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Liu M, Hu SY, Li M, Sun H, Yuan ML. Comparative mitogenomic analysis provides evolutionary insights into Formica (Hymenoptera: Formicidae). PLoS One 2024; 19:e0302371. [PMID: 38857223 PMCID: PMC11164359 DOI: 10.1371/journal.pone.0302371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 04/02/2024] [Indexed: 06/12/2024] Open
Abstract
Formica is a large genus in the family Formicidae with high diversity in its distribution, morphology, and physiology. To better understand evolutionary characteristics of Formica, the complete mitochondrial genomes (mitogenomes) of two Formica species were determined and a comparative mitogenomic analysis for this genus was performed. The two newly sequenced Formica mitogenomes each included 37 typical mitochondrial genes and a large non-coding region (putative control region), as observed in other Formica mitogenomes. Base composition, gene order, codon usage, and tRNA secondary structure were well conserved among Formica species, whereas diversity in sequence size and structural characteristics was observed in control regions. We also observed several conserved motifs in the intergenic spacer regions. These conserved genomic features may be related to mitochondrial function and their highly conserved physiological constraints, while the diversity of the control regions may be associated with adaptive evolution among heterogenous habitats. A negative AT-skew value on the majority chain was presented in each of Formica mitogenomes, indicating a reversal of strand asymmetry in base composition. Strong codon usage bias was observed in Formica mitogenomes, which was predominantly determined by nucleotide composition. All 13 mitochondrial protein-coding genes of Formica species exhibited molecular signatures of purifying selection, as indicated by the ratio of non-synonymous substitutions to synonymous substitutions being less than 1 for each protein-coding gene. Phylogenetic analyses based on mitogenomic data obtained fairly consistent phylogenetic relationships, except for two Formica species that had unstable phylogenetic positions, indicating mitogenomic data are useful for constructing phylogenies of ants. Beyond characterizing two additional Formica mitogenomes, this study also provided some key evolutionary insights into Formica.
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Affiliation(s)
- Min Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Shi-Yun Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Min Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Hao Sun
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Ming-Long Yuan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
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Kim D, Kim G, Shin CR, Park B, Choi EH, Hwang UW. The complete mitochondrial genome of a ground beetle Synuchus nitidus (Carabidae: Harpalinae: Sphodrini) from South Korea. Mitochondrial DNA B Resour 2024; 9:711-715. [PMID: 38855355 PMCID: PMC11159585 DOI: 10.1080/23802359.2024.2361689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/25/2024] [Indexed: 06/11/2024] Open
Abstract
The ground beetle Synuchus nitidus (Motschulsky, 1861) (Carabidae: Harpalinae: Sphodrini) is one of the most common species in the forests of South Korea, which has the potential to be utilized as an environmental indicator. Here, we characterized the complete mitochondrial genome (mitogenome) of S. nitidus, which is the first in the harpaline tribe Sphodrini. Its genome is 16,392 bp in length and composed of 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and an A + T rich region. In addition, we reconstructed a maximum likelihood tree to elucidate the phylogenetic position of Sphodrini among the seven harpaline tribes using nucleotide sequences of the 13 PCGs. The ML tree supported a monophyletic clade of the subfamily Harpalinae and showed a close relationship between Sphodrini and Lebinii with a low bootstrap value. The complete mitogenome of S. nitidus could be helpful for molecular species identification and exploring phylogenetic relationships among carabids.
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Affiliation(s)
- Dooyoung Kim
- Department of Biomedical Convergence Science and Technology, School of Industrial Technology Advances, Kyungpook National University, Daegu, South Korea
| | - Gyeongmin Kim
- School of Life Sciences, Graduate School, Kyungpook National University, Daegu, South Korea
| | - Cho Rong Shin
- Department of Biomedical Convergence Science and Technology, School of Industrial Technology Advances, Kyungpook National University, Daegu, South Korea
| | - Bia Park
- Department of Biology Education, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
| | - Eun Hwa Choi
- Department of Biology Education, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
- Phylomics Inc, Daegu, South Korea
| | - Ui Wook Hwang
- Department of Biomedical Convergence Science and Technology, School of Industrial Technology Advances, Kyungpook National University, Daegu, South Korea
- Department of Biology Education, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
- Phylomics Inc, Daegu, South Korea
- Institute for Korean Herb-Bio Convergence Promotion, Kyungpook National University, Daegu, South Korea
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Gao RR, Lei QL, Jin X, Zafar I, Yang XK, Su CY, Hao JS, Nie RE. Characterization of Four Complete Mitogenomes of Monolepta Species and Their Related Phylogenetic Implications. INSECTS 2024; 15:50. [PMID: 38249056 PMCID: PMC10816406 DOI: 10.3390/insects15010050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024]
Abstract
Monolepta is one of the diverse genera in the subfamily Galerucinae, including 708 species and 6 sub-species worldwide. To explore the information on the mitogenome characteristics and phylogeny of the section "Monoleptites", especially the genus Monolepta, we obtained the newly completed mitochondrial genomes (mitogenomes) of four Monolepta species using high-throughput sequencing technology. The lengths of these four new mitochondrial genomes are 16,672 bp, 16,965 bp, 16,012 bp, and 15,866 bp in size, respectively. All four mitochondrial genomes include 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), and one control region, which is consistent with other Coleoptera. The results of the nonsynonymous with synonymous substitution rates showed that ND6 had the highest evolution rate, while COI displayed the lowest evolution rate. The substitution saturation of three datasets (13 PCGs_codon1, 13 PCGs_codon2, 13 PCGs_codon3) showed that there was no saturation across all datasets. Phylogenetic analyses based on three datasets (ND1, 15 genes of mitogenomes, and 13 PCGs_AA) were carried out using maximum likelihood (ML) and Bayesian inference (BI) methods. The results showed that mitogenomes had a greater capacity to resolve the main clades than the ND1 gene at the suprageneric and species levels. The section "Monoleptites" was proven to be a monophyletic group, while Monolepta was a non-monophyletic group. Based on ND1 data, the newly sequenced species whose antennal segment 2 was shorter than 3 were split into several clades, while, based on the mitogenomic dataset, the four newly sequenced species had close relationships with Paleosepharia. The species whose antennal segment 2 was as long as 3 were split into two clades, which indicated that the characteristic of "antennal segment 2 as long as 3" of the true "Monolepta" evolved multiple times in several subgroups. Therefore, to explore the relationships among the true Monolepta, the most important thing is to perform a thorough revision of Monolepta and related genera in the future.
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Affiliation(s)
- Rong-Rong Gao
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.-R.G.); (X.J.); (I.Z.); (C.-Y.S.)
| | - Qi-Long Lei
- Department of Entomology, China Agricultural University, Beijing 100193, China;
| | - Xu Jin
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.-R.G.); (X.J.); (I.Z.); (C.-Y.S.)
| | - Iqbal Zafar
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.-R.G.); (X.J.); (I.Z.); (C.-Y.S.)
| | - Xing-Ke Yang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou 510260, China
| | - Cheng-Yong Su
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.-R.G.); (X.J.); (I.Z.); (C.-Y.S.)
| | - Jia-Sheng Hao
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.-R.G.); (X.J.); (I.Z.); (C.-Y.S.)
| | - Rui-E Nie
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.-R.G.); (X.J.); (I.Z.); (C.-Y.S.)
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Li K, Yu SW, Hu H, Feng YF, Storey KB, Ma Y, Zhang JY, Yu DN. The Phylogenetic Relationship of Lamiinae (Coleoptera: Cerambycidae) Using Mitochondrial Genomes. Genes (Basel) 2023; 15:13. [PMID: 38275595 PMCID: PMC10815127 DOI: 10.3390/genes15010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Lamiinae is the largest subfamily of the Cerambycidae (longhorn beetles), with approximately 21,863 described species. Previous phylogenetic studies of Lamiinae showed that this subfamily was monophyletic, but the relationship between the tribes of Lamiinae is still controversial. Partial molecular data and species morphological characteristics are not sufficient to resolve species phylogenetic studies perfectly. At the same time, the full mitochondrial genome contains more comprehensive genetic data. Benefiting from the development of next-generation sequencing (NGS), mitochondrial genomes can be easily acquired and used as reliable molecular markers to investigate phylogenetic relationships within Cerambycidae. Using NGS technology, we obtained 11 mitochondrial genome sequences of Lamiinae species. Based on this newly generated mitochondrial genome dataset matrix, we reconstructed the phylogeny of Lamiinae. The Bayesian Inference and Maximum Likelihood analyses strongly support the monophyly of four tribes (Lamiini, Batocerini, Mesosini, and Saperdini), whereas the tribe Acanthocinini was identified as paraphyletic. Other mitochondrial structural features were also observed: the start codon in the nad1 gene of all 11 mitochondrial genomes is TTG; 17-22 bp intergenic spacers (IGS) with a 'TACTA' motif were found between trnS2 and nad1. Moreover, two long IGS were found in Mesosa myops and Batocera sp. Tandem repeats were found in the IGS of Batocera sp.
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Affiliation(s)
- Ke Li
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
| | - Sheng-Wu Yu
- Longquan Protection Center of Qianjiangyuan-Baishanzu National Park, Lishui 323700, China
| | - Hao Hu
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
| | - Yu-Feng Feng
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Yue Ma
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Jia-Yong Zhang
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Dan-Na Yu
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
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Cheng HY, Gao QI, Pan Z. Mitochondrial genomes of three Mylabris (Pseudabris) species (Coleoptera: Meloidae, Mylabrini) and their phylogenetic implications. Zootaxa 2023; 5357:186-204. [PMID: 38220647 DOI: 10.11646/zootaxa.5357.2.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Indexed: 01/16/2024]
Abstract
The complete mitogenomes of the subgenus Mylabris (Pseudabris) Fairmaire, 1894, endemic to the Qinghai-Xizang Plateau, are reported for the first time. Three species out of seven, M. hingstoni Blair, 1927, M. longiventris Blair, 1927, and M. przewalskyi (Dokhtouroff, 1887), were sequenced. The sequencing results of mitogenomes were annotated and analyzed. The gene arrangements were consistent with the putative ancestral insect mitogenomes as understood today, including 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and a noncoding internal control region (CR). The PCGs used the typical start ATN codon and TAA/TAG stop codons. The lengths of three mitogenomes were 15,692 bp, 15,685 bp, and 15,685 bp, with an A + T content of 71.29%, 71.67%, and 71.53%, respectively. The evolution rates of 13 PCGs were compared: The evolution rate of ATP8 was the highest, and that of COX1 was the lowest. Furthermore, the phylogenetic relationships among the genera and tribes of Meloidae were discussed.
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Affiliation(s)
- Hai-Yun Cheng
- Key Laboratory of Zoological Systematics and Application; School of Life Sciences; Institute of Life Science and Green Development; Hebei University; Wusidong Road 180; 071002; Baoding; Hebei Province; China.
| | - Q I Gao
- Key Laboratory of Zoological Systematics and Application; School of Life Sciences; Institute of Life Science and Green Development; Hebei University; Wusidong Road 180; 071002; Baoding; Hebei Province; China.
| | - Zhao Pan
- Key Laboratory of Zoological Systematics and Application; School of Life Sciences; Institute of Life Science and Green Development; Hebei University; Wusidong Road 180; 071002; Baoding; Hebei Province; China.
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Xiao ML, Yuan H, Li TJ, Chen B. Two New Mitogenomes of Bibionidae and Their Comparison within the Infraorder Bibionomorpha (Diptera). Genes (Basel) 2023; 14:1485. [PMID: 37510389 PMCID: PMC10378959 DOI: 10.3390/genes14071485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Despite the worldwide distribution and rich diversity of the infraorder Bibionomorpha in Diptera, the characteristics of mitochondrial genomes (mitogenomes) are still little-known, and the phylogenetics and evolution of the infraorder remains controversial. In the present study, we report complete and annotated mitogenome sequences of Penthetria simplioipes and Plecia hardyi representing Bibionidae. This is the first report of the complete mitogenomes for the superfamily Bibionoidea. There are 37 genes in each of the complete mitogenomes of all 20 studied species from eight families of four superfamilies within infraorder Bibionomorpha. The Ka/Ks analysis suggests that all 13 PCGs have undergone purifying selection. The gene rearrangement events exist in some families (Keroplatidae, Sciaridae, and Cecidomyiidae) but not in Mycetophilidae in Sciaroidea and also in Scatopsoidea, Anisopodoidea, and Bibionoidea, which suggests that these rearrangement events are derived in the late period in the evolution of the Bibionomorpha. The phylogenetic analysis suggests the phylogenetic relationships of Scatopsoidea + (Anisopodoidea + (Bibionoidea + Sciaroidea)) in Bibionomorpha. The divergence time analysis suggests that Bibionomorpha originated in the Triassic, Scatopsoidea and Anisopodoidea in the late Triassic, Bibionoidea in the Jurassic, and Sciaroidea in the Jurassic to the Cretaceous. The work lays a base for the study of mitogenomes in Bibionomorpha but further work and broader taxon sampling are necessary for a better understanding of the phylogenetics and evolution of the infraorder.
