1
|
Shi Q, Xie J, Wu J, Chen S, Sun G, Zhang J. Characterization of the complete mitochondrial genome of an endemic species in China, Aulocera merlina (Lepidoptera: Nymphalidae: Satyrinae) and phylogenetic analysis within Satyrinae. Ecol Evol 2024; 14:e11355. [PMID: 38694754 PMCID: PMC11061544 DOI: 10.1002/ece3.11355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/01/2024] [Accepted: 04/12/2024] [Indexed: 05/04/2024] Open
Abstract
The mitochondrial genome (mitogenome) has been extensively used as molecular markers in determining the insect phylogenetic relationships. In order to resolve the relationships among tribes and subtribes of Satyrinae at the mitochondrial genomic level, we obtained the complete mitogenome of Aulocera merlina (Oberthür, 1890) (Lepidoptera: Nymphalidae: Satyrinae) with a size of 15,259 bp. The mitogenome consisted of 37 typical genes, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an A + T-rich region. The gene organization and arrangement were similar to those of all other known Satyrinae mitogenomes. All PCGs were initiated with the canonical codon pattern ATN, except for the cox1 gene, which used an atypical CGA codon. Nine PCGs used the complete stop codon TAA, while the remaining PCGs (cox1, cox2, nad4, and nad5) were terminated with a single T nucleotide. The canonical cloverleaf secondary structures were found in all tRNAs, except for trnS1 which lacked a dihydrouridine arm. The 448 bp A + T-rich region was located between rrnS and trnM, and it included the motif ATAGA followed by a 19-bp poly-T stretch and a microsatellite-like (TA)6 element preceded by the ATTTA motif. The phylogenetic tree, inferred using Bayesian inference and maximum likelihood methods, generated similar tree topologies, revealing well-supported monophyletic groups at the tribe level and recovering the relationship ((Satyrini + Melanitini) + ((Amathusiini + Elymniini) + Zetherini)). The close relationship between Satyrina and Melanargiina within the Satyrini was widely accepted. Additionally, Lethina, Parargina, and Mycalesina were closely related and collectively formed a sister group to Coenonymphina. Moreover, A. merlina was closely related to Oeneis buddha within the Satyrina. These findings will provide valuable information for future studies aiming to elucidate the phylogenetic relationships of Satyrinae.
Collapse
Affiliation(s)
- Qinghui Shi
- Fujian Provincial Key Laboratory of Resources and Environment Monitoring & Sustainable Management and UtilizationSanming UniversitySanmingChina
| | - Jinling Xie
- Fujian Provincial Key Laboratory of Resources and Environment Monitoring & Sustainable Management and UtilizationSanming UniversitySanmingChina
| | - Jialing Wu
- Fujian Provincial Key Laboratory of Resources and Environment Monitoring & Sustainable Management and UtilizationSanming UniversitySanmingChina
| | - Shengchung Chen
- Fujian Provincial Key Laboratory of Resources and Environment Monitoring & Sustainable Management and UtilizationSanming UniversitySanmingChina
| | - Gang Sun
- Fujian Provincial Key Laboratory of Resources and Environment Monitoring & Sustainable Management and UtilizationSanming UniversitySanmingChina
| | - Juncheng Zhang
- Fujian Provincial Key Laboratory of Resources and Environment Monitoring & Sustainable Management and UtilizationSanming UniversitySanmingChina
- Medical Plant Exploitation and Utilization Engineering Research CenterSanming UniversitySanmingChina
| |
Collapse
|
2
|
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.
Collapse
|
3
|
Zhao Y, Yang L, Chen Y, Zhang X, Li J, Liang D, Jiang S, Gao J, Meng Y. A Comparative Analysis of Bombyx mori (Lepidoptera: Bombycidae) β-fructofuranosidase Homologs Reveals Different Post-Translational Regulations in Glyphodes pyloalis Walker (Lepidoptera: Pyralidae). INSECTS 2022; 13:insects13050410. [PMID: 35621746 PMCID: PMC9143633 DOI: 10.3390/insects13050410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/13/2022] [Accepted: 04/17/2022] [Indexed: 12/03/2022]
Abstract
Simple Summary The β-fructofuranosidase (β-FFase) encoding gene BmSuc1 regulates the glycometabolism of silkworm larvae, and it participates in the resistance of mulberry alkaloids. However, there is no molecular or biochemical information available about the mulberry pest Glyphodespyloalis Walker β-FFase homologs. In this paper, we have obtained five β-FFase homologous genes in G. pyloalis and characterized the expression and the localization of GpSUC1a in the midgut. The β-FFase activity in the midgut of G. pyloalis larvae and GpSUC1a were both confirmed, while recombinant GpSUC1a displayed little activity as compared with the higher activity of BmSUC1. Some putative N-glycosylation sites were found in GpSUC1a but none in BmSUC1, while there was more methylation in BmSUC1 than in GpSUC1a. The results