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Wei K, Guo J, Liu M, Long X, Du C, Liu Y. The complete mitochondrial genome of Sigara lateralis (Leach, 1817) (Nepomorpha: Corixidae). Mitochondrial DNA B Resour 2024; 9:729-733. [PMID: 38859914 PMCID: PMC11164096 DOI: 10.1080/23802359.2024.2363362] [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: 07/14/2023] [Accepted: 05/29/2024] [Indexed: 06/12/2024] Open
Abstract
The Sigara lateralis (Leach, 1817) is a small aquatic insect belonging to the family Corixidae. The study aims to reveal the genomic data of the mitochondrial genome of S. lateralis. The length of its circular mitochondrial genome is 15,725 bp long with an A + T bias (75.96%). The mitogenome comprises 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes, and two rRNA genes. The phylogenetic analyses showed that the S. lateralis is the closest to S. septemlineata. These findings will help the conservation of Corixidae from the perspective of genetic evolution.
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Affiliation(s)
- Ke Wei
- Baotou Teachers College, Baotou, People’s Republic of China
| | - Jinxing Guo
- Baotou Teachers College, Baotou, People’s Republic of China
| | - Mengjiao Liu
- Baotou Teachers College, Baotou, People’s Republic of China
| | - Xu Long
- Baotou Teachers College, Baotou, People’s Republic of China
| | - Chao Du
- Baotou Teachers College, Baotou, People’s Republic of China
| | - Yunpeng Liu
- Baotou Teachers College, Baotou, People’s Republic of China
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2
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Wang W, Dong Z, Du Z, Wu P. Genome-scale approach to reconstructing the phylogenetic tree of psyllids (superfamily Psylloidea) with account of systematic bias. Mol Phylogenet Evol 2023; 189:107924. [PMID: 37699449 DOI: 10.1016/j.ympev.2023.107924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/05/2023] [Accepted: 09/09/2023] [Indexed: 09/14/2023]
Abstract
Psyllids (class Insecta: order Hemiptera: superfamily Psylloidea) are a taxonomically and phylogenetically challenging clade. Recent studies have largely advanced the phylogeny of this group, yet the family-level relationships among Aphalaridae, Carsidaridae, and others remain unresolved. Genome-scale phylogenetic analysis is known to provide a finer resolution for problems like that. However, such phylogenomics also introduces new problems: incorrect trees with high confidence yielded due to systematic error (bias). Here we addressed these issues using hundreds of single-copy orthologous (SCO) genes in psyllid transcriptomes and genomes. Our analyses revealed conflicts between the nucleotide-based and amino-acid-based phylogenetic trees. While the nucleotide-based phylogeny strongly supported the (Aphalaridae + Carsidaridae) + Others relationship, the amino-acid-based one recovered Aphalaridae + (Carsidaridae + Others) with 100% support. Further inspection revealed significant compositional heterogeneity in nucleotide sequences for 67% of SCO genes, but not in the corresponding translated amino acid sequences. We then used different strategies to combat this compositional bias, and found that using the RY-coding strategy (coding the standard nucleotides as purines and pyrimidines) the nucleotide-based phylogeny became consistent with the amino-acid-based one. We further applied RY-coding to a published concatenated nucleotide dataset and recovered the Aphalaridae monophyly (which is refuted by the original literature on non-recoded sequences) at the base of psyllid tree. Moreover, it was found that variations in evolutionary rate could lead to errors in nucleotide-based phylogeny. The fast-evolving Heteropsylla cubana (Psyllidae: Ciriacreminae) was incorrectly placed within the subfamily Psyllinae. This bias can be avoided by using data removal or RY-coding strategies. Together, our results strongly support the family relationship of Aphalaridae + (Carsidaridae + Others), and show that the amino-acid-based concatenation analysis is more robust than nucleotide-based one. Future phylogenomic analysis of psyllid nucleotide sequences should take into account methods such as the RY-coding scheme to address potential systematic biases arising from composition and rate heterogeneities.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zequn Dong
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhong Du
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengxiang Wu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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3
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Zhang M, Zhao Z, Ren D, Yao Y. Three New Species of Velvety Shore Bugs (Hemiptera: Heteroptera: Ochteroidea) From Mid-Cretaceous Kachin Amber Shed Light on the Evolution of Rostrum Length in Ochteroidea. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.892530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Two new genera of velvety shore bugs, Arcochterus Zhang, Ren and Yao gen. nov. and Parvochterus Zhang, Ren and Yao gen. nov. are described, with three new species between them—Arcochterus fuscus Zhang, Ren and Yao sp. nov., Parvochterus reticulatus Ren and Yao sp. nov., and P. lanceolarus Zhang, Ren and Yao sp. nov. Based on the combination of fossil and extant taxa, a cladistic analysis is conducted to confirm the phylogenetic position of these species and allows reconstruction of the inter-genus relationships within the superfamily Ochteroidea. Major conclusions of the phylogenetic analysis: (1) these new species and Grimaldinia pronotalis belong to Ochteridae; (2) Ochteroidea is a monophyletic group, Ochteridae and Gelastocoridae are sister group and monophyletic, respectively. (3) The ancestral character state reconstruction (ACSR) shows that the length of the rostrum has occurred in at least three independent transitions during the evolution of the superfamily Ochteroidea.
