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Wei Z, Shi A. The complete mitochondrial genomes of four lagriine species (Coleoptera, Tenebrionidae) and phylogenetic relationships within Tenebrionidae. PeerJ 2023; 11:e15483. [PMID: 37283890 PMCID: PMC10241167 DOI: 10.7717/peerj.15483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 05/09/2023] [Indexed: 06/08/2023] Open
Abstract
It is common to use whole mitochondrial genomes to analyze phylogenetic relationships among insects. In this study, seven mitogenomes of Tenebrionidae are newly sequenced and annotated. Among them, four species (Cerogira janthinipennis (Fairmaire, 1886), Luprops yunnanus (Fairmaire, 1887), Anaedus unidentasus Wang & Ren, 2007, and Spinolyprops cribricollis Schawaller, 2012) represent the subfamily Lagriinae. In this subfamily, the mitogenomes of the tribes Goniaderini (A. unidentasus) and Lupropini (L. yunnanus and S. cribricollis) were first reported; they were found to be 15,328-16,437 bp in length and encode 37 typical mitochondrial genes (13 PCGs, 2 rRNAs, 22 tRNAs, and a single noncoding control region). Most protein-coding genes in these mitogenomes have typical ATN start codons and TAR or an incomplete stop codon T-. In these four lagriine species, F, L2, I, and N are the most frequently used amino acids. In the 13 PCGs, the gene atp8 (Pi = 0.978) was the most diverse nucleotide, while cox1 was the most conserved gene with the lowest value (Pi = 0.211). The phylogenetic results suggest that Pimelinae, Lagriinae, Blaptinae, Stenochiinae, and Alleculinae are monophyletic, Diaperinae is paraphyletic, and Tenebrioninae appears polyphyletic. In Lagriinae, the tribe Lupropini appears paraphyletic because Spinolyprops is clustered with Anaedus in Goniaderini. These mitogenomic data provide important molecular data for the phylogeny of Tenebrionidae.
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Wei Z, Huang X, Shi A. First mitochondrial genome of subfamily Julodinae (Coleoptera, Buprestidae) with its phylogenetic implications. Zookeys 2023; 1139:165-182. [PMID: 36761279 PMCID: PMC9860506 DOI: 10.3897/zookeys.1139.96216] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
Complete mitochondrial genomes of three species of the family Buprestidae were sequenced, annotated, and analyzed in this study. To explore the mitogenome features of the subfamily Julodinae and verify its phylogenetic position, the complete mitogenome of Julodisvariolaris was sequenced and annotated. The complete mitogenomes of Ptosimachinensis and Chalcophorajaponica were also provided for the phylogenetic analyses within Buprestidae. Compared to the known mitogenomes of Buprestidae species varied from 15,499 bp to 16,771 bp in length, three newly sequenced mitogenomes were medium length (15,759-16,227 bp). These mitogenomes were encoded 37 typical mitochondrial genes. Among the three studied mitogenomes, Leu2 (L2), Ser2 (S2), and Pro (P) were the three most frequently encoded amino acids. Within the Buprestidae, the heterogeneity in sequence divergences of Agrilinae was highest, whereas the sequence homogeneity of Chrysochroinae was highest. Moreover, phylogenetic analyses were performed based on nucleotide matrix (13 PCGs + 2 rRNAs) among the available sequenced species of Buprestidae using Bayesian Inference and Maximum Likelihood methods. The results showed that the Julodinae was closely related to the subfamily Polycestinae. Meanwhile, the genera Melanophila, Dicerca, and Coomaniella were included in Buprestinae, which was inconsistent with the current classification system of Buprestidae. These results could contribute to further studies on genetic diversity and phylogeny of Buprestidae.