indicate that such post-translational modifications (PTMs) are differentially supporting that β-FFase are active in these two mulberry feeding caterpillars, and the activation of GpSUC1a may be controlled by a more complex post-translational regulatory system in G. pyloalis larvae. This is the first report on the characterization of β-FFase genes from G. pyloalis and the first comparison of expression regulation between two mulberry feeding insects B. mori and G. pyloalis. Moreover, this research may provide new ideas for the management of mulberry borers. Abstract The silk-spinning and Lepidopteran model insect Bombyx mori (Bombycidae) is a mulberry specialist. The BmSuc1 gene is the first β-fructofuranosidase (β-FFase) encoding gene identified in animals, and β-FFase acts as an essential sucrase for glycometabolism modulation in the silkworm larvae, involved in resistance to mulberry alkaloids. Glyphodes pyloalis Walker (Lepidoptera: Pyralidae) is an important mulberry pest leading to heavy economic loss of sericulture. However, no molecular or biochemical information is available about G. pyloalis β-FFase homologs. In this study, five β-FFase homologous genes in G. pyloalis were obtained. The genes GpSuc1a and GpSuc2c were expressed in the midgut; GpSuc2c encodes a truncated polypeptide. The expression and the localization of GpSUC1a in the midgut was characterized. Whereas recombinant GpSUC1a expressed in both Escherichia coli and BmN cells displayed little activity as compared with higher activity of BmSUC1, β-FFase activity in the larval midgut of G. pyloalis and GpSUC1a purified from the midgut were both confirmed. The data suggested that the activation of GpSUC1a is probably controlled by a more complicated post-translational regulation system in G. pyloalis larvae than that of BmSUC1 in B. mori. To study post-translational modifications (PTMs), GpSUC1a and BmSUC1 were purified from larval midguts using immunoprecipitation and subjected to LC-MS to perform PTMs analysis. Some putative N-glycosylated sites were found in GpSUC1a but none in BmSUC1, while there was more methylation in BmSUC1 than in GpSUC1a, indicating that such PTMs were supporting the differential β-FFases activities in these two mulberry feeding caterpillars.
Collapse
Affiliation(s)
- Yue Zhao
- School of Life Sciences, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China; (Y.Z.); (L.Y.); (Y.C.); (X.Z.); (J.L.); (D.L.); (S.J.); (J.G.)
- Anhui International Joint Research and Development Center of Sericulture Resources Utilization, 130 West Changjiang Road, Hefei 230036, China
| | - Liangli Yang
- School of Life Sciences, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China; (Y.Z.); (L.Y.); (Y.C.); (X.Z.); (J.L.); (D.L.); (S.J.); (J.G.)
- Anhui International Joint Research and Development Center of Sericulture Resources Utilization, 130 West Changjiang Road, Hefei 230036, China
| | - Yu Chen
- School of Life Sciences, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China; (Y.Z.); (L.Y.); (Y.C.); (X.Z.); (J.L.); (D.L.); (S.J.); (J.G.)
| | - Xinwei Zhang
- School of Life Sciences, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China; (Y.Z.); (L.Y.); (Y.C.); (X.Z.); (J.L.); (D.L.); (S.J.); (J.G.)
- Department of Pathology, Henan Provincial People’s Hospital, 7 Weiwu Road, Zhengzhou 450003, China
| | - Jing Li
- School of Life Sciences, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China; (Y.Z.); (L.Y.); (Y.C.); (X.Z.); (J.L.); (D.L.); (S.J.); (J.G.)
| | - Dan Liang
- School of Life Sciences, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China; (Y.Z.); (L.Y.); (Y.C.); (X.Z.); (J.L.); (D.L.); (S.J.); (J.G.)
- Anhui International Joint Research and Development Center of Sericulture Resources Utilization, 130 West Changjiang Road, Hefei 230036, China
| | - Song Jiang
- School of Life Sciences, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China; (Y.Z.); (L.Y.); (Y.C.); (X.Z.); (J.L.); (D.L.); (S.J.); (J.G.)
- Anhui International Joint Research and Development Center of Sericulture Resources Utilization, 130 West Changjiang Road, Hefei 230036, China
| | - Junshan Gao
- School of Life Sciences, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China; (Y.Z.); (L.Y.); (Y.C.); (X.Z.); (J.L.); (D.L.); (S.J.); (J.G.)
- Anhui International Joint Research and Development Center of Sericulture Resources Utilization, 130 West Changjiang Road, Hefei 230036, China
| | - Yan Meng
- School of Life Sciences, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China; (Y.Z.); (L.Y.); (Y.C.); (X.Z.); (J.L.); (D.L.); (S.J.); (J.G.)
- Anhui International Joint Research and Development Center of Sericulture Resources Utilization, 130 West Changjiang Road, Hefei 230036, China
- Correspondence: ; Tel./Fax: +86-551-65786967
| |
Collapse
|
4
|
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.