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Akita S, Vieira C, Hanyuda T, Rousseau F, Cruaud C, Couloux A, Heesch S, Cock JM, Kawai H. Providing a phylogenetic framework for trait-based analyses in brown algae: Phylogenomic tree inferred from 32 nuclear protein-coding sequences. Mol Phylogenet Evol 2022; 168:107408. [PMID: 35031471 DOI: 10.1016/j.ympev.2022.107408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 12/16/2021] [Accepted: 12/26/2021] [Indexed: 11/23/2022]
Abstract
In the study of the evolution of biological complexity, a reliable phylogenetic framework is needed. Many attempts have been made to resolve phylogenetic relationships between higher groups (i.e., interordinal) of brown algae (Phaeophyceae) based on molecular evidence, but most of these relationships remain unclear. Analyses based on small multi-gene data (including chloroplast, mitochondrial and nuclear sequences) have yielded inconclusive and sometimes contradictory results. To address this problem, we have analyzed 32 nuclear protein-coding sequences in 39 Phaeophycean species belonging to eight orders. The resulting nuclear-based phylogenomic trees provide virtually full support for the phylogenetic relationships within the studied taxa, with few exceptions. The relationships largely confirm phylogenetic trees based on nuclear, chloroplast and mitochondrial sequences, except for the placement of the Sphacelariales with weak bootstrap support. Our study indicates that nuclear protein-coding sequences provide significant support to conclusively resolve phylogenetic relationships among Phaeophyceae, and may be a powerful approach to fully resolve interordinal relationships with increased taxon sampling.
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Affiliation(s)
- Shingo Akita
- Kobe University Research Center for Inland Seas, Rokkodai 1-1, Kobe 657-8501, Japan; Faculty of Fisheries Sciences, Hokkaido University, 3-1-1 Minato, Hakodate, Hokkaido 041-8611, Japan
| | - Christophe Vieira
- Kobe University Research Center for Inland Seas, Rokkodai 1-1, Kobe 657-8501, Japan.
| | - Takeaki Hanyuda
- Kobe University Research Center for Inland Seas, Rokkodai 1-1, Kobe 657-8501, Japan
| | - Florence Rousseau
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 39 75005 Paris, France
| | - Corinne Cruaud
- Génoscope, Centre National de Séquençage, 2 rue G. Crémieux, Evry CP 5706, France
| | - Arnaud Couloux
- Génoscope, Centre National de Séquençage, 2 rue G. Crémieux, Evry CP 5706, France
| | - Svenja Heesch
- CNRS, Sorbonne Université, Algal Genetics Group, UMR 8227 Integrative Biology of Marine Models, Station Biologique, F 29688 Roscoff, France; Universität Rostock Institut für Biowissenschaften Angewandte Ökologie & Phykologie Albert-Einstein-Straße, 21 18059 Rostock, Germany.
| | - J Mark Cock
- CNRS, Sorbonne Université, Algal Genetics Group, UMR 8227 Integrative Biology of Marine Models, Station Biologique, F 29688 Roscoff, France
| | - Hiroshi Kawai
- Kobe University Research Center for Inland Seas, Rokkodai 1-1, Kobe 657-8501, Japan
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Sureshan SC, Tanavade RV, Ghosh S, Ghosh S, Sella RN, Mohideen HS. Complete mitochondrial genome sequencing of Oxycarenus laetus (Hemiptera: Lygaeidae) from two geographically distinct regions of India. Sci Rep 2021; 11:23738. [PMID: 34887433 PMCID: PMC8660866 DOI: 10.1038/s41598-021-02881-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 11/18/2021] [Indexed: 11/09/2022] Open
Abstract
Oxycarenus laetus is a seed-sap sucking pest affecting a variety of crops, including cotton plants. Rising incidence and pesticide resistance by O. laetus have been reported from India and neighbouring countries. In this study, O. laetus samples were collected from Bhatinda and Coimbatore (India). Pure mtDNA was isolated and sequenced using Illumina MiSeq. Both the samples were found to be identical species (99.9%), and the complete genome was circular (15,672 bp), consisting of 13 PCGs, 2 rRNA, 23 tRNA genes, and a 962 bp control region. The mitogenome is 74.1% AT-rich, 0.11 AT, and - 0.19 GC skewed. All the genes had ATN as the start codon except cox1 (TTG), and an additional trnT was predicted. Nearly all tRNAs folded into the clover-leaf structure, except trnS1 and trnV. The intergenic space between trnH and nad4, considered as a synapomorphy of Lygaeoidea, was displaced. Two 5 bp motifs AATGA and ACCTA, two tandem repeats, and a few microsatellite sequences, were also found. The phylogenetic tree was constructed using 36 mitogenomes from 7 super-families of Hemiptera by employing rigorous bootstrapping and ML. Ours is the first study to sequence the complete mitogenome of O. laetus or any Oxycarenus species. The findings from this study would further help in the evolutionary studies of Lygaeidae.
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Affiliation(s)
- Shruthi Chalil Sureshan
- grid.412742.60000 0004 0635 5080Bioinformatics and Entomoinformatics Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203 Tamil Nadu India
| | - Ruchi Vivekanand Tanavade
- grid.412742.60000 0004 0635 5080Bioinformatics and Entomoinformatics Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203 Tamil Nadu India
| | - Sewali Ghosh
- Department of Advanced Zoology and Biotechnology, Guru Nanak College, Chennai, 600042 Tamil Nadu India
| | - Saswati Ghosh
- grid.506009.aDepartment of Virology, King Institute of Preventive Medicine and Research, Chennai, 600032 Tamil Nadu India
| | - Raja Natesan Sella
- grid.412742.60000 0004 0635 5080Membrane Protein Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203 Tamil Nadu India
| | - Habeeb Shaik Mohideen
- Bioinformatics and Entomoinformatics Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Tamil Nadu, India.
