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Iqbal Z, Azad R, Chen XS, Lin XL, Zhou Z, Wang XM, Nie RE. A New Species of Scymnus (Coleoptera, Coccinellidae) from Pakistan with Mitochondrial Genome and Its Phylogenetic Implications. INSECTS 2024; 15:371. [PMID: 38786927 PMCID: PMC11122443 DOI: 10.3390/insects15050371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
In this study, a new species of the subgenus Pullus belonging to the Scymnus genus from Pakistan, Scymnus (Pullus) cardi sp. nov., was described and illustrated, with information on its distribution, host plants, and prey. Additionally, the completed mitochondrial genome (mitogenome) of the new species using high-throughput sequencing technology was obtained. The genome contains the typical 37 genes (13 protein-coding genes, two ribosomal RNAs, and 22 transfer RNAs) and a non-coding control region, and is arranged in the same order as that of the putative ancestor of beetles. The AT content of the mitogenome is approximately 85.1%, with AT skew and GC skew of 0.05 and -0.43, respectively. The calculated values of relative synonymous codon usage (RSCU) determine that the codon UUA (L) has the highest frequency. Furthermore, we explored the phylogenetic relationship among 59 representatives of the Coccinellidae using Bayesian inference and maximum likelihood methods, the results of which strongly support the monophyly of Coccinellinae. The phylogenetic results positioned Scymnus (Pullus) cardi in a well-supported clade with Scymnus (Pullus) loewii and Scymnus (Pullus) rubricaudus within the genus Scymnus and the tribe Scymnini. The mitochondrial sequence of S. (P.) cardi will contribute to the mitochondrial genome database and provide helpful information for the identification and phylogeny of Coccinellidae.
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Affiliation(s)
- Zafar Iqbal
- Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (Z.I.); (X.-L.L.)
| | - Rashid Azad
- Department of Entomology, The University of Haripur, Haripur 22620, Pakistan;
- Department of Entomology, South China Agricultural University, Guangzhou 510640, China
| | - Xiao-Sheng Chen
- Engineering Research Center of Biological Control, Ministry of Education, Guangzhou 510642, China;
- Department of Forest Protection, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Xiao-Ling Lin
- Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (Z.I.); (X.-L.L.)
| | - Zichen Zhou
- Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2BX, UK;
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Xing-Min Wang
- Department of Entomology, South China Agricultural University, Guangzhou 510640, China
- Engineering Technology Research Center of Agricultural Pest Biocontrol of Guangdong Province, Guangzhou 510640, China
| | - Rui-E Nie
- Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (Z.I.); (X.-L.L.)
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Mukherjee A, Ghosh A, Tyagi K, Kumar V, Banerjee D, Naskar A. Characterization of complete mitochondrial genome of three Horse flies of the genus Tabanus (Diptera: Tabanidae): comparative analysis. Mol Biol Rep 2023; 50:9897-9908. [PMID: 37864662 DOI: 10.1007/s11033-023-08837-z] [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: 08/04/2023] [Accepted: 09/25/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Tabanidae (Horse-Flies or Deer-Flies) are one of the most economically important as well as medically significant haematophagous insect family within the order Diptera. Members of this group are also responsible for the mortality of substantial number of live-stock every year. Due to their pathogen transmission potential and vector competencies makes them an important insect group to study. Till now, mitochondrial genome of 18 species of tabanids were available. METHODS AND RESULTS The complete mitogenome of three species T. diversifrons (15,809 bp), T. rubidus (15,878 bp) and T. tenens (15,872 bp) were generated by Next generation sequencing method. They consist 37 genes, with a positive AT skew and a negative GC skew. The gene order of these three species is similar to the typical gene arrangement of infra-order Tabanomorpha. Most of the tRNAs showed typical clover-leaf secondary structure except trnS1, which lacks the DHU arm. The sliding window analysis showed that the nad4L is the most conserved while atp8, and nad6 are the most variable genes. Moreover, the ratios of non-synonymous to synonymous substitution rates indicated that all PCGs under the purifying selection. Phylogeny revealed Chrysops and Haematopota are monophyletic while species of Hybomitra are nested within the polyphyletic clade of Tabanus. T. diversifrons exhibits sister relationship with Atylotus miser. Two morphologically divergent species T. rubidus and T. tenens are found to be genetically similar and indistinguishable by mitochondrial genome. CONCLUSIONS The hypervariable genes like atp8 and nad6 can be used as molecular markers for the identification of recently diverged lineages of family Tabanidae. Further, to address uncertainties arising from the two morphological divergent species, it is imperative to obtain data from nuclear gene markers.
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Affiliation(s)
- Arka Mukherjee
- Diptera Section, Zoological Survey of India, Kolkata, West Bengal, India
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
| | - Abhishek Ghosh
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India.