Collapse
|
5
|
Yang L, Dai J, Gao Q, Yuan G, Liu J, Sun Y, Sun Y, Wang L, Qian C, Zhu B, Liu C, Wei G. Characterization of the complete mitochondrial genome of Orthaga olivacea Warre (Lepidoptera Pyralidae) and comparison with other Lepidopteran insects. PLoS One 2020; 15:e0227831. [PMID: 32142522 PMCID: PMC7059908 DOI: 10.1371/journal.pone.0227831] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 12/30/2019] [Indexed: 02/01/2023] Open
Abstract
Orthaga olivacea Warre (Lepidoptera: Pyralidae) is an important agricultural pest of camphor trees (Cinnamomum camphora). To further supplement the known genome-level features of related species, the complete mitochondrial genome of Orthaga olivacea is amplified, sequenced, annotated, analyzed, and compared with 58 other species of Lepidopteran. The complete sequence is 15,174 bp, containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a putative control region. Base composition is biased toward adenine and thymine (79.02% A+T) and A+T skew are slightly negative. Twelve of the 13 PCGs use typical ATN start codons. The exception is cytochrome oxidase 1 (cox1) that utilizes a CGA initiation codon. Nine PCGs have standard termination codon (TAA); others have incomplete stop codons, a single T or TA nucleotide. All the tRNA genes have the typical clover-leaf secondary structure, except for trnS(AGN), in which dihydrouridine (DHU) arm fails to form a stable stem-loop structure. The A+T-rich region (293 bp) contains a typical Lepidopter motifs 'ATAGA' followed by a 17 bp poly-T stretch, and a microsatellite-like (AT)13 repeat. Codon usage analysis revealed that Asn, Ile, Leu2, Lys, Tyr and Phe were the most frequently used amino acids, while Cys was the least utilized. Phylogenetic analysis suggested that among sequenced lepidopteran mitochondrial genomes, Orthaga olivacea Warre was most closely related to Hypsopygia regina, and confirmed that Orthaga olivacea Warre belongs to the Pyralidae family.
Collapse
Affiliation(s)
- Liangli Yang
- School of Life Sciences, Anhui Agricultural University, Hefei, P. R. China
| | - Junjun Dai
- Sericultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, P. R. China
| | - Qiuping Gao
- School of Life Sciences, Anhui Agricultural University, Hefei, P. R. China
| | - Guozhen Yuan
- School of Life Sciences, Anhui Agricultural University, Hefei, P. R. China
| | - Jiang Liu
- School of Life Sciences, Anhui Agricultural University, Hefei, P. R. China
| | - Yu Sun
- School of Life Sciences, Anhui Agricultural University, Hefei, P. R. China
| | - Yuxuan Sun
- School of Life Sciences, Anhui Agricultural University, Hefei, P. R. China
| | - Lei Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, P. R. China
| | - Cen Qian
- School of Life Sciences, Anhui Agricultural University, Hefei, P. R. China
| | - Baojian Zhu
- School of Life Sciences, Anhui Agricultural University, Hefei, P. R. China
| | - Chaoliang Liu
- School of Life Sciences, Anhui Agricultural University, Hefei, P. R. China
| | - Guoqing Wei
- School of Life Sciences, Anhui Agricultural University, Hefei, P. R. China
| |
Collapse
|
6
|
Complete mitochondrial genome of Atractomorpha sagittaris (Orthoptera: Pyrgomorphidae) and its phylogenetic analysis for Acrididea. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-019-00402-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
7
|
Wang T, Zhang S, Pei T, Yu Z, Liu J. The Complete Mitochondrial Genome and Expression Profile of Mitochondrial Protein-Coding Genes in the Bisexual and Parthenogenetic Haemaphysalis longicornis. Front Physiol 2019; 10:982. [PMID: 31417433 PMCID: PMC6682753 DOI: 10.3389/fphys.2019.00982] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/15/2019] [Indexed: 11/13/2022] Open
Abstract
The tick Haemaphysalis longicornis is widely distributed in eastern Asia, New Zealand and Australia, and is well-known as a vector of multiple zoonotic pathogens. This species exhibits two reproductive strategies, bisexual and obligate parthenogenetic reproduction. Hence, in the current study, the complete mitochondrial genomes of the bisexual and parthenogenetic populations were assembled and analyzed, and the expression of the mitochondrial protein-coding genes was evaluated and compared between the two reproductive populations. The results indicated that the length of the mitochondrial genomes of the two reproductive populations is 14,694 and 14,693 bp in the bisexual and parthenogenetic populations, respectively. The AT content in the mitochondrial genome of the bisexual and obligate parthenogenetic population reached 77.22 and 77.34%, respectively. The phylogenetic tree was constructed combining 13 protein-coding genes, which showed that the genetic distance between the bisexual and parthenogenetic populations was less than that between the subspecies. The expression of the mitochondrial protein-coding genes was quantitatively analyzed at different feeding status for the bisexual and parthenogenetic populations, and the results showed significant differences in the expression patterns of these genes, suggesting that they might trigger specific energy utilization mechanisms due to their different reproductive strategies and environmental pressures.
Collapse
Affiliation(s)
- Tianhong Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Shiqi Zhang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Tingwei Pei
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Zhijun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| |
Collapse
|
8
|
Han Y, Huang Z, Tang J, Chiba H, Fan X. The complete mitochondrial genomes of two skipper genera (Lepidoptera: Hesperiidae) and their associated phylogenetic analysis. Sci Rep 2018; 8:15762. [PMID: 30361496 PMCID: PMC6202373 DOI: 10.1038/s41598-018-34107-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 10/11/2018] [Indexed: 11/08/2022] Open
Abstract
The systematic positions of two hesperiid genera, Apostictopterus and Barca (Lepidoptera: Hesperiidae), remain ambiguous. We sequenced and annotated the two mitogenomes of Apostictopterus fuliginosus and Barca bicolor and inferred the phylogenetic positions of the two genera within the Hesperiidae based on the available mitogenomes. The lengths of the two circular mitogenomes of A. fuliginosus and B. bicolor are 15,417 and 15,574 base pairs (bp), respectively. These two mitogenomes show similar AT skew, GC skew, codon usage and nucleotide bias of AT: the GC skew of the two species is negative, and the AT skew of A. fuliginosus is negative, while the AT skew of B. bicolor is slightly positive. The largest intergenic spacer is located at the same position between trnQ and ND2 in A. fuliginosus (73 bp) and B. bicolor (72 bp). Thirteen protein-coding genes (PCGs) start with ATN codons except for COI, which starts with CGA. The control regions of both mitogenomes possess a long tandem repeat, which is 30 bp long in A. fuliginosus, and 18 bp in B. bicolor. Bayesian inference and maximum likelihood methods were employed to infer the phylogenetic relationships, which suggested that A. fuliginosus and B. bicolor belong in the subfamily Hesperiinae.