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Affiliation(s)
- Zhonghua Wei
- The Key Laboratory of Southwest China Wildlife Resources Conservation of the Ministry of Education, College of Life Sciences, China West Normal University, 637009, Nanchong, Sichuan Province, ChinaChina West Normal UniversityNanchongChina
| | - Xuyan Huang
- The Key Laboratory of Southwest China Wildlife Resources Conservation of the Ministry of Education, College of Life Sciences, China West Normal University, 637009, Nanchong, Sichuan Province, ChinaChina West Normal UniversityNanchongChina
| | - Aimin Shi
- The Key Laboratory of Southwest China Wildlife Resources Conservation of the Ministry of Education, College of Life Sciences, China West Normal University, 637009, Nanchong, Sichuan Province, ChinaChina West Normal UniversityNanchongChina
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Wei F, Huang W, Fang L, He B, Zhao Y, Zhang Y, Shu Z, Su C, Hao J. Spatio-Temporal Evolutionary Patterns of the Pieridae Butterflies (Lepidoptera: Papilionoidea) Inferred from Mitogenomic Data. Genes (Basel) 2022; 14:72. [PMID: 36672814 PMCID: PMC9858963 DOI: 10.3390/genes14010072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/17/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Pieridae is one of the largest and almost cosmopolitan groups of butterflies, which plays an important role in natural ecosystems; however, to date, its phylogeny and evolutionary history have not been fully resolved. In this study, we obtained the complete or nearly complete mitochondrial genomes of 100 pierid taxa (six newly sequenced, sixty extracted from the whole-genome data, and thirty-four directly available from GenBank). At the same time, for the first time, we conducted comparative mitogenomic and phylogenetic analyses based on these mitogenomic data, to further clarify their spatio-temporal evolutionary patterns. Comparative mitogenomic analysis showed that, except for cox2, the GC content of each of the 13 protein-coding genes (PCGs) in the rapidly diverging subfamily Pierinae was higher than in its sister group Coliadinae. Moreover, the dN/dS values of nine genes (atp6, atp8, cox1, cox3, cob, nad1, nad3, nad5, and nad6) in Pierinae were also relatively higher than those in its sister group, Coliadinae. Phylogenetic analysis showed that all the resultant phylogenetic trees were generally in agreement with those of previous studies. The Pierinae family contained six clades in total with the relationship of (Leptosiaini + (((Nepheroniini + Arthocharidini) + Teracolini) + (Pierini + Elodini))). The Pieridae originated in the Palearctic region approximately 72.3 million years ago in the late Cretaceous, and the subfamily Pierinae diverged from this family around 57.9 million years ago in the Oriental region, shortly after the K-Pg mass extinction event; in addition, the spatio-temporal evolutionary patterns of Pierinae were closely correlated with geological events and environmental changes, as well as the host plant coevolutionary scenario in Earth's history. However, some incongruencies were observed between our results and those of previous studies in terms of shallow phylogenies for a few taxa, and should be further investigated.
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Affiliation(s)
- Fanyu Wei
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Wenxiang Huang
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Lin Fang
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Bo He
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Youjie Zhao
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Yingming Zhang
- Guangdong Chebaling National Nature Reserve Administration Bureau, Shaoguan 512500, China
| | - Zufei Shu
- Guangdong Chebaling National Nature Reserve Administration Bureau, Shaoguan 512500, China
| | - Chengyong Su
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jiasheng Hao
- College of Life Sciences, Anhui Normal University, Wuhu 241000, 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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Wei Z. The complete mitochondrial genomes of five Agrilinae (Coleoptera, Buprestidae) species and phylogenetic implications. Zookeys 2022; 1092:195-212. [PMID: 35586288 PMCID: PMC9007928 DOI: 10.3897/zookeys.1092.80993] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/18/2022] [Indexed: 11/22/2022] Open
Abstract
Five complete mitochondrial genomes of five species from the subfamily Agrilinae were sequenced and annotated, including Coraebusdiminutus Gebhardt, 1928 (15,499 bp), Coraebuscloueti Théry, 1893 (15,514 bp), Meliboeussinae Obenberger, 1935 (16,108 bp), Agrilussichuanus Jendek, 2011 (16,521 bp), and Sambusfemoralis Kerremans, 1892 (15,367 bp). These mitogenomes ranged from 15,367 to 16,521 bp in length and encoded 37 typical mitochondrial genes: 13 protein-coding genes (13 PCGs), 2 ribosomal RNA genes (2 rRNAs), 22 transfer RNA genes (22 tRNAs), and a control region (CR). Most of PCGs had typical ATN start codons and terminated with TAR or an incomplete stop codon T–. Among these five mitogenomes, Leu2, Ile, Phe, Ser2, Gly, Met, and Val were the seven most frequently encoded amino acids. Interestingly, in A.sichuanus, a 774 bp insertion was present at trnW and trnC junction, which is unusual in Buprestidae. Additionally, phylogenetic analyses were performed based on three kinds of nucleotide matrixes (13 PCGs, 2 rRNAs, and 13 PCGs + 2 rRNAs) using Bayesian inference and maximum-likelihood methods. The results showed that the clade of Buprestidae was well separated from outgroups and all Agrilinae species formed to a single highly supported clade. The tribe Coraebini was polyphyletic, as the genus Meliboeus (Coraebini) clustered with the genus Trachys (Tracheini). The rRNA genes had important impact for the tree topology of Agrilinae. Compared to the tribes Tracheini and Agrilini, the tribe Coraebini is a younger group.
