic analyses were performed based on nucleotide matrix (13 PCGs + 2 rRNAs) among the available sequenced species of Buprestidae using Bayesian Inference and Maximum Likelihood methods. The results showed that the Julodinae was closely related to the subfamily Polycestinae. Meanwhile, the genera Melanophila, Dicerca, and Coomaniella were included in Buprestinae, which was inconsistent with the current classification system of Buprestidae. These results could contribute to further studies on genetic diversity and phylogeny of Buprestidae.
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Affiliation(s)
- Zhonghua Wei
- The Key Laboratory of Southwest China Wildlife Resources Conservation of the Ministry of Education, College of Life Sciences, China West Normal University, 637009, Nanchong, Sichuan Province, ChinaChina West Normal UniversityNanchongChina
| | - Xuyan Huang
- The Key Laboratory of Southwest China Wildlife Resources Conservation of the Ministry of Education, College of Life Sciences, China West Normal University, 637009, Nanchong, Sichuan Province, ChinaChina West Normal UniversityNanchongChina
| | - Aimin Shi
- The Key Laboratory of Southwest China Wildlife Resources Conservation of the Ministry of Education, College of Life Sciences, China West Normal University, 637009, Nanchong, Sichuan Province, ChinaChina West Normal UniversityNanchongChina
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Yang Y, Kang Y, Tong J, Ge X, Yang X, Liu H. Mitochondrial gene rearrangements suggest a new genus in the subfamily Cantharinae (Coleoptera). ZOOL SCR 2022. [DOI: 10.1111/zsc.12572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yuxia Yang
- Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development Hebei University Baoding China
| | - Ya Kang
- Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development Hebei University Baoding China
| | - Junbo Tong
- Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development Hebei University Baoding China
| | - Xueying Ge
- Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development Hebei University Baoding China
| | - Xingke Yang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology, Chinese Academy of Sciences Beijing China
| | - Haoyu Liu
- Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development Hebei University Baoding China
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Unfolding the mitochondrial genome structure of green semilooper (Chrysodeixis acuta Walker): An emerging pest of onion (Allium cepa L.). PLoS One 2022; 17:e0273635. [PMID: 36040876 PMCID: PMC9426943 DOI: 10.1371/journal.pone.0273635] [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: 05/02/2022] [Accepted: 08/12/2022] [Indexed: 11/19/2022] Open
Abstract
Onion is the most important crop challenged by a diverse group of insect pests in the agricultural ecosystem. The green semilooper (Chrysodeixis acuta Walker), a widespread tomato and soybean pest, has lately been described as an emergent onion crop pest in India. C. acuta whole mitochondrial genome was sequenced in this work. The circular genome of C. acuta measured 15,743 base pairs (bp) in length. Thirteen protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one control region were found in the 37 sequence elements. With an average 395 bp gene length, the maximum and minimum gene length observed was 1749 bp and 63 bp of nad5 and trnR, respectively. Nine of the thirteen PCGs have (ATN) as a stop codon, while the other four have a single (T) as a stop codon. Except for trnS1, all of the tRNAs were capable of producing a conventional clover leaf structure. Conserved ATAGA motif sequences and poly-T stretch were identified at the start of the control region. Six overlapping areas and 18 intergenic spacer regions were found, with sizes ranged from 1 to 20 bp and 1 to 111 bp correspondingly. Phylogenetically, C. acuta belongs to the Plusiinae subfamily of the Noctuidae superfamily, and is closely linked to Trichoplusia ni species from the same subfamily. In the present study, the emerging onion pest C. acuta has its complete mitochondrial genome sequenced for the first time.
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Huang X, Chen B, Wei Z, Shi A. First Report of Complete Mitochondrial Genome in the Tribes Coomaniellini and Dicercini (Coleoptera: Buprestidae) and Phylogenetic Implications. Genes (Basel) 2022; 13:genes13061074. [PMID: 35741836 PMCID: PMC9222259 DOI: 10.3390/genes13061074] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 11/16/2022] Open
Abstract
The complete mitochondrial genomes (mitogenomes) of the tribes Coomaniellini and Dicercini were sequenced and described in this study, including Coomaniella copipes (16,196 bp), Coomaniella dentata (16,179 bp), and Dicerca corrugata (16,276 bp). These complete mitogenomes are very similar in length and encoded 37 typical mitochondrial genes, including 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and 13 protein-coding genes (PCGs). Most of PCGs had typical ATN start codons and terminated with TAR. Among these mitogenomes, Leu2 (L2), Ile (I), Ser2 (S2), and Phe (F) were the four most frequently encoded amino acids. Moreover, phylogenetic analyses were performed based on three kinds of nucleotide matrixes (13 PCGs, 2 rRNAs, and 13 PCGs + 2 rRNAs) among the available sequenced species of the family Buprestidae using Bayesian inference and Maximum-likelihood methods. The results showed that a Chrysochroninae species interspersed in Buprestinae, and Coomaniellini is more closely related to Dicercini than Melanophilini. Moreover, the clade of Buprestidae was well separated from outgroups and the monophyly of Agrilinae is confirmed again. Our whole mitogenome phylogenetic results support that the genus Dicerca can be transferred from Chrysochroinae to Buprestinae; whether Dicercini can be completely transferred remains to be further verified after enriching samples. Our results have produced new complete mitogenomic data, which will provide information for future phylogenetic and taxonomic research.
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Wei Z. The complete mitochondrial genomes of five Agrilinae (Coleoptera, Buprestidae) species and phylogenetic implications. Zookeys 2022; 1092:195-212. [PMID: 35586288 PMCID: PMC9007928 DOI: 10.3897/zookeys.1092.80993] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/18/2022] [Indexed: 11/22/2022] Open
Abstract
Five complete mitochondrial genomes of five species from the subfamily Agrilinae were sequenced and annotated, including Coraebusdiminutus Gebhardt, 1928 (15,499 bp), Coraebuscloueti Théry, 1893 (15,514 bp), Meliboeussinae Obenberger, 1935 (16,108 bp), Agrilussichuanus Jendek, 2011 (16,521 bp), and Sambusfemoralis Kerremans, 1892 (15,367 bp). These mitogenomes ranged from 15,367 to 16,521 bp in length and encoded 37 typical mitochondrial genes: 13 protein-coding genes (13 PCGs), 2 ribosomal RNA genes (2 rRNAs), 22 transfer RNA genes (22 tRNAs), and a control region (CR). Most of PCGs had typical ATN start codons and terminated with TAR or an incomplete stop codon T–. Among these five mitogenomes, Leu2, Ile, Phe, Ser2, Gly, Met, and Val were the seven most frequently encoded amino acids. Interestingly, in A.sichuanus, a 774 bp insertion was present at trnW and trnC junction, which is unusual in Buprestidae. Additionally, phylogenetic analyses were performed based on three kinds of nucleotide matrixes (13 PCGs, 2 rRNAs, and 13 PCGs + 2 rRNAs) using Bayesian inference and maximum-likelihood methods. The results showed that the clade of Buprestidae was well separated from outgroups and all Agrilinae species formed to a single highly supported clade. The tribe Coraebini was polyphyletic, as the genus Meliboeus (Coraebini) clustered with the genus Trachys (Tracheini). The rRNA genes had important impact for the tree topology of Agrilinae. Compared to the tribes Tracheini and Agrilini, the tribe Coraebini is a younger group.