Collapse
Affiliation(s)
- Yuke Han
- Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Zhenfu Huang
- Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Jing Tang
- Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | | | - Xiaoling Fan
- Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
| |
Collapse
|
9
|
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)))).
Collapse
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.
| |
Collapse
|
10
|
Potential of Visible and Near-Infrared Hyperspectral Imaging for Detection of Diaphania pyloalis Larvae and Damage on Mulberry Leaves. SENSORS 2018; 18:s18072077. [PMID: 29958467 PMCID: PMC6068755 DOI: 10.3390/s18072077] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/16/2018] [Accepted: 06/26/2018] [Indexed: 11/17/2022]
Abstract
Mulberry trees are an important crop for sericulture. Pests can affect the yield and quality of mulberry leaves. This study aims to develop a hyperspectral imaging system in visible and near-infrared (NIR) region (400⁻1700 nm) for the rapid identification of Diaphania pyloalis larvae and its damage. The extracted spectra of five region of interests (ROI), namely leaf vein, healthy mesophyll, slight damage, serious damage, and Diaphania pyloalis larva at 400⁻1000 nm (visible range) and 900⁻1700 nm (NIR range), were used to establish a partial least squares discriminant analysis (PLS-DA) and least-squares support vector machines (LS-SVM) models. Successive projections algorithm (SPA), uninformation variable elimination (UVE), UVE-SPA, and competitive adaptive reweighted sampling were used for variable selection. The best models in distinguishing between leaf vein, healthy mesophyll, slight damage and serious damage, leaf vein, healthy mesophyll, and larva, slight damage, serious damage, and larva were all the SPA-LS-SVM models, based on the NIR range data, and their correct rate of prediction (CRP) were all 100.00%. The best model for the identification of all five ROIs was the UVE-SPA-LS-SVM model, based on visible range data, which had the CRP value of 97.30%. In summary, visible and near infrared hyperspectral imaging could distinguish Diaphania pyloalis larvae and their damage from leaf vein and healthy mesophyll in a rapid and non-destructive way.
Collapse
|
11
|
The complete mitochondrial genome of Vanessa indica and phylogenetic analyses of the family Nymphalidae. Genes Genomics 2018; 40:1011-1022. [PMID: 29949077 DOI: 10.1007/s13258-018-0709-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/29/2018] [Indexed: 02/02/2023]
Abstract
Vanessa indica is a small butterfly lacking historical molecular and biological research. Vanessa indica belongs to the family Nymphalidae (Lepidoptera: Papilionoidea), which is the largest group of butterflies and are nearly ubiquitous. However, after more than a century of taxonomic and molecular studies, there is no consensus for family classification, and the phylogenetic relationships within Nymphalidae are controversial. The first objective was to sequence and characterize the complete mitochondrial genome of V. indica. The most important objective was to completely reconstruct the phylogenetic relationships for family members within Nymphalidae. The mitochondrial genomic DNA (mtDNA) of V. indica was extracted and amplified by polymerase chain reaction. The complete mitochondrial sequence was annotated and characterized by analyzing sequences with SeqMan program. The phylogenetic analyses were conducted on thirteen protein coding genes (PCGs) in 95 mtDNA of Nymphalidae downloaded from GenBank for reference using the maximum likelihood method and Bayesian inference to ensure the validity of the results. The complete mitogenome was a circular molecule with 15,191 bp consisting of 13 protein coding genes, two ribosomal RNA genes (16S rRNA and 12S rRNA), 22 transfer RNA (tRNA) genes, and an A + T-rich region (D-loop). The nucleotide composition of the genome was highly biased for A + T content, which accounts for 80.0% of the nucleotides. All the tRNAs have putative secondary structures that are characteristic of mitochondrial tRNAs, except tRNASer(AGN). All the PCGs started with ATN codons, except cytochrome c oxidase subunit 1 (COX1), which was found to start with an unusual CGA codon. Four genes were observed to have unusual codons: COX1 terminated with atypical TT and the other three genes terminated with a single T. The A + T rich region of 327 bp consisted of repetitive sequences, including a ATAGA motif, a 19-bp poly-T stretch, and two microsatellite-like regions (TA)8. The phylogenetic analyses consistently placed Biblidinae as a sister cluster to Heliconiinae and Calinaginae as a sister clade to Satyrinae. Moreover, the phylogenetic tree identified Libytheinae as a monophyletic group within Nymphalidae. The complete mitogenome of V. indica was 15,191 bp with mitochondrial characterizations common for lepidopteran species, which enriched the mitochondria data of Nymphalid species. And the phylogenetic analysis revealed different classifications and relationships than those previously described. Our results are significant because they would be useful in further understanding of the evolutionary biology of Nymphalidae.