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Jiang Y, Li HX, Yu XF, Yang MF. Comparative Analysis of Mitochondrial Genomes among Twelve Sibling Species of the Genus Atkinsoniella Distant, 1908 (Hemiptera: Cicadellidae: Cicadellinae) and Phylogenetic Analysis. INSECTS 2022; 13:insects13030254. [PMID: 35323552 PMCID: PMC8953490 DOI: 10.3390/insects13030254] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/25/2022] [Accepted: 03/01/2022] [Indexed: 02/04/2023]
Abstract
Simple Summary Atkinsoniella is a large genus of 98 species across the world and 88 species recorded in China within the globally distributed subfamily Cicadellinae, which is phytophagous, and some of which have been reported as important agricultural pests. Some Atkinsoniella species are very similar in morphological characteristics, making accurate identification at species level confusing. To provide further evidence toward understanding the relationships within the genus Atkinsoniella and subfamily Cicadellinae, mitogenomes of 12 Atkinsoniella sibling species were obtained and annotated. Their characteristics were comparatively analyzed. In addition, the comprehensive phylogenetic relationship within the subfamily Cicadellinae was determined based on three mitochondrial datasets using both the maximum-likelihood (ML) and Bayesian inference (BI) methods. The results suggested that the genus Atkinsoniella was recovered as a monophyletic group. The branches of the 12 newly sequenced species were clearly separated, with most nodes receiving strong support in all analyses, indicating that mitogenomics is an effective method for identifying closely related species and understanding their phylogenetic and evolutionary relationships. Abstract The herbivorous leafhopper genus Atkinsoniella Distant, 1908 (Hemiptera: Cicadellidae: Cicadellinae), a large genus of subfamily Cicadellinae, consists of 98 valid species worldwide and 88 species recorded in China. Some species of the genus are very similar in morphological characteristics, so they are difficult to identify accurately. In this study, 12 mitochondrial genomes of Atkinsoniella species with similar morphological characteristics were first obtained through high-throughput sequencing, which featured a typical circular molecule of 15,034–15,988 bp in length. The arrangement and orientation of 37 genes were identical to those of typical Cicadellidae mitogenomes. The phylogenetic relationship within the subfamily Cicadellinae was reconstructed using maximum-likelihood (ML) and Bayesian inference (BI) methods based on three concatenated datasets. The topological structures of the six obtained phylogenetic trees were highly consistent. The results suggested that Atkinsoniella was recovered as a monophyletic group and emerged as a sister group with the monophyletic clade of Bothrogonia, Paracrocampsa (part), and Draeculacephala (part). The branches of the 12 newly sequenced species were clearly separated, with most nodes receiving strong support in all analyses. In addition, the key to the 12 Atkinsoniella species was provided to identify species according to morphological characteristics. This study further promotes research on the classification, genetics, evolution, and phylogeny of the genus Atkinsoniella and subfamily Cicadellinae.
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Affiliation(s)
- Yan Jiang
- Institute of Entomology, Guizhou University, Guiyang 550025, China;
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang 550025, China; (H.-X.L.); (X.-F.Y.)
| | - Hao-Xi Li
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang 550025, China; (H.-X.L.); (X.-F.Y.)
- College of Tobacco Sciences, Guizhou University, Guiyang 550025, China
| | - Xiao-Fei Yu
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang 550025, China; (H.-X.L.); (X.-F.Y.)
- College of Tobacco Sciences, Guizhou University, Guiyang 550025, China
| | - Mao-Fa Yang
- Institute of Entomology, Guizhou University, Guiyang 550025, China;
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang 550025, China; (H.-X.L.); (X.-F.Y.)