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Zhang S, Sekerka L, Liao C, Long C, Xu J, Dai X, Guo Q. The First Eight Mitogenomes of Leaf-Mining Dactylispa Beetles (Coleoptera: Chrysomelidae: Cassidinae) Shed New Light on Subgenus Relationships. INSECTS 2021; 12:insects12111005. [PMID: 34821805 PMCID: PMC8624545 DOI: 10.3390/insects12111005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/28/2021] [Accepted: 11/04/2021] [Indexed: 11/16/2022]
Abstract
The taxonomic classification of Dactylispa, a large genus of leaf-mining beetles, is problematic because it is currently based on morphology alone. Here, the first eight mitochondrial genomes of Dactylispa species, which were used to construct the first molecular phylogenies of this genus, are reported. The lengths of the eight mitogenomes range from 17,189 bp to 20,363 bp. All of the mitochondrial genomes include 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and 1 A + T-rich region. According to the nonsynonymous/synonymous mutation ratio (Ka/Ks) of all PCGs, the highest and the lowest evolutionary rates were found for atp8 and cox1, respectively, which is a common phenomenon among animals. According to relative synonymous codon usage, UUA(L) has the highest frequency. With two Gonophorini species as the outgroup, mitogenome-based phylogenetic trees of the eight Dactylispa species were constructed using maximum likelihood (ML) and Bayesian inference (BI) methods based on the PCGs, tRNAs, and rRNAs. Two DNA-based phylogenomic inferences and one protein-based phylogenomic inference support the delimitation of the subgenera Dactylispa s. str. and Platypriella as proposed in the system of Chen et al. (1986). However, the subgenus Triplispa is not recovered as monophyletic. The placement of Triplispa species requires further verification and testing with more species. We also found that both adult body shape and host plant relationship might explain the subgeneric relationships among Dactylispa beetles to a certain degree.
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Affiliation(s)
- Shengdi Zhang
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (S.Z.); (C.L.); (C.L.); (J.X.)
- National Navel-Orange Engineering Research Center, Ganzhou 341000, China
| | - Lukáš Sekerka
- Department of Entomology, National Museum, Natural History Museum, 1740 Cirkusová, Czech Republic;
| | - Chengqing Liao
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (S.Z.); (C.L.); (C.L.); (J.X.)
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
| | - Chengpeng Long
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (S.Z.); (C.L.); (C.L.); (J.X.)
- National Navel-Orange Engineering Research Center, Ganzhou 341000, China
| | - Jiasheng Xu
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (S.Z.); (C.L.); (C.L.); (J.X.)
- National Navel-Orange Engineering Research Center, Ganzhou 341000, China
| | - Xiaohua Dai
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (S.Z.); (C.L.); (C.L.); (J.X.)
- National Navel-Orange Engineering Research Center, Ganzhou 341000, China
- Correspondence: (X.D.); (Q.G.)
| | - Qingyun Guo
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (S.Z.); (C.L.); (C.L.); (J.X.)
- National Navel-Orange Engineering Research Center, Ganzhou 341000, China
- Correspondence: (X.D.); (Q.G.)
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Deyrup ST, Stagnitti NC, Perpetua MJ, Wong-Deyrup SW. Drug Discovery Insights from Medicinal Beetles in Traditional Chinese Medicine. Biomol Ther (Seoul) 2021; 29:105-126. [PMID: 33632986 PMCID: PMC7921859 DOI: 10.4062/biomolther.2020.229] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 12/29/2020] [Accepted: 01/04/2021] [Indexed: 11/23/2022] Open
Abstract
Traditional Chinese medicine (TCM) was the primary source of medical treatment for the people inhabiting East Asia for thousands of years. These ancient practices have incorporated a wide variety of materia medica including plants, animals and minerals. As modern sciences, including natural products chemistry, emerged, there became increasing efforts to explore the chemistry of this materia medica to find molecules responsible for their traditional use. Insects, including beetles have played an important role in TCM. In our survey of texts and review articles on TCM materia medica, we found 48 species of beetles from 34 genera in 14 different families that are used in TCM. This review covers the chemistry known from the beetles used in TCM, or in cases where a species used in these practices has not been chemically studied, we discuss the chemistry of closely related beetles. We also found several documented uses of beetles in Traditional Korean Medicine (TKM), and included them where appropriate. There are 129 chemical constituents of beetles discussed.
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Affiliation(s)
- Stephen T. Deyrup
- Department of Chemistry and Biochemistry, Siena College, Loudonville, NY 12309, USA
| | - Natalie C. Stagnitti
- Department of Chemistry and Biochemistry, Siena College, Loudonville, NY 12309, USA
| | | | - Siu Wah Wong-Deyrup
- The RNA Institute and Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
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Chen L, Wahlberg N, Liao CQ, Wang CB, Ma FZ, Huang GH. Fourteen complete mitochondrial genomes of butterflies from the genus Lethe (Lepidoptera, Nymphalidae, Satyrinae) with mitogenome-based phylogenetic analysis. Genomics 2020; 112:4435-4441. [PMID: 32745503 DOI: 10.1016/j.ygeno.2020.07.042] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 05/16/2020] [Accepted: 07/26/2020] [Indexed: 12/01/2022]
Abstract
The mitochondrial genome (mitogenome) can help us understand the phylogenetic relationships within the genus Lethe and the subfamily Satyrinae. In this study, we sequenced the complete mitogenomes of 14 Lethe species, which range in size from 15,225 to 15,271 bp, with both 37 genes (13 PCGs, 22 tRNAs, 2 rRNAs) and a noncoding A + T-rich region. The gene arrangement and orientation is similar to typical mitogenomes of Lepidoptera. The Ka/Ks ratio shows that cox1 has the slowest evolutionary rate. The secondary structure of trnN lacks the Pseudouracil loop (TψC loop) in most Lethe species. The inferred phylogenetic analyses show that Lethe is a well-supported monophyletic group, and reveal 2 major clades within the genus Lethe, which is consistent with previous morphological classifications.
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Affiliation(s)
- Lu Chen
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, Hunan 410128, China
| | - Niklas Wahlberg
- Systematic Biology Group, Department of Biology, Lund University, Lund, Sweden
| | - Cheng-Qing Liao
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, Hunan 410128, China
| | - Chen-Bin Wang
- State Key Laboratory of Biosafety, Ministry of Environmental Protection, Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing, Jiangsu 210042, China
| | - Fang-Zhou Ma
- State Key Laboratory of Biosafety, Ministry of Environmental Protection, Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing, Jiangsu 210042, China.
| | - Guo-Hua Huang
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, Hunan 410128, China.