Collapse
|
12
|
Liu N, Li N, Yang P, Sun C, Fang J, Wang S. The complete mitochondrial genome of Damora sagana and phylogenetic analyses of the family Nymphalidae. Genes Genomics 2017; 40:109-122. [PMID: 29892904 DOI: 10.1007/s13258-017-0614-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 09/26/2017] [Indexed: 11/30/2022]
Abstract
The monotypic genus Damora (Nymphalidae, Heliconiinae) contains a single species, Damora sagana, which is widely distributed across southern China. Herein, its complete mitogenome was sequenced to further understand lepidopteran mitogenome characteristics, reconstruct the nymphalid family phylogeny, and infer the subdivision of Heliconiinae species. The circular mitogenome was 15,151 bp long, abundant in A and T, and comprised of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and one control region with a gene arrangement typical of lepidopteran mitogenomes. ATN codons initiated all PCGs, except cytochrome c oxidase subunit 1 (COX1), which was initiated by a CGA sequence as has been observed in other lepidopterans. Three PCGs (COX1, COX2 and ND4) employed a single T termination signal, whereas others had the typical complete termination codon (TAA). All tRNA genes were folded into the typical cloverleaf structure except for tRNA-Ser (AGN). The A+T-rich region included the conserved motif 'ATAGA' followed by a 17 bp poly-T stretch, which was also observed in tribe Argynnini mitogenomes. A phylogenetic tree was constructed via multiple methods using the 13 PCGs data of D. sagana and other available mitogenomes of nymphalid species. All three phylogenetic trees yielded the same topology. These results were consistent with those from previous studies of most major nymphalid groups, except those regarding tribe subdivision in certain subfamilies such as Argynnini + (Acraeini + Heliconiini) for Heliconiine. Furthermore, our analyses identified that the genus Cethosia was grouped with the genus Acraea composing the tribe Acraeini with strong support.
Collapse
Affiliation(s)
- Naiyi Liu
- School of Life Sciences, Anhui University, Hefei, China
| | - Na Li
- School of Life Sciences, Anhui University, Hefei, China
| | - Pengyu Yang
- School of Life Sciences, Anhui University, Hefei, China
| | - Chunqin Sun
- School of Life Sciences, Anhui University, Hefei, China
| | - Jie Fang
- School of Life Sciences, Anhui University, Hefei, China.
| | - Shuyan Wang
- School of Life Sciences, Anhui University, Hefei, China.
| |
Collapse
|
13
|
Xin ZZ, Yu-Liu, Zhang DZ, Wang ZF, Zhang HB, Tang BP, Zhou CL, Chai XY, Liu QN. Mitochondrial genome of Helice tientsinensis (Brachyura: Grapsoidea: Varunidae): Gene rearrangements and higher-level phylogeny of the Brachyura. Gene 2017. [DOI: 10.1016/j.gene.2017.06.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Wu L, Xiong X, Wang X, Xin T, Wang J, Zou Z, Xia B. The complete mitochondrial genome of Trabala vishnou guttata (Lepidoptera: Lasiocampidae) and the related phylogenetic analyses. Genetica 2016; 144:675-688. [PMID: 27770241 DOI: 10.1007/s10709-016-9934-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 10/17/2016] [Indexed: 10/20/2022]
Abstract
The bluish yellow lappet moth, Trabala vishnou guttata is an extraordinarily important pest in China. The complete mitochondrial genome is sequenced and determined firstly, which is based on traditional PCR amplification and primer walking methods with a length of 15,281 bp, including 13 protein-coding (PCG) genes, 22 transfer RNA (rRNA) genes, two ribosomal RNA (tRNA) genes, and an A + T-rich region. The gene order and orientation of the T. vishnou guttata mitogenome were identical to the other sequenced Lasiocampidae species. The overall nucleotide composition of T. vishnou guttata is A (40.27 %), T (40.59 %), C (11.58 %) and G (7.56 %), respectively. All the PCGs initiate with the three orthodox start codons ATN except for coxI with CGA start codon. Three PCGs (coxI, coxII and nad4) used incomplete stop codon T, while the other 10 PCGs terminate with complete stop codon TAA. All tRNA genes have a typical clover-leaf structure except for the absence of a dihydrouridine arm in trnS (AGN). The length of A + T-rich region is 383 bp. Phylogeny is established to reveal the genetic relationship between T. vishnou guttata and other lepidopteran species based on 13 PCGs nucleotide sequences of the sequenced species (32 taxa) by Maximum likelihood and Bayesian methods. Phylogenetic analyses presents that T. vishnou guttata and its closely related species (Dendrolimus taxa) are clustered on Lasiocampidae group. It is a sister clade relationship between Lasiocampidae and other families in Bombycoidea with a bootstrap value of 83 % and a posterior probability of 0.75. This study supports that Lasiocampidae may be independent from Bombycoidea.
Collapse
Affiliation(s)
- Liuyu Wu
- College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Xiao Xiong
- College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Xuming Wang
- Plant Protection Unit, Dayu County, Ganzhou, 341500, China
| | - Tianrong Xin
- College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Jing Wang
- College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Zhiwen Zou
- College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Bin Xia
- College of Life Science, Nanchang University, Nanchang, 330031, China.
| |
Collapse
|
16
|
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))))).