- College of Tobacco Sciences, Guizhou University, Guiyang 550025, China
- Correspondence: ; Tel.: +86-139-8407-3566
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Dong X, Yi W, Zheng C, Zhu X, Wang S, Xue H, Ye Z, Bu W. Species delimitation of rice seed bugs complex: Insights from mitochondrial genomes and ddRAD‐seq data. ZOOL SCR 2021. [DOI: 10.1111/zsc.12523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xue Dong
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Wenbo Yi
- Department of Biology Xinzhou Teachers University Xinzhou China
| | - Chenguang Zheng
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Xiuxiu Zhu
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Shujing Wang
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Huaijun Xue
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Zhen Ye
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Wenjun Bu
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
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The Primary Complete Mitochondrial Genome of the Lappet Moth Brahmophthalma hearseyi (Lepidoptera: Brahmaeidae) and Related Phylogenetic Analysis. INSECTS 2021; 12:insects12110973. [PMID: 34821774 PMCID: PMC8620751 DOI: 10.3390/insects12110973] [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: 09/08/2021] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 12/04/2022]
Abstract
Simple Summary In this paper, the complete mitochondrial genome (mitogenome) of B. hearseyi was sequenced using long-PCR and primer-walking methods. The results indicated that the mitogenome is a typical circular molecule that is composed of 15,442 bp. Phylogenetic analysis showed that B. hearseyi is clustered into Brahmaeidae, and the phylogenetic relationships are (Brahmaeidae + Lasiocampidae) + (Bombycidae + (Sphingidae + Saturniidae)). This study provides the first mitogenomic resources for the Brahmaeidae. Abstract Background: Brahmophthalma hearseyi (Lepidoptera: Brahmaeidae) is widely distributed across China. Its larvae damage the leaves of many plants such as those belonging to the Oleaceae family, causing significant economic losses and seriously affecting the survival and reproduction of Cervus nippon; however, genetic data for this species are scarce. Methods: The complete mitochondrial genome (mitogenome) of B. hearseyi was sequenced using long-PCR and primer-walking methods. Phylogenetic analysis that was based on 13 PCGs and two rRNAs was carried out using the neighbor-joining and Bayesian interference methods. Results: The mitogenome is a typical circular molecule that is made up of 15,442 bp, which includes 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and an A + T-rich region (456 bp). All of the PCGs, except for COX1 and COX2, start with ATN codons. COX2 and ND5 use the incomplete termination codon T, and 11 other PCGs use the typical stop codon TAA. All tRNA genes, except for trnS1 and trnS2, display a typical cloverleaf structure; trnS1 lacks the “DHU” arm, whereas trnS2 exhibits two mismatched base pairs in the anticodon stem. Phylogenetic analysis showed that B. hearseyi is clustered into Brahmaeidae, and the phylogenetic relationships are (Brahmaeidae + Lasiocampidae) + (Bombycidae + (Sphingidae + Saturniidae)). Conclusions: This study provides the first mitogenomic resources for the Brahmaeidae.
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First complete mitogenomes of three mayflies in the genus Afronurus (Ephemeroptera: Heptageniidae) and their implications for phylogenetic reconstruction. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00729-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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10
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Li R, Ying X, Deng W, Rong W, Li X. Mitochondrial genomes of eight Scelimeninae species (Orthoptera) and their phylogenetic implications within Tetrigoidea. PeerJ 2021; 9:e10523. [PMID: 33604160 PMCID: PMC7863789 DOI: 10.7717/peerj.10523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 11/17/2020] [Indexed: 11/20/2022] Open
Abstract
Scelimeninae is a key member of the pygmy grasshopper community, and an important ecological indicator. No mitochondrial genomes of Scelimeninae have been reported to date, and the monophyly of Scelimeninae and its phylogenetic relationship within Tetrigidae is still unclear. We sequenced and analyzed eight nearly complete mitochondrial genomes representing eight genera of Scelimeninae. These mitogenomes ranged in size from 13,112 to 16,380 bp and the order of tRNA genes between COII and ATP8 was reversed compared with the ancestral order of insects. The protein-coding genes (PCGs) of tetrigid species mainly with the typical ATN codons and most terminated with complete (TAA or TAG) stop codons. Analyses of pairwise genetic distances showed that ATP8 was the least conserved gene within Tetrigidae, while COI was the most conserved. The longest intergenic spacer (IGS) region in the mitogenomes was always found between tRNASer(UCN) and ND1. Additionally, tandem repeat units were identified in the longest IGS of three mitogenomes. Maximum likelihood (ML) and Bayesian Inference (BI) analyses based on the two datasets supported the monophyly of Tetriginae. Scelimeninae was classified as a non-monophyletic subfamily.