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India.
| | - Dhriti Banerjee
- Diptera Section, Zoological Survey of India, Kolkata, West Bengal, India
| | - Atanu Naskar
- Diptera Section, Zoological Survey of India, Kolkata, West Bengal, India
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Huang X, Gan Y, Wang L, Xu Y, Wei Z, Shi A. The larval, pupal and mitogenomic characteristics of Agrilusadelphinus Kerremans, 1895 (Coleoptera, Buprestidae) from China. Zookeys 2023; 1174:15-33. [PMID: 38318285 PMCID: PMC10843335 DOI: 10.3897/zookeys.1174.105479] [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: 04/25/2023] [Accepted: 07/15/2023] [Indexed: 02/07/2024] Open
Abstract
In this study, the larva and pupa of Agrilusadelphinus are described and illustrated. DNA barcoding (COI gene) was used to associate the larval and pupal stages with adults based on the maximum-likelihood method. In the resulting phylogenetic tree, species from the same species-group were found to be clustered on a branch with high support value. To better understand A.adelphinus, the complete mitochondrial genome of this species was also sequenced and annotated. Comparing this genome to the known mitogenomes of Agrilus species, the newly sequenced genome is shorter, with 15,732 bp. However, its whole mitogenome composition and gene orientation were consistent with that of most species of Buprestidae. In the mitogenome of A.adelphinus, the ATGATAG sequence was observed between ATP8 and ATP6, which is ATGATAA in other insect mitogenomes. Leu2, Phe, Ile, Gly, and Ser2 were the five most frequently encoded amino acids. The results further prove that DNA barcoding can remove the limitation of traditional taxonomy which cannot identify to species all developmental stages. This study also provides valuable molecular and morphological data for species identification and phylogenetic analyses of the genus Agrilus.
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Affiliation(s)
- Xuyan Huang
- College of Life Sciences, China West Normal University, Nanchong 637009, ChinaChina West Normal UniversityNanchongChina
| | - Yujie Gan
- College of Life Sciences, China West Normal University, Nanchong 637009, ChinaChina West Normal UniversityNanchongChina
| | - Lei Wang
- College of Life Sciences, China West Normal University, Nanchong 637009, ChinaChina West Normal UniversityNanchongChina
| | - Yanying Xu
- College of Life Sciences, China West Normal University, Nanchong 637009, ChinaChina West Normal UniversityNanchongChina
| | - Zhonghua Wei
- College of Life Sciences, China West Normal University, Nanchong 637009, ChinaChina West Normal UniversityNanchongChina
| | - Aimin Shi
- College of Life Sciences, China West Normal University, Nanchong 637009, ChinaChina West Normal UniversityNanchongChina
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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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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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A novel gene order and remolded tRNAs revealed in the mitogenome of Asian gecarcinucid freshwater crabs (Brachyura, Gecarcinucidae). Gene 2021; 813:146102. [PMID: 34933078 DOI: 10.1016/j.gene.2021.146102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/13/2021] [Accepted: 11/16/2021] [Indexed: 11/21/2022]
Abstract
Here we report the first mitochondrial genomes (mitogenomes) of four species of gecarcinucid freshwater crabs (FWCs) in two genera, two from China (Somanniathelphusa hainanensis and S. yangshanensis), one from Laos (Esanthelphusa dugasti), and one from Myanmar (Esanthelphusa keyini). A novel gecarcinucid mitochondrial gene order (GMGO2) that was only found in E. dugasti that contains a total of 42 genes, including one pseudogene, two remolded tRNAs and two duplicated tRNAs. The GMGO2 of E. dugasti was compared with the brachyuran ground-pattern mitochondrial gene order (BMGO), revealing the rearrangements of the positions of 10 tRNAs, two PCGs, and one mNCR. The three other gecarcinucids in this study were all found to possess a previously reported gecarcinucid mitochondrial gene order (GMGO1). The phylogenetic tree reconstructed using the secondary structures of 22 tRNAs of the mitogenomes of 41 species of FWCs provides insights into the evolution of the mitogenome of E. dugasti (GMGO2) which includes remolded and duplicated tRNAs.
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Li X, Song N, Zhang H. Comparative and phylogenomic analyses of mitochondrial genomes in Coccinellidae (Coleoptera: Coccinelloidea). PeerJ 2021; 9:e12169. [PMID: 34966567 PMCID: PMC8667754 DOI: 10.7717/peerj.12169] [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: 03/18/2021] [Accepted: 08/26/2021] [Indexed: 11/26/2022] Open
Abstract
The Coccinellidae are one of the most familiar beetle families, the ladybirds. Despite the great ecological and economic significance, the phylogenetic relationships of Coccinellidae remain poorly understood. One of the reasons is that the sequenced mitogenomes available for this family are very limited. We sequenced complete or nearly complete mitogenomes from seven species of the tribe Coccinellini with next-generation sequencing. All species have the same gene content and gene order as the putatively ancestral insect mitogenome. A large intergenic spacer region (> 890 bp) was found located between trnI and trnQ. The potential for using secondary structures of the large and small ribosomal subunits for phylogenetic reconstruction was predicted. The phylogenetic relationships were explored through comparative analyses across more than 30 coccinellid species. We performed phylogenetic analyses with both concatenation methods (Maximum Likelihood and Bayesian Inference) and multispecies coalescent method (ASTRAL). Phylogenetic results strongly supported the monophyly of Coccinellidae. Within Coccinellidae, the Epilachnini and the Coccinellini including Halyziini were monophyletic, while the Scymnini and Coccidulini were non-monophyletic.