Collapse
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
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
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.
Collapse
|
19
|
Shi X, Tian P, Lin R, Huang D, Wang J. Characterization of the Complete Mitochondrial Genome Sequence of the Globose Head Whiptail Cetonurus globiceps (Gadiformes: Macrouridae) and Its Phylogenetic Analysis. PLoS One 2016; 11:e0153666. [PMID: 27093057 PMCID: PMC4836748 DOI: 10.1371/journal.pone.0153666] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 04/01/2016] [Indexed: 11/19/2022] Open
Abstract
The particular environmental characteristics of deep water such as its immense scale and high pressure systems, presents technological problems that have prevented research to broaden our knowledge of deep-sea fish. Here, we described the mitogenome sequence of a deep-sea fish, Cetonurus globiceps. The genome is 17,137 bp in length, with a standard set of 22 transfer RNA genes (tRNAs), two ribosomal RNA genes, 13 protein-coding genes, and two typical non-coding control regions. Additionally, a 70 bp tRNA(Thr)-tRNA(Pro) intergenic spacer is present. The C. globiceps mitogenome exhibited strand-specific asymmetry in nucleotide composition. The AT-skew and GC-skew values in the whole genome of C. globiceps were 0 and -0.2877, respectively, revealing that the H-strand had equal amounts of A and T and that the overall nucleotide composition was C skewed. All of the tRNA genes could be folded into cloverleaf secondary structures, while the secondary structure of tRNA(Ser(AGY)) lacked a discernible dihydrouridine stem. By comparing this genome sequence with the recognition sites in teleost species, several conserved sequence blocks were identified in the control region. However, the GTGGG-box, the typical characteristic of conserved sequence block E (CSB-E), was absent. Notably, tandem repeats were identified in the 3' portion of the control region. No similar repetitive motifs are present in most of other gadiform species. Phylogenetic analysis based on 12 protein coding genes provided strong support that C. globiceps was the most derived in the clade. Some relationships however, are in contrast with those presented in previous studies. This study enriches our knowledge of mitogenomes of the genus Cetonurus and provides valuable information on the evolution of Macrouridae mtDNA and deep-sea fish.
Collapse
Affiliation(s)
- Xiaofeng Shi
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, P.R. China
| | - Peng Tian
- Ocean College, Zhejiang University Hangzhou, P.R. China
| | - Rongcheng Lin
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, P.R. China
| | - Dingyong Huang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, P.R. China
| | - Jianjia Wang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, P.R. China
| |
Collapse
|
20
|
Dong WW, Dong SY, Jiang GF, Huang GH. Characterization of the complete mitochondrial genome of tea tussock moth, Euproctis pseudoconspersa (Lepidoptera: Lymantriidae) and its phylogenetic implications. Gene 2016; 577:37-46. [DOI: 10.1016/j.gene.2015.11.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 10/03/2015] [Accepted: 11/16/2015] [Indexed: 11/15/2022]
|
21
|
Ma L, Dong WW, Jiang GF, Wang X. The Complete Mitochondrial Genome of Brachmia macroscopa (Lepidoptera: Gelechiidae) and Its Related Phylogenetic Analysis. JOURNAL OF INSECT SCIENCE (ONLINE) 2016; 16:9. [PMID: 26810560 PMCID: PMC4725263 DOI: 10.1093/jisesa/iev157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 12/11/2015] [Indexed: 06/05/2023]
Abstract
The sweet potato leaf folder, Brachmia macroscopa, is an important pest in China. The complete mitogenome, which consists of 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and an A + T-rich region, was sequenced and found to be 15,394 bp in length (GeneBank no. KT354968). The gene order and orientation of the B. macroscopa mitogenome were similar to those of other sequenced lepidopteran species. All of the PCGs started with ATN as the canonical start codon except for cox1, which started with CGA. In regard to stop codons, most PCGs stopped at TAA except for cox2, which stopped at TA, and nad4, which stopped at a single T. Thirteen PCGs of the available species (33 taxa) were used to demonstrate phylogenetic relationships. The ditrysian cluster was supported as a monophyletic clade at high levels by using maximum likelihood and Bayesian methods. The apoditrysian group, covering the Gelechioidea, formed a monophyletic clade with a bootstrap value of 88% and a posterior probability of 1.00. The superfamily Gelechioidea was supported as a monophyletic lineage by a posterior probability of 1.00.