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12
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Wei Z, Zhang L, Shi A. A note on the larva of Chalcophora japonica chinensis (Coleoptera, Buprestidae) based on morphological characters and molecular data. Zookeys 2020; 944:147-155. [PMID: 32684778 PMCID: PMC7340638 DOI: 10.3897/zookeys.944.37765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 05/13/2020] [Indexed: 11/12/2022] Open
Abstract
Larvae of Chalcophora japonica chinensis Schaufuss, 1879 were collected from within dead trunks in Hubei Province, China, in February 2019. These specimens created an opportunity to provide the first description of the larval stage of this subspecies; The larva is described and illustrated based on morphological characters and DNA barcoding.
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Affiliation(s)
- Zhonghua Wei
- The Key Laboratory of Southwest China Wildlife Resources Conservation of the Ministry of Education, College of Life Sciences, China West Normal University, 637009, Nanchong, Sichuan Province, China The Key Laboratory of Southwest China Wildlife Resources Conservation of the Ministry of Education, College of Life Sciences, China West Normal University Nanchong China.,College of Life Sciences, Hebei University, 071002, Baoding, Hebei Province, China College of Life Sciences, Hebei University Baoding China
| | - Liumei Zhang
- The Key Laboratory of Southwest China Wildlife Resources Conservation of the Ministry of Education, College of Life Sciences, China West Normal University, 637009, Nanchong, Sichuan Province, China The Key Laboratory of Southwest China Wildlife Resources Conservation of the Ministry of Education, College of Life Sciences, China West Normal University Nanchong China
| | - Aimin Shi
- The Key Laboratory of Southwest China Wildlife Resources Conservation of the Ministry of Education, College of Life Sciences, China West Normal University, 637009, Nanchong, Sichuan Province, China The Key Laboratory of Southwest China Wildlife Resources Conservation of the Ministry of Education, College of Life Sciences, China West Normal University Nanchong China
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13
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Sun H, Zhao W, Lin R, Zhou Z, Huai W, Yao Y. The conserved mitochondrial genome of the jewel beetle (Coleoptera: Buprestidae) and its phylogenetic implications for the suborder Polyphaga. Genomics 2020; 112:3713-3721. [PMID: 32360911 DOI: 10.1016/j.ygeno.2020.04.026] [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: 01/30/2020] [Revised: 04/22/2020] [Accepted: 04/27/2020] [Indexed: 01/04/2023]
Abstract
In this study, we sequenced the mitochondrial (mt) genome of Agrilus mali (Coleoptera: Buprestidae) using next-generation sequencing, and accordingly annotated 13 protein-coding, 22 tRNA, and 2 rRNA genes and a 1458-bp non-coding region. Comparative analysis indicated that the mt genome of A. mali is relatively conserved, with a typical gene content and order identical to those of other coleopterans. However, the newly sequenced mt genome is characterized by a relatively higher A + T content compared with that of other species within the family Buprestidae. Phylogenetic analysis based on Bayesian inference revealed that the evolutionary relationship among the six infraorders of the suborder Polyphaga is (Scirtiformia + (Elateriformia + ((Scarabaeiformia + Staphyliniformia) + (Bostrichiformia + (Cucujiformia))))). However, the topology indicated that the family Buprestidae is a sister group to other Polyphaga infraorders, excluding Scirtiformia as a monophyly, and thus the monophyly of Elateriformia was not supported. This study not only presents the mt genome of a species in the family Buprestidae and a comparative analysis of jewel beetles but also examines the contribution of mt genomes in elucidating phylogenetic relationships within the suborder Polyphaga of Coleoptera.
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Affiliation(s)
- Huiquan Sun
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Wenxia Zhao
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Ruozhu Lin
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Zhongfu Zhou
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Wenxia Huai
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Yanxia Yao
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China.
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14
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Jeong JS, Kim MJ, Kim I. The mitochondrial genome of the dung beetle, Copris tripartitus, with mitogenomic comparisons within Scarabaeidae (Coleoptera). Int J Biol Macromol 2020; 144:874-891. [DOI: 10.1016/j.ijbiomac.2019.09.165] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/22/2019] [Accepted: 09/23/2019] [Indexed: 11/25/2022]
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15
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Xiao L, Zhang S, Long C, Guo Q, Xu J, Dai X, Wang J. Complete Mitogenome of a Leaf-Mining Buprestid Beetle, Trachys auricollis, and Its Phylogenetic Implications. Genes (Basel) 2019; 10:E992. [PMID: 31805706 PMCID: PMC6947639 DOI: 10.3390/genes10120992] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/26/2019] [Accepted: 11/28/2019] [Indexed: 11/16/2022] Open
Abstract
A complete mitogenome of Trachys auricollis is reported, and a mitogenome-based phylogenetic tree of Elateriformia with all protein-coding genes (PCGs), rRNAs, and tRNAs is presented for the first time. The complete mitochondrial genome of T. auricollis is 16,429 bp in size and contains 13 PCGs, two rRNA genes, 22 tRNA genes, and an A + T-rich region. The A + T content of the entire genome is approximately 71.1%, and the AT skew and GC skew are 0.10 and -0.20, respectively. According to the the nonsynonymous substitution rate to synonymous substitution rates (Ka/Ks) of all PCGs, the highest and lowest evolutionary rates were observed for atp8 and cox1, respectively, which is a common finding among animals. The start codons of all PCGs are the typical ATN. Ten PCGs have complete stop codons, but three have incomplete stop codons with T or TA. As calculated based on the relative synonymous codon usage (RSCU) values, UUA(L) is the codon with the highest frequency. Except for trnS1, all 22 tRNA genes exhibit typical cloverleaf structures. The A + T-rich region of T. auricollis is located between rrnS and the trnI-trnG-trnM gene cluster, with six 72-bp tandem repeats. Both maximum likelihood (ML) and Bayesian (BI) trees suggest that Buprestoidea is close to Byrrhoidea and that Buprestoidea and Byrrhoidea are sister groups of Elateroidea, but the position of Psephenidae is undetermined. The inclusion of tRNAs might help to resolve the phylogeny of Coleoptera.
