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Hou YF, Wei JF, Zhao TY, Li CF, Wang F. First complete mitochondrial genome of the tribe Coccini (Hemiptera, Coccomorpha, Coccidae) and its phylogenetic implications. Zookeys 2023; 1180:333-354. [PMID: 38312323 PMCID: PMC10838174 DOI: 10.3897/zookeys.1180.109116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/07/2023] [Indexed: 02/06/2024] Open
Abstract
Soft scale insects (Hemiptera, Coccidae) are important pests of various agricultural and horticultural crops and ornamental plants. They have negative impacts on agriculture and forestry. The tribe Coccini represents one of the most ancient evolutionary lineages of soft scale insects. However, no complete Coccini mitochondrial genome (mitogenome) is available in public databases. Here, we described the complete mitogenome of Coccushesperidum L., 1758. The 15,566 bp mitogenome of C.hesperidum had a high A+T content (83.4%) and contained a typical set of 37 genes, with 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and two ribosomal RNA genes (rRNAs). Only seven tRNAs had the typical clover-leaf secondary structure and the remaining tRNAs lacked the DHU arm, TψC arm or both. Moreover, a comparative analysis of all reported scale insect mitogenomes from GenBank database was performed. The mitogenomes of scale insects showed high similarities in base composition and A+T content. Additionally, our phylogenetic analysis confirmed the monophyly of Coccomorpha and revealed that the archaeococcoids were the most basal lineage within Coccomorpha, while Ericeruspela and Didesmococcuskoreanus, belonging to Coccidae, were often mixed with Aclerdidae, making Coccidae a paraphyletic group. These findings expand the mitogenome database of scale insects and provide new insights on mitogenome evolution for future studies across different insect groups.
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Affiliation(s)
- Yun-Feng Hou
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, China Hebei Normal University Shijiazhuang China
| | - Jiu-Feng Wei
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, 030801, China Shanxi Agricultural University Jinzhong China
| | - Tian-You Zhao
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China China Agricultural University Beijing China
| | - Cai-Feng Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, China Hebei Normal University Shijiazhuang China
| | - Fang Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, China Hebei Normal University Shijiazhuang China
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An JQ, Yu SH, Wei SJ, Zhang HP, Shi YC, Zhao QY, Fu ZY, Yang P. The Complete Mitochondrial Genome of the Chinese White Wax Scale Insect, Ericerus pela Chavannes (Hemiptera: Coccidae), with Novel Gene Arrangement and Truncated tRNA Genes. Insects 2023; 14:290. [PMID: 36975975 PMCID: PMC10055984 DOI: 10.3390/insects14030290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 06/18/2023]
Abstract
The Chinese white wax scale insect, Ericerus pela Chavannes (Hemiptera: Coccidae), is one of the scale insects with great economic value and has been dispersed and reared in China for over one thousand years. Its mitochondrial genome provides essential information for the molecular identification and genetic study of this species. We assembled the complete mitochondrial genome of E. pela based on PacBio sequencing and analyzed its genomic features. The genome was 17,766 bp in length with 13 protein-coding genes, 22 tRNAs, and two rRNA genes. The analysis results showed E. pela had significant gene rearrangements involving tRNAs compared with other Coccoidea species. Furthermore, E. pela's nine tRNAs were identified to have obvious truncated structures. The phylogenetic tree compiled of the species showed a long branch of the Coccoidea lineage, which indicated the high evolutionary rate in this group. Our study revealed the mitochondrial characteristics of E. pela and enriched the mitochondrial genetic information on Coccoidea species. It also determined the occurrence of gene rearrangement for the species in this superfamily.