Collapse
Affiliation(s)
- Li Ma
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Wan-Wei Dong
- Jiangsu Key Laboratory for Bioresource Technology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China, and
| | - Guo-Fang Jiang
- Jiangsu Key Laboratory for Bioresource Technology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China, and
| | - Xing Wang
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan 410128, China ,
| |
Collapse
|
22
|
Ramírez-Ríos V, Franco-Sierra ND, Alvarez JC, Saldamando-Benjumea CI, Villanueva-Mejía DF. Mitochondrial genome characterization of Tecia solanivora (Lepidoptera: Gelechiidae) and its phylogenetic relationship with other lepidopteran insects. Gene 2016; 581:107-16. [PMID: 26802972 DOI: 10.1016/j.gene.2016.01.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 01/13/2016] [Accepted: 01/15/2016] [Indexed: 01/07/2023]
Abstract
The complete mitogenome of the potato tuber moth Tecia solanivora (Lepidoptera: Gelechiidae) was sequenced, annotated, characterized and compared with 140 species of the order Lepidoptera. The circular genome is 15,251 bp, containing 37 genes (13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and an A+T-rich region). The gene arrangement was identical to other lepidopteran mitogenomes but different from the ancestral arrangement found in most insects for the tRNA-Met gene (A+T-region, tRNA-I, tRNA-Q, tRNA-M). The mitogenome of T. solanivora is highly A+T-biased (78.2%) and exhibits negative AT- and GC-skews. All PCGs are initiated by canonical ATN start codons, except for Cytochrome Oxidase subunit 1 (COI), which is initiated by CGA. Most PCGs have a complete typical stop codon (TAA). Only NAD1 has a TAG stop codon and the COII and NAD5 genes have an incomplete stop codon consisting of just a T. The A+T-rich region is 332 bp long and contains common features found in lepidopteran mitogenomes, including the 'ATAGA' motif, a 17 bp poly (T) stretch and a (AT)8 element preceded by the 'ATTTA' motif. Other tandem repeats like (TAA)4 and (TAT)7 were found, as well as (T)6 and (A)10 mononucleotide repeat elements. Finally, this mitogenome has 20 intergenic spacer regions. The phylogenetic relationship of T. solanivora with 28 other lepidopteran families (12 superfamilies) showed that taxonomic classification by morphological features coincides with the inferred phylogeny. Thus, the Gelechiidae family represents a monophyletic group, suggesting that T. solanivora and Pectinophora gossypiella have a recent common ancestor.
Collapse
Affiliation(s)
- Viviana Ramírez-Ríos
- Departamento de Ciencias Biológicas, Escuela de Ciencias, Universidad EAFIT, Medellín, Antioquia, Colombia
| | - Nicolás D Franco-Sierra
- Departamento de Ciencias Biológicas, Escuela de Ciencias, Universidad EAFIT, Medellín, Antioquia, Colombia
| | - Javier Correa Alvarez
- Departamento de Ciencias Biológicas, Escuela de Ciencias, Universidad EAFIT, Medellín, Antioquia, Colombia
| | - Clara I Saldamando-Benjumea
- Escuela de Biociencias, Facultad de Ciencias, Universidad Nacional de Colombia, sede Medellín, Antioquía, Colombia.
| | - Diego F Villanueva-Mejía
- Departamento de Ciencias Biológicas, Escuela de Ciencias, Universidad EAFIT, Medellín, Antioquia, Colombia
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
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]
|
26
|
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]
|
27
|
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.
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
Kong W, Yang J. The complete mitochondrial genome of Diaphania pyloalis Walker (Lepidoptera: Crambidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4044-4045. [PMID: 25629474 DOI: 10.3109/19401736.2014.1003836] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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 Diaphania pyloalis Walker collected from China was reported and characterized. The mitogenome was 14,960 bp in length, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 short A + T-rich region. The A + T content of the mitochondrial genome is 80.77%. All protein-coding genes were initiated by an ATN codon, except for coxI gene which is initiated by CGA. Only coxII gene was terminated with a single T. There are 13 overlaps totaling 52 bp, and 13 intergenic spacer regions totaling 121 bp in the D. pyloalis mitogenome. The short A + T-rich region is 67 bp long, with 91.04% A + T content.
Collapse
Affiliation(s)
- Weiqing Kong
- a The Key Sericultural Laboratory of Shaanxi , Ankang University , Ankang , Shaanxi , PR China
| | - Jinhong Yang
- a The Key Sericultural Laboratory of Shaanxi , Ankang University , Ankang , Shaanxi , PR China
| |
Collapse
|
30
|
Wei L, He J, Jia X, Qi Q, Liang Z, Zheng H, Ping Y, Liu S, Sun J. Analysis of codon usage bias of mitochondrial genome in Bombyx mori and its relation to evolution. BMC Evol Biol 2014; 14:262. [PMID: 25515024 PMCID: PMC4276022 DOI: 10.1186/s12862-014-0262-4] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 12/09/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Synonymous codon usage bias (SCUB) is an inevitable phenomenon in organismic taxa, generally referring to differences in the occurrence frequency of codons across different species or within the genome of the same species. SCUB happens in various degrees under pressure from nature selection, mutation bias and other factors in different ways. It also attaches great significance to gene expression and species evolution, however, a systematic investigation towards the codon usage in Bombyx mori (B. mori) has not been reported yet. Moreover, it is still indistinct about the reasons contributing to the bias or the relationship between the bias and the evolution of B. mori. RESULTS The comparison of the codon usage pattern between the genomic DNA (gDNA) and the mitochondrial DNA (mtDNA) from B. mori suggests that mtDNA has a higher level of codon bias. Furthermore, the correspondence analysis suggests that natural selection, such as gene length, gene function and translational selection, dominates the codon preference of mtDNA, while the composition constraints for mutation bias only plays a minor role. Additionally, the clustering results of the silkworm superfamily suggest a lack of explicitness in the relationship between the codon usage of mitogenome and species evolution. CONCLUSIONS Among the complicated influence factors leading to codon bias, natural selection is found to play a major role in shaping the high bias in the mtDNA of B. mori from our current data. Although the cluster analysis reveals that codon bias correlates little with the species evolution, furthermore, a detailed analysis of codon usage of mitogenome provides better insight into the evolutionary relationships in Lepidoptera. However, more new methods and data are needed to investigate the relationship between the mtDNA bias and evolution.