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Abramson NI, Bodrov SY, Bondareva OV, Genelt-Yanovskiy EA, Petrova TV. A mitochondrial genome phylogeny of voles and lemmings (Rodentia: Arvicolinae): Evolutionary and taxonomic implications. PLoS One 2021; 16:e0248198. [PMID: 34797834 PMCID: PMC8604340 DOI: 10.1371/journal.pone.0248198] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 11/03/2021] [Indexed: 01/04/2023] Open
Abstract
Arvicolinae is one of the most impressive placental radiations with over 150 extant and numerous extinct species that emerged since the Miocene in the Northern Hemisphere. The phylogeny of Arvicolinae has been studied intensively for several decades using morphological and genetic methods. Here, we sequenced 30 new mitochondrial genomes to better understand the evolutionary relationships among the major tribes and genera within the subfamily. The phylogenetic and molecular dating analyses based on 11,391 bp concatenated alignment of protein-coding mitochondrial genes confirmed the monophyly of the subfamily. While Bayesian analysis provided a high resolution across the entire tree, Maximum Likelihood tree reconstruction showed weak support for the ordering of divergence and interrelationships of tribal level taxa within the most ancient radiation. Both the interrelationships among tribes Lagurini, Ellobiusini and Arvicolini, comprising the largest radiation and the position of the genus Dinaromys within it also remained unresolved. For the first time complex relationships between genus level taxa within the species-rich tribe Arvicolini received full resolution. Particularly Lemmiscus was robustly placed as sister to the snow voles Chionomys in the tribe Arvicolini in contrast with a long-held belief of its affinity with Lagurini. Molecular dating of the origin of Arvicolinae and early divergences obtained from the mitogenome data were consistent with fossil records. The mtDNA estimates for putative ancestors of the most genera within Arvicolini appeared to be much older than it was previously proposed in paleontological studies.
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Affiliation(s)
- Natalia I. Abramson
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Semyon Yu. Bodrov
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Olga V. Bondareva
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Evgeny A. Genelt-Yanovskiy
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Tatyana V. Petrova
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
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Xu KK, Chen QP, Ayivi SPG, Guan JY, Storey KB, Yu DN, Zhang JY. Three Complete Mitochondrial Genomes of Orestes guangxiensis, Peruphasma schultei, and Phryganistria guangxiensis (Insecta: Phasmatodea) and Their Phylogeny. INSECTS 2021; 12:779. [PMID: 34564219 PMCID: PMC8471129 DOI: 10.3390/insects12090779] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/26/2021] [Accepted: 08/28/2021] [Indexed: 01/21/2023]
Abstract
Insects of the order Phasmatodea are mainly distributed in the tropics and subtropics and are best known for their remarkable camouflage as plants. In this study, we sequenced three complete mitochondrial genomes from three different families: Orestes guangxiensis, Peruphasma schultei, and Phryganistria guangxiensis. The lengths of the three mitochondrial genomes were 15,896 bp, 16,869 bp, and 17,005 bp, respectively, and the gene composition and structure of the three stick insects were identical to those of the most recent common ancestor of insects. The phylogenetic relationships among stick insects have been chaotic for a long time. In order to discuss the intra- and inter-ordinal relationship of Phasmatodea, we used the 13 protein-coding genes (PCGs) of 85 species for maximum likelihood (ML) and Bayesian inference (BI) analyses. Results showed that the internal topological structure of Phasmatodea had a few differences in both ML and BI trees and long-branch attraction (LBA) appeared between Embioptera and Zoraptera, which led to a non-monophyletic Phasmatodea. Consequently, after removal of the Embioptera and Zoraptera species, we re-performed ML and BI analyses with the remaining 81 species, which showed identical topology except for the position of Tectarchus ovobessus (Phasmatodea). We recovered the monophyly of Phasmatodea and the sister-group relationship between Phasmatodea and Mantophasmatodea. Our analyses also recovered the monophyly of Heteropterygidae and the paraphyly of Diapheromeridae, Phasmatidae, Lonchodidae, Lonchodinae, and Clitumninae. In this study, Peruphasma schultei (Pseudophasmatidae), Phraortes sp. YW-2014 (Lonchodidae), and species of Diapheromeridae clustered into the clade of Phasmatidae. Within Heteropterygidae, O. guangxiensis was the sister clade to O. mouhotii belonging to Dataminae, and the relationship of (Heteropteryginae + (Dataminae + Obriminae)) was recovered.
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Affiliation(s)
- Ke-Ke Xu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (K.-K.X.); (Q.-P.C.); (S.P.G.A.); (J.-Y.G.); (D.-N.Y.)
| | - Qing-Ping Chen
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (K.-K.X.); (Q.-P.C.); (S.P.G.A.); (J.-Y.G.); (D.-N.Y.)
| | - Sam Pedro Galilee Ayivi
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (K.-K.X.); (Q.-P.C.); (S.P.G.A.); (J.-Y.G.); (D.-N.Y.)
| | - Jia-Yin Guan
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (K.-K.X.); (Q.-P.C.); (S.P.G.A.); (J.-Y.G.); (D.-N.Y.)
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Dan-Na Yu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (K.-K.X.); (Q.-P.C.); (S.P.G.A.); (J.-Y.G.); (D.-N.Y.)
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Jia-Yong Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (K.-K.X.); (Q.-P.C.); (S.P.G.A.); (J.-Y.G.); (D.-N.Y.)