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Affiliation(s)
- Jia-Qi An
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, China
- College of Biology and Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Shu-Hui Yu
- College of Agriculture and Life Sciences, Kunming University, Kunming 650214, China
| | - Shu-Jun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Hong-Ping Zhang
- College of Agriculture and Life Sciences, Kunming University, Kunming 650214, China
| | - Yuan-Chong Shi
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, China
| | - Qiu-Yu Zhao
- College of Agriculture and Life Sciences, Kunming University, Kunming 650214, China
| | - Zuo-Yi Fu
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, China
| | - Pu Yang
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, China
- Key Laboratory of Breeding and Utilization of Resource Insects of National Forestry and Grassland Administration, Kunming 650224, China
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Xu H, Liu X, Wang P, Li H, Wu SA. Phylogenetic Implications of Mitogenomic Sequences and Gene Rearrangements of Scale Insects (Hemiptera, Coccoidea). Insects 2023; 14:257. [PMID: 36975942 PMCID: PMC10051623 DOI: 10.3390/insects14030257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/25/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Coccoidea (scale insects) are important plant parasites with high diversity of species. However, the phylogenetic relationship within Coccoidea has not been fully determined. In this study, we sequenced mitogenomes of six species belonging to five coccoid families. With the addition of three previously published mitogenomes, a total of 12 coccoid species were adopted for the phylogenetic reconstruction based on the maximum likelihood and Bayesian inference. The monophyly of Coccoidea was recovered and Aclerdidae and Coccidae were recovered as the sister group, successively sister to Cerococcidae, Kerriidae, and Eriococcidae. In addition, there were gene rearrangements occurring in all mitogenomes of coccoid species studied here. The novel gene rearrangement ND6-trnP and trnI-ND2-trnY supported the monophyly of Coccoidea and the sister relationship of Aclerdidae and Coccidae. This implies that data from the mitogenome can provide new insight for clarifying the deeper level of phylogenetic relationship within Coccoidea.
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Affiliation(s)
- Han Xu
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing 100083, China
| | - Xiaochen Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Pei Wang
- Key Laboratory of Molluscan Quarantine and Identification of GACC, Fuzhou Customs District, Fuzhou 350001, China
| | - Hu Li
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - San-an Wu
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing 100083, China
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4
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Giegé R, Eriani G. The tRNA identity landscape for aminoacylation and beyond. Nucleic Acids Res 2023; 51:1528-1570. [PMID: 36744444 PMCID: PMC9976931 DOI: 10.1093/nar/gkad007] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 02/07/2023] Open
Abstract
tRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily on sets of identities within tRNA molecules composed of determinants and antideterminants preventing mischarging by non-cognate synthetases. Such identity sets were discovered in the tRNAs of a few model organisms, and their properties were generalized as universal identity rules. Since then, the panel of identity elements governing the accuracy of tRNA aminoacylation has expanded considerably, but the increasing number of reported functional idiosyncrasies has led to some confusion. In parallel, the description of other processes involving tRNAs, often well beyond aminoacylation, has progressed considerably, greatly expanding their interactome and uncovering multiple novel identities on the same tRNA molecule. This review highlights key findings on the mechanistics and evolution of tRNA and tRNA-like identities. In addition, new methods and their results for searching sets of multiple identities on a single tRNA are discussed. Taken together, this knowledge shows that a comprehensive understanding of the functional role of individual and collective nucleotide identity sets in tRNA molecules is needed for medical, biotechnological and other applications.
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Affiliation(s)
- Richard Giegé
- Correspondence may also be addressed to Richard Giegé.
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Lu C, Huang X, Deng J. Mitochondrial genomes of soft scales (Hemiptera: Coccidae): features, structures and significance. BMC Genomics 2023; 24:37. [PMID: 36670383 PMCID: PMC9863192 DOI: 10.1186/s12864-023-09131-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/12/2023] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Soft scales (Hemiptera: Coccidae), including important agricultural and forestry pests, are difficult to identify directly by morphological characters. Mitochondrial genomes (mitogenomes) have been widely used in species identification and phylogenetic research. However, only three complete mitogenomes, and very few mitochondrial genes of scale insects (Hemiptera: Coccoidea) can be searched in GenBank. Mitogenome comparisons between scale insects or between scale insects and other hemipteran species have not yet been reported. RESULTS In this study, detailed annotation of three new mitogenomes and comparative analysis of scale insects were completed, as well as comparative analysis of the gene composition, gene arrangement, codon usage and evolutionary forces between scale insects and 488 other hemipteran species for the first time. We found that high A + T content, gene rearrangement and truncated tRNAs are common phenomena in soft scales. The average A + T content and codon usage bias of scale insects are higher and stronger than those of other hemipteran insects, respectively. The atp8 gene of Hemiptera and nine other protein-coding genes of scale insects are under positive selection with higher evolutionary rates. CONCLUSIONS The study revealed the particularity of the scale insect mitogenomes, which will provide a good reference for future research on insect phylogenetic relationships, insect pest control, biogeography and identification.