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Affiliation(s)
- Mei-Ling Xiao
- Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing 401331, China
| | - Huan Yuan
- Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing 401331, China
| | - Ting-Jing Li
- Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing 401331, China
| | - Bin Chen
- Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing 401331, China
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Wu J, Xu D, Wei X, Liao W, Li X, Zhuo Z. Characterization of the complete mitochondrial genome of the longhorn beetle, Batocerahorsfieldi (Coleoptera, Cerambycidae) and its phylogenetic analysis with suitable longhorn beetles. Zookeys 2023; 1168:387-402. [PMID: 37448482 PMCID: PMC10336557 DOI: 10.3897/zookeys.1168.105328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Mitochondrial genome analysis is an important tool for studying insect phylogenetics. The longhorn beetle, Batocerahorsfieldi, is a significant pest in timber, economic and protection forests. This study determined the mitochondrial genome of B.horsfieldi and compared it with the mitochondrial genomes of other Cerambycidae with the aim of exploring the phylogenetic status of the pest and the evolutionary relationships among some Cerambycidae subgroups. The complete mitochondrial genome of B.horsfieldi was sequenced by the Illumina HiSeq platform. The mitochondrial genome was aligned and compared with the existing mitochondrial genomes of Batoceralineolata and B.rubus in GenBank (MF521888, MW629558, OM161963, respectively). The secondary structure of transfer RNA (tRNA) was predicted using tRNAScan-SE server v.1.21 and MITOS WebSever. Thirteen protein-coding genes (PCGs) and two ribosomal RNA gene sequences of 21 longhorn beetles, including B.horsfieldi, plus two outgroups, Dryopsernesti (Dryopidae) and Heterocerusparallelus (Heteroceridae), were analyzed. The phylogenetic tree was constructed using maximum likelihood and Bayesian inference methods. In this study, we successfully obtained the complete mitochondrial genome of B.horsfieldi for the first time, which is 15 425 bp in length. It contains 37 genes and an A + T-rich region, arranged in the same order as the recognized ancestor of longhorn beetles. The genome of B.horsfieldi is composed of 33.12% A bases, 41.64% T bases, 12.08% C bases, and 13.16% G bases. The structure, nucleotide composition, and codon usage of the new mitochondrial genome are not significantly different from other longhorn mitochondrial genomes. Phylogenetic analyses revealed that Cerambycidae formed a highly supported single clade, and Vesperidae was either clustered with Cerambycidae or formed a separate clade. Interestingly, B.horsfieldi, B.rubus and B.lineolata were clustered with Monochamus and Anoplophora species in both analyses, with high node support. Additionally, the VesperidaeSpiniphilusspinicornis and Vesperussanzi and the 19 Cerambycidae species formed a sister clade in the Bayesian analysis. Our results have produced new complete mitogenomic data, which will provide information for future phylogenetic and taxonomic research, and provide a foundation for future relevant research.
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Affiliation(s)
- Junhao Wu
- College of Life Science, China West Normal University, Nanchong, 637002, China China West Normal University Nanchong China
| | - Danping Xu
- College of Life Science, China West Normal University, Nanchong, 637002, China China West Normal University Nanchong China
| | - Xinju Wei
- College of Life Science, China West Normal University, Nanchong, 637002, China China West Normal University Nanchong China
| | - Wenkai Liao
- College of Life Science, China West Normal University, Nanchong, 637002, China China West Normal University Nanchong China
| | - Xiushan Li
- College of Life Science, China West Normal University, Nanchong, 637002, China China West Normal University Nanchong China
| | - Zhihang Zhuo
- College of Life Science, China West Normal University, Nanchong, 637002, China China West Normal University Nanchong China
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Rehman A, Huo QB, Du YZ. The First Complete Mitochondrial Genome of Genus Isocapnia (Plecoptera: Capniidae) and Phylogenetic Assignment of Superfamily Nemouroidea. Genes (Basel) 2023; 14:genes14050965. [PMID: 37239326 DOI: 10.3390/genes14050965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Capniidae are a family of stoneflies, also known as snow flies, who emerge in winter. The phylogeny of Capniidae is widely accepted to be based on morphological analysis. Until now, only five Capniidae mitochondrial genomes have been sequenced so far. In addition, sampling is required to determine an accurate phylogenetic association because the generic classification of this family is still controversial and needs to be investigated further. In this study, the first mitogenome of genus Isocapnia was sequenced with a length of 16,200 bp and contained 37 genes, including a control region, two rRNAs, 22 tRNAs, and 13 PCGs, respectively. Twelve PCGs originated with the common start codon ATN (ATG, ATA, or ATT), while nad5 used GTG. Eleven PCGs had TAN (TAA or TAG) as their last codon; however, cox1 and nad5 had T as their final codon due to a shortened termination codon. All tRNA genes demonstrated the cloverleaf structure, which is distinctive for metazoans excluding the tRNASer1 (AGN) that missed the dihydrouridine arm. A Phylogenetic analysis of the superfamily Nemouroidea was constructed using thirteen PCGs from 32 formerly sequenced Plecoptera species. The Bayesian inference and maximum likelihood phylogeny tree structures derived similar results across the thirteen PCGs. Our findings strongly supported Leuctridae + ((Capniidae + Taeniopterygidae) + (Nemouridae + Notonemouridae)). Ultimately, the best well-supported generic phylogenetic relationship within Capniidae is as follows; (Isocapnia + (Capnia + Zwicknia) + (Apteroperla + Mesocapnia)). These findings will enable us to better understand the evolutionary relationships within the superfamily Nemouroidea and the generic classification and mitogenome structure of the family Capniidae.
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Affiliation(s)
- Abdur Rehman
- College of Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou 225009, China
| | - Qing-Bo Huo
- College of Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou 225009, China
| | - Yu-Zhou Du
- College of Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education, Yangzhou University, Yangzhou 225009, China
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Zhang Z, Pei P, Zhang M, Li F, Tang G. Chromosome-level genome assembly of Dastarcus helophoroides provides insights into CYP450 genes expression upon insecticide exposure. PEST MANAGEMENT SCIENCE 2023; 79:1467-1482. [PMID: 36502364 DOI: 10.1002/ps.7319] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 10/26/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Dastarcus helophoroides is an important natural enemy of cerambycids, and is wildly used in biological control of pests. Nevertheless, the absence of complete genomic information limits the investigation of the underlying molecular mechanisms. Here, a chromosome-level of Dastarcus helophoroides genome is assembled using a combination strategy of Illumina, PacBio, 10x™ Genomics, and Hi-C. RESULTS The final assembly is 609.09 Mb with contig N50, scaffold N50 and GC content of 5.46 Mb, 42.56 Mb and 31.50%, respectively, and 95.25% of the contigs anchor into 13 chromosomes. In total 14 890 protein-coding genes and 65.37% repeat sequences are predicted in the assembly genome. The phylogenetic analysis of single-copy gene families shared among 20 insect species indicates that Dastarcus helophoroides is placed as the sister species to clade (Nitidulidae+Curculionoidea+Chrysomeloidea) + Tenebrionoidea, and diverges from the related species ~242.9 Mya. In total 36 expanded gene families are identified in Dastarcus helophoroides genome, and are functionally related to drug metabolism and metabolism of xenobiotics by cytochrome P450. Some members of CYP4 Clade and CYP6 Clade are up-regulated in Dastarcus helophoroides adults upon insecticide exposure, of which expressions of DhCYP4Q, DhCYP6A14X1 and DhCYP4C1 are significantly up-regulated. The silencing of the three genes leads to adults more sensitive to insecticide and increased knocked-down rate, which may indicate their critical roles in stress resistance and detoxication. CONCLUSION Our study systematically integrated the chromosome-level genome, transcriptome and gene expression of Dastarcus helophoroides, which will provide valuable resources for understanding mechanisms of pesticide metabolism, growth and development, and utilization of the natural enemy in integrated control. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Zhengqing Zhang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
| | - Pei Pei
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
| | - Meng Zhang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
| | - Feifei Li
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
| | - Guanghui Tang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
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Yuan ML, Chen WT, Zhang QL, Li M, Zhang L, Tang PA. Transcriptomic data recover a new superfamily-level phylogeny of Cucujiformia (Coleoptera, Polyphaga). Mol Phylogenet Evol 2023; 179:107679. [PMID: 36539017 DOI: 10.1016/j.ympev.2022.107679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/30/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
Cucujiformia, the largest taxon in the order Coleoptera, exhibits extraordinary morphological, ecological, and behavioral diversity. This infraorder is currently divided into seven superfamilies, but considerably incongruent relationships among superfamilies have been reported by recent phylogenomic studies. Here, we combined the 21 newly sequenced transcriptomes representing six superfamilies with nine previously published cucujiform genomes/transcriptomes to elucidate the phylogeny and evolution of Cucujiformia. The monophyly of each of five superfamilies were consistently supported by all phylogenetic analyses based on the twelve datasets (matrix occupancy, amino acid and nucleotide data) and the two analytical methods (maximum likelihood method and Bayesian inference). Both the amino acid datasets and the RY recoded nucleotide datasets recovered the monophyly of Cucujoidea. Topology test results statistically supported the following robust superfamily-level phylogeny in Cucujiformia: (Coccinelloidea, (Cleroidea, (Tenebrionoidea, (Cucujoidea, (Chrysomeloidea, Curculionoidea))))). Our divergence time analyses recovered a Permian origin of Cucujiformia and a Jurassic-Cretaceous origin of most superfamilies. The diversification of phytophagous beetles that occurred in the Cretaceous can be attributed to its co-evolution with angiosperms, supporting the hypothesis of a Cretaceous Terrestrial Revolution.
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Affiliation(s)
- Ming-Long Yuan
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China.
| | - Wen-Ting Chen
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China
| | - Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Min Li
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China
| | - Li Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China
| | - Pei-An Tang
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, People's Republic of China.
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Chen WT, Li M, Hu SY, Wang SH, Yuan ML. Comparative mitogenomic and evolutionary analysis of Lycaenidae (Insecta: Lepidoptera): Potential association with high-altitude adaptation. Front Genet 2023; 14:1137588. [PMID: 37144132 PMCID: PMC10151513 DOI: 10.3389/fgene.2023.1137588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/03/2023] [Indexed: 05/06/2023] Open
Abstract
Harsh environments (e.g., hypoxia and cold temperatures) of the Qinghai-Tibetan Plateau have a substantial influence on adaptive evolution in various species. Some species in Lycaenidae, a large and widely distributed family of butterflies, are adapted to the Qinghai-Tibetan Plateau. Here, we sequenced four mitogenomes of two lycaenid species in the Qinghai-Tibetan Plateau and performed a detailed comparative mitogenomic analysis including nine other lycaenid mitogenomes (nine species) to explore the molecular basis of high-altitude adaptation. Based on mitogenomic data, Bayesian inference, and maximum likelihood methods, we recovered a lycaenid phylogeny of [Curetinae + (Aphnaeinae + (Lycaeninae + (Theclinae + Polyommatinae)))]. The gene content, gene arrangement, base composition, codon usage, and transfer RNA genes (sequence and structure) were highly conserved within Lycaenidae. TrnS1 not only lacked the dihydrouridine arm but also showed anticodon and copy number diversity. The ratios of non-synonymous substitutions to synonymous substitutions of 13 protein-coding genes (PCGs) were less than 1.0, indicating that all PCGs evolved under purifying selection. However, signals of positive selection were detected in cox1 in the two Qinghai-Tibetan Plateau lycaenid species, indicating that this gene may be associated with high-altitude adaptation. Three large non-coding regions, i.e., rrnS-trnM (control region), trnQ-nad2, and trnS2-nad1, were found in the mitogenomes of all lycaenid species. Conserved motifs in three non-coding regions (trnE-trnF, trnS1-trnE, and trnP-nad6) and long sequences in two non-coding regions (nad6-cob and cob-trnS2) were detected in the Qinghai-Tibetan Plateau lycaenid species, suggesting that these non-coding regions were involved in high-altitude adaptation. In addition to the characterization of Lycaenidae mitogenomes, this study highlights the importance of both PCGs and non-coding regions in high-altitude adaptation.
