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Li J, Yan B, He H, Xu X, Ruan Y, Yang M. Characterization of the Complete Mitochondrial Genome of a Flea Beetle Luperomorpha xanthodera (Coleoptera: Chrysomelidae: Galerucinae) and Phylogenetic Analysis. Genes (Basel) 2023; 14:414. [PMID: 36833341 PMCID: PMC9957443 DOI: 10.3390/genes14020414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
In this study, the mitochondrial genome of Luperomorpha xanthodera was assembled and annotated, which is a circular DNA molecule including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA genes (12S rRNA and 16S rRNA), and 1388 bp non-coding regions (A + T rich region), measuring 16,021 bp in length. The nucleotide composition of the mitochondrial genome is 41.3% adenine (A), 38.7% thymine (T), 8.4% guanine (G), and 11.6% cytosine (C). Most of the protein-coding genes presented a typical ATN start codon (ATA, ATT, ATC, ATG), except for ND1, which showed the start codon TTG. Three-quarters of the protein-coding genes showed the complete stop codon TAR (TAA, TAG), except the genes COI, COII, ND4, and ND5, which showed incomplete stop codons (T- or TA-). All the tRNA genes have the typical clover-leaf structure, except tRNASer1 (AGN), which has a missing dihydrouridine arm (DHU). The phylogenetic results determined by both maximum likelihood and Bayesian inference methods consistently supported the monophyly of the subfamily Galerucinae and revealed that the subtribe Luperina and genus Monolepta are polyphyletic groups. Meanwhile, the classification status of the genus Luperomorpha is controversial.
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Affiliation(s)
- Jingjing Li
- Institute of Entomology, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang 550025, China
| | - Bin Yan
- Institute of Entomology, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang 550025, China
| | - Hongli He
- Institute of Entomology, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang 550025, China
| | - Xiaoli Xu
- Institute of Entomology, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang 550025, China
| | - Yongying Ruan
- Plant Protection Research Center, Shenzhen Polytechnic, Shenzhen 518055, China
| | - Maofa Yang
- Institute of Entomology, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang 550025, China
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Phylogenetic divergence of Lipaphis erysimi pseudobrassicae (Aphididae: Homoptera): a dominant specialist aphid on Rapeseed-mustard, India. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01213-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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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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Zhang C, Zhang K, Peng Y, Zhou J, Liu Y, Liu B. Novel Gene Rearrangement in the Mitochondrial Genome of Three Garra and Insights Into the Phylogenetic Relationships of Labeoninae. Front Genet 2022; 13:922634. [PMID: 35754812 PMCID: PMC9213810 DOI: 10.3389/fgene.2022.922634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/16/2022] [Indexed: 12/04/2022] Open
Abstract
Complete mitochondrial genomes (mitogenomes) can provide valuable information for phylogenetic relationships, gene rearrangement, and molecular evolution. Here, we report the mitochondrial whole genomes of three Garra species and explore the mechanisms of rearrangements that occur in their mitochondrial genomes. The lengths of the mitogenomes’ sequences of Garra dengba, Garra tibetana, and Garra yajiangensis were 16,876, 16,861, and 16,835, respectively. They contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genomes of three Garra species were rearranged compared to other fish mitochondrial genomes. The tRNA-Thr, tRNA-Pro and CR (T-P-CR) genes undergo replication followed by random loss of the tRNA-Thr and tRNA-Pro genes to form tRNA-Thr, CR1, tRNA-Pro and CR2 (T-CR-P-CR). Tandem duplication and random loss best explain this mitochondrial gene rearrangement. These results provide a foundation for future characterization of the mitochondrial gene arrangement of Labeoninae and further phylogenetic studies.
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Affiliation(s)
- Chi Zhang
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Kun Zhang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Ying Peng
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Jianshe Zhou
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Yifan Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
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Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of Saturnia japonica. Biochem Genet 2021; 60:914-936. [PMID: 34553327 DOI: 10.1007/s10528-021-10129-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/21/2021] [Indexed: 10/20/2022]
Abstract
The complete mitochondrial genome (mitogenome) of Saturnia japonica (Lepidoptera: Saturniidae) was sequenced and annotated. It is a circular molecule of 15, 376 bp, composed of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNA), and an adenine (A) + thymine (T)-rich region. All protein-coding genes (PCGs) are initiated by the ATN codon except for cytochrome c oxidase subunit 1 (cox1) gene that is seemingly initiated by the CGA codon. Except for cox2 and nad4, which were terminated by incomplete stop codon T or TA, the rest were terminated by canonical stop codon TAA. The A + T-rich region is high conservative, including 'ATAGA' motif followed by a 19 bp poly-T stretch, a microsatellite-like element (AT)9 and also a poly-A element, with a total length of 332 bp. The Asn codon was the most frequently used codon, followed by Ile, Leu2, Lys, Met, Phe, and Tyr, while Cys was the least frequently used codon. Phylogenetic relationships analysis based on the 13 PCGs by using maximum likelihood (ML) and neighbor Joining (NJ) revealed that S. japonica belongs to the Saturniidae family. In this study, the annotation and characteristics of the mitogenome of S. japonica were resolved for the first time, which laid a foundation for species classification and the molecular evolution of Lepidoptera: Saturniidae.
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Riyaz M, Shah RA, Savarimuthu I, Kuppusamy S. Comparative mitochondrial genome analysis of Eudocima salaminia (Cramer, 1777) (Lepidoptera: Noctuoidea), novel gene rearrangement and phylogenetic relationship within the superfamily Noctuoidea. Mol Biol Rep 2021; 48:4449-4463. [PMID: 34109499 DOI: 10.1007/s11033-021-06465-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 06/01/2021] [Indexed: 10/21/2022]
Abstract
The species Eudocima salaminia (Cramer, 1777) commonly known as the fruit-piercing moth belongs to family Erebidae. Its distribution varies from India and across South-east Asia, pacific islands and parts of Australia. The insect is a devastating pest of citrus, longans and lychees. In the present study, complete mitochondrial genome of Eudocima salaminia was sequenced and analyzed using Illumina sequencer. The phylogenetic tree was reconstructed based on nucleotide sequences of 13 PCGs using Maximum likelihood method-General Reversible mitochondrial (mtREV) model. The mitogenome has 15,597 base pairs (bp) in length, comprising of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and A + T-rich region. All protein-coding genes (PCGs) initiate with canonical start codon ATN. The gene order (trnQ-trnI-trnM) of tRNA shows a different rearrangement compared to ancestral insect gene order (trnI-trnQ-trnM). Almost all tRNAs have a typical cloverleaf secondary structure except for trnS1 (AGN) which lacks the dihydrouridine arm. At the beginning of the control region, we observed a conserved polyT", motif "ATTTA" and microsatellite (TA)n element. There are 21 intergenic regions and five overlapping regions ranging from 1 to 73 bp and 1 to 8 bp, respectively. The phylogenetic relationships based on nucleotide sequences of 13 PCGs using Maximum likelihood method showed the family level relationships as (Notodontidae + (Euteliidae + Noctuidae + (Erebidae + Nolidae))). The present study represents the similarity to phylogenetic analysis of Noctuoidea mitogenome. Moreover, the family Erebidae is the sister to the families of (Euteliidae + Noctuidae + Nolidae).
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Affiliation(s)
- Muzafar Riyaz
- Division of Taxonomy and Biodiversity, Entomology Research Institute, Loyola College, Chennai, Tamil Nadu, 600034, India
| | - Rauf Ahmad Shah
- Division of Taxonomy and Biodiversity, Entomology Research Institute, Loyola College, Chennai, Tamil Nadu, 600034, India
| | | | - Sivasankaran Kuppusamy
- Division of Taxonomy and Biodiversity, Entomology Research Institute, Loyola College, Chennai, Tamil Nadu, 600034, India.