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
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Tihelka E, Thayer MK, Newton AF, Cai C. New Data, Old Story: Molecular Data Illuminate the Tribal Relationships among Rove Beetles of the Subfamily Staphylininae (Coleoptera: Staphylinidae). INSECTS 2020; 11:E164. [PMID: 32143338 PMCID: PMC7143346 DOI: 10.3390/insects11030164] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 02/28/2020] [Accepted: 03/02/2020] [Indexed: 11/17/2022]
Abstract
The megadiverse subfamily Staphylininae traditionally belonged to the best-defined rove beetle taxa, but the advent of molecular phylogenetics in the last decade has brought turbulent changes to the group's classification. Here, we reevaluate the internal relationships among the tribes of Staphylininae by implementing tree inference methods that suppress common sources of systematic error. In congruence with morphological data, and in contrast to some previous phylogenetic studies, we unambiguously recover Staphylininae and Paederinae as monophyletic in the traditional sense. We show that the recently proposed subfamily Platyprosopinae (Arrowinus and Platyprosopus) is a phylogenetic artefact and reinstate Arrowinus as a member of Arrowinini stat. res. and Platyprosopus as a member of Platyprosopini stat. res. We show that several recent changes to the internal classification of the subfamily are phylogenetically unjustified and systematically unnecessary. We, therefore, reestablish Platyprosopini, Staphylinini, and Xantholinini as tribes within Staphylininae (all stat. res.) and recognize Coomaniini as a tribe (stat. nov.) rather than subfamily. Consequently, the traditional ranks of the subtribes Acylophorina, Afroquediina, Amblyopinina, Antimerina, †Baltognathina, Cyrtoquediina, Erichsoniina, Hyptiomina, Indoquediina, Quediina, and Tanygnathinina are restored (all stat. res.). We review the current classification of Staphylininae and discuss sources of incongruence in multigene phylogenies.
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Affiliation(s)
- Erik Tihelka
- Department of Animal Science, Hartpury College, Hartpury GL19 3BE, UK;
| | - Margaret K. Thayer
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA; (M.K.T.); (A.F.N.)
| | - Alfred F. Newton
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA; (M.K.T.); (A.F.N.)
| | - Chenyang Cai
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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Ye Z, Damgaard J, Yang H, Hebsgaard MB, Weir T, Bu W. Phylogeny and diversification of the true water bugs (Insecta: Hemiptera: Heteroptera: Nepomorpha). Cladistics 2020; 36:72-87. [PMID: 34618947 DOI: 10.1111/cla.12383] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2019] [Indexed: 01/29/2023] Open
Abstract
Climate fluctuations and tectonic reconfigurations associated with environmental changes play large roles in determining patterns of adaptation and diversification, but studies documenting how such drivers have shaped the evolutionary history and diversification dynamics of limnic organisms during the Mesozoic are scarce. Members of the heteropteran infraorder Nepomorpha, or aquatic bugs, are ideal for testing the effects of these determinants on their diversification pulses because most species are confined to aquatic environments during their entire life. The group has a relatively mature taxonomy and is well represented in the fossil record. We investigated the evolution of Nepomorpha based on phylogenetic analyses of morphological and molecular characters sampled from 115 taxa representing all 13 families and approximately 40% of recognized genera. Our results were largely congruent with the phylogenetic relationships inferred from morphology. A divergence dating analysis indicated that Nepomorpha began to diversify in the late Permian (approximately 263 Ma), and diversification analyses suggested that palaeoecological opportunities probably promoted lineage diversification in this group.
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Affiliation(s)
- Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Jakob Damgaard
- Natural History Museum of Denmark, Zoological Museum, Universitetsparken 15, Kobenhavn, 2100 Ø, Denmark
| | - Huanhuan Yang
- School of Life Sciences, Ludong University, 264025, Yantai, Shandong, China
| | - Martin B Hebsgaard
- Natural History Museum of Denmark, Zoological Museum, Universitetsparken 15, Kobenhavn, 2100 Ø, Denmark
| | - Tom Weir
- CSIRO Entomology, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
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Yu X, Tan W, Zhang H, Jiang W, Gao H, Wang W, Liu Y, Wang Y, Tian X. Characterization of the Complete Mitochondrial Genome of Harpalus sinicus and Its Implications for Phylogenetic Analyses. Genes (Basel) 2019; 10:E724. [PMID: 31540431 PMCID: PMC6771156 DOI: 10.3390/genes10090724] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/12/2019] [Accepted: 09/13/2019] [Indexed: 01/13/2023] Open
Abstract
In this study, we report the complete mitochondrial genome of Harpalus sinicus (occasionally named as the Chinese ground beetle) which is the first mitochondrial genome for Harpalus. The mitogenome is 16,521 bp in length, comprising 37 genes, and a control region. The A + T content of the mitogenome is as high as 80.6%. A mitochondrial origins of light-strand replication (OL)-like region is found firstly in the insect mitogenome, which can form a stem-loop hairpin structure. Thirteen protein-coding genes (PCGs) share high homology, and all of them are under purifying selection. All tRNA genes (tRNAs) can be folded into the classic cloverleaf secondary structures except tRNA-Ser (GCU), which lacks a dihydrouridine (DHU) stem. The secondary structure of two ribosomal RNA genes (rRNAs) is predicted based on previous insect models. Twelve types of tandem repeats and two stem-loop structures are detected in the control region, and two stem-loop structures may be involved in the initiation of replication and transcription. Additionally, phylogenetic analyses based on mitogenomes suggest that Harpalus is an independent lineage in Carabidae, and is closely related to four genera (Abax, Amara, Stomis, and Pterostichus). In general, this study provides meaningful genetic information for Harpalus sinicus and new insights into the phylogenetic relationships within the Carabidae.