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Affiliation(s)
- Lifang Xiao
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China;
| | - Shengdi Zhang
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
| | - Chengpeng Long
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
| | - Qingyun Guo
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
| | - Jiasheng Xu
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
| | - Xiaohua Dai
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
- National Navel-Orange Engineering Research Center, Ganzhou 341000, China
| | - Jianguo Wang
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China;
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Liu HY, Kang ZX, Zhang F, Ge XY, Yang YX. The complete mitogenome of Lycostomus sp. (Elateroidea: Lycidae). Mitochondrial DNA B Resour 2019; 4:3813-3815. [PMID: 33366200 PMCID: PMC7707448 DOI: 10.1080/23802359.2019.1682483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 10/13/2019] [Indexed: 11/11/2022] Open
Abstract
The complete mitochondrial genome of a net-winged beetle was sequenced, Lycostomus sp. (Coleoptera: Lycidae). The total length of this mitogenome is 16096 bp and the composition of each base is A (41.1%), T (31.9%), C (17.1%), G (9.9%), respectively. The gene arrangement of this beetle mt genome is the same as other insects. The phylogenetic tree shows that Lycostomus sp. is closest to Platerodrilus sp. with robust statistical support, which confirms the monophyly of Lycidae.
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Affiliation(s)
- Hao-Yu Liu
- The Key Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding, Hebei Province, China
| | - Zi-Xuan Kang
- The Key Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding, Hebei Province, China
| | - Fang Zhang
- The Key Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding, Hebei Province, China
| | - Xue-Ying Ge
- The Key Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding, Hebei Province, China
| | - Yu-Xia Yang
- The Key Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding, Hebei Province, China
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17
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Wang P, Yuan LL, Ge XY, Liu HY, Yang YX. The complete mitochondrial genome sequence and phylogenetic analysis of Lycocerus asperipennis (Coleoptera, Cantharidae). Mitochondrial DNA B Resour 2019; 4:3768-3769. [PMID: 33366182 PMCID: PMC7707410 DOI: 10.1080/23802359.2019.1682478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 10/13/2019] [Indexed: 12/05/2022] Open
Abstract
The complete mitochondrial genome of a common Chinese soldier beetle was sequenced, Lycocerus asperipennis (Coleoptera, Cantharidae, Cantharinae). The mitogenome is a double-stranded circular molecule, and the obtained sequence with 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA subunits, and an AT-rich region, as in other insects. Total length of this mitogenome is 16162 bp and the composition of each base is A (41.5%), T (37.7%), C (12.4%), G (8.4%), respectively. The phylogenetic tree analysis using 16 species of Elateriformia shows that L. asperipennis is closest to Chauliognathus opacus, which belongs to the subfamily Chauliognathinae of Cantharidae.
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Affiliation(s)
- Ping Wang
- College of Agriculture, Yangtze University, Jingzhou, Hubei Province, China
| | - Li-Lan Yuan
- College of Agriculture, Yangtze University, Jingzhou, Hubei Province, China
- Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding, Hebei Province, China
| | - Xue-Ying Ge
- Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding, Hebei Province, China
| | - Hao-Yu Liu
- Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding, Hebei Province, China
| | - Yu-Xia Yang
- College of Agriculture, Yangtze University, Jingzhou, Hubei Province, China
- Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding, Hebei Province, China
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Cao L, Wang X. The complete mitochondrial genome of the jewel beetle Trachys variolaris (Coleoptera: Buprestidae). Mitochondrial DNA B Resour 2019; 4:3042-3043. [PMID: 33365847 PMCID: PMC7706562 DOI: 10.1080/23802359.2019.1666053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 08/16/2019] [Indexed: 10/26/2022] Open
Abstract
The complete mitochondrial genome (mitogenome) of the jewel beetle, Trachys variolaris, was sequenced and described. The mitogenome of T. variolaris is a typical circular DNA molecule with 16,771 bp in length. It contains the typical 37 mitochondrial genes (13 protein-coding genes, two rRNA genes, and 22 tRNA genes) and a long non-coding region called the control region. Twelve protein-coding genes initiate with ATN codons except ND1 uses TTG. Most of the protein-coding genes use TAA or TAG as the stop codon, but COII, COIII, ND4, and ND5 terminate with a single T-- or TA-. The length of the 22 tRNAs ranges from 61 to 70 bp and they all have the clover-leaf structure except for tRNASer(AGN) . The control region is 2155 bp long with the A + T content of 69.4%. The result of our phylogenetic analysis showed that Buprestoidea is monophyletic, and it is the sister group to (Byrrhoidea + Elateroidea).
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Affiliation(s)
- Liangming Cao
- The Key Laboratory of Forest Protection, State Forestry and Grassland Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Xiaoyi Wang
- The Key Laboratory of Forest Protection, State Forestry and Grassland Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
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19
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Cao L, Wang X. The complete mitochondrial genome of the jewel beetle Coraebus cavifrons (Coleoptera: Buprestidae). Mitochondrial DNA B Resour 2019; 4:2407-2408. [PMID: 33365565 PMCID: PMC7687635 DOI: 10.1080/23802359.2019.1636730] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 06/22/2019] [Indexed: 11/20/2022] Open
Abstract
The complete mitochondrial genome (mitogenome) of the jewel beetle, Coraebus cavifrons, was sequenced and described in the present study. The mitogenome of Coraebus cavifrons is a typical circular DNA molecule of 15,686 bp. All of the 37 mitochondrial genes (13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes) were annotated and a putative control region with 1135 bp in length was found between tRNAIle and srRNA. Protein-coding genes all initiate with ATN codons except for COII uses GTG. Most of the protein-coding genes use TAA or TAG as the stop codon, but COII, COIII, and ND5 terminate with a single T. All tRNAs have the clover-leaf structure except for tRNASer(AGN) and the length of them range from 60 to 71 bp. Genome organization and nucleotide composition of the mitogenome were also noted. Our phylogenetic analysis of Elateriformia supported the monophyly of Buprestoidea and the sister relationship between Buprestoidea and (Byrrhoidea + Elateroidea).
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Affiliation(s)
- Liangming Cao
- The Key Laboratory of Forest Protection, State Forestry and Grassland Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Xiaoyi Wang
- The Key Laboratory of Forest Protection, State Forestry and Grassland Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
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20
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Sun Y, Liu D, Xiao B, Jiang G. The comparative mitogenomics and phylogenetics of the two grouse-grasshoppers (Insecta, Orthoptera, Tetrigoidea). Biol Res 2017; 50:34. [PMID: 28982393 PMCID: PMC5629798 DOI: 10.1186/s40659-017-0132-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 09/04/2017] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE This study aimed to reveal the mitochondrial genomes (mtgenomes) of Tetrix japonica and Alulatettix yunnanensis, and the phylogenetics of Orthoptera species. METHODS The mtgenomes of A. yunnanensis and T. japonica were firstly sequenced and assembled through partial sequences amplification, and then the genome organization and gene arrangement were analyzed. Based on nucleotide/amino acid sequences of 13 protein-coding genes and whole mtgenomes, phylogenetic trees were established on 37 Orthoptera species and 5 outgroups, respectively. RESULTS Except for a regulation region (A+T rich region), a total of 37 genes were found in mtgenomes of T. japonica and A. yunnanensis, including 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes, which exhibited similar characters with other Orthoptera species. Phylogenetic tree based on 13 concatenated protein-coding nucleotide sequences were considered to be more suitable for phylogenetic reconstruction of Orthoptera species than amino acid sequences and mtgenomes. The phylogenetic relationships of Caelifera species were Acridoidea and Pamphagoidea > Pyrgomorphoidea > Pneumoroidea > Eumastacoidea > Tetrigoidea > Tridactyloidea. Besides, a sister-group relationship between Tettigonioidea and Rhaphidophoroidea was revealed in Ensifera. CONCLUSION Concatenated protein-coding nucleotide sequences of 13 genes were suitable for reconstruction of phylogenetic relationship in orthopteroid species. Tridactyloidea was a sister group of Tetrigoidea in Caelifera, and Rhaphidophoroidea was a sister group of Tettigonioidea in Ensifera.