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Affiliation(s)
- Wen-Ting Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Min Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Shi-Yun Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou, Gansu, China
| | - Su-Hao Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Ming-Long Yuan
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou, Gansu, China
- *Correspondence: Ming-Long Yuan,
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Li M, Liu M, Hu SY, Luo FZ, Yuan ML. Comparative mitogenomic analyses provide evolutionary insights into the retrolateral tibial apophysis clade (Araneae: Entelegynae). Front Genet 2022; 13:974084. [PMID: 36186478 PMCID: PMC9515440 DOI: 10.3389/fgene.2022.974084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
The retrolateral tibial apophysis (RTA) clade is the largest spider lineage within Araneae. To better understand the diversity and evolution, we newly determined mitogenomes of ten RTA species from six families and performed a comparative mitogenomics analysis by combining them with 40 sequenced RTA mitogenomes available on GenBank. The ten mitogenomes encoded 37 typical mitochondrial genes and included a large non-coding region (putative control region). Nucleotide composition and codon usage were well conserved within the RTA clade, whereas diversity in sequence length and structural features was observed in control region. A reversal of strand asymmetry in nucleotide composition, i.e., negative AT-skews and positive GC-skews, was observed in each RTA species, likely resulting from mitochondrial gene rearrangements. All protein-coding genes were evolving under purifying selection, except for atp8 whose Ka/Ks was larger than 1, possibly due to positive selection or selection relaxation. Both mutation pressure and natural selection might contribute to codon usage bias of 13 protein-coding genes in the RTA lineage. Phylogenetic analyses based on mitogenomic data recovered a family-level phylogeny within the RTA; {[(Oval calamistrum clade, Dionycha), Marronoid clade], Sparassidae}. This study characterized RTA mitogenomes and provided some new insights into the phylogeny and evolution of the RTA clade.
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Affiliation(s)
- Min Li
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Min Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Shi-Yun Hu
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Fang-Zhen Luo
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Ming-Long Yuan
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
- *Correspondence: Ming-Long Yuan,
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Xu M, Zhou S, Wan X. Phylogenetic Implication of Large Intergenic Spacers: Insights from a Mitogenomic Comparison of Prosopocoilus Stag Beetles (Coleoptera: Lucanidae). Animals (Basel) 2022; 12:ani12131595. [PMID: 35804495 PMCID: PMC9264858 DOI: 10.3390/ani12131595] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/12/2022] [Accepted: 06/18/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Insect mitochondrial genomes (mitogenomes) show high diversity in some lineages. In the mitogenome of some Coleoptera species, a large intergenic spacer (IGS) has been identified. However, very little is known about mitogenomes of lucanid beetles. In this work, to provide further insight into the phylogenic relationships among species in lucanid beetles (genus Prosopocoilus), two Prosopocoilus species (Prosopocoilus castaneus and Prosopocoilus laterotarsus) were newly sequenced and comparatively analyzed. Significantly, the two newly sequenced Prosopocoilus species contained a large IGS located between trnI and trnQ. Our phylogenomic analyses showed that P. castaneus and P. laterotarsus were clustered in a clade with typical Prosopocoilus species (Prosopocoilus confucius, Prosopocoilus blanchardi, and Prosopocoilusastacoides). These results provide valuable data for the future study of the phylogenetic relationships in this genus. Abstract To explore the characteristics of mitogenomes and discuss the phylogenetic relationships within the genus Prosopocoilus, the mitogenomes of two species (P. castaneus and P. laterotarsus) were newly sequenced and comparatively analyzed. The arrangement of the mitogenome in these two lucanid beetles was the same as that in the inferred ancestral insect, and the nucleotide composition was highly biased towards A + T as in other lucanids. The evolutionary rates of 13 protein-coding genes (PCGs) suggested that their evolution was based on purifying selection. Notably, we found evidence of the presence of a large IGS between trnI and trnQ genes, whose length varied from 375 bp (in P. castaneus) to 158 bp (in P. laterotarsus). Within the large IGS region, a short sequence (TAAAA) was found to be unique among these two species, providing insights into phylogenomic reconstruction. Phylogenetic analyses were performed using the maximum likelihood (IQ-TREE) and Bayesian (PhyloBayes) methods based on 13 protein-coding genes (PCGs) in nucleotides and amino acids (AA) from published mitogenomes (n = 29). The genus Prosopocoilus was found to constitute a distinct clade with high nodal support. Overall, our findings suggested that analysis of the characteristics of the large IGS (presence or absence, size, and location) in mitogenomes of the genus Prosopocoilus may be informative for the phylogenetic and taxonomic analyses and for evaluation of the genus Prosopocoilus, despite the dense sampling materials needed.
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Affiliation(s)
- Mengqiong Xu
- Department of Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (M.X.); (S.Z.)
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Hefei 230601, China
| | - Shiju Zhou
- Department of Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (M.X.); (S.Z.)
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Hefei 230601, China
| | - Xia Wan
- Department of Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (M.X.); (S.Z.)
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Hefei 230601, China
- Correspondence: ; Tel.: +86-136-3709-1923
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14
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Huang X, Chen B, Wei Z, Shi A. First Report of Complete Mitochondrial Genome in the Tribes Coomaniellini and Dicercini (Coleoptera: Buprestidae) and Phylogenetic Implications. Genes (Basel) 2022; 13:genes13061074. [PMID: 35741836 PMCID: PMC9222259 DOI: 10.3390/genes13061074] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 11/16/2022] Open
Abstract
The complete mitochondrial genomes (mitogenomes) of the tribes Coomaniellini and Dicercini were sequenced and described in this study, including Coomaniella copipes (16,196 bp), Coomaniella dentata (16,179 bp), and Dicerca corrugata (16,276 bp). These complete mitogenomes are very similar in length and encoded 37 typical mitochondrial genes, including 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and 13 protein-coding genes (PCGs). Most of PCGs had typical ATN start codons and terminated with TAR. Among these mitogenomes, Leu2 (L2), Ile (I), Ser2 (S2), and Phe (F) were the four most frequently encoded amino acids. Moreover, phylogenetic analyses were performed based on three kinds of nucleotide matrixes (13 PCGs, 2 rRNAs, and 13 PCGs + 2 rRNAs) among the available sequenced species of the family Buprestidae using Bayesian inference and Maximum-likelihood methods. The results showed that a Chrysochroninae species interspersed in Buprestinae, and Coomaniellini is more closely related to Dicercini than Melanophilini. Moreover, the clade of Buprestidae was well separated from outgroups and the monophyly of Agrilinae is confirmed again. Our whole mitogenome phylogenetic results support that the genus Dicerca can be transferred from Chrysochroinae to Buprestinae; whether Dicercini can be completely transferred remains to be further verified after enriching samples. Our results have produced new complete mitogenomic data, which will provide information for future phylogenetic and taxonomic research.
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15
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Nethavhani Z, Straeuli R, Hiscock K, Veldtman R, Morton A, Oberprieler RG, van Asch B. Mitogenomics and phylogenetics of twelve species of African Saturniidae (Lepidoptera). PeerJ 2022; 10:e13275. [PMID: 35462770 PMCID: PMC9022641 DOI: 10.7717/peerj.13275] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/24/2022] [Indexed: 01/13/2023] Open
Abstract
African Saturniidae (Lepidoptera) include numerous species consumed at the caterpillar stage throughout the continent, and their importance to local communities as a source of nutrition and seasonal income cannot be overestimated. However, baseline genetic data with utility for the characterization of their diversity, phylogeography and phylogenetic relationships have remained scarce compared to their Asian counterparts. To bridge this gap, we sequenced the mitochondrial genomes of 12 species found in southern Africa for comparative mitogenomics and phylogenetic reconstruction of the family, including the first representatives of the tribes Eochroini and Micragonini. Mitochondrial gene content and organization were conserved across all Saturniidae included in the analyses. The phylogenetic positions of the 12 species were assessed in the context of publicly available mitogenomes using Bayesian inference and maximum likelihood (ML) methods. The monophyly of the tribes Saturniini, Attacini, Bunaeini and Micragonini, the sister relationship between Saturniini and Attacini, and the placement of Eochroa trimenii and Rhodinia fugax in the tribes Eochroini and Attacini, respectively, were strongly supported. These results contribute to significantly expanding genetic data available for African Saturniidae and allow for the development of new mitochondrial markers in future studies.
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Affiliation(s)
- Zwannda Nethavhani
- Department of Genetics, University of Stellenbosch, Stellenbosch, Western Cape, South Africa
| | - Rieze Straeuli
- Department of Genetics, University of Stellenbosch, Stellenbosch, Western Cape, South Africa
| | - Kayleigh Hiscock
- Department of Genetics, University of Stellenbosch, Stellenbosch, Western Cape, South Africa
| | - Ruan Veldtman
- Department of Conservation Ecology and Entomology, University of Stellenbosch, Stellenbosch, Western Cape, South Africa,Kirstenbosch Research Centre, South African National Biodiversity Institute, Cape Town, Western Cape, South Africa
| | | | - Rolf G. Oberprieler
- Australian National Insect Collection, Commonwealth Scientific and Industrial Research Organisation, Canberra, Australia
| | - Barbara van Asch
- Department of Genetics, University of Stellenbosch, Stellenbosch, Western Cape, South Africa
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Cai C, Tihelka E, Giacomelli M, Lawrence JF, Ślipiński A, Kundrata R, Yamamoto S, Thayer MK, Newton AF, Leschen RAB, Gimmel ML, Lü L, Engel MS, Bouchard P, Huang D, Pisani D, Donoghue PCJ. Integrated phylogenomics and fossil data illuminate the evolution of beetles. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211771. [PMID: 35345430 PMCID: PMC8941382 DOI: 10.1098/rsos.211771] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/15/2022] [Indexed: 05/03/2023]
Abstract
Beetles constitute the most biodiverse animal order with over 380 000 described species and possibly several million more yet unnamed. Recent phylogenomic studies have arrived at considerably incongruent topologies and widely varying estimates of divergence dates for major beetle clades. Here, we use a dataset of 68 single-copy nuclear protein-coding (NPC) genes sampling 129 out of the 193 recognized extant families as well as the first comprehensive set of fully justified fossil calibrations to recover a refined timescale of beetle evolution. Using phylogenetic methods that counter the effects of compositional and rate heterogeneity, we recover a topology congruent with morphological studies, which we use, combined with other recent phylogenomic studies, to propose several formal changes in the classification of Coleoptera: Scirtiformia and Scirtoidea sensu nov., Clambiformia ser. nov. and Clamboidea sensu nov., Rhinorhipiformia ser. nov., Byrrhoidea sensu nov., Dryopoidea stat. res., Nosodendriformia ser. nov. and Staphyliniformia sensu nov., and Erotyloidea stat. nov., Nitiduloidea stat. nov. and Cucujoidea sensu nov., alongside changes below the superfamily level. Our divergence time analyses recovered a late Carboniferous origin of Coleoptera, a late Palaeozoic origin of all modern beetle suborders and a Triassic-Jurassic origin of most extant families, while fundamental divergences within beetle phylogeny did not coincide with the hypothesis of a Cretaceous Terrestrial Revolution.