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Zhongying Q, Huihui C, Hao Y, Yuan H, Huimeng L, Xia L, Xingchun G. Comparative mitochondrial genomes of four species of Sinopodisma and phylogenetic implications (Orthoptera, Melanoplinae). Zookeys 2020; 969:23-42. [PMID: 33013166 PMCID: PMC7515930 DOI: 10.3897/zookeys.969.49278] [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: 12/11/2019] [Accepted: 08/14/2020] [Indexed: 11/12/2022] Open
Abstract
In this study, the whole mitochondrial genomes (mitogenomes) from four species were sequenced. The complete mitochondrial genomes of Sinopodisma pieli, S. houshana, S. qinlingensis, and S. wulingshanensis are 15,857 bp, 15,818 bp, 15,843 bp, and 15,872 bp in size, respectively. The 13 protein-coding genes (PCGs) begin with typical ATN codons, except for COXI in S. qinlingensis, which begins with ACC. The highest A+T content in all the sequenced orthopteran mitogenomes is 76.8% (S. qinlingensis), followed by 76.5% (S. wulingshanensis), 76.4% (S. pieli) and 76.4% (S. houshana) (measured on the major strand). The long polythymine stretches (T-stretch) in the A+T-rich region of the four species are not adjacent to the trnI locus but are inside the stem-loop sequences on the major strand. Moreover, several repeated elements are found in the A+T-rich region of the four species. Phylogenetic analysis based on 53 mitochondrial genomes using Bayesian Inference (BI) and Maximum Likelihood (ML) revealed that Melanoplinae (Podismini) was a monophyletic group; however, the monophyly of Sinopodisma was not supported. These data will provide important information for a better understanding of the phylogenetic relationship of Melanoplinae.
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Affiliation(s)
- Qiu Zhongying
- Shaanxi Key Laboratory of Brain Disorders &School of Basic Medical Sciences, Xi'an Medical University, Xi'an,710021, China Xi'an Medical University Xi'an China
| | - Chang Huihui
- Shaanxi Key Laboratory of Brain Disorders &School of Basic Medical Sciences, Xi'an Medical University, Xi'an,710021, China Xi'an Medical University Xi'an China
| | - Yuan Hao
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China Shaanxi Normal University Xi'an China
| | - Huang Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China Shaanxi Normal University Xi'an China
| | - Lu Huimeng
- Key Laboratory for Space Bioscience & Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China Northwestern Polytechnical University Xi'an China
| | - Li Xia
- Huizhou No.8 High School, Hui'zhou 516001, China Huizhou No.8 High School Hui'zhou China
| | - Gou Xingchun
- Shaanxi Key Laboratory of Brain Disorders &School of Basic Medical Sciences, Xi'an Medical University, Xi'an,710021, China Xi'an Medical University Xi'an China
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Zhou M, Yu J, Li B, Ouyang B, Yang J. The complete mitochondrial genome of Budorcas taxicolor tibetana (Artiodactyla: Bovidae) and comparison with other Caprinae species: Insight into the phylogeny of the genus Budorcas. Int J Biol Macromol 2019; 121:223-232. [DOI: 10.1016/j.ijbiomac.2018.10.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 10/28/2022]
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Huang Y, Liu Y, Zhu XY, Xin ZZ, Zhang HB, Zhang DZ, Wang JL, Tang BP, Zhou CL, Liu QN, Dai LS. Comparative mitochondrial genome analysis of Grammodes geometrica and other noctuid insects reveals conserved mitochondrial genome organization and phylogeny. Int J Biol Macromol 2018; 125:1257-1265. [PMID: 30240711 DOI: 10.1016/j.ijbiomac.2018.09.104] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 09/16/2018] [Accepted: 09/17/2018] [Indexed: 12/01/2022]
Abstract
The mitochondrial genome (mitogenome) plays an important role in revealing molecular evolution. In this study, the complete mitogenome of Grammodes geometrica (G. geometrica) (Lepidoptera: Erebidae) was sequenced and characterized. The nucleotide composition of the genome is highly A + T biased, accounting for 80.49%. Most protein-coding genes (PCGs) are initiated by ATN codons except for the cytochrome oxidase subunit 1 (cox1) gene, which was initiated by CGA. The order and orientation of genes with the order trnM-trnI-trnQ-nad2 is a typical rearrangement compared with those ancestral insects in which trnM is located between trnQ and nad2. Most tRNA genes were folded into the typical cloverleaf structure except for trnS1 (AGN). The A + T-rich region contains the conserved motif "ATAGA" followed by a 19 bp poly-T stretch, which was also observed in other Noctuoidea species. In addition, we reconstructed phylogenetic trees among the nucleotide alignments of five families of Noctuoidea species except the Oenosandridae. Finally, we achieved a well-supported tree, which showed that G. geometrica belongs to the Erebidae family. Moreover, the relationships at the family-level can be displayed as follows: (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))).
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Affiliation(s)
- Yan Huang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224007, People's Republic of China; School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, People's Republic of China; Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, People's Republic of China
| | - Yu Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224007, People's Republic of China; College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing 210009, People's Republic of China
| | - Xiao-Yu Zhu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224007, People's Republic of China
| | - Zhao-Zhe Xin
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224007, People's Republic of China; College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing 210009, People's Republic of China
| | - Hua-Bin Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224007, People's Republic of China.
| | - Dai-Zhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224007, People's Republic of China
| | - Jia-Lian Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224007, People's Republic of China
| | - Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224007, People's Republic of China
| | - Chun-Lin Zhou
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224007, People's Republic of China
| | - Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224007, People's Republic of China.
| | - Li-Shang Dai
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, People's Republic of China.
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Yang M, Song L, Mao J, Shi Y, Wu C, Zhang Y, Huang L, Peng W, Liu X. Complete mitochondrial genome of the soybean leaffolder, Omiodes indicata (Lepidoptera: Pyraloidea: Crambidae), and phylogenetic analysis for Pyraloidea. Int J Biol Macromol 2018. [PMID: 29540301 DOI: 10.1016/j.ijbiomac.2018.03.041] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Complete mitochondrial genome (mitogenome) of the Omiodes indicata was sequenced and characterized. The circular mitogenome is 15,367bp long, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an A+T-rich region. Nucleotide composition is highly biased toward A+T nucleotides (81.6%). All 13 PCGs initiate with canonical start codon (ATN), except for cox1 that initiates with CGA. All tRNAs have a typical clover-leaf structure, except for trnS1 (AGN) in which the base pairs of the dihydrouridine (DHU) arm are reduced. In O. indicata, the motifs "ATGATAA" and "ATACTAA" between atp8 and atp6, trnS2 and nad1, respectively, and the motifs "ATAG" and "ATTTA" in the A+T-rich region can be identified. Comparative phylogenetic analyses based on four datasets show that the dataset including all coding positions of 13 PCGs exhibit the highest informativeness in resolving higher phylogeny of Pyraloidea. Bayesian inference (BI) and maximum likelihood (ML) analyses yield generally well-supported phylogenetic relationships among the eleven pyraloid subfamilies involved. However, the relationships among the five subfamilies (Acentropinae, Crambinae, Glaphyriinae, Schoenobiinae and Scopariinae) in ML analysis are ambiguous, which might be resolved by ample sampling in future mitogenome-based phylogenetic studies.
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Affiliation(s)
- Mingsheng Yang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan 466001, China
| | - Lu Song
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan 466001, China
| | - Jianhang Mao
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan 466001, China
| | - Yuxia Shi
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan 466001, China
| | - Changjing Wu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan 466001, China
| | - Yunxia Zhang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan 466001, China
| | - Li Huang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan 466001, China
| | - Weifeng Peng
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan 466001, China
| | - Xiaomeng Liu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan 466001, China.
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Shantibala T, Devi KM, Lokeshwari RK, Anju S, Luikham R. Complete mitochondrial genome of a latent wild oak tasar silkworm, Antheraea frithi (Lepidoptera: Saturniidae). MITOCHONDRIAL DNA PART B-RESOURCES 2017; 3:15-16. [PMID: 33490481 PMCID: PMC7800305 DOI: 10.1080/23802359.2017.1413290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Antheraea frithi mitogenome was sequenced to understand its phylogenetic and evolutionary relationship. It comprises 22 tRNAs, 13 protein-coding genes, two rRNAs and a AT rich region. The arrangement of mitogenome gene follows the pattern of dytrysian lepidoptera. rrnL gene consists of two unique long consensus repeats copy. tRNAs like structure of trnL and trnP are present in rrnL gene and AT rich region, respectively. The phylogenetic analysis by maximum-likelihood method showed that A. frithi was clustered with A. pernyi and A. yamamai, the commercialized wild silkworms.