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Affiliation(s)
- Yufang Sun
- School of Biology and Basic Medical Sciences, Medical College, Soochow University, 199 Ren’ai Road, Suzhou, 215123 Jiangsu China
| | - Dianfeng Liu
- Department of Bioengineering and Food Engineering, Puyang Vocational & Technical Institute, Puyang, 457000 Henan China
| | - Bo Xiao
- Key Laboratory for Ecology and Pollution Control of Coastal Wetlands, School of Environmental Science and Engineering, Yancheng Institute of Technology, No.9, Yingbin Road, Yancheng, 224051 Jiangsu China
| | - Guofang Jiang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, 362000 Fujian China
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Yuan ML, Zhang QL, Zhang L, Guo ZL, Liu YJ, Shen YY, Shao R. High-level phylogeny of the Coleoptera inferred with mitochondrial genome sequences. Mol Phylogenet Evol 2016; 104:99-111. [DOI: 10.1016/j.ympev.2016.08.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 07/26/2016] [Accepted: 08/02/2016] [Indexed: 01/03/2023]
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22
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Ibrahim KS, Momin MD, Lalrotluanga R, Rosangliana D, Ghatak S, Zothansanga R, Kumar NS, Gurusubramanian G. Influence of shifting cultivation practices on soil-plant-beetle interactions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:16201-16229. [PMID: 27154839 DOI: 10.1007/s11356-016-6782-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 04/27/2016] [Indexed: 06/05/2023]
Abstract
Shifting cultivation (jhum) is a major land use practice in Mizoram. It was considered as an eco-friendly and efficient method when the cycle duration was long (15-30 years), but it poses the problem of land degradation and threat to ecology when shortened (4-5 years) due to increased intensification of farming systems. Studying beetle community structure is very helpful in understanding how shifting cultivation affects the biodiversity features compared to natural forest system. The present study examines the beetle species diversity and estimates the effects of shifting cultivation practices on the beetle assemblages in relation to change in tree species composition and soil nutrients. Scarabaeidae and Carabidae were observed to be the dominant families in the land use systems studied. Shifting cultivation practice significantly (P < 0.05) affected the beetle and tree species diversity as well as the soil nutrients as shown by univariate (one-way analysis of variance (ANOVA), correlation and regression, diversity indices) and multivariate (cluster analysis, principal component analysis (PCA), detrended correspondence analysis (DCA), canonical variate analysis (CVA), permutational multivariate analysis of variance (PERMANOVA), permutational multivariate analysis of dispersion (PERMDISP)) statistical analyses. Besides changing the tree species composition and affecting the soil fertility, shifting cultivation provides less suitable habitat conditions for the beetle species. Bioindicator analysis categorized the beetle species into forest specialists, anthropogenic specialists (shifting cultivation habitat specialist), and habitat generalists. Molecular analysis of bioindicator beetle species was done using mitochondrial cytochrome oxidase subunit I (COI) marker to validate the beetle species and describe genetic variation among them in relation to heterogeneity, transition/transversion bias, codon usage bias, evolutionary distance, and substitution pattern. The present study revealed the fact that shifting cultivation practice significantly affects the beetle species in terms of biodiversity pattern as well as evolutionary features. Spatiotemporal assessment of soil-plant-beetle interactions in shifting cultivation system and their influence in land degradation and ecology will be helpful in making biodiversity conservation decisions in the near future.
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Affiliation(s)
| | - Marcy D Momin
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - R Lalrotluanga
- Department of Zoology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - David Rosangliana
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Souvik Ghatak
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - R Zothansanga
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
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Amaral DT, Mitani Y, Oliveira G, Ohmiya Y, Viviani VR. Revisiting Coleoptera a + T-rich region: structural conservation, phylogenetic and phylogeographic approaches in mitochondrial control region of bioluminescent Elateridae species (Coleoptera). Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:671-680. [PMID: 27159725 DOI: 10.3109/24701394.2016.1174220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The control region (CR) or A + T-rich region in Coleoptera mt genome is poorly characterized, including the Elateroidea bioluminescent species. Here, we provided the first attempt to characterize and compare the structure and organization of the CR of different species within Elateridae. We also revisited some sequenced Coleoptera CR and observed consensus T-stretches, non-conserved sequences near the stem-loop and unusual inner tRNAs-like sequences. All these features are probably involved in the replication start of the mt genome. The phylogenetic relationships in Elateridae bioluminescent groups using partial sequence of CR showed the monophyly of Pyrearinus pumilus group and Pyrearinus as a polyphyletic genus, corroborating our previous results. The wider genetic variation obtained by CR analysis could separate two different lineages that occur within P. termitilluminans populations. In Elateridae, the CR exhibited high polymorphism within and between populations, which was also observed in other Coleoptera species, suggesting that the CR could be described as a suitable molecular marker to be applied in phylogenetic and phylogeographic studies.
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Affiliation(s)
- Danilo T Amaral
- a Graduate School of Biotechnology and Environmental Monitoring (UFSCar) , Sorocaba , SP , Brazil.,b Graduate School of Evolutive Genetics and Molecular Biology , Federal University of São Carlos (UFSCar) , São Carlos , SP , Brazil
| | - Yasuo Mitani
- c Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba , Japan
| | - Gabriela Oliveira
- a Graduate School of Biotechnology and Environmental Monitoring (UFSCar) , Sorocaba , SP , Brazil.,b Graduate School of Evolutive Genetics and Molecular Biology , Federal University of São Carlos (UFSCar) , São Carlos , SP , Brazil
| | - Yoshihiro Ohmiya
- d Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba , Japan
| | - Vadim R Viviani
- a Graduate School of Biotechnology and Environmental Monitoring (UFSCar) , Sorocaba , SP , Brazil.,b Graduate School of Evolutive Genetics and Molecular Biology , Federal University of São Carlos (UFSCar) , São Carlos , SP , Brazil
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Niu FF, Zhu L, Wang S, Wei SJ. The mitochondrial genome of the multicolored Asian lady beetle Harmonia axyridis (Pallas) and a phylogenetic analysis of the Polyphaga (Insecta: Coleoptera). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2725-7. [PMID: 26057015 DOI: 10.3109/19401736.2015.1046165] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Here, we report the mitochondrial genome sequence of the multicolored Asian lady beetle Harmonia axyridis (Pallas, 1773) (Coleoptera: Coccinellidae) (GenBank accession No. KR108208). This is the first species with sequenced mitochondrial genome from the genus Harmonia. The current length with partitial A + T-rich region of this mitochondrial genome is 16,387 bp. All the typical genes were sequenced except the trnI and trnQ. As in most other sequenced mitochondrial genomes of Coleoptera, there is no re-arrangement in the sequenced region compared with the pupative ancestral arrangement of insects. All protein-coding genes start with ATN codons. Five, five and three protein-coding genes stop with termination codon TAA, TA and T, respectively. Phylogenetic analysis using Bayesian method based on the first and second codon positions of the protein-coding genes supported that the Scirtidae is a basal lineage of Polyphaga. The Harmonia and the Coccinella form a sister lineage. The monophyly of Staphyliniformia, Scarabaeiformia and Cucujiformia was supported. The Buprestidae was found to be a sister group to the Bostrichiformia.