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Affiliation(s)
- Congcong Lu
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiaolei Huang
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jun Deng
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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Hu K, Yu S, Zhang N, Tian M, Ban Q, Fan Z, Qiu J. The first complete mitochondrial genome of Matsucoccidae (Hemiptera, Coccoidea) and implications for its phylogenetic position. Biodivers Data J 2022; 10:e94915. [PMID: 36761530 PMCID: PMC9836553 DOI: 10.3897/bdj.10.e94915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/23/2022] [Indexed: 11/11/2022] Open
Abstract
The mitochondrial genome (mitogenome) has been extensively used to better understand the phylogenetic relationships within the hemipteran suborder Sternorrhyncha, but sequenced mitogenomes remain unavailable for the entire family Matsucoccidae to date. To address this, here we sequenced the complete mitogenome of Matsucoccusmatsumurae; the first for this family. The mitogenome is 15,360 bp in size and comprises the typical set of 37 mitochondrial genes and a large non-coding region (AT-rich region). Gene order, nucleotide composition and codon usage of protein-coding genes (PCGs) of M.matsumurae differ considerably from those of the other two sequenced Coccidae species. All PCGs were initiated by the ATN start codons and ended with the TAA/G or single T-- stop codons. Nine transfer RNA genes could be folded into typical clover-leaf secondary structures. The length and AT content of the ribosomal RNA genes are highly conserved in the Coccoidea mitogenomes. In contrast, the AT-rich control region is highly variable in size and in the number of tandem repeats. The sliding window analysis showed that the cox1 gene is the most conserved amongst the 13 PCGs, while the ratios of non-synonymous to synonymous substitution rates indicated that the evolution of this mitogenome has been dominated by positive selection. Phylogenetic analyses, based on nucleotide sequence data of 37 mitochondrial genes and amino acid sequence data of 13 PCGs using Bayesian Inference and Maximum Likelihood methods, showed that Matsucoccidae diverged before the Coccidae.
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Affiliation(s)
- Kai Hu
- Guizhou Academy of Forestry, Guiyang, ChinaGuizhou Academy of ForestryGuiyangChina
| | - Sanpeng Yu
- Guizhou Academy of Forestry, Guiyang, ChinaGuizhou Academy of ForestryGuiyangChina
| | - Niannian Zhang
- Guizhou Academy of Forestry, Guiyang, ChinaGuizhou Academy of ForestryGuiyangChina
| | - Maojuan Tian
- Guizhou Academy of Forestry, Guiyang, ChinaGuizhou Academy of ForestryGuiyangChina
| | - Qiming Ban
- Forestry Administration of Wangmo County, Qianxinan, ChinaForestry Administration of Wangmo CountyQianxinanChina
| | - Zhongliang Fan
- Forestry Administration of Huichuan District, Zunyi, ChinaForestry Administration of Huichuan DistrictZunyiChina
| | - Jiansheng Qiu
- Guizhou Academy of Forestry, Guiyang, ChinaGuizhou Academy of ForestryGuiyangChina
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Zhang H, Lu C, Liu Q, Zou T, Qiao G, Huang X. Insights into the Evolution of Aphid Mitogenome Features from New Data and Comparative Analysis. Animals (Basel) 2022; 12:ani12151970. [PMID: 35953959 PMCID: PMC9367533 DOI: 10.3390/ani12151970] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022] Open
Abstract
The complete mitochondrial genomes and their rearrangement patterns can provide useful information for inferring evolutionary history of organisms. Aphids are one of the insect groups with some unique mitogenome features. In this study, to examine whether some features in aphid mitogenomes are independent species-specific evolutionary events or clade-specific events at certain taxonomic levels, we sequenced three new aphid mitogenomes (Hormaphidinae: Ceratovacuna keduensis, Pseudoregma panicola; Lachninae: Nippolachnus piri) and compared them with all known aphid mitogenomes. The three mitogenomes are 16,059–17,033 bp in length, with a set of 37 typical mitochondrial genes, a non-coding control region and a tandem repeat region. The gene orders of them are all highly rearranged. Within the subfamily Hormaphidinae, the presence of repeat region and mitogenome rearrangement in Cerataphidini species but not in the other two tribes indicate that these may be Cerataphidini-specific features. The same gene rearrangement pattern in the two Lachninae species, N. piri (Tuberolachnini) and Stomaphis sinisalicis (Stomaphidini), supports that this feature should be at least derived from the common ancestor of two tribes. Overall, our data and analyses provide new insights into the evolutionary patterns of gene rearrangement and repeat region in aphid mitogenomes, and further corroborate the potential role of gene rearrangement in elucidating the evolutionary history of different insect lineages.