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Affiliation(s)
- Tourangbam Shantibala
- Animal Bioresources Division, Institute of Bioresources and Sustainable Development, Imphal, India
| | | | - R K Lokeshwari
- Animal Bioresources Division, Institute of Bioresources and Sustainable Development, Imphal, India
| | - Shamurailatpam Anju
- Animal Bioresources Division, Institute of Bioresources and Sustainable Development, Imphal, India
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Sivasankaran K, Mathew P, Anand S, Ceasar SA, Mariapackiam S, Ignacimuthu S. Complete mitochondrial genome sequence of fruit-piercing moth Eudocima phalonia (Linnaeus, 1763) (Lepidoptera: Noctuoidea). GENOMICS DATA 2017; 14:66-81. [PMID: 29021958 PMCID: PMC5633087 DOI: 10.1016/j.gdata.2017.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 09/18/2017] [Accepted: 09/23/2017] [Indexed: 02/01/2023]
Abstract
The complete mitochondrial genome of the fruit piercing moth Eudocima phalonia (Linnaeus, 1763) (Lepidoptera: Noctuoidea) was sequenced and characterized (Genbank Accession No: KY196412). The complete mitogenome is a circular molecule of 15,575 bp length, consisting of 13 protein-coding genes (PCGs), two ribosomal RNA genes (rrnS and rrnL), 22 transfer RNA (tRNA) genes and an A + T-rich region (D-loop). The nucleotide composition of the genome is highly A + T biased, accounting for 80.67% of nucleotides. All tRNAs have putative secondary structures that are characteristic of mitochondrial tRNA. Most of the PCGs were initiated by typical ATN codons. Five genes were initiated by unusual codons. Cox1 gene was initiated by an unusual CGA codon and terminated by the typical stop codon GAA. Six genes ended with a single T. The A + T-rich region of 336 bp consisted of repetitive sequences, including two ATAGA motifs, a 19 bp poly-T stretch and three microsatellite-like regions ((TA)4, (TA)6 and two (TA)7). Moreover, three large tandem (one 40 bp and two 25 bp) repeated elements were identified in A + T-rich region. Phylogenetic analysis using PCGs revealed that Superfamily Noctuoidea is a monophyletic group.
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Affiliation(s)
- Kuppusamy Sivasankaran
- Entomology Research Institute, Loyola College, University of Madras, Chennai 600 034, Tamil Nadu, India
| | - Pratheesh Mathew
- Entomology Research Institute, Loyola College, University of Madras, Chennai 600 034, Tamil Nadu, India
| | - Sekar Anand
- Entomology Research Institute, Loyola College, University of Madras, Chennai 600 034, Tamil Nadu, India
| | - Stanislaus Antony Ceasar
- Entomology Research Institute, Loyola College, University of Madras, Chennai 600 034, Tamil Nadu, India
- Centre for Plant Sciences, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS29JT, United Kingdom
| | | | - Savarimuthu Ignacimuthu
- Entomology Research Institute, Loyola College, University of Madras, Chennai 600 034, Tamil Nadu, India
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Tang BP, Liu Y, Xin ZZ, Zhang DZ, Wang ZF, Zhu XY, Wang Y, Zhang HB, Zhou CL, Chai XY, Liu QN. Characterisation of the complete mitochondrial genome of Helice wuana (Grapsoidea: Varunidae) and comparison with other Brachyuran crabs. Genomics 2017; 110:S0888-7543(17)30099-X. [PMID: 28982639 DOI: 10.1016/j.ygeno.2017.10.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/29/2017] [Accepted: 10/02/2017] [Indexed: 11/28/2022]
Abstract
The mitochondrial genome (mitogenome) provides important information for phylogenetic analysis and understanding evolutionary origins. Herein, we sequenced, annotated, and characterised the mitogenome of the crab Helice wuana to better understand its molecular evolution and phylogeny. The 16,359bp mitogenome includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one control region. The genome composition is highly A+T biased 68.42%, and exhibits a negative AT-skew (-0.036) and GC-skew (-0.269) among Brachyura crabs. Gene rearrangements were detected, as was tandem duplication followed by random loss, which explains the translocation of mitochondrial genes. Phylogenetic analysis showed that H. wuana and H. tientsinensis clustered on one branch with high nodal support values. These results confirm that the placement of H. wuana within the Varunidae family of Thoracotrematan crabs. This study will provided a better understanding for gene rearrangements and crab evolution in the further.
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Affiliation(s)
- Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Yu Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Zhao-Zhe Xin
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Dai-Zhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Zheng-Fei Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Xiao-Yu Zhu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Ying Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Hua-Bin Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Chun-Lin Zhou
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Xin-Yue Chai
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China.
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14
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Dai LS, Kausar S, Abbas MN, Wang TT. Complete sequence and characterization of the Ectropis oblique mitochondrial genome and its phylogenetic implications. Int J Biol Macromol 2017; 107:1142-1150. [PMID: 28962847 DOI: 10.1016/j.ijbiomac.2017.09.093] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 09/21/2017] [Accepted: 09/22/2017] [Indexed: 10/18/2022]
Abstract
In the present study, we sequenced the entire mitochondrial genome (mitogenome) of Ectropis oblique using PCR amplification and sequencing methods The entire mitogenome is 15,356bp long, including 13 protein coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and A+T rich element. The base composition and gene arrangement are identical to those of other lepidopterans. Of these 37 genes, twenty three are resided on heavy strand, while fourteen located on light strand. The newly sequenced mitogenome displayed a biased Adenine/thymine 84.94% usage versus guanine/cytosine. The AT skewness is 0.030 and the GC skewness is -0.180. Twelve out of 13 PCGs initiated with canonical start codon (ATN), while cox1 started with CGA. The A+T rich element of E. oblique is 363bp long and contains of many features common to lepidopteran insects, including the 'ATAGA' motif, a 22bp poly (T) stretch and a microsatellite-like (AT)8 element upstream of trnM. Further, this mitogenome comprises 15 intergenic spacer and overlapping regions. Phylogenetic analyses showed that E. oblique belongs to Geometridae, and that the monophyly of Lepidoptera superfamilies is well supported.
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Affiliation(s)
- Li-Shang Dai
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, PR China.
| | - Saima Kausar
- Department of Zoology and Fisheries, University of Agriculture, Faisalabad 38000, Pakistan
| | - Muhammad Nadeem Abbas
- Department of Zoology and Fisheries, University of Agriculture, Faisalabad 38000, Pakistan
| | - Tian-Tian Wang
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, PR China
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15
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The mitogenome of the brown pod-sucking bug Clavigralla tomentosicollis Stäl (Hemiptera: Coreidae). ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.aggene.2017.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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16
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Liu SQ, Gu XS, Wang X. The complete mitochondrial genome of Bombyx lemeepauli (Lepidoptera: Bombycidae) and its phylogenetic relationship. Mitochondrial DNA B Resour 2017; 2:518-519. [PMID: 33473882 PMCID: PMC7800946 DOI: 10.1080/23802359.2017.1361360] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The complete mitochondrial genome (mitogenome) of Bombyx lemmepauli Lemée has been sequenced with 15,801 bp in length (Genbank no. KY620270), and has a base composition of A (43.17%), G (7.40%), C (11.90%), and T (37.86%). Similar to other bombyciod species, it contains a typically conserved structure including 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and an A + T-rich region. Excepting cox1 started with CGA, the start codons of the other 12 PCGs were ATN. Eleven of the 13 PCGs ended with TAA, expect for cox1 and cox2, which ended with a single T. The complete mitogenome sequence provided here would be useful for further understanding the evolutional position of B. lemeepauli, which is a key species to relate the famous resource insect B. mori and the important insect pest Rondotia menciana (Lepidoptera: Bombycidae).