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Affiliation(s)
- Xinghao Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan, China
| | - Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan, China
| | - Heng Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan, China
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Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of Saturnia japonica. Biochem Genet 2021; 60:914-936. [PMID: 34553327 DOI: 10.1007/s10528-021-10129-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/21/2021] [Indexed: 10/20/2022]
Abstract
The complete mitochondrial genome (mitogenome) of Saturnia japonica (Lepidoptera: Saturniidae) was sequenced and annotated. It is a circular molecule of 15, 376 bp, composed of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNA), and an adenine (A) + thymine (T)-rich region. All protein-coding genes (PCGs) are initiated by the ATN codon except for cytochrome c oxidase subunit 1 (cox1) gene that is seemingly initiated by the CGA codon. Except for cox2 and nad4, which were terminated by incomplete stop codon T or TA, the rest were terminated by canonical stop codon TAA. The A + T-rich region is high conservative, including 'ATAGA' motif followed by a 19 bp poly-T stretch, a microsatellite-like element (AT)9 and also a poly-A element, with a total length of 332 bp. The Asn codon was the most frequently used codon, followed by Ile, Leu2, Lys, Met, Phe, and Tyr, while Cys was the least frequently used codon. Phylogenetic relationships analysis based on the 13 PCGs by using maximum likelihood (ML) and neighbor Joining (NJ) revealed that S. japonica belongs to the Saturniidae family. In this study, the annotation and characteristics of the mitogenome of S. japonica were resolved for the first time, which laid a foundation for species classification and the molecular evolution of Lepidoptera: Saturniidae.
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Jiang L, Zhang M, Deng L, Xu Z, Shi H, Jia X, Lai Z, Ruan Q, Chen W. Characteristics of the mitochondrial genome of Rana omeimontis and related species in Ranidae: Gene rearrangements and phylogenetic relationships. Ecol Evol 2020; 10:12817-12837. [PMID: 33304496 PMCID: PMC7713938 DOI: 10.1002/ece3.6824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/16/2020] [Accepted: 08/20/2020] [Indexed: 12/01/2022] Open
Abstract
The Omei wood frog (Rana omeimontis), endemic to central China, belongs to the family Ranidae. In this study, we achieved detail knowledge about the mitogenome of the species. The length of the genome is 20,120 bp, including 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a noncoding control region. Similar to other amphibians, we found that only nine genes (ND6 and eight tRNA genes) are encoded on the light strand (L) and other genes on the heavy strand (H). Totally, The base composition of the mitochondrial genome included 27.29% A, 28.85% T, 28.87% C, and 15.00% G, respectively. The control regions among the Rana species were found to exhibit rich genetic variability and A + T content. R. omeimontis was clustered together with R. chaochiaoensis in phylogenetic tree. Compared to R. amurensis and R. kunyuensi, it was more closely related to R. chaochiaoensis, and a new way of gene rearrangement (ND6-trnE-Cytb-D-loop-trnL2 (CUN)-ND5-D-loop) was also found in the mitogenome of R. amurensis and R. kunyuensi. Our results about the mitochondrial genome of R. omeimontis will contribute to the future studies on phylogenetic relationship and the taxonomic status of Rana and related Ranidae species.
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Affiliation(s)
- Lichun Jiang
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangChina
| | - Min Zhang
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Lu Deng
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Zhongwen Xu
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Hongyan Shi
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Xiaodong Jia
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Zhenli Lai
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Qiping Ruan
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Wei Chen
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangChina
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Salazar K, Nattier R. New Light on Historical Specimens Reveals a New Species of Ladybird (Coleoptera: Coccinellidae): Morphological, Museomic, and Phylogenetic Analyses. INSECTS 2020; 11:E766. [PMID: 33172182 PMCID: PMC7694756 DOI: 10.3390/insects11110766] [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] [Received: 10/02/2020] [Revised: 10/24/2020] [Accepted: 10/27/2020] [Indexed: 11/22/2022]
Abstract
Natural history collections house an important source of genetic data from yet unexplored biological diversity. Molecular data from museum specimens remain underexploited, which is mainly due to the degradation of DNA from specimens over time. However, Next-Generation Sequencing (NGS) technology can now be used to sequence "old" specimens. Indeed, many of these specimens are unique samples of nomenclatural types and can be crucial for resolving systematic or biogeographic scientific questions. Two ladybird beetle specimens from Patagonia corresponding to a new species of the genus Eriopis Mulsant were found in the collections of the Muséum national d'Histoire naturelle (MNHN), Paris. Here, we describe Eriopis patagonia Salazar, sp. nov. Total DNA of one of the two specimens was sequenced by NGS using a paired-end Illumina approach. We reconstruct and characterize the mitochondrial genome of this species (16,194 bp). Then, the protein-coding genes (PCGs) and ribosomal RNAs (rRNAs) were used to infer by maximum likelihood and Bayesian Inference the phylogenetic position of E. patagonia among 27 representatives of Coccinellidae. Phylogenetic analysis confirmed the position of Eriopis as sister group to Cycloneda Crotch. Hence, we highlight the high potential of sequencing technology for extracting molecular information from old specimens, which are used here for the systematic study of a genus, while demonstrating the importance of preserving biological collections.
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Affiliation(s)
- Karen Salazar
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005 Paris, France;
- Grupo de Investigación Insectos de Colombia, Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Ciudad Universitaria, Bogotá 111321, Colombia
| | - Romain Nattier
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005 Paris, France;
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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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Andrianov BV, Romanov DA, Gorelova TV, Goryacheva II. Sequence Polymorphism of the Mitochondrial DNA Control Region in Native and Invasive Populations of Harmonia axyridis (Coleoptera, Coccinellidae). RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419070032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Wang Q, Tang G. The mitochondrial genomes of two walnut pests, Gastrolina depressa depressa and G. depressa thoracica (Coleoptera: Chrysomelidae), and phylogenetic analyses. PeerJ 2018; 6:e4919. [PMID: 29888134 PMCID: PMC5993032 DOI: 10.7717/peerj.4919] [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: 11/23/2017] [Accepted: 05/16/2018] [Indexed: 11/20/2022] Open
Abstract
In this study, the mitochondrial genomes (mitogenomes) of two walnut leaf insect pests, Gastrolina depressa depressa and G. depressa thoracica, were sequenced by Sanger sequencing technology. The mitogenome of G. depressa thoracica was complete at 16,109 bp in length, while the mitogenome of G. depressa depressa (14,277 bp) was partial. The genomic analyses indicated that both mitogenomes have the typical gene content and arrangement. The formerly identified elements, 'TAGTA' between trnSer(UCN) and nad2, and 'ATGATAA' between atp8 and atp6, were more conserved than that between nad4L and nad4, which was 'ATGTTAA' in Coleoptera excluding Polyphaga. Phylogenetic analyses of the 13 protein-coding genes from 36 coleopteran species well supported a close affinity between the subfamily Chrysomelinae including G. depressa thoracica and G. depressa depressa and Galerucinae, as well as a sister relationship of ((Eumolpinae + Cryptocephalinae) + Cassidinae) within Chrysomelidae.