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Affiliation(s)
- Chenyang Cai
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Erik Tihelka
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Mattia Giacomelli
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - John F. Lawrence
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Adam Ślipiński
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Robin Kundrata
- Department of Zoology, Faculty of Science, Palacký University, 17. listopadu 50, 771 46 Olomouc, Czech Republic
| | - Shûhei Yamamoto
- Hokkaido University Museum, Hokkaido University, Kita 8, Nishi 5, Kita-ku, Sapporo 060-0808, Japan
| | - Margaret K. Thayer
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Alfred F. Newton
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Richard A. B. Leschen
- Manaaki Whenua Landcare Research, New Zealand Arthropod Collection, Private Bag 92170, Auckland, New Zealand
| | - Matthew L. Gimmel
- Invertebrate Zoology Department, Santa Barbara Museum of Natural History, 2559 Puesta del Sol Road, Santa Barbara, CA 93105, USA
| | - Liang Lü
- College of Life Science, Hebei Normal University, Shijiazhuang 050024, People's Republic of China
| | - Michael S. Engel
- Division of Entomology, Natural History Museum, and Department of Ecology & Evolutionary Biology, University of Kansas, 1501 Crestline Drive – Suite 140, Lawrence, KS 66045, USA
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Patrice Bouchard
- Division of Entomology, Natural History Museum, and Department of Ecology & Evolutionary Biology, University of Kansas, 1501 Crestline Drive – Suite 140, Lawrence, KS 66045, USA
| | - Diying Huang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Philip C. J. Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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17
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López-Estrada EK, Sanmartín I, Uribe JE, Abalde S, Jiménez-Ruiz Y, García-París M. Mitogenomics and hidden-trait models reveal the role of phoresy and host shifts in the diversification of parasitoid blister beetles (Coleoptera: Meloidae). Mol Ecol 2022; 31:2453-2474. [PMID: 35146829 PMCID: PMC9305437 DOI: 10.1111/mec.16390] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 01/24/2022] [Accepted: 01/31/2022] [Indexed: 11/28/2022]
Abstract
Changes in life history traits are often considered speciation triggers and can have dramatic effects on the evolutionary history of a lineage. Here, we examine the consequences of changes in two life history traits, host‐type and phoresy, in the hypermetamorphic blister beetles, Meloidae. Subfamilies Nemognathinae and Meloinae exhibit a complex life cycle involving multiple metamorphoses and parasitoidism. Most genera and tribes are bee‐parasitoids, and include phoretic or nonphoretic species, while two tribes feed on grasshopper eggs. These different life strategies are coupled with striking differences in species richness among clades. We generated a mitogenomic phylogeny for Nemognathinae and Meloinae, confirming the monophyly of these two clades, and used the dated phylogeny to explore the association between diversification rates and changes in host specificity and phoresy, using state‐dependent speciation and extinction (SSE) models that include the effect of hidden traits. To account for the low taxon sampling, we implemented a phylogenetic‐taxonomic approach based on birth‐death simulations, and used a Bayesian framework to integrate parameter and phylogenetic uncertainty. Results show that the ancestral hypermetamorphic Meloidae was a nonphoretic bee‐parasitoid, and that transitions towards a phoretic bee‐parasitoid and grasshopper parasitoidism occurred multiple times. Nonphoretic bee‐parasitoid lineages exhibit significantly higher relative extinction and lower diversification rates than phoretic bee‐and grasshopper‐parasitoids, but no significant differences were found between the latter two strategies. This suggests that Orthopteran host shifts and phoresy contributed jointly to the evolutionary success of the parasitoid meloidae. We also demonstrate that SSE models can be used to identify hidden traits coevolving with the focal trait in driving a lineage's diversification dynamics.
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Affiliation(s)
- E K López-Estrada
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, 28006, Madrid, España.,Real Jardín Botánico (RJB-CSIC). Plaza de Murillo, 2, 28014. Madrid, España
| | - I Sanmartín
- Real Jardín Botánico (RJB-CSIC). Plaza de Murillo, 2, 28014. Madrid, España
| | - J E Uribe
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, 28006, Madrid, España
| | - S Abalde
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, 28006, Madrid, España.,Centro de Estudios Avanzados de Blanes (CEAB-CSIC). Accéss, Cala Sant Francesc, 14, 17300, Blanes, España
| | - Y Jiménez-Ruiz
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, 28006, Madrid, España
| | - M García-París
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, 28006, Madrid, España
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Yuan L, Liu H, Ge X, Yang G, Xie G, Yang Y. A Mitochondrial Genome Phylogeny of Cleridae (Coleoptera, Cleroidea). INSECTS 2022; 13:insects13020118. [PMID: 35206692 PMCID: PMC8878092 DOI: 10.3390/insects13020118] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/16/2022] [Accepted: 01/19/2022] [Indexed: 01/22/2023]
Abstract
The predaceous beetle family Cleridae includes a large and widely distributed rapid radiation, which is vital for the ecosystem. Despite its important role, a number of problems remain to be solved regarding the phylogenetic inter-relationships, the timing of divergence, and the mitochondrial biology. Mitochondrial genomes have been widely used to reconstruct phylogenies of various insect groups, but never introduced to Cleridae until now. Here, we generated 18 mitochondrial genomes to address these issues, which are all novel to the family. In addition to phylogenomic analysis, we have leveraged our new sources to study the mitochondrial biology in terms of nucleotide composition, codon usage and substitutional rate, to understand how these vital cellular components may have contributed to the divergence of the Cleridae. Our results recovered Korynetinae sister to the remaining clerids, and the calde of Clerinae+Hydnocerinae is indicated more related to Tillinae. A time-calibrated phylogeny estimated the earliest divergence time of Cleridae was soon after the origin of the family, not later than 160.18 Mya (95% HPD: 158.18–162.07 Mya) during the mid-Jurassic. This is the first mitochondrial genome-based phylogenetic study of the Cleridae that covers nearly all subfamily members, which provides an alternative evidence for reconstructing the phylogenetic relationships.
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Affiliation(s)
- Lilan Yuan
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (L.Y.); (X.G.)
- College of Agriculture, Yangtze University, Jingzhou 434025, China;
| | - Haoyu Liu
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (L.Y.); (X.G.)
- Correspondence: (H.L.); (Y.Y.)
| | - Xueying Ge
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (L.Y.); (X.G.)
| | - Ganyan Yang
- Beijing Dabu Biotechnology Service Co., Ltd., Beijing 100085, China;
| | - Guanglin Xie
- College of Agriculture, Yangtze University, Jingzhou 434025, China;
| | - Yuxia Yang
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (L.Y.); (X.G.)
- Correspondence: (H.L.); (Y.Y.)
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Xing K, Chen K, Zhao XJ, Zhao F. The complete mitochondrial genome of Lixus subtilis Boheman, 1835 (Coleoptera, Curculionidae) and its phylogenetic implications. Mitochondrial DNA B Resour 2022; 7:35-36. [PMID: 34912964 PMCID: PMC8667946 DOI: 10.1080/23802359.2021.2008278] [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] [Indexed: 11/05/2022] Open
Abstract
The first complete mitochondrial genome of Lixus subtilis Boheman is reported in this study. The circular genome is 15,223 bp long, including a standard set of 21 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), 13 protein-coding genes, and a non-coding control region. The trnI gene was not found in the L. subtilis mitogenome. All tRNAs had the typical cloverleaf structure, except for trnS1, which lacked the dihydrouridine arm. The phylogenetic tree of 13 Curculionidae species based on the concatenated nucleotide sequences of complete mitochondrial genomes strongly supported that L. subtilis is closely related to Curculioninae and Molytinae.
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Affiliation(s)
- Kun Xing
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, College of Plant Protection, Shanxi Agricultural University, Taiyuan, China
| | - Kang Chen
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, College of Plant Protection, Shanxi Agricultural University, Taiyuan, China
| | - Xiao-jun Zhao
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, College of Plant Protection, Shanxi Agricultural University, Taiyuan, China
| | - Fei Zhao
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, College of Plant Protection, Shanxi Agricultural University, Taiyuan, China
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Mitochondrial Genomes of the Genus Claassenia (Plecoptera: Perlidae) and Phylogenetic Assignment to Subfamily Perlinae. Genes (Basel) 2021; 12:genes12121986. [PMID: 34946934 PMCID: PMC8701382 DOI: 10.3390/genes12121986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 11/29/2021] [Accepted: 12/10/2021] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial genomes of three stoneflies, e.g., Claassenia magna Wu, 1948, Claassenia sp. 2 and Claassenia xucheni Chen, 2019 were sequenced in this study with 15,774, 15,777 and 15,746 bp in length, respectively. Each mitogenome contained 37 genes including 22 tRNAs, two ribosomal RNAs, 13 protein-coding genes (PCGs), and a noncoding control region (CR). In general, standard ATN start and TAN termination codons were evident in the PCGs. Although the dihydrouridine arm was absent in trnSer, the remaining 21 tRNAs displayed the characteristic cloverleaf secondary structure. Stem-loop structures were identified in the CRs of all three mitogenomes, but tandem repeats were only apparent in Claassenia xucheni. The mitogenomes of three Claassenia species were analyzed and compared with mitogenomes in 21 other stoneflies from the Perlidae and three Euholognatha species (Rhopalopsole bulbifera, Capnia zijinshana and Amphinemura longispina) as outgroups. Phylogenetic analyses using maximum likelihood and Bayesian inference. Phylogenetic analysis supported that Claassenia was recovered as the sister group of other Perlinae and Claassenia+Perlinae emerged from the paraphyletic Acroneuriinae. The final results supported that Claassenia was classified into subfamily Perlinae and proposed Claassenia represent a transitional group of the subfamilies Acroneuriinae and Perlinae. This study provided new molecular evidence for exploring the debatable taxonomic position of the genus Claassenia in Perlidae.
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Zhang S, Sekerka L, Liao C, Long C, Xu J, Dai X, Guo Q. The First Eight Mitogenomes of Leaf-Mining Dactylispa Beetles (Coleoptera: Chrysomelidae: Cassidinae) Shed New Light on Subgenus Relationships. INSECTS 2021; 12:insects12111005. [PMID: 34821805 PMCID: PMC8624545 DOI: 10.3390/insects12111005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/28/2021] [Accepted: 11/04/2021] [Indexed: 11/16/2022]
Abstract
The taxonomic classification of Dactylispa, a large genus of leaf-mining beetles, is problematic because it is currently based on morphology alone. Here, the first eight mitochondrial genomes of Dactylispa species, which were used to construct the first molecular phylogenies of this genus, are reported. The lengths of the eight mitogenomes range from 17,189 bp to 20,363 bp. All of the mitochondrial genomes include 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and 1 A + T-rich region. According to the nonsynonymous/synonymous mutation ratio (Ka/Ks) of all PCGs, the highest and the lowest evolutionary rates were found for atp8 and cox1, respectively, which is a common phenomenon among animals. According to relative synonymous codon usage, UUA(L) has the highest frequency. With two Gonophorini species as the outgroup, mitogenome-based phylogenetic trees of the eight Dactylispa species were constructed using maximum likelihood (ML) and Bayesian inference (BI) methods based on the PCGs, tRNAs, and rRNAs. Two DNA-based phylogenomic inferences and one protein-based phylogenomic inference support the delimitation of the subgenera Dactylispa s. str. and Platypriella as proposed in the system of Chen et al. (1986). However, the subgenus Triplispa is not recovered as monophyletic. The placement of Triplispa species requires further verification and testing with more species. We also found that both adult body shape and host plant relationship might explain the subgeneric relationships among Dactylispa beetles to a certain degree.
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Affiliation(s)
- Shengdi Zhang
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (S.Z.); (C.L.); (C.L.); (J.X.)
- National Navel-Orange Engineering Research Center, Ganzhou 341000, China
| | - Lukáš Sekerka
- Department of Entomology, National Museum, Natural History Museum, 1740 Cirkusová, Czech Republic;
| | - Chengqing Liao
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (S.Z.); (C.L.); (C.L.); (J.X.)
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
| | - Chengpeng Long
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (S.Z.); (C.L.); (C.L.); (J.X.)
- National Navel-Orange Engineering Research Center, Ganzhou 341000, China
| | - Jiasheng Xu
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (S.Z.); (C.L.); (C.L.); (J.X.)
- National Navel-Orange Engineering Research Center, Ganzhou 341000, China
| | - Xiaohua Dai
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (S.Z.); (C.L.); (C.L.); (J.X.)
- National Navel-Orange Engineering Research Center, Ganzhou 341000, China
- Correspondence: (X.D.); (Q.G.)
| | - Qingyun Guo
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (S.Z.); (C.L.); (C.L.); (J.X.)
- National Navel-Orange Engineering Research Center, Ganzhou 341000, China
- Correspondence: (X.D.); (Q.G.)