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Affiliation(s)
- Shuang-Qing Liu
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China.,Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan, China
| | - Xing-Shi Gu
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China.,Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan, China
| | - Xing Wang
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China.,Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan, China
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17
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Xin ZZ, Yu Liu, Zhu XY, Wang Y, Zhang HB, Zhang DZ, Zhou CL, Tang BP, Liu QN. Mitochondrial Genomes of Two Bombycoidea Insects and Implications for Their Phylogeny. Sci Rep 2017; 7:6544. [PMID: 28747720 PMCID: PMC5529375 DOI: 10.1038/s41598-017-06930-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 06/22/2017] [Indexed: 11/21/2022] Open
Abstract
The mitochondrial genome (mt genome) provides important information for understanding molecular evolution and phylogenetics. As such, the two complete mt genomes of Ampelophaga rubiginosa and Rondotia menciana were sequenced and annotated. The two circular genomes of A. rubiginosa and R. menciana are 15,282 and 15,636 bp long, respectively, including 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and an A + T-rich region. The nucleotide composition of the A. rubiginosa mt genome is A + T rich (81.5%) but is lower than that of R. menciana (82.2%). The AT skew is slightly positive and the GC skew is negative in these two mt genomes. Except for cox1, which started with CGA, all other 12PCGs started with ATN codons. The A + T-rich regions of A. rubiginosa and R. menciana were 399 bp and 604 bp long and consist of several features common to Bombycoidea insects. The order and orientation of A. rubiginosa and R. menciana mitogenomes with the order trnM-trnI-trnQ-nad2 is different from the ancestral insects in which trnM is located between trnQ and nad2 (trnI-trnQ-trnM-nad2). Phylogenetic analyses indicate that A. rubiginosa belongs in the Sphingidae family, and R. menciana belongs in the Bombycidae family.
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Affiliation(s)
- Zhao-Zhe Xin
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Yu Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Xiao-Yu Zhu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Ying Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Hua-Bin Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Dai-Zhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Chun-Lin Zhou
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China.
| | - Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China.
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18
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Zhu XY, Xin ZZ, Wang Y, Zhang HB, Zhang DZ, Wang ZF, Zhou CL, Tang BP, Liu QN. The complete mitochondrial genome of Clostera anachoreta (Lepidoptera: Notodontidae) and phylogenetic implications for Noctuoidea species. Genomics 2017; 109:221-226. [DOI: 10.1016/j.ygeno.2017.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 04/10/2017] [Accepted: 04/19/2017] [Indexed: 10/19/2022]
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19
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Sun Y, Chen C, Gao J, Abbas MN, Kausar S, Qian C, Wang L, Wei G, Zhu BJ, Liu CL. Comparative mitochondrial genome analysis of Daphnis nerii and other lepidopteran insects reveals conserved mitochondrial genome organization and phylogenetic relationships. PLoS One 2017; 12:e0178773. [PMID: 28598968 PMCID: PMC5466310 DOI: 10.1371/journal.pone.0178773] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/18/2017] [Indexed: 11/24/2022] Open
Abstract
In the present study, the complete sequence of the mitochondrial genome (mitogenome) of Daphnis nerii (Lepidoptera: Sphingidae) is described. The mitogenome (15,247 bp) of D.nerii encodes13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and an adenine (A) + thymine (T)-rich region. Its gene complement and order is similar to that of other sequenced lepidopterans. The 12 PCGs initiated by ATN codons except for cytochrome c oxidase subunit 1 (cox1) gene that is seemingly initiated by the CGA codon as documented in other insect mitogenomes. Four of the 13 PCGs have the incomplete termination codon T, while the remainder terminated with the canonical stop codon. This mitogenome has six major intergenic spacers, with the exception of A+T-rich region, spanning at least 10 bp. The A+T-rich region is 351 bp long, and contains some conserved regions, including 'ATAGA' motif followed by a 17 bp poly-T stretch, a microsatellite-like element (AT)9 and also a poly-A element. Phylogenetic analyses based on 13 PCGs using maximum likelihood (ML) and Bayesian inference (BI) revealed that D. nerii resides in the Sphingidae family.
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Affiliation(s)
- Yu Sun
- College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Chen Chen
- College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Jin Gao
- College of Life Sciences, Anhui Agricultural University, Hefei, China
| | | | - Saima Kausar
- College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Cen Qian
- College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Lei Wang
- College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Guoqing Wei
- College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Bao-Jian Zhu
- College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Chao-Liang Liu
- College of Life Sciences, Anhui Agricultural University, Hefei, China
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20
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Liu QN, Xin ZZ, Bian DD, Chai XY, Zhou CL, Tang BP. The first complete mitochondrial genome for the subfamily Limacodidae and implications for the higher phylogeny of Lepidoptera. Sci Rep 2016; 6:35878. [PMID: 27767191 PMCID: PMC5073316 DOI: 10.1038/srep35878] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 10/07/2016] [Indexed: 11/08/2022] Open
Abstract
The mitochondrial genome (mitogenome) provides important information for understanding molecular evolution and phylogeny. To determine the systematic status of the family Limacodidae within Lepidoptera, we infer a phylogenetic hypothesis based on the complete mitogenome of Monema flavescens (Lepidoptera: Limacodidae). The mitogenome of M. flavescens is 15,396 base pairs (bp), and includes 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (CR). The AT skew of this mitogenome is slightly negative and the nucleotide composition is also biased towards A + T nucleotides (80.5%). All PCGs are initiated by ATN codons, except for the cytochrome c oxidase subunit 1 (cox1) gene, which is initiated by CGA. All tRNAs display the typical clover-leaf structure characteristic of mitochondrial tRNAs, with the exception of trnS1 (AGN). The mitogenome CR is 401 bp and consists of several features common to Lepidoptera. Phylogenetic analysis using Bayesian Inference (BI) and Maximum Likelihood (ML) based on nucleotide and amino acid sequences of 13 mitochondrial PCGs indicates that M. flavescens belongs to Zygaenoidea. We obtain a well-supported phylogenetic tree consisting of Yponomeutoidea + (Tortricoidea + Zygaenoidea + (Papilionoidea + (Pyraloidea + (Noctuoidea + (Geometroidea + Bombycoidea))))).
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Affiliation(s)
- Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, P. R. China
| | - Zhao-Zhe Xin
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, P. R. China
| | - Dan-Dan Bian
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, P. R. China
| | - Xin-Yue Chai
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, P. R. China
| | - Chun-Lin Zhou
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, P. R. China
| | - Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, P. R. China
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21
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Dai LS, Li S, Yu HM, Wei GQ, Wang L, Qian C, Zhang CF, Li J, Sun Y, Zhao Y, Zhu BJ, Liu CL. Mitochondrial genome of the sweet potato hornworm, Agrius convolvuli (Lepidoptera: Sphingidae), and comparison with other Lepidoptera species. Genome 2016; 60:128-138. [PMID: 28084809 DOI: 10.1139/gen-2016-0058] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In the present study, we sequenced the complete mitochondrial genome (mitogenome) of Agrius convolvuli (Lepidoptera: Sphingidae) and compared it with previously sequenced mitogenomes of lepidopteran species. The mitogenome was a circular molecule, 15 349 base pairs (bp) long, containing 37 genes. The order and orientation of genes in the A. convolvuli mitogenome were similar to those in sequenced mitogenomes of other lepidopterans. All 13 protein-coding genes (PCGs) were initiated by ATN codons, except for the cytochrome c oxidase subunit 1 (cox1) gene, which seemed to be initiated by the codon CGA, as observed in other lepidopterans. Three of the 13 PCGs had the incomplete termination codon T, while the remainder terminated with TAA. Additionally, the codon distributions of the 13 PCGs revealed that Asn, Ile, Leu2, Lys, Phe, and Tyr were the most frequently used codon families. All transfer RNAs were folded into the expected cloverleaf structure except for tRNASer(AGN), which lacked a stable dihydrouridine arm. The length of the adenine (A) + thymine (T)-rich region was 331 bp. This region included the motif ATAGA followed by a 19-bp poly-T stretch and a microsatellite-like (TA)8 element next to the motif ATTTA. Phylogenetic analyses (maximum likelihood and Bayesian methods) showed that A. convolvuli belongs to the family Sphingidae.
