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Zheng C, Zhu X, Wang Y, Dong X, Yang R, Tang Z, Bu W. Mitogenomes Provide Insights into the Species Boundaries and Phylogenetic Relationships among Three Dolycoris Sloe Bugs (Hemiptera: Pentatomidae) from China. INSECTS 2024; 15:134. [PMID: 38392553 PMCID: PMC10889809 DOI: 10.3390/insects15020134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
(1) Background: The three sloe bugs, Dolycoris baccarum, Dolycoris indicus, and Dolycoris penicillatus, are found in the Chinese mainland and are morphologically similar. The species boundaries and phylogenetic relationships of the three species remain uncertain; (2) Methods: In this study, we generated multiple mitochondrial genomes (mitogenomes) for each of the three species and conducted comparative mitogenomic analysis, species delimitation, and phylogenetic analysis based on these data; (3) Results: Mitogenomes of the three Dolycoris species are conserved in nucleotide composition, gene arrangement, and codon usage. All protein-coding genes (PCGs) were found to be under purifying selection, and the ND4 evolved at the fastest rate. Most species delimitation analyses based on the COI gene and the concatenated 13 PCGs retrieved three operational taxonomic units (OTUs), which corresponded well with the three Dolycoris species identified based on morphological characters. A clear-cut barcode gap was discovered between the interspecific and intraspecific genetic distances of the three Dolycoris species. Phylogenetic analyses strongly supported the monophyly of Dolycoris, with interspecific relationship inferred as (D. indicus + (D. baccarum + D. penicillatus)); (4) Conclusions: Our study provides the first insight into the species boundaries and phylogenetic relationships of the three Dolycoris species distributed across the Chinese mainland.
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Affiliation(s)
- Chenguang Zheng
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Xiuxiu Zhu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Ying Wang
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Xue Dong
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Ruijuan Yang
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Zechen Tang
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
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Wei Z, Shi A. The complete mitochondrial genomes of four lagriine species (Coleoptera, Tenebrionidae) and phylogenetic relationships within Tenebrionidae. PeerJ 2023; 11:e15483. [PMID: 37283890 PMCID: PMC10241167 DOI: 10.7717/peerj.15483] [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: 10/13/2022] [Accepted: 05/09/2023] [Indexed: 06/08/2023] Open
Abstract
It is common to use whole mitochondrial genomes to analyze phylogenetic relationships among insects. In this study, seven mitogenomes of Tenebrionidae are newly sequenced and annotated. Among them, four species (Cerogira janthinipennis (Fairmaire, 1886), Luprops yunnanus (Fairmaire, 1887), Anaedus unidentasus Wang & Ren, 2007, and Spinolyprops cribricollis Schawaller, 2012) represent the subfamily Lagriinae. In this subfamily, the mitogenomes of the tribes Goniaderini (A. unidentasus) and Lupropini (L. yunnanus and S. cribricollis) were first reported; they were found to be 15,328-16,437 bp in length and encode 37 typical mitochondrial genes (13 PCGs, 2 rRNAs, 22 tRNAs, and a single noncoding control region). Most protein-coding genes in these mitogenomes have typical ATN start codons and TAR or an incomplete stop codon T-. In these four lagriine species, F, L2, I, and N are the most frequently used amino acids. In the 13 PCGs, the gene atp8 (Pi = 0.978) was the most diverse nucleotide, while cox1 was the most conserved gene with the lowest value (Pi = 0.211). The phylogenetic results suggest that Pimelinae, Lagriinae, Blaptinae, Stenochiinae, and Alleculinae are monophyletic, Diaperinae is paraphyletic, and Tenebrioninae appears polyphyletic. In Lagriinae, the tribe Lupropini appears paraphyletic because Spinolyprops is clustered with Anaedus in Goniaderini. These mitogenomic data provide important molecular data for the phylogeny of Tenebrionidae.