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Guo J, Yan ZT, Fu WB, Yuan H, Li XD, Chen B. Complete mitogenomes of Anopheles peditaeniatus and Anopheles nitidus and phylogenetic relationships within the genus Anopheles inferred from mitogenomes. Parasit Vectors 2021; 14:452. [PMID: 34488869 PMCID: PMC8420037 DOI: 10.1186/s13071-021-04963-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/17/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite the medical importance of mosquitoes of the genus Anopheles in the transmission of malaria and other human diseases, its phylogenetic relationships are not settled, and the characteristics of mitochondrial genome (mitogenome) are not thoroughly understood. METHODS The present study sequenced and analyzed the complete mitogenomes of An. peditaeniatus and An. nitidus, investigated genome characteristics, and inferred the phylogenetic relationships of 76 Anopheles spp. RESULTS The complete mitogenomes of An. peditaeniatus and An. nitidus are 15,416 and 15,418 bp long, respectively, and both include 13 PCGs, 22 tRNAs, two tRNAs and one control region (CR). Mitogenomes of Anopheles spp. are similar to those of other insects in general characteristics; however, the trnR and trnA have been reversed to "trnR-trnA," as has been reported in other mosquito genera. Genome variations mainly occur in CR length (493-886 bp) with six repeat unit types identified for the first time that demonstrate an evolutionary signal. The subgenera Lophopodomyia, Stethomyia, Kerteszia, Nyssorhynchus, Anopheles and Cellia are inferred to be monophyletic, and the phylogenetic analyses support a new phylogenetic relationship among the six subgenera investigated, in that subgenus Lophopodomyia is the sister to all other five subgenera, and the remaining five subgenera are divided into two clades, one of which is a sister-taxon subgenera Stethomyia + Kerteszia, and the other consists of subgenus Nyssorhynchus as the sister to a sister-group subgenera Anopheles + Cellia. Four series (Neomyzomyia, Pyretophorus, Neocellia and Myzomyia) of the subgenus Cellia, and two series (Arribalzagia and Myzorhynchus) of the subgenus Anopheles were found to be monophyletic, whereas three sections (Myzorhynchella, Argyritarsis and Albimanus) and their subdivisions of the subgenus Nyssorhynchus were polyphyletic or paraphyletic. CONCLUSIONS The study comprehensively uncovered the characteristics of mitogenome and the phylogenetics based on mitogenomes in the genus Anopheles, and provided information for further study on the mitogenomes, phylogenetics and taxonomic revision of the genus.
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Affiliation(s)
- Jing Guo
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331 People’s Republic of China
| | - Zhen-Tian Yan
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331 People’s Republic of China
| | - Wen-Bo Fu
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331 People’s Republic of China
| | - Huan Yuan
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331 People’s Republic of China
| | - Xu-Dong Li
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331 People’s Republic of China
| | - Bin Chen
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331 People’s Republic of China
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Wang L, Ding S, Cameron SL, Li X, Liu Y, Yao G, Yang D. Middle Jurassic origin in India: a new look at evolution of Vermileonidae and time-scaled relationships of lower brachyceran flies. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Vermileonidae (wormlions) comprises 61 described species in 12 genera and is one of the oddest and most rarely collected dipteran families. Larvae of Vermileonidae are famous for their pitfall prey behaviour, whereas the adults are rarely seen. Here we report, for the first time, the complete mitochondrial genome from members of Vermileonidae. Phylogenetic reconstruction based on a representative sampling of the order reveals new insights into relationships between the Vermileonidae and other members of lower brachyceran flies. A sister-group relationship between Vermileonidae and Xylophagidae is supported, and the higher-level clade relationships are Tabanomorpha + (Muscomorpha + (Xylophagomorpha + Stratiomyomorpha)). Combining mitochondrial genome data with a morphological phylogeny, geographical distribution and geological history, we propose that the Vermileonidae originated in India during the Middle Jurassic, spreading to Africa via land bridges during the Late Jurassic, to the Palaearctic after the collision of India with Laurasia in the Late Oligocene, and to the Nearctic in the Early Miocene, via either North Atlantic or Beringian land bridges. Wet forested regions have proved to be barriers to their dispersal, explaining their absence from Central Africa, South America and eastern North America.
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Affiliation(s)
- Liang Wang
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Shuangmei Ding
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Stephen L Cameron
- Department of Entomology, Purdue University, West Layfayette, IN, USA
| | - Xin Li
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Yue Liu
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Gang Yao
- Jinhua Polytechnic, Jinhua, Zhejiang, China
| | - Ding Yang
- College of Plant Protection, China Agricultural University, Beijing, China
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24
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Mello CADA, Amorim IC, Silva AFD, Medeiros GRD, Wallau GL, Moura RDCD. Mitogenome of Coprophanaeus ensifer and phylogenetic analysis of the Scarabaeidae family (Coleoptera). Genet Mol Biol 2021; 44:e20200417. [PMID: 34387299 PMCID: PMC8361247 DOI: 10.1590/1678-4685-gmb-2020-0417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 05/02/2021] [Indexed: 12/02/2022] Open
Abstract
Several studies about the phylogenetic relationships of the Scarabaeinae subfamily (Coleoptera: Scarabaeidae) have been performed, but some phylogenetic uncertainties persist including the relationship and monophyly of different tribes and some genera. The aim of this study was to characterize the mitogenome of Coprophanaeus ensifer in order to establish its position within the Scarabaeidae family and to contribute to the resolution of some phylogenetic uncertainties. The mitogenome was sequenced on the Illumina HiSeq 4000, assembled using the Mitobim software and annotated in MITOS WebServer. The phylogenetic trees were reconstructed by Bayesian inference. The C. ensifer mitogenome is a molecule of 14,964 bp that contains the number and organization of the genes similar to those of most Coleoptera species. Phylogenetic reconstruction suggests monophyly of the tribe Phanaeini and supports the hypothesis that Coprini is a sister group of Phanaeini. The results also revealed the position of the tribe Oniticellini which is grouped with Onthophagini and Onitini. The geographic distribution of these species that form the most ancestral clade suggests with Scarabaeinae originated in Africa.
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Affiliation(s)
| | - Igor Costa Amorim
- Universidade de Pernambuco, Instituto de Ciências Biológicas, Laboratório de Biodiversidade e Genética de Insetos, Recife, PE, Brazil
| | | | - Giuliene Rocha de Medeiros
- Universidade de Pernambuco, Instituto de Ciências Biológicas, Laboratório de Biodiversidade e Genética de Insetos, Recife, PE, Brazil
| | - Gabriel Luz Wallau
- Departamento de Entomologia, Instituto Aggeu Magalhães - FIOCRUZ, Recife, Pernambuco, Brazil
| | - Rita de Cássia de Moura
- Universidade de Pernambuco, Instituto de Ciências Biológicas, Laboratório de Biodiversidade e Genética de Insetos, Recife, PE, Brazil
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Seo Y, Chae J, Ki JS. The complete mitochondrial genome of the hydrozoan jellyfish Turritopsis lata Lendenfeld, 1885 (Cnidaria; Hydrozoa; Anthoathecata) with molecular phylogenetic analysis. Mitochondrial DNA B Resour 2021; 6:1992-1993. [PMID: 34179492 PMCID: PMC8205065 DOI: 10.1080/23802359.2021.1938725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/27/2021] [Indexed: 11/20/2022] Open
Abstract
In this study, we sequenced and analyzed the complete mitochondrial genome (mtgenome) of the hydrozoan jellyfish Turritopsis lata. The mtgenome was a complete linear form (15,047 bp in length, 30.9% A, 42.1% T, 12.5% C, and 14.5% G), including 13 protein coding genes (PCGs) (cox1, cox2, cox3, atp6, atp8, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, and cytb), 2 tRNAs (tRNAMet and tRNATrp), and 2 rRNAs (12S and 16S rRNA). The genome structure of the T. lata was completely identical to those of other species within the subclass Hydroidolina. In addition, our molecular phylogenetic analysis using 13 PCGs within hydrozoans showed that T. lata was the closest to Turritopsis dohrnii.
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Affiliation(s)
- Yoseph Seo
- Department of Biotechnology, Sangmyung University, Seoul, South Korea
| | - Jinho Chae
- Marine Environmental Research and Information Laboratory, Gunpo, South Korea
| | - Jang-Seu Ki
- Department of Biotechnology, Sangmyung University, Seoul, South Korea
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Deyrup ST, Stagnitti NC, Perpetua MJ, Wong-Deyrup SW. Drug Discovery Insights from Medicinal Beetles in Traditional Chinese Medicine. Biomol Ther (Seoul) 2021; 29:105-126. [PMID: 33632986 PMCID: PMC7921859 DOI: 10.4062/biomolther.2020.229] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 12/29/2020] [Accepted: 01/04/2021] [Indexed: 11/23/2022] Open
Abstract
Traditional Chinese medicine (TCM) was the primary source of medical treatment for the people inhabiting East Asia for thousands of years. These ancient practices have incorporated a wide variety of materia medica including plants, animals and minerals. As modern sciences, including natural products chemistry, emerged, there became increasing efforts to explore the chemistry of this materia medica to find molecules responsible for their traditional use. Insects, including beetles have played an important role in TCM. In our survey of texts and review articles on TCM materia medica, we found 48 species of beetles from 34 genera in 14 different families that are used in TCM. This review covers the chemistry known from the beetles used in TCM, or in cases where a species used in these practices has not been chemically studied, we discuss the chemistry of closely related beetles. We also found several documented uses of beetles in Traditional Korean Medicine (TKM), and included them where appropriate. There are 129 chemical constituents of beetles discussed.
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Affiliation(s)
- Stephen T Deyrup
- Department of Chemistry and Biochemistry, Siena College, Loudonville, NY 12309, USA
| | - Natalie C Stagnitti
- Department of Chemistry and Biochemistry, Siena College, Loudonville, NY 12309, USA
| | - Mackenzie J Perpetua
- Department of Chemistry and Biochemistry, Siena College, Loudonville, NY 12309, USA
| | - Siu Wah Wong-Deyrup
- The RNA Institute and Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
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Narakusumo RP, Riedel A, Pons J. Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils. PeerJ 2020; 8:e10017. [PMID: 33083123 PMCID: PMC7566755 DOI: 10.7717/peerj.10017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/01/2020] [Indexed: 11/20/2022] Open
Abstract
Mitochondrial genomes of twelve species of Trigonopterus weevils are presented, ten of them complete. We describe their gene order and molecular features and test their potential for reconstructing the phylogeny of this hyperdiverse genus comprising > 1,000 species. The complete mitochondrial genomes examined herein ranged from 16,501 bp to 21,007 bp in length, with an average AT content of 64.2% to 69.7%. Composition frequencies and skews were generally lower across species for atp6, cox1-3, and cob genes, while atp8 and genes coded on the minus strand showed much higher divergence at both nucleotide and amino acid levels. Most variation within genes was found at the codon level with high variation at third codon sites across species, and with lesser degree at the coding strand level. Two large non-coding regions were found, CR1 (between rrnS and trnI genes) and CR2 (between trnI and trnQ), but both with large variability in length; this peculiar structure of the non-coding region may be a derived character of Curculionoidea. The nad1 and cob genes exhibited an unusually high interspecific length variation of up to 24 bp near the 3' end. This pattern was probably caused by a single evolutionary event since both genes are only separated by trnS2 and length variation is extremely rare in mitochondrial protein coding genes. We inferred phylogenetic trees using protein coding gene sequences implementing both maximum likelihood and Bayesian approaches, each for both nucleotide and amino acid sequences. While some clades could be retrieved from all reconstructions with high confidence, there were also a number of differences and relatively low support for some basal nodes. The best partition scheme of the 13 protein coding sequences obtained by IQTREE suggested that phylogenetic signal is more accurate by splitting sequence variation at the codon site level as well as coding strand, rather than at the gene level. This result corroborated the different patterns found in Trigonopterus regarding to A+T frequencies and AT and GC skews that also greatly diverge at the codon site and coding strand levels.