Collapse
Affiliation(s)
- Lei Wei
- Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
| | - Jian He
- Guangzhou East Campus Lab Center, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Xian Jia
- Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
| | - Qi Qi
- Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
| | - Zhisheng Liang
- Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
| | - Hao Zheng
- Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
| | - Yao Ping
- Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
| | - Shuyu Liu
- Guangzhou East Campus Lab Center, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Jingchen Sun
- Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
| |
Collapse
|
31
|
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.
Collapse
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
| |
Collapse
|
32
|
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%.
Collapse
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
| |
Collapse
|
33
|
Dong WW, Jiang GF. Characterization of the mitochondrial genome of the threatened alpine butterfly, Parnassius nomion (Lepidoptera: Papilionidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1107-8. [PMID: 24989052 DOI: 10.3109/19401736.2014.933322] [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 sequenced mitochondrial genome of the threatened alpine butterfly Parnassius nomion includes 13 protein-coding genes (ND1-6, COI-III, ATP6, ATP8, ND4, ND4L, CTYB), 2 ribosomal RNAs (12 S and 16 S), 22 transfer RNAs, which is 14,547 bp in length. Its gene order and orientation are identical to the common type found in most of other completely sequenced lepidopteran mitogenomes. All protein-coding genes are initiated by ATN codons, except for COI, which uses CGA as its start codon. Eleven PCGs use the standard TAA as their termination codon, and COI, COII use the incomplete termination codon T.
Collapse
Affiliation(s)
- Wan-Wei Dong
- a Jiangsu Key Laboratory for Bioresource Technology , College of Life Sciences, Nanjing Normal University , Nanjing , P.R. China
| | - Guo-Fang Jiang
- a Jiangsu Key Laboratory for Bioresource Technology , College of Life Sciences, Nanjing Normal University , Nanjing , P.R. China
| |
Collapse
|
34
|
Dong WW, Feng XJ, Huang GH, Jiang GF. Characterization of the mitochondrial genome of the cabbage webworm, Hellula undalis (Lepidoptera: Pyralidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:931-2. [PMID: 24919505 DOI: 10.3109/19401736.2014.926491] [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 sequenced mitochondrial genome of the cabbage webworm Hellula undalis includes 13 protein-coding genes (PCGs) (nad1-6, cox1-3, atp6, atp8, nad4L and cob), two ribosomal RNAs (12S and 16S) and 19 transfer RNAs, which is 14,678 bp in length. Its gene order and orientation are identical to the common types found in most of the other completely sequenced lepidopteran mitogenomes. Thirteen PCGs start with a typical ATN codon, while cox1 uses CGA as its start codon. Some PCGs use the standard TAA as their termination codon, while others use the incomplete termination codon T (cox1, cox2 and nad4).
Collapse
Affiliation(s)
- Wan-Wei Dong
- a Jiangsu Key Laboratory for Bioresource Technology , College of Life Sciences, Nanjing Normal University , Nanjing , Jiangsu , China and
| | - Xiao-Jing Feng
- a Jiangsu Key Laboratory for Bioresource Technology , College of Life Sciences, Nanjing Normal University , Nanjing , Jiangsu , China and
| | - Guo-Hua Huang
- b Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests , Hunan Agricultural University , Changsha , Hunan , China
| | - Guo-Fang Jiang
- a Jiangsu Key Laboratory for Bioresource Technology , College of Life Sciences, Nanjing Normal University , Nanjing , Jiangsu , China and
| |
Collapse
|
35
|
Niu FF, Fan XL, Wei SJ. Complete mitochondrial genome of theGrapholita dimorphaKomai (Lepidoptera: Tortricidae). ACTA ACUST UNITED AC 2014; 27:775-6. [DOI: 10.3109/19401736.2014.915536] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
36
|
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.
Collapse
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
| |
Collapse
|
37
|
Idiosyncrasies in decoding mitochondrial genomes. Biochimie 2014; 100:95-106. [PMID: 24440477 DOI: 10.1016/j.biochi.2014.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 01/06/2014] [Indexed: 11/24/2022]
Abstract
Mitochondria originate from the α-proteobacterial domain of life. Since this unique event occurred, mitochondrial genomes of protozoans, fungi, plants and metazoans have highly derived and diverged away from the common ancestral DNA. These resulting genomes highly differ from one another, but all present-day mitochondrial DNAs have a very reduced coding capacity. Strikingly however, ATP production coupled to electron transport and translation of mitochondrial proteins are the two common functions retained in all mitochondrial DNAs. Paradoxically, most components essential for these two functions are now expressed from nuclear genes. Understanding how mitochondrial translation evolved in various eukaryotic models is essential to acquire new knowledge of mitochondrial genome expression. In this review, we provide a thorough analysis of the idiosyncrasies of mitochondrial translation as they occur between organisms. We address this by looking at mitochondrial codon usage and tRNA content. Then, we look at the aminoacyl-tRNA-forming enzymes in terms of peculiarities, dual origin, and alternate function(s). Finally we give examples of the atypical structural properties of mitochondrial tRNAs found in some organisms and the resulting adaptive tRNA-protein partnership.
Collapse
|