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Vidal JAD, Sassi FDMC, de Moraes RLR, Artoni RF, Liehr T, Cioffi MB, de Almeida MC. Giant Sex Chromosomes in Omophoita Species (Coleoptera, Chrysomelidae): Structural and Evolutionary Relationships Revealed by Zoo-FISH and Comparative Genomic Hybridization (CGH). INSECTS 2023; 14:insects14050440. [PMID: 37233068 DOI: 10.3390/insects14050440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 04/29/2023] [Accepted: 05/02/2023] [Indexed: 05/27/2023]
Abstract
The beetles of the subtribe Oedionychina (Chrysomelidae, Alticinae) are the only ones that have the atypical giant and achiasmatic sex chromosomes, which are substantially larger than the autosomes. Previous cytogenetic analyses suggest a large accumulation of repetitive DNA in the sex chromosomes. In this study, we examined the similarity of X and Y chromosomes in four Omophoita species and compared genomic differentiation to better understand the evolutionary process and the giant sex chromosomes origin. Intraspecific genomic comparation using male and female genomes of O. octoguttata and interespecific analyses using genomic DNA of O. octoguttata, O. sexnotata, O. magniguttis, and O. personata were performed. In addition, whole chromosome painting (WCP) experiments were performed with X and Y chromosome probes of O. octogutatta. CGH analysis revealed great genomic similarity between the sexes and a sex-specific region on the Y chromosome, and interspecific analysis revealed a genomic divergence between species. In contrast, WCP results revealed that the sex chromosomes of O. octoguttata have high intra- and interspecific similarity with the studied species. Our data support a common origin under the canonical evolution of the sex chromosomes in this group, as they have high genomic similarity between them.
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Affiliation(s)
- Jhon A D Vidal
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, Brazil
- Laboratório de Genética e Evolução, Departamento de Biologia Estrutural Molecular e Genética, Universidade Estadual de Ponta Grossa (UEPG), Av. Carlos Cavalcanti, 4748, Ponta Grossa 84030-900, Brazil
| | - Francisco de M C Sassi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, Brazil
| | - Renata L R de Moraes
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, Brazil
| | - Roberto F Artoni
- Laboratório de Genética e Evolução, Departamento de Biologia Estrutural Molecular e Genética, Universidade Estadual de Ponta Grossa (UEPG), Av. Carlos Cavalcanti, 4748, Ponta Grossa 84030-900, Brazil
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany
| | - Marcelo B Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, Brazil
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany
| | - Mara C de Almeida
- Laboratório de Genética e Evolução, Departamento de Biologia Estrutural Molecular e Genética, Universidade Estadual de Ponta Grossa (UEPG), Av. Carlos Cavalcanti, 4748, Ponta Grossa 84030-900, Brazil
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Li J, Yan B, He H, Xu X, Ruan Y, Yang M. Characterization of the Complete Mitochondrial Genome of a Flea Beetle Luperomorpha xanthodera (Coleoptera: Chrysomelidae: Galerucinae) and Phylogenetic Analysis. Genes (Basel) 2023; 14:414. [PMID: 36833341 PMCID: PMC9957443 DOI: 10.3390/genes14020414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
In this study, the mitochondrial genome of Luperomorpha xanthodera was assembled and annotated, which is a circular DNA molecule including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA genes (12S rRNA and 16S rRNA), and 1388 bp non-coding regions (A + T rich region), measuring 16,021 bp in length. The nucleotide composition of the mitochondrial genome is 41.3% adenine (A), 38.7% thymine (T), 8.4% guanine (G), and 11.6% cytosine (C). Most of the protein-coding genes presented a typical ATN start codon (ATA, ATT, ATC, ATG), except for ND1, which showed the start codon TTG. Three-quarters of the protein-coding genes showed the complete stop codon TAR (TAA, TAG), except the genes COI, COII, ND4, and ND5, which showed incomplete stop codons (T- or TA-). All the tRNA genes have the typical clover-leaf structure, except tRNASer1 (AGN), which has a missing dihydrouridine arm (DHU). The phylogenetic results determined by both maximum likelihood and Bayesian inference methods consistently supported the monophyly of the subfamily Galerucinae and revealed that the subtribe Luperina and genus Monolepta are polyphyletic groups. Meanwhile, the classification status of the genus Luperomorpha is controversial.