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Affiliation(s)
- Qiqi Wang
- Key Laboratory of State Forestry Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guanghui Tang
- Key Laboratory of State Forestry Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
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Characterization of the complete mitochondrial genome of Biston marginata (Lepidoptera: Geometridae) and phylogenetic analysis among lepidopteran insects. Int J Biol Macromol 2018; 113:961-970. [PMID: 29462677 DOI: 10.1016/j.ijbiomac.2018.02.110] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 02/14/2018] [Accepted: 02/16/2018] [Indexed: 01/05/2023]
Abstract
The complete mitochondrial genome (mitogenome) of Biston marginata (Lepidoptera: Geometridae) was determined and annotated. The circular genome is 15,470bp long and it contains the entire set of 37 genes usually present in lepidopteran mitogenomes. The nucleotide composition of the genome is highly A+T biased, accounting for 81.20%, with a slightly positive AT skewness (0.028), indicating the occurrence of more As than Ts, as found in other Geometridae species. Except for cox1 gene starts with non-canonical initial codon CGA, all protein-coding genes start with ATN codon. Three of the 13 PCGs (protein coding gene) had an incomplete termination codon, T or TA, while the others terminated with TAA. All tRNA genes are predicted to fold into typical clover-leaf secondary structure, except for the trnS1 (AGN), in which the dihydrouridine (DHU) arm could not form a stable stem-loop structure. The A+T-rich region of 343bp is comprised of non-repetitive sequences, but have several distinctive features, including the motif "ATAGA" followed by a 19bp poly-T stretch, a microsatellite-like (TA)7 element next to the ATTTA motif. The phylogenetic analyses support the view that the B. marginata is closely related to the Biston pantrinaria, and confirm that Biston marginata belongs to the family Geometridae.
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Jia XN, Xu SX, Bai J, Wang YF, Nie ZH, Zhu CC, Wang Y, Cai YX, Zou JX, Zhou XM. The complete mitochondrial genome of Somanniathelphusa boyangensis and phylogenetic analysis of Genus Somanniathelphusa (Crustacea: Decapoda: Parathelphusidae). PLoS One 2018; 13:e0192601. [PMID: 29438407 PMCID: PMC5810993 DOI: 10.1371/journal.pone.0192601] [Citation(s) in RCA: 17] [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: 10/27/2017] [Accepted: 01/28/2018] [Indexed: 11/18/2022] Open
Abstract
In this study, the authors first obtained the mitochondrial genome of Somanniathelphusa boyangensis. The results showed that the mitochondrial genome is 17,032bp in length, included 13 protein-coding genes, 2 rRNAs genes, 22 tRNAs genes and 1 putative control region, and it has the characteristics of the metazoan mitochondrial genome A+T bias. All tRNA genes display the typical clover-leaf secondary structure except tRNASer(AGN), which has lost the dihydroxyuridine arm. The GenBank database contains the mitochondrial genomes of representatives of approximately 22 families of Brachyura, comprising 56 species, including 4 species of freshwater crab. The authors established the phylogenetic relationships using the maximum likelihood and Bayesian inference methods. The phylogenetic relationship indicated that the molecular taxonomy of S. boyangensis is consistent with current morphological classification, and Parathelphusidae and Potamidae are derived within the freshwater clade or as part of it. In addition, the authors used the COX1 sequence of Somanniathelphusa in GenBank and the COX1 sequence of S. boyangensis to estimated the divergence time of this genus. The result displayed that the divergence time of Somanniathelphusa qiongshanensis is consistent with the separation of Hainan Island from mainland China in the Beibu Gulf, and the divergence time for Somanniathelphusa taiwanensis and Somanniathelphusa amoyensis is consistent with the separation of Taiwan Province from Mainland China at Fujian Province. These data indicate that geologic events influenced speciation of the genus Somanniathelphusa.