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Affiliation(s)
- Xiaolei Yu
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Wei Tan
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Huanyu Zhang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Weiling Jiang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Han Gao
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Wenxiu Wang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yuxia Liu
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yu Wang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Xiaoxuan Tian
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
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11
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Li M, Wang F, Li R, Zhao C, Zhang H. Next generation sequencing yields the complete mitochondrial genome of Notonecta montandoni Motschulsky (Hemiptera: Notonectidae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1561228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Min Li
- Department of Biology, Taiyuan Normal University, Taiyuan, China
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Fang Wang
- Department of Biology, Taiyuan Normal University, Taiyuan, China
| | - Rongrong Li
- Department of Biology, Taiyuan Normal University, Taiyuan, China
| | - Chenjing Zhao
- Department of Biology, Taiyuan Normal University, Taiyuan, China
| | - Hufang Zhang
- Department of Biology, Xinzhou Teachers University, Xinzhou, China
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Zhang DL, Li M, Li T, Yuan JJ, Bu WJ. A mitochondrial genome of Micronectidae and implications for its phylogenetic position. Int J Biol Macromol 2018; 119:747-757. [PMID: 30075212 DOI: 10.1016/j.ijbiomac.2018.07.191] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 06/05/2018] [Accepted: 07/31/2018] [Indexed: 11/27/2022]
Abstract
The mitochondrial genome (mitogenome) has been extensively used to better understand the phylogenetic relationships within the heteropteran infraorder Nepomorpha (Hemiptera), but no mitogenome in Micronectidae has been sequenced to date. Here we describe the first complete mitogenome of Micronecta sahlbergii (Jakovlev, 1881). The mitogenome is 15,005 bp in size, containing 13 typical PCGs, 22 tRNAs, two rRNAs and a control region (CR). All genes are arranged in the same gene order as the most other known heteropteran mitogenome. The phylogenetic relationships based on mitogenomes using Bayesian inference and Maximum likelihood methods showed that Micronecta sahlbergii was sister to Sigara septemlineata, suggesting that Micronecta sahlbergii belongs to Corixoidea. Corixoidea was basal within Nepomorpha. The PCG12 and PCG12RT matrices of BI and ML analyses yielded the consistent topology, respectively. Whereas there was no consistent conclusions in PCG123 and PCG123RT matrices. Saturation tests showed that PCG12 and PCG12RT were free of saturation in evaluation of transition and transversion substitution, while PCG123 and PCG123RT exhibited a plateau revealing saturation of transition suggesting that the third codon positions of PCGs were not suitable for addressing relationships at the superfamily level in Nepomorpha. So our results supported the phylogenetic analysis of PCG12 and PCG12RT in Nepomorpha.
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Affiliation(s)
- Dan-Li Zhang
- Department of Biology, Taiyuan Normal University, Jinzhong 030619, PR China; Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Min Li
- Department of Biology, Taiyuan Normal University, Jinzhong 030619, PR China
| | - Teng Li
- Institute of Zoology and Developmental Biology, College of Life Sciences, Lanzhou University, Lanzhou 730000, PR China
| | - Juan-Juan Yuan
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Wen-Jun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, PR China.
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13
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Yang H, Li T, Dang K, Bu W. Compositional and mutational rate heterogeneity in mitochondrial genomes and its effect on the phylogenetic inferences of Cimicomorpha (Hemiptera: Heteroptera). BMC Genomics 2018; 19:264. [PMID: 29669515 PMCID: PMC5907366 DOI: 10.1186/s12864-018-4650-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 04/08/2018] [Indexed: 01/24/2023] Open
Abstract
Background Mitochondrial genome (mt-genome) data can potentially return artefactual relationships in the higher-level phylogenetic inference of insects due to the biases of accelerated substitution rates and compositional heterogeneity. Previous studies based on mt-genome data alone showed a paraphyly of Cimicomorpha (Insecta, Hemiptera) due to the positions of the families Tingidae and Reduviidae rather than the monophyly that was supported based on morphological characters, morphological and molecular combined data and large scale molecular datasets. Various strategies have been proposed to ameliorate the effects of potential mt-genome biases, including dense taxon sampling, removal of third codon positions or purine-pyrimidine coding and the use of site-heterogeneous models. In this study, we sequenced the mt-genomes of five additional Tingidae species and discussed the compositional and mutational rate heterogeneity in mt-genomes and its effect on the phylogenetic inferences of Cimicomorpha by implementing the bias-reduction strategies mentioned above. Results Heterogeneity in nucleotide composition and mutational biases were found in mt protein-coding genes, and the third codon exhibited high levels of saturation. Dense taxon sampling of Tingidae and Reduviidae and the other common strategies mentioned above were insufficient to recover the monophyly of the well-established group Cimicomorpha. When the sites with weak phylogenetic signals in the dataset were removed, the remaining dataset of mt-genomes can support the monophyly of Cimicomorpha; this support demonstrates that mt-genomes possess strong phylogenetic signals for the inference of higher-level phylogeny of this group. Comparison of the ratio of the removal of amino acids for each PCG showed that ATP8 has the highest ratio while CO1 has the lowest. This pattern is largely congruent with the evolutionary rate of 13 PCGs that ATP8 represents the highest evolutionary rate, whereas CO1 appears to be the lowest. Notably, the value of Ka/Ks ratios of all PCGs is less than 1, indicating that these genes are likely evolving under purifying selection. Conclusions Our results demonstrate that mt-genomes have sites with strong phylogenetic signals for the inference of higher-level phylogeny of Cimicomorpha. Consequently, bioinformatic approaches to removing sites with weak phylogenetic signals in mt-genome without relying on an a priori tree topology would greatly improve this field. Electronic supplementary material The online version of this article (10.1186/s12864-018-4650-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Huanhuan Yang
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Teng Li
- Institute of Zoology and Developmental Biology, College of Life Sciences, Lanzhou University, 222 Tianshui South Road, Lanzhou, 730000, China.