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Affiliation(s)
- Ran Li
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoli Ying
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Weian Deng
- School of Chemistry and Bioengineering, Hechi University, Yizhou, China
| | - Wantao Rong
- School of Chemistry and Bioengineering, Hechi University, Yizhou, China
| | - Xiaodong Li
- School of Chemistry and Bioengineering, Hechi University, Yizhou, China
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Li R, Zhang W, Ma Z, Zhou C. Novel gene rearrangement pattern in the mitochondrial genomes of Torleya mikhaili and Cincticostella fusca (Ephemeroptera: Ephemerellidae). Int J Biol Macromol 2020; 165:3106-3114. [PMID: 33098898 DOI: 10.1016/j.ijbiomac.2020.10.124] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 10/23/2022]
Abstract
The mayfly family Ephemerellidae (Insecta: Ephemeroptera) is distributed around the world and has very high species diversity. However, its evolution pattern of mitogenome and phylogenetic relationships within Ephemeroptera remain unclear. In this study, the complete mitochondrial genomes (mitogenomes) of Torleya mikhaili (15,042 bp) and Cincticostella fusca (15,135 bp) were firstly determined and analyzed. Two ephemerellid mitogenomes shared similar gene organization with 37 typical genes as well as a putative control region. Compared with other reported mitogenomes of mayflies, the unique gene order (I'-CR-Q-M) was found in these two mitogenomes. Although the observed rearrangement pattern is novel within ephemeropteran mitogenomes, it could be explained presumably by the mechanisms of tandem duplication-random loss and recombination. The phylogenetic analyses using both Bayesian inference (BI) and maximum likelihood (ML) methods based on four nucleotide datasets placed three ephemerellid species together. Furthermore, the phylogenetic relationships of the three genera were recovered as ((Ephemerella + Cincticostella) + Torleya).
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Affiliation(s)
- Ran Li
- The Key Laboratory of Jiangsu Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, PR China
| | - Wei Zhang
- The Key Laboratory of Jiangsu Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, PR China
| | - Zhenxing Ma
- The Key Laboratory of Jiangsu Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, PR China
| | - Changfa Zhou
- The Key Laboratory of Jiangsu Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, PR China.
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Liu QN, Tang YY, Yang TT, Li YT, Yu XM. Phylogenetic relationships of Grapsoidea and insights into the higher phylogeny of Brachyuran. Genomics 2020; 113:429-439. [PMID: 32889043 DOI: 10.1016/j.ygeno.2020.08.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 08/10/2020] [Accepted: 08/27/2020] [Indexed: 10/23/2022]
Abstract
Decapoda is one of the most diverse crustacean orders, and has become an important research subject. However, the phylogenetic relationships among the main lineages of Decapoda remain uncertain, especially in the order Brachyura. Herein, we sequenced the whole mitochondrial genome of V. litterata and constructed a phylogenetic tree to understand its phylogenetic relationships with other species. The results showed that the mitochondrial genome of V. litterata was generally similar to mitogenomes of Metazoa reported in the literature, with a size of 16,247 bp, 37 genes, and a control region. Both AT-skew and GC-skew were negative, indicating more abundant Cs and Ts than Gs and As. The gene arrangement of V. litterata is identical to those of Eriocheir hepuensis, Cyclograpsus granulosus, Hemigrapsus sanguineus, Helicana wuana, and Helice tientsinensis but differs from the pancrustacean ground pattern and typical arrangement of Brachyuran crabs. Phylogenetic reconstruction showed that V. litterata belongs to the Varunidae.
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Affiliation(s)
- Qiu-Ning Liu
- School of Wetland, Yancheng Teachers University, Yancheng 224007, People's Republic of China; School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, People's Republic of China.
| | - Ying-Yu Tang
- School of Wetland, Yancheng Teachers University, Yancheng 224007, People's Republic of China
| | - Ting-Ting Yang
- School of Wetland, Yancheng Teachers University, Yancheng 224007, People's Republic of China
| | - Yue-Tian Li
- School of Wetland, Yancheng Teachers University, Yancheng 224007, People's Republic of China
| | - Xiao-Min Yu
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, People's Republic of China.