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Affiliation(s)
- Raden Pramesa Narakusumo
- State Museum of Natural History Karlsruhe, Karlsruhe, Germany.,Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | | | - Joan Pons
- Diversidad Animal y Microbiana, Instituto Mediterráneo de Estudios Avanzados IMEDEA (CSIC-UIB), Esporles, Balearic Islands, Spain
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28
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Gao XJ, Wang HL, Zu JH. The complete mitochondrial genome of Psylliodes balyi Jacoby (Coleoptera: Chrysomelidae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2909-2910. [PMID: 33457998 PMCID: PMC7781982 DOI: 10.1080/23802359.2020.1791752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The complete mitogenome of Psylliodes balyi Jacoby (GenBank accession number MT644112) is 14,561 bp in length, and contains 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes, and a putative control region. The gene content and orientation of P. balyi were identical to other beetle mitogenomes. ATT, ATA, and ATG were initiation codons and TAA, TAG, and T were termination codons. All the 22 tRNAs have the typical cloverleaf secondary structure, except for trnS1 which lacked the dihydrouracil (DHU) arm. The phylogenetic relationship based on the neighbor-joining method showed that P. balyi is closely related to Agasicles hygrophila, which agrees with the conventional classification.
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Affiliation(s)
- Xin-Ju Gao
- Henan Key Laboratory of Crop Pest Control, IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, International Joint Research Laboratory for Crop Protection of Henan, Biological Pesticides Engineering Research Center of Henan Province, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Heng-Liang Wang
- Henan Key Laboratory of Crop Pest Control, IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, International Joint Research Laboratory for Crop Protection of Henan, Biological Pesticides Engineering Research Center of Henan Province, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Jun-Huai Zu
- Henan Key Laboratory of Crop Pest Control, IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, International Joint Research Laboratory for Crop Protection of Henan, Biological Pesticides Engineering Research Center of Henan Province, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, China
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29
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Choi EH, Mun S, Baek SY, Hwang J, Hwang UW. The complete mitochondrial genome of a whiter-spotted flower chafer, Protaetia brevitarsis (Coleoptera: Scarabaeidae). Mitochondrial DNA B Resour 2020; 5:3602-3604. [PMID: 33367026 PMCID: PMC7594739 DOI: 10.1080/23802359.2020.1824592] [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] [Indexed: 11/29/2022] Open
Abstract
The complete mitochondrial genome of Protaetia brevitarsis, an important Scarabaeidae insect that is distributed across most Asian countries, was characterized using long template PCR methods. It was 17,783 bp in length being composed of 13 protein coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a non-coding region. The phylogenetic tree reconstructed based on the maximum likelihood (ML) method confirmed that P. brevitarsis was placed within the clade of Scarabaeidae and Polyphaga species forming a complete monophyly.
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Affiliation(s)
- Eun Hwa Choi
- Department of Biology Education, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, Republic of Korea
| | - Sohyun Mun
- Department of Biology Education, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, Republic of Korea
| | - Su Youn Baek
- Department of Biology Education, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, Republic of Korea
- Institute for Korean Herb-Bio Convergence Promotion, Kyungpook National University, Daegu, Republic of Korea
| | - Jihye Hwang
- Department of Biology Education, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, Republic of Korea
| | - Ui Wook Hwang
- Department of Biology Education, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, Republic of Korea
- Institute for Korean Herb-Bio Convergence Promotion, Kyungpook National University, Daegu, Republic of Korea
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Song X, Yang T, Yan X, Zheng F, Xu X, Zhou C. Comparison of microsatellite distribution patterns in twenty-nine beetle genomes. Gene 2020; 757:144919. [PMID: 32603771 DOI: 10.1016/j.gene.2020.144919] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 06/15/2020] [Accepted: 06/20/2020] [Indexed: 01/20/2023]
Abstract
Simple sequence repeats (SSRs) represent an important source of genetic variation that provides a basis for adaptation to different environments in organisms. In this study, we examined the distribution patterns of SSRs in twenty-nine beetle genomes and carried out Gene Ontology (GO) analysis of CDSs embedded with perfect SSRs (P-SSRs). The results demonstrated that imperfect SSRs (I-SSRs) represented the most abundant SSR category in beetle genomes and in different genomic regions (CDS, exon, and intron regions). The numbers of P-SSRs, I-SSRs, compound SSRs, and variable number tandem repeats were positively correlated with beetle genome size, whereas neither the frequency nor the density of the SSRs was correlated with genome size. Moreover, our results demonstrated that common genomic features of P-SSRs within the same suborder or family of Coleoptera were rare. Mono-, di-, tri-, or tetranucleotide SSRs were the most abundant P-SSR categories in beetle genomes. The preferred predominant repeat motif among the mononucleotide P-SSRs was (A)n, but the most frequent repeat motifs for other length classes varied differentially among these genomes. Furthermore, the P-SSR type with the highest GC content differed in the beetle genomes and in different genomic regions. CV (coefficient of variability) analysis demonstrated that the repeat copy numbers of P-SSRs presented relatively higher variation in introns than in CDSs and exons. The GO terms of CDSs containing P-SSRs for molecular functions were mainly enriched in "binding" and "transcription". Our findings will be useful for studying the functional roles of microsatellite heterogeneity in beetle adaptation.
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Affiliation(s)
- Xuhao Song
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China.
| | - Tingbang Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China
| | - Xianghui Yan
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China
| | - Fake Zheng
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China
| | - Xiaoqin Xu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China
| | - Caiquan Zhou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China.
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Tang PA, Feng RQ, Zhang L, Wang J, Wang XT, Zhang LJ, Yuan ML. Mitochondrial genomes of three Bostrichiformia species and phylogenetic analysis of Polyphaga (Insecta, Coleoptera). Genomics 2020; 112:2970-2977. [PMID: 32417292 DOI: 10.1016/j.ygeno.2020.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 10/24/2022]
Abstract
Here we determined mitogenomes of three Bostrichiformia species. These data were combined with 51 previously sequenced Polyphaga mitogenomes to explore the higher-level relationships within Polyphaga by using four different mitogenomic datasets and three tree inference approaches. Among Polyphaga mitogenomes we observed heterogeneity in nucleotide composition and evolutionary rates, which may have affected phylogenetic inferences across the different mitogenomic datasets. Elateriformia, Cucujiformia, and Scarabaeiformia were each inferred to be monophyletic by all analyses, as was Bostrichiformia by most analyses based on two datasets with low heterogeneity. The large series Staphyliniformia was never recovered as monophyletic in our analyses. The Bayesian tree using a degenerated nucleotide dataset (P123_Degen) and a site-heterogeneous mixture model in PhyloBayes was supported as the best Polyphaga phylogeny: (Scirtiformia, (Elateriformia, ((Bostrichiformia, Cucujiformia), (Scarabaeiformia + Staphyliniformia)))). For Cucujiformia, the largest series, we inferred a superfamily-level phylogeny: ((Cleroidea, Coccinelloidea), (Tenebrionoidea, (Cucujoidea + Curculionoidea + Chrysomeloidea))).
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Affiliation(s)
- Pei-An Tang
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, People's Republic of China
| | - Run-Qiu Feng
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China
| | - Li Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China
| | - Juan Wang
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China
| | - Xiao-Tong Wang
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China
| | - Li-Jun Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China
| | - Ming-Long Yuan
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China.
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Sun H, Zhao W, Lin R, Zhou Z, Huai W, Yao Y. The conserved mitochondrial genome of the jewel beetle (Coleoptera: Buprestidae) and its phylogenetic implications for the suborder Polyphaga. Genomics 2020; 112:3713-3721. [PMID: 32360911 DOI: 10.1016/j.ygeno.2020.04.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/22/2020] [Accepted: 04/27/2020] [Indexed: 01/04/2023]
Abstract
In this study, we sequenced the mitochondrial (mt) genome of Agrilus mali (Coleoptera: Buprestidae) using next-generation sequencing, and accordingly annotated 13 protein-coding, 22 tRNA, and 2 rRNA genes and a 1458-bp non-coding region. Comparative analysis indicated that the mt genome of A. mali is relatively conserved, with a typical gene content and order identical to those of other coleopterans. However, the newly sequenced mt genome is characterized by a relatively higher A + T content compared with that of other species within the family Buprestidae. Phylogenetic analysis based on Bayesian inference revealed that the evolutionary relationship among the six infraorders of the suborder Polyphaga is (Scirtiformia + (Elateriformia + ((Scarabaeiformia + Staphyliniformia) + (Bostrichiformia + (Cucujiformia))))). However, the topology indicated that the family Buprestidae is a sister group to other Polyphaga infraorders, excluding Scirtiformia as a monophyly, and thus the monophyly of Elateriformia was not supported. This study not only presents the mt genome of a species in the family Buprestidae and a comparative analysis of jewel beetles but also examines the contribution of mt genomes in elucidating phylogenetic relationships within the suborder Polyphaga of Coleoptera.
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Affiliation(s)
- Huiquan Sun
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Wenxia Zhao
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Ruozhu Lin
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Zhongfu Zhou
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Wenxia Huai
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Yanxia Yao
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China.
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Sun X, Yu D, Xie Z, Dong J, Ding Y, Yao H, Greenslade P. Phylomitogenomic analyses on collembolan higher taxa with enhanced taxon sampling and discussion on method selection. PLoS One 2020; 15:e0230827. [PMID: 32282807 PMCID: PMC7153868 DOI: 10.1371/journal.pone.0230827] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/09/2020] [Indexed: 12/20/2022] Open
Abstract
Collembola are a basal group of Hexapoda renowned for both unique morphological characters and significant ecological roles. However, a robust and plausible phylogenetic relationship between its deeply divergent lineages has yet to be achieved. We carried out a mitophylogenomic study based on a so far the most comprehensive mitochondrial genome dataset. Our data matrix contained mitogenomes of 31 species from almost all major families of all four orders, with 16 mitogenomes newly sequenced and annotated. We compared the linear arrangements of genes along mitochondria across species. Then we conducted 13 analyses each under a different combination of character coding, partitioning scheme and heterotachy models, and assessed their performance in phylogenetic inference. Several hypothetical tree topologies were also tested. Mitogenomic structure comparison revealed that most species share the same gene order of putative ancestral pancrustacean pattern, while seven species from Onychiuridae, Poduridae and Symphypleona bear different levels of gene rearrangements, indicating phylogenetic signals. Tomoceroidea was robustly recovered for the first time in the presence of all its families and subfamilies. Monophyly of Onychiuroidea was supported using unpartitioned models alleviating LBA. Paronellidae was revealed polyphyletic with two subfamilies inserted independently into Entomobryidae. Although Entomobryomorpha has not been well supported, more than half of the analyses obtained convincing topologies by placing Tomoceroidea within or near remaining Entomobryomorpha. The relationship between elongate-shaped and spherical-shaped collembolans still remained ambiguous, but Neelipleona tend to occupy the basal position in most trees. This study showed that mitochondrial genomes could provide important information for reconstructing the relationships among Collembola when suitable analytical approaches are implemented. Of all the data refining and model selecting schemes used in this study, the combination of nucleotide sequences, partitioning model and exclusion of third codon positions performed better in generating more reliable tree topology and higher node supports than others.
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Affiliation(s)
- Xin Sun
- J.F. Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Daoyuan Yu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- * E-mail: ,
| | - Zhijing Xie
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Dong
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yinhuan Ding
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Haifeng Yao
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Penelope Greenslade
- Environmental Management, School of Applied and Biomedical Science, Federation University, Ballarat, Victoria, Australia
- Division of Biology, Australian National University, Australian Capital Territory, Australia
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Liu YY, Zhou ZC, Chen XS. Characterization of the Complete Mitochondrial Genome of Epicauta impressicornis (Coleoptera: Meloidae) and Its Phylogenetic Implications for the Infraorder Cucujiformia. JOURNAL OF INSECT SCIENCE (ONLINE) 2020; 20:16. [PMID: 32302386 PMCID: PMC7164779 DOI: 10.1093/jisesa/ieaa021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Indexed: 06/11/2023]
Abstract
The complete mitochondrial genome (mitogenome) of Epicauta impressicornis Pic (Coleoptera: Meloidae) was determined. The circular genome is 15,713-bp long, and encodes 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (CR). The 13 PCGs start with the typical ATN codon and terminate with the typical stop codon TAA (ND2, ND4L, ND6, ATP6, ATP8, and CYTB), TAG (ND1 and ND3), and T- (COX1, COX2, COX3, ND4, and ND5). The two rRNA genes (rrn12S and rrn16S) are encoded on the minority strand. All tRNAs genes except trnS1 (AGN) are predicted to fold into the typical cloverleaf structure. The longest overlap (10 bp) is observed between ATP8 and ATP6. CR mainly harbors a conserved poly-T stretch (15 bp), a short repeat unit (17 bp), some universal microsatellite-like repeats, and a canonical poly-A tail. Phylogenetic analysis using Bayesian inferences and maximum likelihood based on nucleotide and corresponding amino acid sequences of the 13 PCGs showed that E. impressicornis is closely related to E. chinensis, this relationship is and supported within Cucujiformia belonging to Meloidae (Tenebrionoidea). Our results further confirmed the monophyly of Tenebrionoidea, Lymexyloidea, Curculionoidea, Chrysomeloidea, Cucujoidea, Coccinelloidea, and Cleroidea within Cucujiformia, and revealed the sister relationships of (Cleroidea + Coccinelloidea), (Lymexyloidea + Tenebrionoidea), and ((Chrysomeloidea + Cucujoidea) + Curculionoidea). We believe that the complete mitogenome of E. impressicornis will contribute to further studies on molecular bases for the classification and phylogeny of Meloidae or even Cucujiformia.