| | - Kai Dang
- 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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14
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Zhao Q, Wang J, Wang MQ, Cai B, Zhang HF, Wei JF. Complete Mitochondrial Genome of Dinorhynchus dybowskyi (Hemiptera: Pentatomidae: Asopinae) and Phylogenetic Analysis of Pentatomomorpha Species. JOURNAL OF INSECT SCIENCE (ONLINE) 2018; 18:4970868. [PMID: 29718506 PMCID: PMC5905379 DOI: 10.1093/jisesa/iey031] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Indexed: 05/30/2023]
Abstract
Dinorhynchus dybowskyi (Hemiptera: Pentatomidae: Asopinae) is used as a biological control agent against various insect pests for its predatory. In the present study, the complete mitochondrial genome (mitogenome) of the species was sequenced using the next-generation sequencing technology. The results showed that the mitogenome is 15,952 bp long, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and a control region. Furthermore, the gene order and orientation of this mitogenome are identical to those of most heteropterans. There are 21 intergenic spacers (of length 1-28 bp) and 13 overlapping regions (of length 1-23 bp) throughout the genome. The control region is 1,291 bp long. The start codon of the PCGs is ATN, except cox1 (TTG), and stop codon is TAA, except nad1 (TAG). The 22 tRNAs exhibit a typical cloverleaf secondary structure, except trnS1, which lacks a dihydrouridine (DHU) arm and trnV, where the DHU arm forms a simple loop. The analyses based on nucleotide sequences of the 13 PCGs by Bayesian Inference and maximum likelihood methods. The results support the monophyly of five superfamilies Aradoidea, Pentatomoidea, Pyrrhocoroidea, Lygaeoidea, and Coreoidea. Within Pentatomoidea, the relationship observed is as follows: (Plataspidae + Urostylididae) + (Pentatomidae + (Acanthosomatidae + (Cydnidae + (Scutelleridae + (Dinidoridae + Tessaratomidae))))), and D. dybowskyi was placed in Pentatomidae and close to Eurydema gebleri.
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Affiliation(s)
- Qing Zhao
- Department of Entomology, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Juan Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Meng-Qing Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bo Cai
- Hainan Entry-Exit Inspection and Quarantine Bureau, Haikou, Hainan, China
| | - Hu-Fang Zhang
- Department of Entomology, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Jiu-Feng Wei
- Department of Entomology, Shanxi Agricultural University, Taigu, Shanxi, China
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15
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Weirauch C, Schuh RT, Cassis G, Wheeler WC. Revisiting habitat and lifestyle transitions in Heteroptera (Insecta: Hemiptera): insights from a combined morphological and molecular phylogeny. Cladistics 2018; 35:67-105. [DOI: 10.1111/cla.12233] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2017] [Indexed: 11/28/2022] Open
Affiliation(s)
- Christiane Weirauch
- Department of Entomology University of California Riverside 900 University Avenue Riverside CA 92521 USA
| | - Randall T. Schuh
- Division of Invertebrate Zoology American Museum of Natural History New York NY 10024‐5192 USA
| | - Gerasimos Cassis
- Evolution & Ecology Research Center School of Biological, Earth, and Environmental Sciences University of New South Wales Sydney NSW 2052 Australia
| | - Ward C. Wheeler
- Division of Invertebrate Zoology American Museum of Natural History New York NY 10024‐5192 USA
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16
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Li T, Yang J, Li Y, Cui Y, Xie Q, Bu W, Hillis DM. A Mitochondrial Genome of Rhyparochromidae (Hemiptera: Heteroptera) and a Comparative Analysis of Related Mitochondrial Genomes. Sci Rep 2016; 6:35175. [PMID: 27756915 PMCID: PMC5069475 DOI: 10.1038/srep35175] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/26/2016] [Indexed: 11/23/2022] Open
Abstract
The Rhyparochromidae, the largest family of Lygaeoidea, encompasses more than 1,850 described species, but no mitochondrial genome has been sequenced to date. Here we describe the first mitochondrial genome for Rhyparochromidae: a complete mitochondrial genome of Panaorus albomaculatus (Scott, 1874). This mitochondrial genome is comprised of 16,345 bp, and contains the expected 37 genes and control region. The majority of the control region is made up of a large tandem-repeat region, which has a novel pattern not previously observed in other insects. The tandem-repeats region of P. albomaculatus consists of 53 tandem duplications (including one partial repeat), which is the largest number of tandem repeats among all the known insect mitochondrial genomes. Slipped-strand mispairing during replication is likely to have generated this novel pattern of tandem repeats. Comparative analysis of tRNA gene families in sequenced Pentatomomorpha and Lygaeoidea species shows that the pattern of nucleotide conservation is markedly higher on the J-strand. Phylogenetic reconstruction based on mitochondrial genomes suggests that Rhyparochromidae is not the sister group to all the remaining Lygaeoidea, and supports the monophyly of Lygaeoidea.