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Affiliation(s)
- Li-Shang Dai
- College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, P.R. China.,College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, P.R. China
| | - Sheng Li
- College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, P.R. China.,College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, P.R. China
| | - Hui-Min Yu
- College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, P.R. China.,College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, P.R. China
| | - Guo-Qing Wei
- College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, P.R. China.,College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, P.R. China
| | - Lei Wang
- College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, P.R. China.,College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, P.R. China
| | - Cen Qian
- College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, P.R. China.,College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, P.R. China
| | - Cong-Fen Zhang
- College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, P.R. China.,College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, P.R. China
| | - Jun Li
- College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, P.R. China.,College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, P.R. China
| | - Yu Sun
- College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, P.R. China.,College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, P.R. China
| | - Yue Zhao
- College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, P.R. China.,College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, P.R. China
| | - Bao-Jian Zhu
- College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, P.R. China.,College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, P.R. China
| | - Chao-Liang Liu
- College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, P.R. China.,College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, P.R. China
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Gu XS, Ma L, Wang X, Huang GH. Analysis on the Complete Mitochondrial Genome of Andraca theae (Lepidoptera: Bombycoidea). JOURNAL OF INSECT SCIENCE (ONLINE) 2016; 16:iew090. [PMID: 27694403 PMCID: PMC5045664 DOI: 10.1093/jisesa/iew090] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/03/2016] [Indexed: 06/06/2023]
Abstract
The bombycid moth, Andraca theae (Matsumura) (Lepidoptera: Bombycoidea) is an important pest of tea in southeastern China. In the present study, the mitochondrial genome (mitogenome) of A. theae was amplified by polymerase chain reaction and sequenced. The complete mitogenome of A. theae, encoding 37 genes, was 15,737 bp in length (Genbank no. KX365419), and consisted of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 ribosomal RNA genes and an adenine (A) + thymine (T)-rich region (AT-rich region). The gene order of A. theae mitogenome was typical for Lepidoptera mitogenomes. Except for cox1, which started with CGA, all other 12 PCGs started with ATN. Eleven of the 13 PCGs ended with TAA, expect for cox1 and cox2, which ended with a single T. The maximum likelihood method and the Bayesian method were used to analyze the phylogenetic relationship among 22 representative bombycoid species with a matrix consisting of the 13 PCGs of the mitogenomes of the 22 species. The topological structures of the two phylogenetic trees we constructed were almost identical, with the results indicating that the bombycid species, including A. theae, clustered into a single clade with a bootstrap value of 58% and a posterior probability of 0.98. The phylogenetic relationship among the Bombycoidea species analyzed was Lasiocampidae + (Bombycidae + (Saturniidae + Sphingidae)) which was supported by a high bootstrap value of 100% and a posterior probability of 1.00.
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Affiliation(s)
- Xing-Shi Gu
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China (; ; ; ) Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Li Ma
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China (; ; ; ) Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Xing Wang
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China (; ; ; ) Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Guo-Hua Huang
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China (; ; ; ) Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan 410128, China
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Comparative Mitochondrial Genome Analysis of Eligma narcissus and other Lepidopteran Insects Reveals Conserved Mitochondrial Genome Organization and Phylogenetic Relationships. Sci Rep 2016; 6:26387. [PMID: 27222440 PMCID: PMC4879558 DOI: 10.1038/srep26387] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 04/29/2016] [Indexed: 11/08/2022] Open
Abstract
In this study, we sequenced the complete mitochondrial genome of Eligma narcissus and compared it with 18 other lepidopteran species. The mitochondrial genome (mitogenome) was a circular molecule of 15,376 bp containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and an adenine (A) + thymine (T) − rich region. The positive AT skew (0.007) indicated the occurrence of more As than Ts. The arrangement of 13 PCGs was similar to that of other sequenced lepidopterans. All PCGs were initiated by ATN codons, except for the cytochrome c oxidase subunit 1 (cox1) gene, which was initiated by the CGA sequence, as observed in other lepidopterans. The results of the codon usage analysis indicated that Asn, Ile, Leu, Tyr and Phe were the five most frequent amino acids. All tRNA genes were shown to be folded into the expected typical cloverleaf structure observed for mitochondrial tRNA genes. Phylogenetic relationships were analyzed based on the nucleotide sequences of 13 PCGs from other insect mitogenomes, which confirmed that E. narcissus is a member of the Noctuidae superfamily.
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Liu QN, Chai XY, Jiang SH, Zhou CL, Xuan FJ, Zhang DZ, Tang BP. Identification of the complete mitochondrial genome of the pacific white shrimp Litopenaeus vannamei (Decapoda: Penaeidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4693-4695. [PMID: 26709974 DOI: 10.3109/19401736.2015.1106506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome (mitogenome) of Litopenaeus vannamei was determined to be 15 989 bp in size, it contains 22 tRNA genes, 13 protein-coding genes (PCGs), two rRNA genes and a D-loop region. The nucleotide composition was biased toward A + T nucleotides (67.8%) and the AT skew of this mitogenome was slightly negative (-0.025). All tRNA genes displayed a typical clover-leaf structure, except for trnS1 (AGN). Thirteen PCGs were initiated by ATN codons, except for cox1 gene which was initiated by ACG. Four of the 13 PCGs had the incomplete termination codon by T. The rrnL was 1371 bp and the rrnS was 853 bp, and the AT content of the combined rRNA genes was 70.9%. The D-loop region of the mitogenome was 985 bp in length and the A + T content was 82.7%, and no tandem repeat was found in this region. Phylogenetic analysis showed that the placement of L. vannamei was within the Penaeidae.
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Affiliation(s)
- Qiu-Ning Liu
- a Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University , Yancheng , PR China
| | - Xin-Yue Chai
- a Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University , Yancheng , PR China
| | - Sen-Hao Jiang
- a Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University , Yancheng , PR China
| | - Chun-Lin Zhou
- a Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University , Yancheng , PR China
| | - Fu-Jun Xuan
- a Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University , Yancheng , PR China
| | - Dai-Zhen Zhang
- a Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University , Yancheng , PR China
| | - Bo-Ping Tang
- a Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University , Yancheng , PR China
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Liu QN, Chai XY, Bian DD, Zhou CL, Tang BP. The complete mitochondrial genome of Plodia interpunctella (Lepidoptera: Pyralidae) and comparison with other Pyraloidea insects. Genome 2015; 59:37-49. [PMID: 26701149 DOI: 10.1139/gen-2015-0079] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The mitochondrial (mt) genome can provide important information for the understanding of phylogenetic relationships. The complete mt genome of Plodia interpunctella (Lepidoptera: Pyralidae) has been sequenced. The circular genome is 15 287 bp in size, encoding 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a control region. The AT skew of this mt genome is slightly negative, and the nucleotide composition is biased toward A+T nucleotides (80.15%). All PCGs start with the typical ATN (ATA, ATC, ATG, and ATT) codons, except for the cox1 gene which may start with the CGA codon. Four of the 13 PCGs harbor the incomplete termination codon T or TA. All the tRNA genes are folded into the typical clover-leaf structure of mitochondrial tRNA, except for trnS1 (AGN) in which the DHU arm fails to form a stable stem-loop structure. The overlapping sequences are 35 bp in total and are found in seven different locations. A total of 240 bp of intergenic spacers are scattered in 16 regions. The control region of the mt genome is 327 bp in length and consisted of several features common to the sequenced lepidopteran insects. Phylogenetic analysis based on 13 PCGs using the Maximum Likelihood method shows that the placement of P. interpunctella was within the Pyralidae.