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Affiliation(s)
- Jingjing Li
- Institute of Entomology, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang 550025, China
| | - Bin Yan
- Institute of Entomology, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang 550025, China
| | - Hongli He
- Institute of Entomology, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang 550025, China
| | - Xiaoli Xu
- Institute of Entomology, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang 550025, China
| | - Yongying Ruan
- Plant Protection Research Center, Shenzhen Polytechnic, Shenzhen 518055, China
| | - Maofa Yang
- Institute of Entomology, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang 550025, China
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Wei Z, Huang X, Shi A. First mitochondrial genome of subfamily Julodinae (Coleoptera, Buprestidae) with its phylogenetic implications. Zookeys 2023; 1139:165-182. [PMID: 36761279 PMCID: PMC9860506 DOI: 10.3897/zookeys.1139.96216] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
Complete mitochondrial genomes of three species of the family Buprestidae were sequenced, annotated, and analyzed in this study. To explore the mitogenome features of the subfamily Julodinae and verify its phylogenetic position, the complete mitogenome of Julodisvariolaris was sequenced and annotated. The complete mitogenomes of Ptosimachinensis and Chalcophorajaponica were also provided for the phylogenetic analyses within Buprestidae. Compared to the known mitogenomes of Buprestidae species varied from 15,499 bp to 16,771 bp in length, three newly sequenced mitogenomes were medium length (15,759-16,227 bp). These mitogenomes were encoded 37 typical mitochondrial genes. Among the three studied mitogenomes, Leu2 (L2), Ser2 (S2), and Pro (P) were the three most frequently encoded amino acids. Within the Buprestidae, the heterogeneity in sequence divergences of Agrilinae was highest, whereas the sequence homogeneity of Chrysochroinae was highest. Moreover, phylogenetic analyses were performed based on nucleotide matrix (13 PCGs + 2 rRNAs) among the available sequenced species of Buprestidae using Bayesian Inference and Maximum Likelihood methods. The results showed that the Julodinae was closely related to the subfamily Polycestinae. Meanwhile, the genera Melanophila, Dicerca, and Coomaniella were included in Buprestinae, which was inconsistent with the current classification system of Buprestidae. These results could contribute to further studies on genetic diversity and phylogeny of Buprestidae.
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Affiliation(s)
- Zhonghua Wei
- The Key Laboratory of Southwest China Wildlife Resources Conservation of the Ministry of Education, College of Life Sciences, China West Normal University, 637009, Nanchong, Sichuan Province, ChinaChina West Normal UniversityNanchongChina
| | - Xuyan Huang
- The Key Laboratory of Southwest China Wildlife Resources Conservation of the Ministry of Education, College of Life Sciences, China West Normal University, 637009, Nanchong, Sichuan Province, ChinaChina West Normal UniversityNanchongChina
| | - Aimin Shi
- The Key Laboratory of Southwest China Wildlife Resources Conservation of the Ministry of Education, College of Life Sciences, China West Normal University, 637009, Nanchong, Sichuan Province, ChinaChina West Normal UniversityNanchongChina
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Argopistes sexvittatus and Argopistes capensis (Chrysomelidae: Alticini): Mitogenomics and Phylogeny of Two Flea Beetles Affecting Olive Trees. Genes (Basel) 2022; 13:genes13122195. [PMID: 36553462 PMCID: PMC9777630 DOI: 10.3390/genes13122195] [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: 08/30/2022] [Revised: 10/06/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022] Open
Abstract