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Affiliation(s)
- Teng Li
- Institute of Zoology and Developmental Biology, College of Life Sciences, Lanzhou University, 222 Tianshui South Road, Lanzhou 730000, China
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Jie Yang
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Yinwan Li
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Ying Cui
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Qiang Xie
- 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
| | - David M. Hillis
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
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17
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Zhang D, Xie T, Li T, Bu W. The complete mitochondrial genome of Nepa hoffmanni (Hemiptera: Heteroptera: Nepidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3770-1. [PMID: 26403708 DOI: 10.3109/19401736.2015.1079898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome (mt-genome) of Nepa hoffmanni has been reported in this study. This mitochondrial genome is 15 774 bp long, with an A + T content of 72.04%, containing the typical 37 genes (13 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes) and a control region. All genes are arranged in the same gene order as most other known heteropteran mt-genome. This is the second completely sequenced mt-genome from the family Nepidae of Nepomorpha. Bayesian analyses were performed using the mt-genome of Nepa hoffmanni and its relatives, including 17 taxa, showing a reasonable placement of Nepa hoffmanni.
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Affiliation(s)
- Danli Zhang
- a Institute of Entomology, College of Life Sciences, Nankai University , Tianjin , China and
| | - Tongyin Xie
- a Institute of Entomology, College of Life Sciences, Nankai University , Tianjin , China and
| | - Teng Li
- b Institute of Zoology and Developmental Biology, College of Life Sciences, Lanzhou University , Lanzhou , China
| | - Wenjun Bu
- a Institute of Entomology, College of Life Sciences, Nankai University , Tianjin , China and
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18
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Wang Y, Cui Y, Rédei D, Baňař P, Xie Q, Štys P, Damgaard J, Chen P, Yi W, Wang Y, Dang K, Li C, Bu W. Phylogenetic divergences of the true bugs (Insecta: Hemiptera: Heteroptera), with emphasis on the aquatic lineages: the last piece of the aquatic insect jigsaw originated in the Late Permian/Early Triassic. Cladistics 2015; 32:390-405. [DOI: 10.1111/cla.12137] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2015] [Indexed: 11/26/2022] Open
Affiliation(s)
- Yan‐hui Wang
- Institute of Entomology College of Life Sciences Nankai University 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Ying Cui
- Tianjin State Key Laboratory of Modern Chinese Medicine Tianjin University of Traditional Chinese Medicine Tianjin 300193 China
| | - Dávid Rédei
- Institute of Entomology College of Life Sciences Nankai University 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Petr Baňař
- Department of Entomology Moravian Museum Hviezdoslavova 29 CZ‐627 00 Czech Republic
| | - Qiang Xie
- Institute of Entomology College of Life Sciences Nankai University 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Pavel Štys
- Faculty of Science Department of Zoology Charles University in Prague Viničná 7 CZ‐128 44 Praha 2 Czech Republic
| | - Jakob Damgaard
- Natural History Museum of Denmark Universitetsparken 15 2100 Copenhagen Ø Denmark
| | - Ping‐ping Chen
- Netherlands Centre of Biodiversity Naturalis 2300 RA Leiden Netherlands
| | - Wen‐bo Yi
- Institute of Entomology College of Life Sciences Nankai University 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Ying Wang
- Institute of Entomology College of Life Sciences Nankai University 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Kai Dang
- Institute of Entomology College of Life Sciences Nankai University 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Chuan‐ren Li
- College of Agriculture Yangtze University Jingzhou Hubei 434025 China
| | - Wen‐jun Bu
- Institute of Entomology College of Life Sciences Nankai University 94 Weijin Road, Nankai District Tianjin 300071 China
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19
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Yuan ML, Zhang QL, Guo ZL, Wang J, Shen YY. Comparative mitogenomic analysis of the superfamily Pentatomoidea (Insecta: Hemiptera: Heteroptera) and phylogenetic implications. BMC Genomics 2015; 16:460. [PMID: 26076960 PMCID: PMC4469028 DOI: 10.1186/s12864-015-1679-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 06/01/2015] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Insect mitochondrial genomes (mitogenomes) are the most extensively used genetic marker for evolutionary and population genetics studies of insects. The Pentatomoidea superfamily is economically important and the largest superfamily within Pentatomomorpha with over 7,000 species. To better understand the diversity and evolution of pentatomoid species, we sequenced and annotated the mitogenomes of Eurydema gebleri and Rubiconia intermedia, and present the first comparative analysis of the 11 pentatomoid mitogenomes that have been sequenced to date. RESULTS We obtained the complete mitogenome of Eurydema gebleri (16,005 bp) and a nearly complete mitogenome of Rubiconia intermedia (14,967 bp). Our results show that gene content, gene arrangement, base composition, codon usage, and mitochondrial transcription termination factor sequences are highly conserved in pentatomoid species, especially for species in the same family. Evolutionary rate analyses of protein-coding genes reveal that the highest and lowest rates are found in atp8 and cox1 and distinctive evolutionary patterns are significantly correlated with the G + C content of genes. We inferred the secondary structures for two rRNA genes for eleven pentatomoid species, and identify some conserved motifs of RNA structures in Pentatomidea. All tRNA genes in pentatomoid mitogenomes have a canonical cloverleaf secondary structure, except for two tRNAs (trnS1 and trnV) which appear to lack the dihydrouridine arm. Regions that are A + T-rich have several distinct characteristics (e.g. size variation and abundant tandem repeats), and have potential as species or population level molecular markers. Phylogenetic analyses based on mitogenomic data strongly support the monophyly of Pentatomoidea, and the estimated phylogenetic relationships are: (Urostylididae + (Plataspidae + (Pentatomidae + (Cydnidae + (Dinidoridae + Tessaratomidae))))). CONCLUSIONS This comparative mitogenomic analysis sheds light on the architecture and evolution of mitogenomes in the superfamily Pentatomoidea. Mitogenomes can be effectively used to resolve phylogenetic relationships of pentatomomorphan insects at various taxonomic levels. Sequencing more mitogenomes at various taxonomic levels, particularly from closely related species, will improve the annotation accuracy of mitochondrial genes, as well as greatly enhance our understanding of mitogenomic evolution and phylogenetic relationships in pentatomoids.