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Affiliation(s)
- Hui Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.L.); (Q.L.); (T.Z.)
| | - Congcong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.L.); (Q.L.); (T.Z.)
| | - Qian Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.L.); (Q.L.); (T.Z.)
| | - Tianmin Zou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.L.); (Q.L.); (T.Z.)
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;
- Correspondence: (G.Q.); (X.H.)
| | - Xiaolei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.L.); (Q.L.); (T.Z.)
- Correspondence: (G.Q.); (X.H.)
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Ge XY, Liu T, Kang Y, Liu HY, Yang YX. First complete mitochondrial genomes of Ototretinae (Coleoptera, Lampyridae) with evolutionary insights into the gene rearrangement. Genomics 2022; 114:110305. [DOI: 10.1016/j.ygeno.2022.110305] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 01/09/2022] [Accepted: 02/01/2022] [Indexed: 11/26/2022]
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Wang W, Zhang H, Constant J, Bartlett CR, Qin D. Characterization, Comparative Analysis and Phylogenetic Implications of Mitogenomes of Fulgoridae (Hemiptera: Fulgoromorpha). Genes (Basel) 2021; 12:genes12081185. [PMID: 34440359 PMCID: PMC8394797 DOI: 10.3390/genes12081185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023] Open
Abstract
The complete mitogenomes of nine fulgorid species were sequenced and annotated to explore their mitogenome diversity and the phylogenetics of Fulgoridae. All species are from China and belong to five genera: Dichoptera Spinola, 1839 (Dichoptera sp.); Neoalcathous Wang and Huang, 1989 (Neoalcathous huangshanana Wang and Huang, 1989); Limois Stål, 1863 (Limois sp.); Penthicodes Blanchard, 1840 (Penthicodes atomaria (Weber, 1801), Penthicodes caja (Walker, 1851), Penthicodes variegata (Guérin-Méneville, 1829)); Pyrops Spinola, 1839 (Pyrops clavatus (Westwood, 1839), Pyrops lathburii (Kirby, 1818), Pyrops spinolae (Westwood, 1842)). The nine mitogenomes were 15,803 to 16,510 bp in length with 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and a control region (A + T-rich region). Combined with previously reported fulgorid mitogenomes, all PCGs initiate with either the standard start codon of ATN or the nonstandard GTG. The TAA codon was used for termination more often than the TAG codon and the incomplete T codon. The nad1 and nad4 genes varied in length within the same genus. A high percentage of F residues were found in the nad4 and nad5 genes of all fulgorid mitogenomes. The DHU stem of trnV was absent in the mitogenomes of all fulgorids sequenced except Dichoptera sp. Moreover, in most fulgorid mitogenomes, the trnL2, trnR, and trnT genes had an unpaired base in the aminoacyl stem and trnS1 had an unpaired base in the anticodon stem. The similar tandem repeat regions of the control region were found in the same genus. Phylogenetic analyses were conducted based on 13 PCGs and two rRNA genes from 53 species of Fulgoroidea and seven outgroups. The Bayesian inference and maximum likelihood trees had a similar topological structure. The major results show that Fulgoroidea was divided into two groups: Delphacidae and ((Achilidae + (Lophopidae + (Issidae + (Flatidae + Ricaniidae)))) + Fulgoridae). Furthermore, the monophyly of Fulgoridae was robustly supported, and Aphaeninae was divided into Aphaenini and Pyropsini, which includes Neoalcathous, Pyrops, Datua Schmidt, 1911, and Saiva Distant, 1906. The genus Limois is recovered in the Aphaeninae, and the Limoisini needs further confirmation; Dichoptera sp. was the earliest branch in the Fulgoridae.