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Affiliation(s)
- Fang-Fang Niu
- a Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences , Beijing , China
| | - Liang Zhu
- a Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences , Beijing , China
| | - Su Wang
- a Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences , Beijing , China
| | - Shu-Jun Wei
- a Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences , Beijing , China
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Wang Y, Chen Y, Xia C, Xia X, Chen X, Hao J. The complete mitochondrial genome of Parnassius imperator (Lepidoptera: Papilionidae: Parnassiinae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1900-1. [PMID: 25329273 DOI: 10.3109/19401736.2014.971277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome (mitogenome) of Parnassius imperator (Lepidoptera: Parnassiinae) is a circular molecule of 15,424 bp in length, containing 37 typical insect mitochondrial genes and one non-coding A + T-rich region. Its gene order and arrangement are identical to the common type found in most lepidopteran mitogenomes. All protein-coding genes (PCGs) start with a typical ATN initiation codon, except for the cox1, which is initiated by the CGA codon as observed in other lepidopteran species. Some PCGs use standard TAA, while others use TAG (nad1) or incomplete codon T (cox1 and cox2), as their termination codons. 15 intergenic spacers (175 bp in total) and 10 overlapping sequences (29 bp in total) are dispersed throughout the whole genome. The 491 bp long A+ T-rich region contains some conserved structures similar to those found in other lepidopteran mitogenomes, such as the motif ATAGA followed by an 18-bp poly-T stretch, a microsatellite-like (AT)6 element preceded by the ATTTA motif. In addition, a 36 bp sequence stretch potential to form stem-loop structures is also found in the A+ T-rich region.
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Affiliation(s)
- Yunliang Wang
- a Laboratory of Molecular Evolution and Biodiversity , College of Life Sciences, Anhui Normal University , Wuhu , People's Republic of China
| | - Yanhong Chen
- a Laboratory of Molecular Evolution and Biodiversity , College of Life Sciences, Anhui Normal University , Wuhu , People's Republic of China
| | - Chenchen Xia
- a Laboratory of Molecular Evolution and Biodiversity , College of Life Sciences, Anhui Normal University , Wuhu , People's Republic of China
| | - Xueqin Xia
- a Laboratory of Molecular Evolution and Biodiversity , College of Life Sciences, Anhui Normal University , Wuhu , People's Republic of China
| | - Xiao Chen
- a Laboratory of Molecular Evolution and Biodiversity , College of Life Sciences, Anhui Normal University , Wuhu , People's Republic of China
| | - Jiasheng Hao
- a Laboratory of Molecular Evolution and Biodiversity , College of Life Sciences, Anhui Normal University , Wuhu , People's Republic of China
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Special issue on stem cells: "the end of the beginning". Exp Neurol 2014; 260:1-2. [PMID: 24950181 DOI: 10.1016/j.expneurol.2014.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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27
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Zhang B, Ma C, Edwards O, Fuller S, Kang L. The mitochondrial genome of the Russian wheat aphid Diuraphis noxia: Large repetitive sequences between trnE and trnF in aphids. Gene 2014; 533:253-60. [DOI: 10.1016/j.gene.2013.09.064] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 09/11/2013] [Accepted: 09/17/2013] [Indexed: 10/26/2022]
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Kim MJ, Kim KG, Kim I. Description of Nearly Completed Mitochondrial Genome Sequences of the Garden Chafer Polyphylla laticollis manchurica, Endangered in Korea (Insecta: Coleoptera). ACTA ACUST UNITED AC 2013. [DOI: 10.7852/ijie.2013.27.1.185] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Timmermans MJ, Vogler AP. Phylogenetically informative rearrangements in mitochondrial genomes of Coleoptera, and monophyly of aquatic elateriform beetles (Dryopoidea). Mol Phylogenet Evol 2012; 63:299-304. [DOI: 10.1016/j.ympev.2011.12.021] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 12/22/2011] [Accepted: 12/27/2011] [Indexed: 11/15/2022]
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30
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Xiao B, Chen AH, Zhang YY, Jiang GF, Hu CC, Zhu CD. Complete mitochondrial genomes of two cockroaches, Blattella germanica and Periplaneta americana, and the phylogenetic position of termites. Curr Genet 2012; 58:65-77. [PMID: 22311390 DOI: 10.1007/s00294-012-0365-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 01/14/2012] [Accepted: 01/23/2012] [Indexed: 10/14/2022]
Abstract
The mitochondrial genomes are one of the most information-rich markers in phylogenetics. The relationships within superorder Dictyoptera have been debated in the literature. However, the closely related termites (Isoptera) are retained as unranked taxon within the order Blattaria (cockroaches). In this work, we sequenced the complete mitogenomes of two cockroaches, reconstructed the molecular phylogeny and attempted to infer the phylogenetic position of termites in Blattaria more reliably. The complete mtDNA nucleotide sequences of the peridomestic American cockroach (Periplaneta americana L.) and the domestic German cockroach (Blattella germanica L.) are 15,025 and 15,584 bp in size, respectively. The genome shares the gene order and orientation with previously known Blattaria mitogenomes. Most tRNAs could be folded into the typical cloverleaf secondary structure, but the tRNA-Ser (AGN) of P. americana appears to be missing the dihydrouridine arm. Using nucleotide and amino acid sequences as phylogenetic markers, we proposed that termites should be treated as a superfamily (Termitoidea) of cockroaches. We suggested that Polyphagoidea was the sister group of Termitoidea in Blattaria and supported that the suborder Caelifera is more closely related to the Phasmatodea than to the suborder Ensifera of Orthoptera.