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Affiliation(s)
- Xin-nan Jia
- Research lab of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi, PR China
| | - Shu-xin Xu
- Research lab of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi, PR China
| | - Jun Bai
- Research lab of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi, PR China
| | - Yi-fan Wang
- Institute of Pathogen Biology, Jiangxi Academy of Medical Sciences, Nanchang, Jiangxi, PR China
| | - Zong-heng Nie
- Research lab of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi, PR China
| | - Chun-chao Zhu
- Research lab of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi, PR China
| | - Yan Wang
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang, Jiangxi, PR China
| | - Yi-xiong Cai
- National Biodiversity Centre, National Parks Board, Singapore, Singapore
| | - Jie-xin Zou
- Research lab of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi, PR China
| | - Xian-min Zhou
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang, Jiangxi, PR China
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16
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Yao J, Yang H, Dai R. Characterization of the complete mitochondrial genome of Acanthoscelides obtectus (Coleoptera: Chrysomelidae: Bruchinae) with phylogenetic analysis. Genetica 2017; 145:397-408. [PMID: 28730527 DOI: 10.1007/s10709-017-9975-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 07/04/2017] [Indexed: 11/26/2022]
Abstract
Acanthoscelides obtectus is a common species of the subfamily Bruchinae and a worldwide-distributed seed-feeding beetle. The complete mitochondrial genome of A. obtectus is 16,130 bp in length with an A + T content of 76.4%. It contains a positive AT skew and a negative GC skew. The mitogenome of A. obtectus contains 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes and a non-coding region (D-loop). All PCGs start with an ATN codon, and seven (ND3, ATP6, COIII, ND3, ND4L, ND6, and Cytb) of them terminate with TAA, while the remaining five (COI, COII, ND1, ND4, and ND5) terminate with a single T, ATP8 terminates with TGA. Except tRNA Ser , the secondary structures of 21 tRNAs that can be folded into a typical clover-leaf structure were identified. The secondary structures of lrRNA and srRNA were also predicted in this study. There are six domains with 48 helices in lrRNA and three domains with 32 helices in srRNA. The control region of A. obtectus is 1354 bp in size with the highest A + T content (83.5%) in a mitochondrial gene. Thirteen PCGs in 19 species have been used to infer their phylogenetic relationships. Our results show that A. obtectus belongs to the family Chrysomelidae (subfamily-Bruchinae). This is the first study on phylogenetic analyses involving the mitochondrial genes of A. obtectus and could provide basic data for future studies of mitochondrial genome diversities and the evolution of related insect lineages.
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Affiliation(s)
- Jie Yao
- The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Hong Yang
- The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Renhuai Dai
- The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, 550025, Guizhou, People's Republic of China.
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17
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Zhang Z, Chang Y, Li M. Genetic Population Structure of Dastarcus helophoroides (Coleoptera: Bothrideridae) From Different Long-Horned Beetle Hosts Based on Complete Sequences of Mitochondrial COI. JOURNAL OF ECONOMIC ENTOMOLOGY 2017; 110:1275-1283. [PMID: 28334247 DOI: 10.1093/jee/tox059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Indexed: 06/06/2023]
Abstract
Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae) is an important natural enemy of long-horned beetles in China, Japan, and Korea. In this study, the genetic sequence of cytochrome oxidase subunit Ι was used to investigate the genetics and relationships within and among D. helophoroides populations collected from five different geographic locations. We used principal component analysis, heatmap, and Venn diagram results to determine the relationship between haplotypes and populations. In total, 26 haplotypes with 51 nucleotide polymorphic sites were defined, and low genetic diversity was found among the different populations. Significant genetic variations were observed mainly within populations, and no correlation was found between genetic distribution and geographical distance. Low pairwise fixation index values (-0.01424 to 0.04896) and high gene flows show that there was high gene exchange between populations. The codistributed haplotype DH01 was suggested to be the most ancestral haplotype, and other haplotypes were thought to have evolved from it through several mutations. In four of the populations, both common haplotypes (DH01, DH03, and DH22) and unique haplotypes were found. Low genetic diversity among different populations is related to a relatively high flight capacity, host movement, and human-aided dispersal of D. helophoroides. The high gene exchange and typically weak population genetic structure among five populations, especially among populations of Anoplophora glabripennis (Motschulsky), Monochamus alternatus (Hope), and Massicus raddei (Blessig), may suggest that these populations cross naturally in the field.
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Affiliation(s)
- Zhengqing Zhang
- Laboratory of Forestry Pests Biological Control, College of Forestry, Northwest Agriculture and Forestry University, No. 3 Taicheng Road, Yangling, Shaanxi 712100, Republic of China (; ; )
| | - Yong Chang
- Laboratory of Forestry Pests Biological Control, College of Forestry, Northwest Agriculture and Forestry University, No. 3 Taicheng Road, Yangling, Shaanxi 712100, Republic of China (; ; )
| | - Menglou Li
- Laboratory of Forestry Pests Biological Control, College of Forestry, Northwest Agriculture and Forestry University, No. 3 Taicheng Road, Yangling, Shaanxi 712100, Republic of China ( ; ; )
- Corresponding author, e-mail:
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18
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Zhou Z, Zhao L, Liu N, Guo H, Guan B, Di J, Shi F. Towards a higher-level Ensifera phylogeny inferred from mitogenome sequences. Mol Phylogenet Evol 2017; 108:22-33. [PMID: 28188878 DOI: 10.1016/j.ympev.2017.01.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 01/24/2017] [Accepted: 01/31/2017] [Indexed: 11/15/2022]
Abstract
Although mitogenomes are useful tools for inferring evolutionary history, only a few representative ones can be used for most Ensifera lineages. Thirty-two ensiferan mitogenomes were determined using ABI Sanger sequencing and standard primer walking of 2-3 overlapping Long-PCR fragments, or Illumina® HiSeq2000 for "shotgun" sequenced long-PCR-amplified mitochondrial or total genomic DNA. Six patterns of gene arrangements, including the novel trnR-trnSAGN-trnA-trnN-trnG-nad3 in Lipotactes tripyrga (Lipotactinae), were identified from 59 ensiferan mitogenomes. The results suggest that trnM-trnI-trnQ and trnA-trnR-trnE-trnSAGN-trnN-trnF rearrangements might be a shared derived character in Pseudophyllinae and Gryllidae, respectively. We found base composition biases in our dataset, which potentially complicate the inference of higher-level ensiferan phylogeny. Site-heterogeneous Bayesian inference (BI) and site-homogeneous maximum likelihood (ML) analyses recovered all ensiferan superfamilies as monophyletic. The site-homogeneous BI analysis failed to recover the monophyly of Stenopelmatoidea. As Schizodactyloidea was only represented by Comicus campestris, its monophyly could not be tested. In the Triassic/Jurassic boundary, Ensifera diverged into grylloid and non-grylloid clades. All analyses confirmed Grylloidea and Gryllotalpoidea as sister groups. Site-heterogeneous BI analysis found Schizodactyloidea as the most basal lineage and sister to the clade formed by Grylloidea and Gryllotalpoidea, but the site-homogeneous analyses placed it basally to the non-grylloid clade and recovered a sister relationship between Tettigonioidea and (Hagloidea, Rhaphidophoroidea, Stenopelmatoidea), although this clade had a low support. The site-heterogeneous BI analysis found Tettigonioidea and Hagloidea were sister groups (posterior probability (PP)=0.99), Stenopelmatoidea was sister to (Tettigonioidea, Hagloidea) (PP>0.91), and Rhaphidophoroidea was basal to the non-grylloid clade. At a lower level, all analyses divided Tettigonioidea into Phaneropteridae and Tettigoniidae.