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Affiliation(s)
- Wenqian Wang
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Xianyang 712100, China; (W.W.); (H.Z.)
| | - Huan Zhang
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Xianyang 712100, China; (W.W.); (H.Z.)
| | - Jérôme Constant
- O.D. Phylogeny and Taxonomy, Entomology, Royal Belgian Institute of Natural Sciences, Vautier Street 29, 1000 Brussels, Belgium;
| | - Charles R. Bartlett
- Department of Entomology and Wildlife Ecology, University of Delaware, 250 Townsend Hall, 531 S. College Ave., Newark, DE 9716-2160, USA;
| | - Daozheng Qin
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Xianyang 712100, China; (W.W.); (H.Z.)
- Correspondence:
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Ye F, Li H, Xie Q. Mitochondrial Genomes from Two Specialized Subfamilies of Reduviidae (Insecta: Hemiptera) Reveal Novel Gene Rearrangements of True Bugs. Genes (Basel) 2021; 12:1134. [PMID: 34440308 PMCID: PMC8392325 DOI: 10.3390/genes12081134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/11/2021] [Accepted: 07/22/2021] [Indexed: 11/16/2022] Open
Abstract
Reduviidae, a hyper-diverse family, comprise 25 subfamilies with nearly 7000 species and include many natural enemies of crop pests and vectors of human disease. To date, 75 mitochondrial genomes (mitogenomes) of assassin bugs from only 11 subfamilies have been reported. The limited sampling of mitogenome at higher categories hinders a deep understanding of mitogenome evolution and reduviid phylogeny. In this study, the first mitogenomes of Holoptilinae (Ptilocnemus lemur) and Emesinae (Ischnobaenella hainana) were sequenced. Two novel gene orders were detected in the newly sequenced mitogenomes. Combined 421 heteropteran mitogenomes, we identified 21 different gene orders and six gene rearrangement units located in three gene blocks. Comparative analyses of the diversity of gene order for each unit reveal that the tRNA gene cluster trnI-trnQ-trnM is the hotspot of heteropteran gene rearrangement. Furthermore, combined analyses of the gene rearrangement richness of each unit and the whole mitogenome among heteropteran lineages confirm Reduviidae as a 'hot-spot group' of gene rearrangement in Heteroptera. The phylogenetic analyses corroborate the current view of phylogenetic relationships between basal groups of Reduviidae with high support values. Our study provides deeper insights into the evolution of mitochondrial gene arrangement in Heteroptera and the early divergence of reduviids.
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Affiliation(s)
- Fei Ye
- Department of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Qiang Xie
- Department of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
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Zheng CG, Zhu XX, Yan LP, Yao Y, Bu WJ, Wang XH, Lin XL. First complete mitogenomes of Diamesinae, Orthocladiinae, Prodiamesinae, Tanypodinae (Diptera: Chironomidae) and their implication in phylogenetics. PeerJ 2021; 9:e11294. [PMID: 33996279 PMCID: PMC8106913 DOI: 10.7717/peerj.11294] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/27/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The mitochondrial genome (mitogenome) has been extensively used for phylogenetic and evolutionary analysis in Diptera, but the study of mitogenome is still scarce in the family Chironomidae. METHODS Here, the first complete mitochondrial genomes of four Chironomid species representing Diamesinae, Orthocladiinae, Prodiamesinae and Tanypodinae are presented. Coupled with published mitogenomes of two, a comparative mitochondrial genomic analysis between six subfamilies of Chironomidae was carried out. RESULTS Mitogenomes of Chironomidae are conserved in structure, each contains 37 typical genes and a control region, and all genes arrange the same gene order as the ancestral insect mitogenome. Nucleotide composition is highly biased, the control region displayed the highest A + T content. All protein coding genes are under purifying selection, and the ATP8 evolves at the fastest rate. In addition, the phylogenetic analysis covering six subfamilies within Chironomidae was conducted. The monophyly of Chironomidae is strongly supported. However, the topology of six subfamilies based on mitogenomes in this study is inconsistent with previous morphological and molecular studies. This may be due to the high mutation rate of the mitochondrial genetic markers within Chironomidae. Our results indicate that mitogenomes showed poor signals in phylogenetic reconstructions at the subfamily level of Chironomidae.