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Affiliation(s)
- Yang-Yang Liu
- Institute of Entomology and Special Key Laboratory for Development and Utilization of Insect Resources of Guizhou, Guizhou University, Guiyang, China
| | - Zhi-Cheng Zhou
- Institute of Entomology and Special Key Laboratory for Development and Utilization of Insect Resources of Guizhou, Guizhou University, Guiyang, China
| | - Xiang-Sheng Chen
- Institute of Entomology and Special Key Laboratory for Development and Utilization of Insect Resources of Guizhou, Guizhou University, Guiyang, China
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Magro A, Lecompte E, Hemptinne J, Soares AO, Dutrillaux A, Murienne J, Fürsch H, Dutrillaux B. First case of parthenogenesis in ladybirds (Coleoptera: Coccinellidae) suggests new mechanisms for the evolution of asexual reproduction. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12339] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Alexandra Magro
- Laboratoire Evolution et Diversité biologique UMR EDB 5174 CNRS / UT3 / IRDToulouse France
- Ecole Nationale Supérieure de Formation de l'Enseignement Agricole Auzeville-Tolosane France
| | - Emilie Lecompte
- Laboratoire Evolution et Diversité biologique UMR EDB 5174 CNRS / UT3 / IRDToulouse France
- Université Toulouse III‐Paul Sabatier Toulouse France
| | - Jean‐Louis Hemptinne
- Laboratoire Evolution et Diversité biologique UMR EDB 5174 CNRS / UT3 / IRDToulouse France
- Ecole Nationale Supérieure de Formation de l'Enseignement Agricole Auzeville-Tolosane France
| | - Antonio O. Soares
- Centre for Ecology, Evolution and Environmental Changes Azorean Biodiversity Group University of the Azores Ponta Delgada, Azores Portugal
| | - Anne‐Marie Dutrillaux
- Institut de Systématique, Evolution, Biodiversité UMR ISYEB 7205 CNRS / MNHN / UPMC / EPHE Museum National d'Histoire Naturelle Paris France
| | - Jérôme Murienne
- Laboratoire Evolution et Diversité biologique UMR EDB 5174 CNRS / UT3 / IRDToulouse France
- Université Toulouse III‐Paul Sabatier Toulouse France
| | | | - Bernard Dutrillaux
- Institut de Systématique, Evolution, Biodiversité UMR ISYEB 7205 CNRS / MNHN / UPMC / EPHE Museum National d'Histoire Naturelle Paris France
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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]
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Song N, Li X, Yin X, Li X, Yin S, Yang M. The mitochondrial genome of Apion squamigerum (Coleoptera, Curculionoidea, Brentidae) and the phylogenetic implications. PeerJ 2020; 8:e8386. [PMID: 31976182 PMCID: PMC6964704 DOI: 10.7717/peerj.8386] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/11/2019] [Indexed: 11/20/2022] Open
Abstract
In this article, we present the nearly complete mitochondrial genome (mitogenome) of the weevil beetle Apion squamigerum (Curculionoidea, Brentidae), assembled using data from Illumina next generation sequencing (NGS). This mitogenome was found to be very large, with the total length of 18,562 bp. Two trnM genes were identified. A large non-coding intergenic spacer spanning 1,949 bp occurred between trnI and trnM2. Combined with 111 existing weevil mitogenomes, we conducted phylogenetic reconstructions based on various datasets under maximum likelihood and Bayesian inference. Firstly, phylogenetic analyses robustly supported a sister group of A. squamigerum and Rhopalapion longirostre, namely, that two species of Apioninae (Brentidae) formed a clade. Within the entire Curculionoidea, the Nemonychidae diverged firstly, following the families Anthribidae and Attelabidae. In addition, a large clade comprising the sister families Brentidae and Curculionidae was strongly supported in all trees.
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Affiliation(s)
- Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Xinxin Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Xinming Yin
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Xinghao Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Shengjun Yin
- Department of Chinese Medicine, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Mingsheng Yang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
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Feng RQ, Zhang LJ, Li M, Liu J, Wen CL, Yuan ML. Mitochondrial genome of Chrysochares punctatus (Coleoptera: Chrysomelidae: Eumolpinae) and phylogenetic analysis. Mitochondrial DNA B Resour 2020; 5:667-668. [PMID: 33366695 PMCID: PMC7748835 DOI: 10.1080/23802359.2020.1711823] [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] [Indexed: 11/25/2022] Open
Abstract
Here, we determined the nearly complete mitochondrial genome (mitogenome) of Chrysochares punctatus (Coleoptera: Chrysomelidae: Eumolpinae), an important insect pest on Apocynum venetum in Northwestern China. This mitogenome was 14,451 bp long, encoding 13 protein-coding genes (PCGs), 21 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes. The C. punctatus mitogenome presented an A + T content of 75.11%, with a positive AT-skew (0.064) and a negative GC-skew (−0.192). Ten PCGs started with a typical ATN codon, whereas the remaining three PCGs started with AAC (cox1) and TTG (nad1 and nad2). All tRNAs had a typical secondary cloverleaf structure, except for trnS1 which lacked the dihydrouridine arm. Bayesian phylogenetic analysis based on the nucleotide sequences of 13 PCGs recovered a phylogeny within Chrysomelidae: (((Chrysomelinae + Galerucinae), (((Eumolpinae, Lamprosomatinae), Cassidinae), Criocerinae)), Bruchinae).
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Affiliation(s)
- Run-Qiu Feng
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, People's Republic of China
| | - Li-Jun Zhang
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, People's Republic of China
| | - Min Li
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, People's Republic of China
| | - Jia Liu
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, People's Republic of China
| | - Chun-Li Wen
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, People's Republic of China
| | - Ming-Long Yuan
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, People's Republic of China
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Yuan M, Zhang L, Zhang Q, Zhang L, Li M, Wang X, Feng R, Tang P. Mitogenome evolution in ladybirds: Potential association with dietary adaptation. Ecol Evol 2020; 10:1042-1053. [PMID: 32015863 PMCID: PMC6988538 DOI: 10.1002/ece3.5971] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 11/26/2019] [Accepted: 12/06/2019] [Indexed: 12/20/2022] Open
Abstract
Dietary shifts can alter the relative availability of different nutrients and are therefore associated with metabolic adaptation in animals. The Coccinellidae (ladybirds) exhibits three major types of feeding habits and provides a useful model to study the effects of dietary changes on the evolution of mitogenomes, which encode proteins directly involved in energy metabolism. Here, mitogenomes of three coccinellid species were newly sequenced. These data were combined with other ten previously sequenced coccinellid mitogenomes to explore the relationship between mitogenome evolution and diets. Our results indicate that mitogenomic data can be effectively used to resolve phylogenetic relationships of Coccinellidae. Strong codon usage bias in coccinellid mitogenomes was predominantly determined by nucleotide composition. The 13 mitochondrial protein-coding genes (PCGs) globally evolved under negative constraints, with some PCGs showing a stronger purifying selection. Six PCGs (nad3, nad4L, and nad5 from Complex I; cox1 and cox3 from Complex IV; and atp6 from Complex V) displayed signs of positive selection. Of these, adaptive changes in cox3 were potentially associated with metabolic differences resulting from dietary shifts in Coccinellidae. Our results provide insights into the adaptive evolution of coccinellid mitogenomes in response to both dietary shifts and other life history traits.
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Affiliation(s)
- Ming‐Long Yuan
- State Key Laboratory of Grassland Agro‐EcosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Li‐Jun Zhang
- State Key Laboratory of Grassland Agro‐EcosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Qi‐Lin Zhang
- Faculty of Life Science and TechnologyKunming University of Science and TechnologyKunmingChina
| | - Li Zhang
- State Key Laboratory of Grassland Agro‐EcosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Min Li
- State Key Laboratory of Grassland Agro‐EcosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Xiao‐Tong Wang
- State Key Laboratory of Grassland Agro‐EcosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Run‐Qiu Feng
- State Key Laboratory of Grassland Agro‐EcosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Pei‐An Tang
- Collaborative Innovation Center for Modern Grain Circulation and SafetyCollege of Food Science and EngineeringNanjing University of Finance and EconomicsNanjingChina
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Oh DJ, Yang KS, Jung YH. The mitochondrial genome of the Jeju ground beetle Carabus smaragdinus monilifer (Coleoptera, Carabidae). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 5:39-40. [PMID: 33366412 PMCID: PMC7721059 DOI: 10.1080/23802359.2019.1692708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The complete mitochondrial genome of the Jeju ground beetle Carabus smaragdinus monilifer was analyzed to determine its structure, morphology, and other characteristics. The 16,737-bp long mitochondrial genome consisted of 37 genes, including 13 protein-coding genes, two rRNAs, and 22 tRNAs. The order, encoding direction, and the initiation and termination codons of the 37 genes of C. smaragdinus monilifer were identical to those of other species in the family Carabidae. Phylogenetic analysis revealed that C. smaragdinus monilifer is clustered with Carabus lafossei. Herein, we have provided the complete mitochondrial genome sequence of C. smaragdinus monilifer to understand the phylogeny of Carabidae.
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Affiliation(s)
- Dae-Ju Oh
- Biodiversity Research Institute, Jeju Technopark, Seogwipo, Republic of Korea
| | - Kyoung-Sik Yang
- Biodiversity Research Institute, Jeju Technopark, Seogwipo, Republic of Korea
| | - Yong-Hwan Jung
- Biodiversity Research Institute, Jeju Technopark, Seogwipo, Republic of Korea
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Li R, Shu X, Li X, Meng L, Li B. Comparative mitogenome analysis of three species and monophyletic inference of Catantopinae (Orthoptera: Acridoidea). Genomics 2019; 111:1728-1735. [DOI: 10.1016/j.ygeno.2018.11.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/10/2018] [Accepted: 11/27/2018] [Indexed: 12/29/2022]
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Yang WJ, Yan SY, Jin DC. The complete mitochondrial genome of Smaragdina nigrifrons (Coleoptera: Eumolpidae): characterization and phylogenetic position. Mitochondrial DNA B Resour 2019; 4:3981-3982. [PMID: 33366280 PMCID: PMC7707656 DOI: 10.1080/23802359.2019.1688710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 10/27/2019] [Indexed: 12/04/2022] Open
Abstract
The complete mitogenome of Smaragdina nigrifrons (GenBank accession number MN584924) is 15,903 bp in length, and includes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes, and a control region. The overall base composition was as follows: A, 38.18%; T, 35.25%; C, 15.97%; and G, 10.60%, with a total of A + T content of 73.43%. Eleven reading frame overlaps and thirteen intergenic regions were found in the mitogenome of S. nigrifrons. All 13 PCGs are initiated with the typical ATN codons, and are terminated with either the complete TAA/TAG codons or a single T residue. All tRNAs possess the typical cloverleaf secondary structures except for trnS1 (AGN). Phylogenetic analyses showed that S. nigrifrons was closely related to Cucujus clavipes, which was consistent with the conventional taxonomy.