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Affiliation(s)
- Zhijun Zhou
- Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China.
| | - Ling Zhao
- College of Life Sciences and Biotechnology, Mianyang Normal University, Mianyang, Sichuan 621000, China
| | - Nian Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710062, China
| | - Huifang Guo
- Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Bei Guan
- Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Juanxia Di
- Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Fuming Shi
- Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China.
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19
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Sun YX, Wang L, Wei GQ, Qian C, Dai LS, Sun Y, Abbas MN, Zhu BJ, Liu CL. Characterization of the Complete Mitochondrial Genome of Leucoma salicis (Lepidoptera: Lymantriidae) and Comparison with Other Lepidopteran Insects. Sci Rep 2016; 6:39153. [PMID: 27974854 PMCID: PMC5156926 DOI: 10.1038/srep39153] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 11/18/2016] [Indexed: 11/19/2022] Open
Abstract
The complete mitochondrial genome (mitogenome) of Leucoma salicis (Lepidoptera: Lymantriidae) was sequenced and annotated. It is a circular molecule of 15,334 bp, containing the 37 genes usually present in insect mitogenomes. All protein-coding genes (PCGs) are initiated by ATN codons, other than cox1, which is initiated by CGA. Three of the 13 PCGs had an incomplete termination codon, T or TA, while the others terminated with TAA. The relative synonymous codon usage of the 13 protein-coding genes (PCGs) was consistent with those of published lepidopteran sequences. All tRNA genes had typical clover-leaf secondary structures, except for the tRNASer (AGN), in which the dihydrouridine (DHU) arm could not form a stable stem-loop structure. The A + T-rich region of 325 bp had several distinctive features, including the motif 'ATAGA' followed by an 18 bp poly-T stretch, a microsatellite-like (AT)7 element, and an 11-bp poly-A present immediately upstream of tRNAMet. Relationships among 32 insect species were determined using Maximum Likelihood (ML), Neighbor Joining (NJ) and Bayesian Inference (BI) phylogenetic methods. These analyses confirm that L. salicis belongs to the Lymantriidae; and that Lymantriidae is a member of Noctuoidea, and is a sister taxon to Erebidae, Nolidae and Noctuidae, most closely related to Erebidae.
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MESH Headings
- Animals
- Base Sequence
- Bayes Theorem
- Codon, Terminator
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/isolation & purification
- DNA, Mitochondrial/metabolism
- Genome, Mitochondrial
- Lepidoptera/classification
- Lepidoptera/genetics
- Likelihood Functions
- Moths/classification
- Moths/genetics
- Nucleic Acid Conformation
- Open Reading Frames/genetics
- Phylogeny
- RNA, Ribosomal/classification
- RNA, Ribosomal/genetics
- RNA, Transfer/chemistry
- RNA, Transfer/classification
- RNA, Transfer/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Yu-Xuan Sun
- College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui Province, P. R. China
| | - Lei Wang
- College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui Province, P. R. China
| | - Guo-Qing Wei
- College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui Province, P. R. China
| | - Cen Qian
- College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui Province, P. R. China
| | - Li-Shang Dai
- College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui Province, P. R. China
| | - Yu Sun
- College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui Province, P. R. China
| | - Muhammad Nadeem Abbas
- College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui Province, P. R. China
| | - Bao-Jian Zhu
- College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui Province, P. R. China
| | - Chao-Liang Liu
- College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui Province, P. R. China
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Yang S, Feng X, Jiao Z, Lu D, Duan M, Wang G. The complete mitochondrial genome of Caenorhabditis remanei (Rhabditida: Rhabditoidae), in comparison with four other Caenorhabditis species. GENE REPORTS 2016. [DOI: 10.1016/j.genrep.2016.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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21
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Yang WJ, Cai XY, Xu KK, Cao Y, Meng YL, Li C. The complete mitochondrial genome of Stegobium paniceum (Coleoptera: Anobiidae). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:815-816. [PMID: 33473638 PMCID: PMC7800607 DOI: 10.1080/23802359.2016.1241679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The complete mitochondrial genome of Stegobium paniceum (Coleoptera: Anobiidae) is a circular DNA molecule of 15,271 bp (GenBank accession number XK819317), and its nucleotide composition is biased towards A + T nucleotides (78.32%). This genome comprises 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA (tRNA) genes, and an A + T-rich region. The gene order of S. paniceum was similar to those found in other known Coleoptera species. Sixteen reading frame overlaps and six intergenic regions were found in the mitochondrial genome of S. paniceum. All 22 tRNA genes have the typical cloverleaf secondary structure, with an exception for trnS1 (AGN). The phylogenetic relationships based on neighbour-joining method revealed that S. paniceum is closely related to Apatides fortis, which is consistent with the traditional morphological classification.