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Affiliation(s)
| | - Xiu-Xiu Zhu
- College of Life Sciences, Nankai University, Tianjin, China
| | - Li-Ping Yan
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yuan Yao
- College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Wen-Jun Bu
- College of Life Sciences, Nankai University, Tianjin, China
| | - Xin-Hua Wang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Xiao-Long Lin
- College of Life Sciences, Nankai University, Tianjin, China
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Zhang H, Liu Q, Lu C, Deng J, Huang X. The First Complete Mitochondrial Genome of Lachninae Species and Comparative Genomics Provide New Insights into the Evolution of Gene Rearrangement and the Repeat Region. Insects 2021; 12:55. [PMID: 33440807 PMCID: PMC7828084 DOI: 10.3390/insects12010055] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/08/2021] [Accepted: 01/08/2021] [Indexed: 12/14/2022]
Abstract
Complete mitochondrial genomes are valuable resources for different research fields such as genomics, molecular evolution and phylogenetics. The subfamily Lachninae represents one of the most ancient evolutionary lineages of aphids. To date, however, no complete Lachninae mitogenome is available in public databases. Here we report the Stomaphis sinisalicis mitogenome, representing the first complete mitogenome of Lachninae. The S. sinisalicis mitogenome is consist of 13 protein-coding genes (PCGs), two rRNA genes (rRNAs), 22 tRNA genes (tRNAs), a control region and a large tandem repeat region. Strikingly, the mitogenome exhibits a novel, highly rearranged gene order between trnE and nad1 compared with that of other aphids. The presence of repeat region in the basal Lachninae may further indicate it is probably an ancestral feature of aphid mitogenomes. Collectively, this study provides new insights on mitogenome evolution and valuable data for future comparative studies across different insect lineages.
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Affiliation(s)
| | | | | | | | - Xiaolei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Z.); (Q.L.); (C.L.); (J.D.)
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Garin S, Levi O, Cohen B, Golani-Armon A, Arava YS. Localization and RNA Binding of Mitochondrial Aminoacyl tRNA Synthetases. Genes (Basel) 2020; 11:genes11101185. [PMID: 33053729 PMCID: PMC7600831 DOI: 10.3390/genes11101185] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 12/15/2022] Open
Abstract
Mitochondria contain a complete translation machinery that is used to translate its internally transcribed mRNAs. This machinery uses a distinct set of tRNAs that are charged with cognate amino acids inside the organelle. Interestingly, charging is executed by aminoacyl tRNA synthetases (aaRS) that are encoded by the nuclear genome, translated in the cytosol, and need to be imported into the mitochondria. Here, we review import mechanisms of these enzymes with emphasis on those that are localized to both mitochondria and cytosol. Furthermore, we describe RNA recognition features of these enzymes and their interaction with tRNA and non-tRNA molecules. The dual localization of mitochondria-destined aaRSs and their association with various RNA types impose diverse impacts on cellular physiology. Yet, the breadth and significance of these functions are not fully resolved. We highlight here possibilities for future explorations.