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Affiliation(s)
- Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture; Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, P.R. China.,Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture; Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, P.R. China
| | - Xin-Yue Chai
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture; Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, P.R. China.,Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture; Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, P.R. China
| | - Dan-Dan Bian
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture; Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, P.R. China.,Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture; Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, P.R. China
| | - Chun-Lin Zhou
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture; Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, P.R. China.,Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture; Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, P.R. China
| | - Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture; Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, P.R. China.,Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture; Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, P.R. China
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Liu QN, Chai XY, Bian DD, Ge BM, Zhou CL, Tang BP. The complete mitochondrial genome of fall armyworm Spodoptera frugiperda (Lepidoptera:Noctuidae). Genes Genomics 2015. [DOI: 10.1007/s13258-015-0346-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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27
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Liu QN, Zhang HB, Jiang SH, Xuan FJ, Li CF, Zhang DZ, Zhou CL, Tang BP. The complete mitochondrial genome of Eriocheir japonica sinensis (Decapoda: Varunidae) and its phylogenetic analysis. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Characterization of the Complete Mitochondrial Genome of Cerura menciana and Comparison with Other Lepidopteran Insects. PLoS One 2015; 10:e0132951. [PMID: 26309239 PMCID: PMC4550444 DOI: 10.1371/journal.pone.0132951] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 06/20/2015] [Indexed: 11/19/2022] Open
Abstract
The complete mitochondrial genome (mitogenome) of Cerura menciana (Lepidoptera: Notodontidae) was sequenced and analyzed in this study. The mitogenome is a circular molecule of 15,369 bp, containing 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and a A+T-rich region. The positive AT skew (0.031) indicated that more As than Ts were present. All PCGs were initiated by ATN codons, except for the cytochrome c oxidase subunit 1 (cox1) gene, which was initiated by CAG. Two of the 13 PCGs contained the incomplete termination codon T or TA, while the others were terminated with the stop codon TAA. The A+T-rich region was 372 bp in length and consisted of an ‘ATAGA’ motif followed by an 18 bp poly-T stretch, a microsatellite-like (AT)8 and a poly-A element upstream of the trnM gene. Results examining codon usage indicated that Asn, Ile, Leu2, Lys, Tyr and Phe were the six most frequently occurring amino acids, while Cys was the rarest. Phylogenetic relationships, analyzed based on the nucleotide sequences of the 13 PCGs from other insect mitogenomes, confirmed that C. menciana belongs to the Notodontidae family.
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Liu QN, Chai XY, Jiang SH, Zhou CL, Xuan FJ, Tang BP. Characterization of the complete mitochondrial genome of the red crayfish, Procambarus clarkii (Decapoda: Cambaridae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3458-9. [PMID: 26258501 DOI: 10.3109/19401736.2015.1066346] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Here we present the complete mitochondrial (mt) genome of Procambarus clarkii (Decapoda: Cambaridae) and provide its annotation. The complete mt genome was determined to be 15 929 bp and contains 22 tRNA genes, 13 protein-coding genes (PCGs), two rRNA genes, and a D-loop region. The nucleotide composition was biased toward A + T nucleotides (72.91%) and the AT skew of this mt genome was slightly negative. All the 22 tRNA genes displayed a typical clover-leaf structure, with the exception of trnS1 (AGN). About 13 PCGs were initiated by ATN codons, except for cox1 and nad2 genes which were initiated by ACG and GTG, respectively. Six of the 13 PCGs harbor the incomplete termination codon by T or TA. The D-loop region of the mt genome was 1188 bp in length and the A + T content was 81.08%. Phylogenetic analysis showed that the placement of P. clarkii was within the Cambaridae. This mt genome sequence will provide a better understanding for crayfish evolution in the future.
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Affiliation(s)
- Qiu-Ning Liu
- a Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Key Laboratory for Bioresources of Saline Soils, Yancheng Teachers University , Yancheng , PR China
| | - Xin-Yue Chai
- a Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Key Laboratory for Bioresources of Saline Soils, Yancheng Teachers University , Yancheng , PR China
| | - Sen-Hao Jiang
- a Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Key Laboratory for Bioresources of Saline Soils, Yancheng Teachers University , Yancheng , PR China
| | - Chun-Lin Zhou
- a Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Key Laboratory for Bioresources of Saline Soils, Yancheng Teachers University , Yancheng , PR China
| | - Fu-Jun Xuan
- a Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Key Laboratory for Bioresources of Saline Soils, Yancheng Teachers University , Yancheng , PR China
| | - Bo-Ping Tang
- a Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Key Laboratory for Bioresources of Saline Soils, Yancheng Teachers University , Yancheng , PR China
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Kong W, Yang J. The complete mitochondrial genome of Rondotia menciana (Lepidoptera: Bombycidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2015; 15:iev032. [PMID: 25888706 PMCID: PMC4535477 DOI: 10.1093/jisesa/iev032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 03/23/2015] [Indexed: 06/04/2023]
Abstract
The mulberry white caterpillar, Rondotia menciana Moore (Lepidoptera: Bombycidae) is a species with closest relationship with Bombyx mori and Bombyx mandarina, and the genetic information of R. menciana is important for understanding the diversity of the Bombycidae. In this study, the mitochondrial genome (mitogenome) of R. menciana was amplified by polymerase chain reaction and sequenced. The mitogenome of R. menciana was determined to be 15,301 bp, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes, and an AT-rich region. The A+T content (78.87%) was lower than that observed for other Bombycidae insects. All PCGs were initiated by ATN codons and terminated with the canonical stop codons, except for coxII, which was terminated by a single T. All the tRNA genes displayed a typical clover-leaf structure of mitochondrial tRNA. The length of AT-rich region (360 bp) of R. menciana mitogenome is shorter than that of other Bombycidae species. Phylogenetic analysis showed that the R. menciana was clustered on one branch with B. mori and B. mandarina from Bombycidae.
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Affiliation(s)
- Weiqing Kong
- The Key Sericultural Laboratory of Shaanxi, Ankang University, Ankang, Shaanxi 725099, People's Republic of China
| | - Jinhong Yang
- The Key Sericultural Laboratory of Shaanxi, Ankang University, Ankang, Shaanxi 725099, People's Republic of China
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Guan DL, Xu SQ. Complete mitochondrial genome of the geophilous grasshopper Trilophidia annulata (Acrididae: Oedipodinae: Trilophidia). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3143-4. [PMID: 25690056 DOI: 10.3109/19401736.2015.1007304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitogenome of the geophilous grasshopper Trilophidia annulata was reconstructed from whole-genome Illumina sequencing data. After annotation, the circular genome was obtained with 16,501 bp in length, and typically consisted of 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs) and 1 D-loop region. All PCGs were initiated with ATN codons, except ND2 with the start codon GTG. Most of the PCGs used TAA as their stop codons, while the others used TAG as stop codons (COX1, COX3&ND1). The nucleotide composition was asymmetric (42.3% A, 15.0% C, 11.0% G, 31.8% T) with an overall GC content of 25.9%. These data would contribute to the design of novel molecular markers for population and evolutionary research of T. annulata.
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Affiliation(s)
- De-Long Guan
- a College of Life Sciences, Shaanxi Normal University , Xi'an , Shaanxi , P. R. China
| | - Sheng-Quan Xu
- a College of Life Sciences, Shaanxi Normal University , Xi'an , Shaanxi , P. R. China
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Zhang YL, Zhao JH, Zhou QM. The complete mitochondrial genome of Bombyx mori strain Yu39 (Lepidoptera: Bombycidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3163-4. [PMID: 25676361 DOI: 10.3109/19401736.2015.1007316] [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 of Bombyx mori strain Yu39 (Lepidoptera: Bombycidae) is a circular molecule of 15,652 bp in length, containing 37 typical mitochondrial genes: 13 protein-coding genes (PCGs), 22 transfer RNAs, 2 ribosomal RNAs and a non-coding AT-rich region. Its gene order and arrangement are identical to the common type found in most insect mitogenomes. All PCGs start with a typical ATN codon, except for the cox1 gene, which begins with uncertained codon. All PCGs terminate in the common stop codon TAA, except for the cox1 and cox2, which use single T as their stop codons. The non-coding AT-rich region is 494-bp long, located between rrnS and trnM genes. It contains some structures of repeated motifs and microsatellite-like elements characteristic of the other lepidopterons.