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Affiliation(s)
- Wen-Jia Yang
- Key & Special Laboratory of Guizhou Education Department for Pest Control and Resource Utilization, College of Biology and Environmental Engineering, Guiyang University, Guiyang, China
| | - Xing-Ying Cai
- Key & Special Laboratory of Guizhou Education Department for Pest Control and Resource Utilization, College of Biology and Environmental Engineering, Guiyang University, Guiyang, China
| | - Kang-Kang Xu
- Key & Special Laboratory of Guizhou Education Department for Pest Control and Resource Utilization, College of Biology and Environmental Engineering, Guiyang University, Guiyang, China
| | - Yu Cao
- Key & Special Laboratory of Guizhou Education Department for Pest Control and Resource Utilization, College of Biology and Environmental Engineering, Guiyang University, Guiyang, China
| | - Yong-Lu Meng
- Key & Special Laboratory of Guizhou Education Department for Pest Control and Resource Utilization, College of Biology and Environmental Engineering, Guiyang University, Guiyang, China
| | - Can Li
- Key & Special Laboratory of Guizhou Education Department for Pest Control and Resource Utilization, College of Biology and Environmental Engineering, Guiyang University, Guiyang, China
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22
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Yuan ML, Zhang QL, Zhang L, Guo ZL, Liu YJ, Shen YY, Shao R. High-level phylogeny of the Coleoptera inferred with mitochondrial genome sequences. Mol Phylogenet Evol 2016; 104:99-111. [DOI: 10.1016/j.ympev.2016.08.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 07/26/2016] [Accepted: 08/02/2016] [Indexed: 01/03/2023]
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23
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Amaral DT, Mitani Y, Oliveira G, Ohmiya Y, Viviani VR. Revisiting Coleoptera a + T-rich region: structural conservation, phylogenetic and phylogeographic approaches in mitochondrial control region of bioluminescent Elateridae species (Coleoptera). Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:671-680. [PMID: 27159725 DOI: 10.3109/24701394.2016.1174220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The control region (CR) or A + T-rich region in Coleoptera mt genome is poorly characterized, including the Elateroidea bioluminescent species. Here, we provided the first attempt to characterize and compare the structure and organization of the CR of different species within Elateridae. We also revisited some sequenced Coleoptera CR and observed consensus T-stretches, non-conserved sequences near the stem-loop and unusual inner tRNAs-like sequences. All these features are probably involved in the replication start of the mt genome. The phylogenetic relationships in Elateridae bioluminescent groups using partial sequence of CR showed the monophyly of Pyrearinus pumilus group and Pyrearinus as a polyphyletic genus, corroborating our previous results. The wider genetic variation obtained by CR analysis could separate two different lineages that occur within P. termitilluminans populations. In Elateridae, the CR exhibited high polymorphism within and between populations, which was also observed in other Coleoptera species, suggesting that the CR could be described as a suitable molecular marker to be applied in phylogenetic and phylogeographic studies.
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Affiliation(s)
- Danilo T Amaral
- a Graduate School of Biotechnology and Environmental Monitoring (UFSCar) , Sorocaba , SP , Brazil.,b Graduate School of Evolutive Genetics and Molecular Biology , Federal University of São Carlos (UFSCar) , São Carlos , SP , Brazil
| | - Yasuo Mitani
- c Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba , Japan
| | - Gabriela Oliveira
- a Graduate School of Biotechnology and Environmental Monitoring (UFSCar) , Sorocaba , SP , Brazil.,b Graduate School of Evolutive Genetics and Molecular Biology , Federal University of São Carlos (UFSCar) , São Carlos , SP , Brazil
| | - Yoshihiro Ohmiya
- d Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba , Japan
| | - Vadim R Viviani
- a Graduate School of Biotechnology and Environmental Monitoring (UFSCar) , Sorocaba , SP , Brazil.,b Graduate School of Evolutive Genetics and Molecular Biology , Federal University of São Carlos (UFSCar) , São Carlos , SP , Brazil
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24
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Du C, He S, Song X, Liao Q, Zhang X, Yue B. The complete mitochondrial genome of Epicauta chinensis (Coleoptera: Meloidae) and phylogenetic analysis among Coleopteran insects. Gene 2016; 578:274-80. [DOI: 10.1016/j.gene.2015.12.036] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 12/07/2015] [Accepted: 12/16/2015] [Indexed: 11/15/2022]
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25
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The mitochondrial genome of Atrijuglans hetaohei Yang (Lepidoptera: Gelechioidea) and related phylogenetic analyses. Gene 2016; 581:66-74. [PMID: 26800782 DOI: 10.1016/j.gene.2016.01.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 01/11/2016] [Accepted: 01/16/2016] [Indexed: 01/28/2023]
Abstract
Complete mitochondrial genome sequences are of great importance for better understanding the genome-level characteristics and phylogenetic relationships among related species. In this study, the complete mitochondrial genome of Atrijuglans hetaohei Yang is sequenced and analyzed, which is 15,379bp in length (GenBank: KT581634) and contains a typical set of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and a non-coding region (control region). Except for cox1 gene that is initiated by CGA codon, all protein-coding genes start with ATN codons and end with the stop codon T, TA or TAA. All tRNAs have a typical clover-leaf secondary structure, except for trnS1, of which the DHU arm could not form a stable stem-loop structure. The secondary structure of rrnL and rrnS consists of 49 helices and 33 helices, respectively. Phylogenetic analyses of the complete mitochondrial genome sequences and of the amino acid sequences for 13 mitochondrial protein-coding genes among related species support the view that A. hetaohei is more closely related to the Gelechioidea than Yponomeutoidea. This result is consistent with a previous classification based on morphology.