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Affiliation(s)
- Wen-Jia Yang
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang, P. R. China
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, College of Biology and Environmental Engineering, Guiyang University, Guiyang, P. R. China
| | - Shu-Yan Yan
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, College of Biology and Environmental Engineering, Guiyang University, Guiyang, P. R. China
| | - Dao-Chao Jin
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang, P. R. China
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Sun S, Sha Z, Wang Y. Divergence history and hydrothermal vent adaptation of decapod crustaceans: A mitogenomic perspective. PLoS One 2019; 14:e0224373. [PMID: 31661528 PMCID: PMC6818795 DOI: 10.1371/journal.pone.0224373] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 10/13/2019] [Indexed: 01/08/2023] Open
Abstract
Decapod crustaceans, such as alvinocaridid shrimps, bythograeid crabs and galatheid squat lobsters are important fauna in the hydrothermal vents and have well adapted to hydrothermal vent environments. In this study, eighteen mitochondrial genomes (mitogenomes) of hydrothermal vent decapods were used to explore the evolutionary history and their adaptation to the hydrothermal vent habitats. BI and ML algorithms produced consistent phylogeny for Decapoda. The phylogenetic relationship revealed more evolved positions for all the hydrothermal vent groups, indicating they migrated from non-vent environments, instead of the remnants of ancient hydrothermal vent species, which support the extinction/repopulation hypothesis. The divergence time estimation on the Alvinocarididae, Bythograeidae and Galatheoidea nodes are located at 75.20, 56.44 and 47.41–50.43 Ma, respectively, which refers to the Late Cretaceous origin of alvinocaridid shrimps and the Early Tertiary origin of bythograeid crabs and galatheid squat lobsters. These origin stories are thought to associate with the global deep-water anoxic/dysoxic events. Total eleven positively selected sites were detected in the mitochondrial OXPHOS genes of three lineages of hydrothermal vent decapods, suggesting a link between hydrothermal vent adaption and OXPHOS molecular biology in decapods. This study adds to the understanding of the link between mitogenome evolution and ecological adaptation to hydrothermal vent habitats in decapods.
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Affiliation(s)
- Shao’e Sun
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Science, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Zhongli Sha
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Science, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- * E-mail:
| | - Yanrong Wang
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Science, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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Novel gene rearrangement in the mitochondrial genome of Coenobita brevimanus (Anomura: Coenobitidae) and phylogenetic implications for Anomura. Genomics 2019; 112:1804-1812. [PMID: 31655177 DOI: 10.1016/j.ygeno.2019.10.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 11/24/2022]
Abstract
The complete mitochondrial genomes (mitogenomes) can indicate phylogenetic relationships among organisms, as well as useful information about the process of molecular evolution and gene rearrangement mechanisms. However, knowledge on the complete mitogenome of Coenobitidae (Decapoda: Anomura) is quite scarce. Here, we describe in detail the complete mitogenome of Coenobita brevimanus, which is 16,393 bp in length, and contains 13 protein-coding genes, two ribosomal RNA, 22 transfer RNA genes, as well as a putative control region. The genome composition shows a moderate A + T bias (65.0%), and exhibited a negative AT-skew (-0.148) and a positive GC-skew (0.183). Five gene clusters (or genes) involving eleven tRNAs and two PCGs were found to have rearranged with respect to the pancrustacean ground pattern gene order. Duplication-random loss and recombination models were determined as most likely to explain the observed large-scale gene rearrangements. Phylogenetic analysis placed all Coenobitidae species into one clade. The polyphyly of Paguroidea was well supported, whereas the non-monophyly of Galatheoidea was inconsistence with previous findings on Anomura. Taken together, our results help to better understand gene rearrangement process and the evolutionary status of C. brevimanus and lay a foundation for further phylogenetic studies of Anomura.
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Wang J, Dai XY, Xu XD, Zhang ZY, Yu DN, Storey KB, Zhang JY. The complete mitochondrial genomes of five longicorn beetles (Coleoptera: Cerambycidae) and phylogenetic relationships within Cerambycidae. PeerJ 2019; 7:e7633. [PMID: 31534857 PMCID: PMC6732212 DOI: 10.7717/peerj.7633] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/06/2019] [Indexed: 12/23/2022] Open
Abstract
Cerambycidae is one of the most diversified groups within Coleoptera and includes nearly 35,000 known species. The relationships at the subfamily level within Cerambycidae have not been convincingly demonstrated and the gene rearrangement of mitochondrial genomes in Cerambycidae remains unclear due to the low numbers of sequenced mitogenomes. In the present study, we determined five complete mitogenomes of Cerambycidae and investigated the phylogenetic relationship among the subfamilies of Cerambycidae based on mitogenomes. The mitogenomic arrangement of all five species was identical to the ancestral Cerambycidae type without gene rearrangement. Remarkably, however, two large intergenic spacers were detected in the mitogenome of Pterolophia sp. ZJY-2019. The origins of these intergenic spacers could be explained by the slipped-strand mispairing and duplication/random loss models. A conserved motif was found between trnS2 and nad1 gene, which was proposed to be a binding site of a transcription termination peptide. Also, tandem repeat units were identified in the A + T-rich region of all five mitogenomes. The monophyly of Lamiinae and Prioninae was strongly supported by both MrBayes and RAxML analyses based on nucleotide datasets, whereas the Cerambycinae and Lepturinae were recovered as non-monophyletic.
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Affiliation(s)
- Jun Wang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Xin-Yi Dai
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Xiao-Dong Xu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Zi-Yi Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Dan-Na Yu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
- Key lab of wildlife biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang, China
| | | | - Jia-Yong Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
- Key lab of wildlife biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang, China
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Li R, Wang Y, Shu X, Meng L, Li B. Complete mitochondrial genomes of three Oxya grasshoppers (Orthoptera) and their implications for phylogenetic reconstruction. Genomics 2019; 112:289-296. [PMID: 30790624 DOI: 10.1016/j.ygeno.2019.02.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/02/2019] [Accepted: 02/09/2019] [Indexed: 11/15/2022]
Abstract
Oxya is a genus of grasshoppers (Orthoptera: Acridoidea) attacking rice and other gramineous plants in Africa and Asia. In the present study, we characterized complete mitochondrial genomes (mitogenomes) of three species, Oxya japonica japonica (15,427 bp), Oxya hainanensis (15,443 bp) and Oxya agavisa robusta (15,552 bp) collected from China. The three mitogenomes contained a typical gene set of metazoan mitogenomes and shared the same gene order with other Acridid grasshoppers, including the rearrangement of tRNAAsp and tRNALys. Analyses of pairwise genetic distances showed that ATP8 was the least conserved gene, while COI the most conserved. To determine the position of Oxya grasshoppers in the phylogeny of Acrididae, we reconstructed phylogenetic trees among 64 species from across 11 subfamilies using nucleotide sequences of mitogenomes. While the tree confirms traditional classifications of Acrididae at major higher-levels, it suggests a few modifications for classifications at lower-levels.
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Affiliation(s)
- Ran Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Yuqi Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Xiaohan Shu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Ling Meng
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Baoping Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China.
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47
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Li R, Deng WA, Shu XH, Hu HW, Li XD. Characterization of the complete mitochondrial genome of Dnopherula yuanmowensis (Orthoptera: Acrididae) and its phylogenetic implications. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1574671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Ran Li
- School of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, P. R. China
| | - Wei-An Deng
- School of Chemistry and Bioengineering, Hechi University, Yizhou, Guangxi, 546300, P. R. China
| | - Xiao-Han Shu
- Lanxi Plant Protection and Quarantine Station, Lanxi, Zhejiang, 321100, P. R. China
| | - Hao-Wu Hu
- School of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, P. R. China
| | - Xiao-Dong Li
- School of Chemistry and Bioengineering, Hechi University, Yizhou, Guangxi, 546300, P. R. China
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Zhang QL, Zhang GL, Yuan ML, Dong ZX, Li HW, Guo J, Wang F, Deng XY, Chen JY, Lin LB. A Phylogenomic Framework and Divergence History of Cephalochordata Amphioxus. Front Physiol 2018; 9:1833. [PMID: 30618839 PMCID: PMC6305399 DOI: 10.3389/fphys.2018.01833] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 12/06/2018] [Indexed: 11/21/2022] Open
Abstract
Amphioxus, or cephalochordates, are often used as the living invertebrate proxy of vertebrate ancestors and are widely used as evolutionary biology models of chordates. However, their phylogeny, divergence history, and speciation characteristics remain poorly understood, and phylogenomic studies to explore these problems lacking entirely from the literature. Here, we determined a new transcriptome of Branchiostoma japonicum. Combined with mass sequences of all other 18 species, a 19-way phylogeny was constructed via multiple methods (ML, BI, PhyloBayes, and ASTRAL), consistently supporting a phylogeny of [(B. belcheri + B. japonicum) + (B. lanceolatum + B. floridae) + Asymmetron lucayanum] in amphioxus. Congruent phylogenetic signals were found across mitochondrial genes, 12S RNA, and complete mitochondrial genomes according to previous reports, indicating that 12S RNA may have potential as a molecular marker for phylogenetic analysis in amphioxus. Molecular dating analysis indicated a radiation of the cephalochordates during the Cretaceous (∼104-61 million years ago), supporting an association between the diversification and speciation of cephalochordates with continental drift and associated changes in their respective habitats during this time. The identified functional enrichment analysis for species-specific domains indicated that their function mainly involves immune response, apoptosis, and lipid metabolism and utilization, signaling that pathogens and changes of energy requirements are an important driving force for amphioxus speciation. This study represents the first large-scale phylogenomic analysis of most major amphioxus genera based on phylogenomic data, providing a new perspective on both phylogeny and divergence speciation of cephalochordates.
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Affiliation(s)
- Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.,Evo-Devo Institute, School of Life Sciences, Nanjing University, Nanjing, China
| | - Guan-Ling Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Ming-Long Yuan
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhi-Xiang Dong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Hong-Wei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jun Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Feng Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xian-Yu Deng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jun-Yuan Chen
- Evo-Devo Institute, School of Life Sciences, Nanjing University, Nanjing, China.,State Key Laboratory of Palaeobiology and Stratigraphy (LPS), Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
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Huang J, Ma T. Comparative analysis of two mitochondrial genomes of flesh flies (Sarcophaga antilope and Sarcophaga dux) with phylogeny and evolutionary timescale for Sarcophagidae. Int J Biol Macromol 2018; 120:1955-1964. [DOI: 10.1016/j.ijbiomac.2018.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/29/2018] [Accepted: 10/01/2018] [Indexed: 11/28/2022]
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Xu K, Chen X, Xu L, Yang W, Wang Y, Li C. The complete mitochondrial genome of a walnut weevil, Alcidodes juglans Chao (Coleoptera: Curculionidae). Mitochondrial DNA B Resour 2018; 4:27-28. [PMID: 33365406 PMCID: PMC7510617 DOI: 10.1080/23802359.2018.1535854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 09/19/2018] [Indexed: 11/03/2022] Open
Abstract
The walnut weevil, Alcidodes juglans Chao (Coleoptera: Curculionidae), is an important agricultural pest and distributed widely in China. The complete mitochondrial genome of A. juglans is 15,638 bp long, and consists of 13 protein-coding genes (PCGs), two ribosomal RNA genes, 21 transfer RNA (tRNA) genes and a putative control region (GenBank accession No. MH819192). The trnI gene has not been observed in the A. juglans mitogenome. The nucleotide composition is significantly biased (A, G, C, and T was 38.35%, 10.02%, 14.96%, and 36.67%, respectively) with A + T contents of 75.02%. All of the 21 tRNAs have the typical cloverleaf structure, with an exception for trnS1 (AGN). All PCGs are initiated by ATN codons, except for cox1 with AAT instead. Ten PCGs use a common stop codon of TAA or TAG, whereas the remaining three were terminated with a single T. The phylogenetic relationships based on neighbour-joining method showed that A. juglans is closely related to Naupactus xanthographus, which is in accordance with the traditional morphological classification.
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Affiliation(s)
- Kangkang Xu
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, College of Biology and Environmental Engineering, Guiyang University, Guiyang, China
| | - Xiaoyulong Chen
- College of Tobacco Science, Guizhou University, Guiyang, China
| | - Lin Xu
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, College of Biology and Environmental Engineering, Guiyang University, Guiyang, China
| | - Wenjia Yang
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, College of Biology and Environmental Engineering, Guiyang University, Guiyang, China
| | - Yawei Wang
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, College of Biology and Environmental Engineering, Guiyang University, Guiyang, China
| | - Can Li
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, College of Biology and Environmental Engineering, Guiyang University, Guiyang, China
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