The genus Argopistes (Chrysomelidae: Alticini) is the only group of flea beetles specialized in plant hosts in the family Oleaceae. In southern Africa, Argopistes are often found feeding on African Wild Olive (Olea europaea subsp. cuspidata) and European cultivated olive (O. e. subsp. europaea), and heavy infestations can be devastating to mature trees and compromise the development of young trees. Despite their negative agricultural impact, African Argopistes are an understudied group for which no genetic data were available. We assessed the species diversity of olive flea beetles in the Western Cape province of South Africa, the largest olive-producing region in sub-Saharan Africa, by collecting adult specimens on wild and cultivated olive trees between 2015 and 2017. Argopistes sexvittatus Bryant, 1922 (n = 289) dominated at all sampling sites, and Argopistes capensis Bryant, 1944 (n = 2) was found only once. Argopistes oleae Bryant, 1922, a third species previously reported in the region, was not found. The complete mitogenomes of one A. capensis and two A. sexvittatus (striped and black morphotypes) individuals were sequenced for phylogenetic reconstruction in the context of other 64 species. The two olive flea beetle species form a monophyletic clade with other Argopistes, supporting the hypothesis that the exclusive feeding habit on Oleaceae is an evolutionary adaptation in this genus.
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Zhu X, Zheng C, Dong X, Zhang H, Ye Z, Xue H, Bu W. Species boundary and phylogeographical pattern provide new insights into the management efforts of Megacopta cribraria (Hemiptera: Plataspidae), a bean bug invading North America. PEST MANAGEMENT SCIENCE 2022; 78:4871-4881. [PMID: 36181419 DOI: 10.1002/ps.7108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 07/26/2022] [Accepted: 07/31/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Correct identification together with information on distribution range, geographical origin and evolutionary history are the necessary basis for the management and control of invasive species. The bean bug Megacopta cribraria is a crucial agricultural pest of soybean. Recently, M. cribraria has invaded the United States and spread rapidly, causing severe reductions in soybean yields. However, the species boundary and phylogeographical pattern of this invasive bean bug are still unclear. RESULTS The results of different species delimitation methods (Automatic Barcode Gap Discovery, Assemble Species by Automatic Partitioning, Bayesian Poisson Tree Processes and Bayesian Phylogenetics and Phylogeography) strongly demonstrated that M. cribraria and Megacopta punctatissima represent the same species. M. punctatissima should not be considered a distinct species but rather a variety of M. cribraria. Phylogenetic analyses revealed three well-supported clades (Southeast Asia [SEA], East Asia continent [EAC] and Japan [JA]) with distinct geographical structures in the M. cribraria-M. punctatissima complex. The SEA clade was at the base of the phylogenetic tree, and the sister relationship between the EAC clade and JA clade was strongly supported. The split between the EAC clade and JA clade occurred at approximately 0.71 Ma, corresponding to the submergence period of the East China Sea land bridge. CONCLUSION This study clarified the species boundary between M. cribraria and its closely related species and revealed the phylogeographical pattern and evolutionary history of M. cribraria. The species delimitation and phylogeography results achieved in this study could provide new insights into the monitoring and management of this agricultural pest. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Xiuxiu Zhu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Chenguang Zheng
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Xue Dong
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | | | - Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Huaijun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
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Zhang LJ, Li YJ, Ge XY, Li XY, Yang YX, Bai M, Ge SQ. Mitochondrial genomes of Sternochetus species (Coleoptera: Curculionidae) and the phylogenetic implications. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2022; 111:e21898. [PMID: 35434835 DOI: 10.1002/arch.21898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 02/25/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
The three weevil species, Sternochetus gravis, S. mangiferae, and S. olivieri, have all been reported to be serious pests of mango fruits. Morphology, biology, and various management approaches of these economically important weevils have been well studied. However, no mitochondrial genomes have been reported from the genus Sternochetus. Herein, we assembled mitogenomes of all the three Sternochetus species to reveal their mitogenomic characteristics. A DNA library of 350 bp insert size was constructed and sequenced in Illumina's HiSeq 6000 platform with a pair-end 150 bp sequencing strategy by Novogene. The sequence reads were assembled using GetOrganelle v1.7.1 and the genes were annotated by Geneious Prime 2021.0.3 and MITOS Web Server. Coupled