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The complete mitochondrial genomes of five Eimeria species infecting domestic rabbits. Exp Parasitol 2015; 159:67-71. [PMID: 26358270 DOI: 10.1016/j.exppara.2015.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 06/16/2015] [Accepted: 09/03/2015] [Indexed: 11/21/2022]
Abstract
Rabbit coccidiosis caused by members of the genus Eimeria can cause enormous economic impact worldwide, but the genetics, epidemiology and biology of these parasites remain poorly understood. In the present study, we sequenced and annotated the complete mitochondrial (mt) genomes of five Eimeria species that commonly infect the domestic rabbits. The complete mt genomes of Eimeria intestinalis, Eimeria flavescens, Eimeria media, Eimeria vejdovskyi and Eimeria irresidua were 6261bp, 6258bp, 6168bp, 6254bp, 6259bp in length, respectively. All of the mt genomes consist of 3 genes for proteins (cytb, cox1, and cox3), 14 gene fragments for the large subunit (LSU) rRNA and 11 gene fragments for the small subunit (SSU) rRNA, but no transfer RNA (tRNA) genes. The gene order of the mt genomes is similar to that of Plasmodium, but distinct from Haemosporida and Theileria. Phylogenetic analyses based on full nucleotide sequences using Bayesian analysis revealed that the monophyly of the Eimeria of rabbits was strongly statistically supported with a Bayesian posterior probabilities. These data provide novel mtDNA markers for studying the population genetics and molecular epidemiology of the Eimeria species, and should have implications for the molecular diagnosis, prevention and control of coccidiosis in rabbits.
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Sun TY, Li L, Xin T, Wang Y, Xia B. The complete mitochondrial genome of Cryptolestes ferrugineus (Stephens) (Coleoptera: Laemophloeidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3676-7. [PMID: 26330111 DOI: 10.3109/19401736.2015.1079851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We determined the complete mitochondrial genome (mitogenome) sequence of Cryptolestes ferrugineus (GenBank accession number KT182067) by the long PCR and primer walking method. The mitochondrial genome is a typical circular DNA molecule of 15 511 bp in length, and contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a A + T-rich region (D-loop). The order of 37 genes was typical of insect mitochondrial DNA sequences described to date. The base composition of the genome is A (39.17%), T (37.24%), C (14.22%), and G (9.37%) with an A + T-rich hallmark as that of other invertebrate mitochondrial genomes. All protein-coding genes start with ATN codon and terminate with the stop codon T (AA) or TAG. The A + T-rich region is located between 12S rRNA and tRNA(Ile). In this study, the phylogenetic relationships of Coleoptera species were constructed based on the nucleotides sequences of 13 PCGs of mitogenomes. The molecular-based phylogeny supported the traditional morphological classification on relationships within Coleoptera species.
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Affiliation(s)
- Tian Yi Sun
- a College of Life Science, Nanchang University , Nanchang , China
| | - Lei Li
- a College of Life Science, Nanchang University , Nanchang , China
| | - Tianrong Xin
- a College of Life Science, Nanchang University , Nanchang , China
| | - Yayu Wang
- a College of Life Science, Nanchang University , Nanchang , China
| | - Bin Xia
- a College of Life Science, Nanchang University , Nanchang , China
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Niu FF, Zhu L, Wang S, Wei SJ. The mitochondrial genome of the multicolored Asian lady beetle Harmonia axyridis (Pallas) and a phylogenetic analysis of the Polyphaga (Insecta: Coleoptera). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2725-7. [PMID: 26057015 DOI: 10.3109/19401736.2015.1046165] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Here, we report the mitochondrial genome sequence of the multicolored Asian lady beetle Harmonia axyridis (Pallas, 1773) (Coleoptera: Coccinellidae) (GenBank accession No. KR108208). This is the first species with sequenced mitochondrial genome from the genus Harmonia. The current length with partitial A + T-rich region of this mitochondrial genome is 16,387 bp. All the typical genes were sequenced except the trnI and trnQ. As in most other sequenced mitochondrial genomes of Coleoptera, there is no re-arrangement in the sequenced region compared with the pupative ancestral arrangement of insects. All protein-coding genes start with ATN codons. Five, five and three protein-coding genes stop with termination codon TAA, TA and T, respectively. Phylogenetic analysis using Bayesian method based on the first and second codon positions of the protein-coding genes supported that the Scirtidae is a basal lineage of Polyphaga. The Harmonia and the Coccinella form a sister lineage. The monophyly of Staphyliniformia, Scarabaeiformia and Cucujiformia was supported. The Buprestidae was found to be a sister group to the Bostrichiformia.
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Affiliation(s)
- Fang-Fang Niu
- a Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences , Beijing , China
| | - Liang Zhu
- a Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences , Beijing , China
| | - Su Wang
- a Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences , Beijing , China
| | - Shu-Jun Wei
- a Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences , Beijing , China
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