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Affiliation(s)
- Bo Xiao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Wenyuan Road 1, Nanjing 210046, China
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HAN TAEMAN, KANG TAEHWA, JEONG JONGCHEL, LEE YOUNGBO, CHUNG HYOJUNG, PARK SANGWOOK, LEE SEUNGHWAN, KIM KIGYOUNG, PARK HAECHUL. Pseudocryptic speciation of Chrysochroa fulgidissima (Coleoptera: Buprestidae) with two new species from Korea, China and Vietnam. Zool J Linn Soc 2012. [DOI: 10.1111/j.1096-3642.2011.00763.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Kim MJ, Kang AR, Jeong HC, Kim KG, Kim I. Reconstructing intraordinal relationships in Lepidoptera using mitochondrial genome data with the description of two newly sequenced lycaenids, Spindasis takanonis and Protantigius superans (Lepidoptera: Lycaenidae). Mol Phylogenet Evol 2011; 61:436-45. [DOI: 10.1016/j.ympev.2011.07.013] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Revised: 07/09/2011] [Accepted: 07/19/2011] [Indexed: 11/30/2022]
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The mitochondrial genome of the ascalaphid owlfly Libelloides macaronius and comparative evolutionary mitochondriomics of neuropterid insects. BMC Genomics 2011; 12:221. [PMID: 21569260 PMCID: PMC3115881 DOI: 10.1186/1471-2164-12-221] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Accepted: 05/10/2011] [Indexed: 11/18/2022] Open
Abstract
Background The insect order Neuroptera encompasses more than 5,700 described species. To date, only three neuropteran mitochondrial genomes have been fully and one partly sequenced. Current knowledge on neuropteran mitochondrial genomes is limited, and new data are strongly required. In the present work, the mitochondrial genome of the ascalaphid owlfly Libelloides macaronius is described and compared with the known neuropterid mitochondrial genomes: Megaloptera, Neuroptera and Raphidioptera. These analyses are further extended to other endopterygotan orders. Results The mitochondrial genome of L. macaronius is a circular molecule 15,890 bp long. It includes the entire set of 37 genes usually present in animal mitochondrial genomes. The gene order of this newly sequenced genome is unique among Neuroptera and differs from the ancestral type of insects in the translocation of trnC. The L. macaronius genome shows the lowest A+T content (74.50%) among known neuropterid genomes. Protein-coding genes possess the typical mitochondrial start codons, except for cox1, which has an unusual ACG. Comparisons among endopterygotan mitochondrial genomes showed that A+T content and AT/GC-skews exhibit a broad range of variation among 84 analyzed taxa. Comparative analyses showed that neuropterid mitochondrial protein-coding genes experienced complex evolutionary histories, involving features ranging from codon usage to rate of substitution, that make them potential markers for population genetics/phylogenetics studies at different taxonomic ranks. The 22 tRNAs show variable substitution patterns in Neuropterida, with higher sequence conservation in genes located on the α strand. Inferred secondary structures for neuropterid rrnS and rrnL genes largely agree with those known for other insects. For the first time, a model is provided for domain I of an insect rrnL. The control region in Neuropterida, as in other insects, is fast-evolving genomic region, characterized by AT-rich motifs. Conclusions The new genome shares many features with known neuropteran genomes but differs in its low A+T content. Comparative analysis of neuropterid mitochondrial genes showed that they experienced distinct evolutionary patterns. Both tRNA families and ribosomal RNAs show composite substitution pathways. The neuropterid mitochondrial genome is characterized by a complex evolutionary history.
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Yin J, Hong GY, Wang AM, Cao YZ, Wei ZJ. Mitochondrial genome of the cotton bollworm Helicoverpa armigera (Lepidoptera: Noctuidae) and comparison with other Lepidopterans. ACTA ACUST UNITED AC 2011; 21:160-9. [PMID: 20958224 DOI: 10.3109/19401736.2010.503242] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We present the complete sequence of the mitochondrial genome (mitogenome) of the cotton bollworm Helicoverpa armigera. The 15,347-bp mitogenome of H. armigera was arranged in the same order described for all other sequenced lepidopterans, which differs from the most common type found in insects, due to the movement of trnM to a position 5'-upstream of trnI. The gene overlap in the H. armigera mitogenome is totally 23 bp in six locations. The H. armigera mitogenome has a total of 175 bp of intergenic spacer sequences spread over 14 regions ranging in size from 1 to 45 bp. The nucleotide composition of the whole mitogenome of H. armigera is highly A+T biased, accounting for 80.97%, with a slightly positive AT skewness and negative GC skewness, indicating the occurrence of more A than T, C more than G. The protein-encoding genes have typical mitochondrial start codons, except for cox1, which contains the unusual CGA. The cox1, cox2, and nad4 genes have incomplete stop codons (T). The lrRNA and srRNA genes are 1395 and 794-bp long, respectively. All tRNAs have a typical cloverleaf structure of mitochondrial tRNAs, except for trnS1(AGN), the dihydrouridine arm of which could not form a stable stem-loop structure. The H. armigera A+T-rich region contains a conserved structure combining the motif ATAGA and a 19-bp poly-T stretch, but absence of the 9-bp poly-A element upstream of trnM.
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Affiliation(s)
- Jiao Yin
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
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Timmermans MJTN, Dodsworth S, Culverwell CL, Bocak L, Ahrens D, Littlewood DTJ, Pons J, Vogler AP. Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics. Nucleic Acids Res 2010; 38:e197. [PMID: 20876691 PMCID: PMC2995086 DOI: 10.1093/nar/gkq807] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 08/09/2010] [Accepted: 08/29/2010] [Indexed: 02/03/2023] Open
Abstract
Mitochondrial genome sequences are important markers for phylogenetics but taxon sampling remains sporadic because of the great effort and cost required to acquire full-length sequences. Here, we demonstrate a simple, cost-effective way to sequence the full complement of protein coding mitochondrial genes from pooled samples using the 454/Roche platform. Multiplexing was achieved without the need for expensive indexing tags ('barcodes'). The method was trialled with a set of long-range polymerase chain reaction (PCR) fragments from 30 species of Coleoptera (beetles) sequenced in a 1/16th sector of a sequencing plate. Long contigs were produced from the pooled sequences with sequencing depths ranging from ∼10 to 100× per contig. Species identity of individual contigs was established via three 'bait' sequences matching disparate parts of the mitochondrial genome obtained by conventional PCR and Sanger sequencing. This proved that assembly of contigs from the sequencing pool was correct. Our study produced sequences for 21 nearly complete and seven partial sets of protein coding mitochondrial genes. Combined with existing sequences for 25 taxa, an improved estimate of basal relationships in Coleoptera was obtained. The procedure could be employed routinely for mitochondrial genome sequencing at the species level, to provide improved species 'barcodes' that currently use the cox1 gene only.