with 61 published mitogenomes from 13 subfamilies of Curculionidae, we reconstructed phylogenetic trees to resolve evolutionary relationships of these closely related species and also examined subfamily-level classification among Curculionidae. All three mitogenomes are double-stranded circular molecules with 22 transfer RNA genes, 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 1 noncoding control region as in other insects. Higher interspecific nucleotide divergence (about 10%) of 13 PCGs indicated these three Sternochetus species diverged a long time ago. Phylogenetic analyses using both maximum likelihood and Bayesian inference methods showed that Sternochetus falls into the basal clade of Cryptorhynchini, a tribe in the subfamily Molytinae. The relationship of S. olivieri as a sister species to S. gravis + S. mangiferae was strongly supported. The monophyly of Cryptorhynchini was also well supported whereas Molytinae was suggested to be a polyphyletic group.
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Affiliation(s)
- Li-Jie Zhang
- Institute of plant quarantine, Science and Technical Research Center of China Customs, Beijing, China
| | - Yu-Jie Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xue-Ying Ge
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Xue-Yan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yu-Xia Yang
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Ming Bai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Si-Qin Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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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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Xue HJ, Niu YW, Segraves KA, Nie RE, Hao YJ, Zhang LL, Cheng XC, Zhang XW, Li WZ, Chen RS, Yang XK. The draft genome of the specialist flea beetle Altica viridicyanea (Coleoptera: Chrysomelidae). BMC Genomics 2021; 22:243. [PMID: 33827435 PMCID: PMC8028732 DOI: 10.1186/s12864-021-07558-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 03/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Altica (Coleoptera: Chrysomelidae) is a highly diverse and taxonomically challenging flea beetle genus that has been used to address questions related to host plant specialization, reproductive isolation, and ecological speciation. To further evolutionary studies in this interesting group, here we present a draft genome of a representative specialist, Altica viridicyanea, the first Alticinae genome reported thus far. RESULTS The genome is 864.8 Mb and consists of 4490 scaffolds with a N50 size of 557 kb, which covered 98.6% complete and 0.4% partial insect Benchmarking Universal Single-Copy Orthologs. Repetitive sequences accounted for 62.9% of the assembly, and a total of 17,730 protein-coding gene models and 2462 non-coding RNA models were predicted. To provide insight into host plant specialization of this monophagous species, we examined the key gene families involved in chemosensation, detoxification of plant secondary chemistry, and plant cell wall-degradation. CONCLUSIONS The genome assembled in this work provides an important resource for further studies on host plant adaptation and functionally affiliated genes. Moreover, this work also opens the way for comparative genomics studies among closely related Altica species, which may provide insight into the molecular evolutionary processes that occur during ecological speciation.
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Affiliation(s)
- Huai-Jun Xue
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Yi-Wei Niu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kari A Segraves
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
- Archbold Biological Station, 123 Main Drive, Venus, FL, 33960, USA
| | - Rui-E Nie
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ya-Jing Hao
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Li Zhang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin-Chao Cheng
- Biomarker Technologies Corporation, Floor 8, Shunjie Building, 12 Fuqian Road, Nanfaxin Town, Shunyi District, Beijing, 101300, China
| | - Xue-Wen Zhang
- Biomarker Technologies Corporation, Floor 8, Shunjie Building, 12 Fuqian Road, Nanfaxin Town, Shunyi District, Beijing, 101300, China
| | - Wen-Zhu Li
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Run-Sheng Chen
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xing-Ke Yang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
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