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Affiliation(s)
- Yong-Liang Zhang
- a College of Life Science and Agronomy, Zhoukou Normal University , Zhoukou City , Henan Province , China and
| | - Jin-Hui Zhao
- a College of Life Science and Agronomy, Zhoukou Normal University , Zhoukou City , Henan Province , China and
| | - Qi-Ming Zhou
- b Sericultural Science Research Institute of Henan province , Nanyang City , Henan Province , China
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Zhang YL, Zhao JH, Zhou QM. The complete mitochondrial genome of Bombyx mori strain Yu5 (Lepidoptera: Bombycidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4128-4129. [PMID: 25629482 DOI: 10.3109/19401736.2014.1003876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of Bombyx mori strain Yu5 (Lepidoptera: Bombycidae) is a circular molecule of 15,644 bp in length, containing 37 typical coding genes and one non-coding AT-rich region. The overall composition of the mitogenome was A (43.07%), G (7.34%), C (11.33%), and T (38.26%). Its gene order and content were identical to the common type found in most insect mitogenomes. All protein coding genes (PCGs) started with a typical ATN initiation codon, except for the cox1 gene, which began with CGA codon. Eleven genes used standard complete termination codon TAA, whereas the cox1 and cox2 genes ended with single T. All tRNA genes displayed typical secondary cloverleaf structures as those of other insects. Additionally, the 494 bp long AT-rich region contained several structures common to the other lepidopterons, such as some structures of repeated motifs and microsatellite-like elements and a poly-A element upstream of transfer RNA M (trnM) gene.
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Affiliation(s)
- Yong-Liang Zhang
- a College of Life Science and Agronomy, Zhoukou Normal University , Zhoukou City , Henan Province , China and
| | - Jin-Hui Zhao
- a College of Life Science and Agronomy, Zhoukou Normal University , Zhoukou City , Henan Province , China and
| | - Qi-Ming Zhou
- b Sericultural Science Research Institute of Henan Province , Nanyang City , Henan Province , China
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Zhang YL, Wu AQ. The complete mitochondrial genome of Bombyx mori strain Chunyun (Lepidoptera: Bombycidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4082-4083. [PMID: 25629475 DOI: 10.3109/19401736.2014.1003854] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, the complete mitochondrial genome sequence of Bombyx mori strain Chunyun (Lepidoptera: Bombycidae) has been reported for the first time. The total length of the mitogenome was 15,659 bp with 37 typical animal mitochondrial genes and 1 non-coding A + T-rich region. Its gene content and order were identical to those of other lepidopteran mitochondrial genomes. All protein-coding genes (PCGs) were initiated by ATN codons except for the COI gene, which began with CGA codon. Eleven PCGs stopped with termination codon TAA, whereas the COI and COII genes ended with single T. All tRNAs have typical structures of insect mitochondrial tRNAs. The 494 bp AT-rich region contains several features common to other lepidopterans, such as some structures of repeated motifs and microsatellite-like elements and a poly-A element upstream of transfer RNA M (trnM) gene.
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Affiliation(s)
- Yong-Liang Zhang
- a College of Life Science and Agronomy, Zhoukou Normal University , Zhoukou City , Henan Province , China
| | - An-Quan Wu
- a College of Life Science and Agronomy, Zhoukou Normal University , Zhoukou City , Henan Province , China
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Zhang YL, Zhao JH, Zhou QM. The complete mitochondrial genome of Bombyx mori strain Jin6 (Lepidoptera: Bombycidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4168-4169. [PMID: 25600750 DOI: 10.3109/19401736.2014.1003896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, the complete mitochondrial genome of Bombyx mori strain Jin6 (Lepidoptera: Bombycidae) has been reported for the first time. It was a circular molecule of 15,648 bp in length, containing 37 typical coding genes and one non-coding AT-rich region. The overall composition of the mitogenome was A (43.05%), G (7.30%), C (11.35%), and T (38.29%). Its gene order and content were identical to the common type found in most insect mitogenomes. All protein coding genes (PCGs) started with a typical ATN initiation codon, except for the cox1 gene, which began with CGA codon. Eleven genes used standard complete termination codon TAA, whereas the cox1 and cox2 genes ended with single T. All tRNA genes displayed typical secondary cloverleaf structures as those of other insects. Additionally, the 494 bp long AT-rich region contained several structures common to the other lepidopterons, such as some structures of repeated motifs and microsatellite-like elements.
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Affiliation(s)
- Yong-Liang Zhang
- a College of Life Science and Agronomy, Zhoukou Normal University , Zhoukou City , Henan Province , China and
| | - Jin-Hui Zhao
- a College of Life Science and Agronomy, Zhoukou Normal University , Zhoukou City , Henan Province , China and
| | - Qi-Ming Zhou
- b Sericultural Science Research Institute of Henan Province , Nanyang City , Henan Province , China
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Zhang YL, Zhou QM. The complete mitochondrial genome of Bombyx mori strain Huayu (Lepidoptera: Bombycidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:2155-6. [PMID: 25431820 DOI: 10.3109/19401736.2014.982603] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of Bombyx mori strain Huayu (Lepidoptera: Bombycidae) is determined in this study. The genome was 15,666 bp long, with 37 typical animal mitochondrial genes and 1 non-coding A + T-rich region. Its gene content and order were identical to those of other lepidopteran mitochondrial genomes. All protein-coding genes (PCGs) were initiated by ATN codons except for the COI gene, which began with uncertained codon. Eleven PCGs stopped with termination codon TAA, whereas the COI and COII genes ended with single T. All tRNAs have typical structures of insect mitochondrial tRNAs. The 494 bp AT-rich region contains several features common to other lepidopterans, such as the motif ATAGA followed by an 18 bp poly-T stretch and an 11 bp poly-A element upstream of transfer RNA M (trnM) gene.
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Affiliation(s)
- Yong-Liang Zhang
- a College of Life Science and Agriculture, Zhoukou Normal University , Zhoukou City , Henan Province , China and
| | - Qi-Ming Zhou
- b Sericultural Science Research Institute of Henan province , Nanyang City , Henan Province , China
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Chen SC, Wei DD, Shao R, Shi JX, Dou W, Wang JJ. Evolution of multipartite mitochondrial genomes in the booklice of the genus Liposcelis (Psocoptera). BMC Genomics 2014; 15:861. [PMID: 25282613 PMCID: PMC4197233 DOI: 10.1186/1471-2164-15-861] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 09/29/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genus Liposcelis (Psocoptera: Troctomorpha) has more than 120 species with a worldwide distribution and they pose a risk for global food security. The organization of mitochondrial (mt) genomes varies between the two species of booklice investigated in the genus Liposcelis. Liposcelis decolor has its mt genes on a single chromosome, like most other insects; L. bostrychophila, however, has a multipartite mt genome with genes on two chromosomes. RESULTS To understand how multipartite mt genome organization evolved in the genus Liposcelis, we sequenced the mt genomes of L. entomophila and L. paeta in this study. We found that these two species of booklice also have multipartite mt genomes, like L. bostrychophila, with the mt genes we identified on two chromosomes. Numerous pseudo mt genes and non-coding regions were found in the mt genomes of these two booklice, and account for 30% and 10% respectively of the entire length we sequenced. In L. bostrychophila, the mt genes are distributed approximately equally between the two chromosomes. In L. entomophila and L. paeta, however, one mt chromosome has most of the genes we identified whereas the other chromosome has largely pseudogenes and non-coding regions. L. entomophila and L. paeta differ substantially from each other and from L. bostrychophila in gene content and gene arrangement in their mt chromosomes. CONCLUSIONS Our results indicate unusually fast evolution in mt genome organization in the booklice of the genus Liposcelis, and reveal different patterns of mt genome fragmentation among L. bostrychophila, L. entomophila and L. paeta.
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Affiliation(s)
| | | | | | | | | | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, P, R, China.
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Dai LS, Zhu BJ, Qian C, Zhang CF, Li J, Wang L, Wei GQ, Liu CL. The complete mitochondrial genome of the diamondback moth, Plutella xylostella (Lepidoptera: Plutellidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1512-3. [PMID: 25187437 DOI: 10.3109/19401736.2014.953116] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [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 Plutella xylostella (Lepidoptera: Plutellidae) was determined (GenBank accession No. KM023645). The length of this mitogenome is 16,014 bp with 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes and an A + T-rich region. It presents the typical gene organization and order for completely sequenced lepidopteran mitogenomes. The nucleotide composition of the genome is highly A + T biased, accounting for 81.48%, with a slightly positive AT skewness (0.005). All PCGs are initiated by typical ATN codons, except for the gene cox1, which uses CGA as its start codon. Some PCGs harbor TA (nad5) or incomplete termination codon T (cox1, cox2, nad2 and nad4), while others use TAA as their termination codons. The A + T-rich region is located between rrnS and trnM with a length of 888 bp.