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Affiliation(s)
- M. J. T. N. Timmermans
- Department of Entomology, Natural History Museum, Cromwell Road, London SW7 5BD, Division of Biology, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK, Department of Zoology, Science Faculty, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Department of Zoology, Natural History Museum, Cromwell Road, London SW7 5BD, UK and IMEDEA (CSIC-UIB), Miquel Marqués, 21 Esporlas, 07190 Illes Balears, Spain
| | - S. Dodsworth
- Department of Entomology, Natural History Museum, Cromwell Road, London SW7 5BD, Division of Biology, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK, Department of Zoology, Science Faculty, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Department of Zoology, Natural History Museum, Cromwell Road, London SW7 5BD, UK and IMEDEA (CSIC-UIB), Miquel Marqués, 21 Esporlas, 07190 Illes Balears, Spain
| | - C. L. Culverwell
- Department of Entomology, Natural History Museum, Cromwell Road, London SW7 5BD, Division of Biology, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK, Department of Zoology, Science Faculty, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Department of Zoology, Natural History Museum, Cromwell Road, London SW7 5BD, UK and IMEDEA (CSIC-UIB), Miquel Marqués, 21 Esporlas, 07190 Illes Balears, Spain
| | - L. Bocak
- Department of Entomology, Natural History Museum, Cromwell Road, London SW7 5BD, Division of Biology, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK, Department of Zoology, Science Faculty, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Department of Zoology, Natural History Museum, Cromwell Road, London SW7 5BD, UK and IMEDEA (CSIC-UIB), Miquel Marqués, 21 Esporlas, 07190 Illes Balears, Spain
| | - D. Ahrens
- Department of Entomology, Natural History Museum, Cromwell Road, London SW7 5BD, Division of Biology, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK, Department of Zoology, Science Faculty, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Department of Zoology, Natural History Museum, Cromwell Road, London SW7 5BD, UK and IMEDEA (CSIC-UIB), Miquel Marqués, 21 Esporlas, 07190 Illes Balears, Spain
| | - D. T. J. Littlewood
- Department of Entomology, Natural History Museum, Cromwell Road, London SW7 5BD, Division of Biology, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK, Department of Zoology, Science Faculty, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Department of Zoology, Natural History Museum, Cromwell Road, London SW7 5BD, UK and IMEDEA (CSIC-UIB), Miquel Marqués, 21 Esporlas, 07190 Illes Balears, Spain
| | - J. Pons
- Department of Entomology, Natural History Museum, Cromwell Road, London SW7 5BD, Division of Biology, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK, Department of Zoology, Science Faculty, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Department of Zoology, Natural History Museum, Cromwell Road, London SW7 5BD, UK and IMEDEA (CSIC-UIB), Miquel Marqués, 21 Esporlas, 07190 Illes Balears, Spain
| | - A. P. Vogler
- Department of Entomology, Natural History Museum, Cromwell Road, London SW7 5BD, Division of Biology, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK, Department of Zoology, Science Faculty, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Department of Zoology, Natural History Museum, Cromwell Road, London SW7 5BD, UK and IMEDEA (CSIC-UIB), Miquel Marqués, 21 Esporlas, 07190 Illes Balears, Spain
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Kim MI, Baek JY, Kim MJ, Jeong HC, Kim KG, Bae CH, Han YS, Jin BR, Kim I. Complete nucleotide sequence and organization of the mitogenome of the red-spotted apollo butterfly, Parnassius bremeri (Lepidoptera: Papilionidae) and comparison with other lepidopteran insects. Mol Cells 2009; 28:347-63. [PMID: 19823774 DOI: 10.1007/s10059-009-0129-5] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Accepted: 08/04/2009] [Indexed: 11/30/2022] Open
Abstract
The 15,389-bp long complete mitogenome of the endangered red-spotted apollo butterfly, Parnassius bremeri (Lepidoptera: Papilionidae) was determined in this study. The start codon for the COI gene in insects has been extensively discussed, and has long remained a matter of some controversy. Herein, we propose that the CGA (arginine) sequence functions as the start codon for the COI gene in lepidopteran insects, on the basis of complete mitogenome sequences of lepidopteran insects, including P. bremeri, as well as additional sequences of the COI start region from a diverse taxonomic range of lepidopteran species (a total of 53 species from 15 families). In our extensive search for a tRNA-like structure in the A+T-rich region, one tRNA(Trp)-like sequence and one tRNA(Leu) (UUR)-like sequence were detected in the P. bremeri A+T-rich region, and one or more tRNA-like structures were detected in the A+T-rich region of the majority of other sequenced lepidopteran insects, thereby indicating that such features occur frequently in the lepidopteran mitogenomes. Phylogenetic analysis using the concatenated 13 amino acid sequences and nucleotide sequences of PCGs of the four macrolepidopteran superfamilies together with the Tortricoidea and Pyraloidea resulted in the successful recovery of a monophyly of Papilionoidea and a monophyly of Bombycoidea. However, the Geometroidea were unexpectedly identified as a sister group of the Bombycoidea, rather than the Papilionoidea.
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Affiliation(s)
- Man Il Kim
- College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Korea
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Kim KG, Hong MY, Kim MJ, Im HH, Kim MI, Bae CH, Seo SJ, Lee SH, Kim I. Complete mitochondrial genome sequence of the yellow-spotted long-horned beetle Psacothea hilaris (Coleoptera: Cerambycidae) and phylogenetic analysis among coleopteran insects. Mol Cells 2009; 27:429-41. [PMID: 19390824 DOI: 10.1007/s10059-009-0064-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Revised: 03/03/2009] [Accepted: 03/04/2009] [Indexed: 11/28/2022] Open
Abstract
We have determined the complete mitochondrial genome of the yellow-spotted long horned beetle, Psacothea hilaris (Coleoptera: Cerambycidae), an endangered insect species in Korea. The 15,856-bp long P. hilaris mitogenome harbors gene content typical of the animal mitogenome and a gene arrangement identical to the most common type found in insect mitogenomes. As with all other sequenced coleopteran species, the 5-bp long TAGTA motif was also detected in the intergenic space sequence located between tRNA(Ser)(UCN) and ND1 of P. hilaris. The 1,190-bp long non-coding A+T-rich region harbors an unusual series of seven identical repeat sequences of 57-bp in length and several stretches of sequences with the potential to form stem-and-loop structures. Furthermore, it contains one tRNA(Arg)-like sequence and one tRNA(Lys)-like sequence. Phylogenetic analysis among available coleopteran mitogenomes using the concatenated amino acid sequences of PCGs appear to support the sister group relationship of the suborder Polyphaga to all remaining suborders, including Adephaga, Myxophaga, and Archostemata. Among the two available infraorders in Polyphaga, a monophyletic Cucujiformia was confirmed, with the placement of Cleroidea as the basal lineage for Cucujiformia. On the other hand, the infraorder Elateriformia was not identified as monophyletic, thereby indicating that Scirtoidea and Buprestoidea are the basal lineages for Cucujiformia and the remaining Elateriformia.
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Affiliation(s)
- Ki-Gyoung Kim
- Biological Resources Research Department, National Institute of Biological Resources, Incheon, Korea
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