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Liu HL, Chen QD, Chen S, Pu DQ, Chen ZT, Liu YY, Liu X. The highly rearranged mitochondrial genomes of three economically important scale insects and the mitochondrial phylogeny of Coccoidea (Hemiptera: Sternorrhyncha). PeerJ 2020; 8:e9932. [PMID: 33083111 PMCID: PMC7546225 DOI: 10.7717/peerj.9932] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/22/2020] [Indexed: 11/20/2022] Open
Abstract
The mitochondrial genomes (mitogenomes) of scale insects are less known in comparison to other insects, which hinders the phylogenetic and evolutionary studies of Coccoidea and higher taxa. Herein, the complete mitogenomes of Unaspis yanonensis, Planococcus citri and Ceroplastes rubens were sequenced for Coccoidea. The 15,220-bp long mitogenome of U. yanonensis contained the typical set of 37 genes including 13 PCGs, 22 tRNA genes and two rRNA genes; the 15,549-bp long mitogenome of P. citri lacked the tRNA gene trnV; the 15,387-bp long mitogenome of C. rubens exhibited several shortened PCGs and lacked five tRNA genes. The mitochondrial gene arrangement of the three mitogenomes was different from other scale insects and Drosophila yakuba. Most PCGs used standard ATN (ATA, ATT, ATC and ATG) start codons and complete TAN (TAA or TAG) termination codons. The ND4L had the highest evolutionary rate but COX1 and CYTB were the lowest. Most tRNA genes had cloverleaf secondary structures, whereas the reduction of dihydrouridine (DHU) arms and TψC arms were detected. Tandem repeats, stem-loop (SL) structures and poly-[TA]n stretch were found in the control regions (CRs) of the three mitogenomes. The phylogenetic analyses using Bayesian inference (BI) and maximum likelihood methods (ML) showed identical results, both supporting the inner relationship of Coccoidea as Coccidae + (Pseudococcidae + Diaspididae).
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Affiliation(s)
- Hong-Ling Liu
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of integrated pest management of Southwest crops, Ministry of Agriculture, Chengdu, China
| | - Qing-Dong Chen
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of integrated pest management of Southwest crops, Ministry of Agriculture, Chengdu, China
| | - Song Chen
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of integrated pest management of Southwest crops, Ministry of Agriculture, Chengdu, China
| | - De-Qiang Pu
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of integrated pest management of Southwest crops, Ministry of Agriculture, Chengdu, China
| | - Zhi-Teng Chen
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yue-Yue Liu
- Analysis and testing center of Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Xu Liu
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of integrated pest management of Southwest crops, Ministry of Agriculture, Chengdu, China
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Wang C, Chen H, Tian S, Yang C, Chen X. Novel Gene Rearrangement and the Complete Mitochondrial Genome of Cynoglossus monopus: Insights into the Envolution of the Family Cynoglossidae (Pleuronectiformes). Int J Mol Sci 2020; 21:E6895. [PMID: 32962212 PMCID: PMC7555148 DOI: 10.3390/ijms21186895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/10/2020] [Accepted: 09/16/2020] [Indexed: 11/26/2022] Open
Abstract
Cynoglossus monopus, a small benthic fish, belongs to the Cynoglossidae, Pleuronectiformes. It was rarely studied due to its low abundance and cryptical lifestyle. In order to understand the mitochondrial genome and the phylogeny in Cynoglossidae, the complete mitogenome of C. monopus has been sequenced and analyzed for the first time. The total length is 16,425 bp, typically containing 37 genes with novel gene rearrangements. The tRNA-Gln gene is inverted from the light to the heavy strand and translocated from the downstream of tRNA-Ile gene to its upstream. The control region (CR) translocated downstream to the 3'-end of ND1 gene adjoining to inverted to tRNA-Gln and left a 24 bp trace fragment in the original position. The phylogenetic trees were reconstructed by Bayesian inference (BI) and maximum likelihood (ML) methods based on the mitogenomic data of 32 tonguefish species and two outgroups. The results support the idea that Cynoglossidae is a monophyletic group and indicate that C. monopus has the closest phylogenetic relationship with C. puncticeps. By combining fossil records and mitogenome data, the time-calibrated evolutionary tree of families Cynoglossidae and Soleidae was firstly presented, and it was indicated that Cynoglossidae and Soleidae were differentiated from each other during Paleogene, and the evolutionary process of family Cynoglossidae covered the Quaternary, Neogene and Paleogene periods.
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Affiliation(s)
- Chen Wang
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China; (C.W.); (S.T.); (C.Y.)
| | - Hao Chen
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Silin Tian
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China; (C.W.); (S.T.); (C.Y.)
| | - Cheng Yang
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China; (C.W.); (S.T.); (C.Y.)
| | - Xiao Chen
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China; (C.W.); (S.T.); (C.Y.)
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agriculture University, Guangzhou 510642, China
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