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Affiliation(s)
- Ming-Long Yuan
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, 730020, People's Republic of China.
| | - Qi-Lin Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, 730020, People's Republic of China.
| | - Zhong-Long Guo
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, 730020, People's Republic of China.
| | - Juan Wang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, 730020, People's Republic of China.
| | - Yu-Ying Shen
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, 730020, People's Republic of China.
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20
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Que S, Yu L, Xin T, Zou Z, Hu L, Xia B. Complete mitochondrial genome of Cacopsylla coccinae (Hemiptera: Psyllidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3169-70. [PMID: 25693718 DOI: 10.3109/19401736.2015.1007319] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, the first complete mitochondrial genome (mitogenome) sequence of Cacopsylla coccinae was determined by long PCR and primer walking methods. The complete mitochondrial genome is 14,832 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes as well as a control region. The overall base composition of the genome is A (38.16%), T (33.88%), C (17.95%) and G (10.01%). Stop codon was incomplete for coxII gene and ND1 gene. The gene overlaps were suggested between 13 pairs of the contiguous genes in C. coccinae. The mitogenome would contribute to resolving phylogenetic position and interrelationships of Cacopsylla.
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Affiliation(s)
- Shengquan Que
- a School of Life Sciences, Nanchang University , Nanchang , China .,b Center for Watershed Ecology, Institute of Life Sciences, Nanchang University , Nanchang , China , and
| | - Liping Yu
- a School of Life Sciences, Nanchang University , Nanchang , China
| | - Tianrong Xin
- a School of Life Sciences, Nanchang University , Nanchang , China .,b Center for Watershed Ecology, Institute of Life Sciences, Nanchang University , Nanchang , China , and
| | - Zhiwen Zou
- a School of Life Sciences, Nanchang University , Nanchang , China
| | - Liangxiong Hu
- c School of Life Sciences, Jiujiang University , Jiujiang , China
| | - Bin Xia
- a School of Life Sciences, Nanchang University , Nanchang , China .,b Center for Watershed Ecology, Institute of Life Sciences, Nanchang University , Nanchang , China , and
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21
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Li T, Hua J, Wright AM, Cui Y, Xie Q, Bu W, Hillis DM. Long-branch attraction and the phylogeny of true water bugs (Hemiptera: Nepomorpha) as estimated from mitochondrial genomes. BMC Evol Biol 2014; 14:99. [PMID: 24884699 PMCID: PMC4101842 DOI: 10.1186/1471-2148-14-99] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 04/29/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most previous studies of morphological and molecular data have consistently supported the monophyly of the true water bugs (Hemiptera: Nepomorpha). An exception is a recent study by Hua et al. (BMC Evol Biol 9: 134, 2009) based on nine nepomorphan mitochondrial genomes. In the analysis of Hua et al. (BMC Evol Biol 9: 134, 2009), the water bugs in the group Pleoidea formed the sister group to a clade that consisted of Nepomorpha (the remaining true water bugs) + Leptopodomorpha (shore bugs) + Cimicomorpha (assassin bugs and relatives) + Pentatomomorpha (stink bugs and relatives), thereby suggesting that fully aquatic hemipterans evolved independently at least twice. Based on these results, Hua et al. (BMC Evol Biol 9: 134, 2009) elevated the Pleoidea to a new infraorder, the Plemorpha. RESULTS Our reanalysis suggests that the lack of support for the monophyly of the true water bugs (including Pleoidea) by Hua et al. (BMC Evol Biol 9: 134, 2009) likely resulted from inadequate taxon sampling. In particular, long-branch attraction (LBA) between the distant outgroup taxa and Pleoidea, as well as LBA among taxa in the ingroup, made Nepomorpha appear to be polyphyletic. We used three complementary strategies to test and alleviate the effects of LBA: (1) the removal of distant outgroups from the analysis; (2) the addition of closely related outgroups; and (3) the addition of a mitochondrial genome from a second family of Pleoidea. We also performed likelihood-ratio tests to examine the support for monophyly of Nepomorpha with different combinations of taxa included in the analysis. Furthermore, we found that specimens of Helotrephes sp. were misidentified as Paraplea frontalis (Fieber, 1844) by Hua et al. (BMC Evol Biol 9: 134, 2009). CONCLUSIONS All analyses that included the addition of more taxa significantly and consistently supported the placement of Pleoidea within the Nepomorpha (i.e., supported the monophyly of the traditional true water bugs). Our analyses further support a close relationship between Notonectoidea and Pleoidea within Nepomorpha, and the superfamilies Nepoidea, Ochteroidea, Naucoroidea, and Pleoidea are resolved as monophyletic in all trees with strong support. Our results also confirmed that monophyly of Nepomorpha clearly is not refuted by the mitochondrial genome data.
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Affiliation(s)
- Teng Li
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Jimeng Hua
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - April M Wright
- Department of Integrative Biology, University of Texas at Austin, Austin TX 78712, USA
| | - Ying Cui
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Qiang Xie
- 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
| | - David M Hillis
- Department of Integrative Biology, University of Texas at Austin, Austin TX 78712, USA
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