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Affiliation(s)
- Li-Shang Dai
- a College of Life Science, Anhui Agricultural University , Hefei , China
| | - Bao-Jian Zhu
- a College of Life Science, Anhui Agricultural University , Hefei , China
| | - Cen Qian
- a College of Life Science, Anhui Agricultural University , Hefei , China
| | - Cong-Fen Zhang
- a College of Life Science, Anhui Agricultural University , Hefei , China
| | - Jun Li
- a College of Life Science, Anhui Agricultural University , Hefei , China
| | - Lei Wang
- a College of Life Science, Anhui Agricultural University , Hefei , China
| | - Guo-Qing Wei
- a College of Life Science, Anhui Agricultural University , Hefei , China
| | - Chao-Liang Liu
- a College of Life Science, Anhui Agricultural University , Hefei , China
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Liu QN, Bian DD, Jiang SH, Li ZX, Ge BM, Xuan FJ, Yang L, Li CF, Zhang DZ, Zhou CL, Tang BP. The complete mitochondrial genome of the red flour beetle, Tribolium castaneum (Coleoptera: Tenebrionidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1525-7. [PMID: 25162515 DOI: 10.3109/19401736.2014.953122] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome (mitogenome) of Tribolium castaneum (Coleoptera: Tenebrionidae) was determined to be 15,883 bp (GenBank accession No. KM009121), which contains 22 tRNA genes, 13 protein-coding genes (PCGs), 2 rRNA genes and a major non-coding A + T-rich region. It has the typical gene organization and order of mitogenomes from ancestral insects. The nucleotide composition was also biased toward A + T nucleotides (71.72%) and the AT skew of this mitogenome was slightly positive. All of the 22 tRNA genes displayed a typical clover-leaf structure, with the exception of trnS1 (AGN). Thirteen PCGs were initiated by ATN codons, except for cytochrome c oxidase subunit 1 (cox1) gene which was initiated by AAT. Eight of the 13 PCGs harbor the incomplete termination codon by T or TA. The A + T-rich region of the mitogenome was 1237 bp in length and the A + T content was 82.30%.
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Affiliation(s)
- Qiu-Ning Liu
- a Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources , Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University , Yancheng , P.R. China
| | - Dan-Dan Bian
- a Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources , Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University , Yancheng , P.R. China
| | - Sen-Hao Jiang
- a Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources , Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University , Yancheng , P.R. China
| | - Zhen-Xing Li
- a Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources , Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University , Yancheng , P.R. China
| | - Bao-Ming Ge
- a Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources , Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University , Yancheng , P.R. China
| | - Fu-Jun Xuan
- a Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources , Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University , Yancheng , P.R. China
| | - Li Yang
- a Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources , Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University , Yancheng , P.R. China
| | - Chao-Feng Li
- a Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources , Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University , Yancheng , P.R. China
| | - Dai-Zhen Zhang
- a Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources , Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University , Yancheng , P.R. China
| | - Chun-Lin Zhou
- a Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources , Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University , Yancheng , P.R. China
| | - Bo-Ping Tang
- a Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources , Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University , Yancheng , P.R. China
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Liu S, Xue D, Cheng R, Han H. The complete mitogenome of Apocheima cinerarius (Lepidoptera: Geometridae: Ennominae) and comparison with that of other lepidopteran insects. Gene 2014; 547:136-44. [PMID: 24967940 DOI: 10.1016/j.gene.2014.06.044] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 05/22/2014] [Accepted: 06/21/2014] [Indexed: 10/25/2022]
Abstract
The complete mitochondrial genome (mitogenome) of a female flightless geometrid moth Apocheima cinerarius was found to be 15,722 bp in length, containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region. The A+T content of the complete mitogenome is 80.83%. The AT skew value ([A-T]/[A+T]) is 0.027. The 13 PCGs of the mitogenome start with typical ATN codons, except for cox1 with the start codon CGA. All the tRNA genes have typical cloverleaf secondary structures, except for trnSer(AGN). The secondary structures of rrnL and rrnS were predicted. Six structural domains including conserved regions (IV, V) and variable regions (I, II, III, VI) were identified in the secondary structure of rrnL. The secondary structure of rrnS consists of 3 structural domains. The control region of A. cinerarius begins with conserved motifs of "ATAGA"+19-bp poly T. It also contains a microsatellite-like (TA)26, a stem-and-loop structure, and a poly-A stretch. Phylogenetic analysis showed that Geometroidea is more closely related to Bombycoidea than to Noctuoidea. A. cinerarius is more closely related to Biston panterinaria than to Phthonandria atrilineata, which is in accordance with the conventional morphology-based classification.
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Affiliation(s)
- Shuxian Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
| | - Dayong Xue
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Rui Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hongxiang Han
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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Liu QN, Zhu BJ, Dai LS, Wang L, Qian C, Wei GQ, Liu CL. The complete mitochondrial genome of the common cutworm, Spodoptera litura (Lepidoptera: Noctuidade). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:122-3. [PMID: 24491094 DOI: 10.3109/19401736.2013.873934] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome (mitogenome) of Spodoptera litura (Lepidoptera: Noctuidae) was determined to be 15,374 bp (GenBank accession No. KF543065), including 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and an A + T-rich region. It has the typical gene organization and order of mitogenomes from lepidopteran insects. The AT skew of this mitogenome was slightly positive and the nucleotide composition was also biased toward A + T nucleotides (81.03%). All PCGs were initiated by ATN codons, except for cytochrome c oxidase subunit 1 (cox1) gene which was initiated by CGA. Four of the 13 PCGs harbor the incomplete termination codon by T. All the tRNA genes displayed a typical clover-leaf structure of mitochondrial tRNA, with the exception of trnS1 (AGN). The A + T-rich region of the mitogenome was 326 bp in length.
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Affiliation(s)
- Qiu-Ning Liu
- a College of Life Science, Anhui Agricultural University , Hefei , People's Republic of China
| | - Bao-Jian Zhu
- a College of Life Science, Anhui Agricultural University , Hefei , People's Republic of China
| | - Li-Shang Dai
- a College of Life Science, Anhui Agricultural University , Hefei , People's Republic of China
| | - Lei Wang
- a College of Life Science, Anhui Agricultural University , Hefei , People's Republic of China
| | - Cen Qian
- a College of Life Science, Anhui Agricultural University , Hefei , People's Republic of China
| | - Guo-Qing Wei
- a College of Life Science, Anhui Agricultural University , Hefei , People's Republic of China
| | - Chao-Liang Liu
- a College of Life Science, Anhui Agricultural University , Hefei , People's Republic of China
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Zhu BJ, Liu QN, Dai LS, Wang L, Sun Y, Lin KZ, Wei GQ, Liu CL. Characterization of the complete mitochondrial genome of Diaphania pyloalis (Lepidoptera: Pyralididae). Gene 2013; 527:283-91. [PMID: 23810944 DOI: 10.1016/j.gene.2013.06.035] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/13/2013] [Accepted: 06/15/2013] [Indexed: 11/18/2022]
Abstract
The complete mitochondrial genome (mitogenome) of Diaphania pyloalis (Lepidoptera: Pyralididae) was determined to be 15,298 bp and has the typical gene organization of mitogenomes from lepidopteran insects. It consists of 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and an A+T-rich region. The A+T content of this mitogenome is 80.83% and the AT skew is slightly positive. All PCGs are initiated by ATN codons, except for cytochrome c oxidase subunit 1 (cox1) gene which is initiated by CGA. Only the cox2 gene has an incomplete stop codon consisting of just a T. All the tRNA genes display a typical clover-leaf structure of mitochondrial tRNA. The A+T-rich region of the mitogenome is 332 bp in length, including several common features found in lepidopteran mitogenomes. Phylogenetic analysis showed that the D. pyloalis is close to Pyralididae.
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Affiliation(s)
- Bao-Jian Zhu
- College of Life Science, Anhui Agricultural University, 130 Changjiang West Road, 230036, PR China
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