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Zhang S, Shen S, Peng J, Zhou X, Kong X, Ren P, Liu F, Han L, Zhan S, Huang Y, Zhang A, Zhang Z. Chromosome‐level genome assembly of an important pine defoliator,
Dendrolimus punctatus
(Lepidoptera; Lasiocampidae). Mol Ecol Resour 2020; 20:1023-1037. [DOI: 10.1111/1755-0998.13169] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 02/29/2020] [Accepted: 04/09/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Sufang Zhang
- Key Laboratory of Forest Protection of State Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection Chinese Academy of Forestry Beijing China
| | - Sifan Shen
- Key Laboratory of Forest Protection of State Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection Chinese Academy of Forestry Beijing China
| | - Jiong Peng
- Nextomics Biosciences Institute Wuhan China
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health College of Plant Protection China Agricultural University Beijing China
| | - Xiangbo Kong
- Key Laboratory of Forest Protection of State Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection Chinese Academy of Forestry Beijing China
| | | | - Fu Liu
- Key Laboratory of Forest Protection of State Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection Chinese Academy of Forestry Beijing China
| | | | - Shuai Zhan
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China
| | - Yongping Huang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China
| | - Aibing Zhang
- College of Life Sciences Capital Normal University Beijing China
| | - Zhen Zhang
- Key Laboratory of Forest Protection of State Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection Chinese Academy of Forestry Beijing China
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Han X, He H, Shen H, Tang J, Dong W, Shi Y, Wu S, Zhang F, Liang G. Comparative mitochondrial genome analysis of Dendrolimus houi (Lepidoptera: Lasiocampidae) and phylogenetic relationship among Lasiocampidae species. PLoS One 2020; 15:e0232527. [PMID: 32407393 PMCID: PMC7224488 DOI: 10.1371/journal.pone.0232527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 04/16/2020] [Indexed: 11/18/2022] Open
Abstract
Dendrolimus houi is one of the most common caterpillars infesting Gymnosperm trees, and widely distributed in several countries in Southeast Asia, and exists soley or coexists with several congeners and some Lasiocampidae species in various forest habitats. However, natural hybrids occasionally occur among some closely related species in the same habitat, and host preference, extreme climate stress, and geographic isolation probably lead to their uncertain taxonomic consensus. The mitochondrial DNA (mtDNA) of D. houi was extracted and sequenced by using high-throughput technology, and the mitogenome composition and characteristics were compared and analyzed of these species, then the phylogenetic relationship was constructed using the maximum likelihood method (ML) and the Bayesian method (BI) based on their 13 protein-coding genes (PCGs) dataset, which were combined and made available to download which were combined and made available to download among global Lasiocampidae species data. Mitogenome of D. houi was 15,373 bp in length, with 37 genes, including 13 PCGs, 22 tRNA genes (tRNAs) and 2 rRNA genes (rRNAs). The positions and sequences of genes were consistent with those of most known Lasiocampidae species. The nucleotide composition was highly A+T biased, accounting for ~80% of the whole mitogenome. All start codons of PCGs belonged to typical start codons ATN except for COI which used CGA, and most stop codons ended with standard TAA or TAG, while COI, COII, ND4 ended with incomplete T. Only tRNASer (AGN) lacked DHU arm, while the remainder formed a typical "clover-shaped" secondary structure. For Lasiocampidae species, their complete mitochondrial genomes ranged from 15,281 to 15,570 bp in length, and all first genes started from trnM in the same direction. And base composition was biased toward A and T. Finally, both two methods (ML and BI) separately revealed that the same phylogenetic relationship of D. spp. as ((((D. punctatus + D. tabulaeformis) + D. spectabilis) + D. superans) + (D. kikuchii of Hunan population + D. houi) as in previous research, but results were different in that D. kikuchii from a Yunnan population was included, indicating that different geographical populations of insects have differentiated. And the phylogenetic relationship among Lasiocampidae species was ((((Dendrolimus) + Kunugia) + Euthrix) + Trabala). This provides a better theoretical basis for Lasiocampidae evolution and classification for future research directions.
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Affiliation(s)
- Xiaohong Han
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Huan He
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Haiyan Shen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Jinhan Tang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Wanying Dong
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yufei Shi
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Songqing Wu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Feiping Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Guanghong Liang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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15
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Zhou N, Dong Y, Qiao P, Yang Z. Complete Mitogenomic Structure and Phylogenetic Implications of the Genus Ostrinia (Lepidoptera: Crambidae). INSECTS 2020; 11:E232. [PMID: 32272743 PMCID: PMC7240680 DOI: 10.3390/insects11040232] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 04/01/2020] [Accepted: 04/03/2020] [Indexed: 12/12/2022]
Abstract
To understand mitogenome characteristics and reveal phylogenetic relationships of the genus Ostrinia, including several notorious pests of great importance for crops, we sequenced the complete mitogenomes of four species: Ostrinia furnacalis (Guenée, 1854), Ostrinia nubilalis (Hübner, 1796), Ostrinia scapulalis (Walker, 1859) and Ostrinia zealis (Guenée, 1854). Results indicate that the four mitogenomes-O. furnacalis, O. nubilalis, O. scapulalis, and O. zealis-are 15,245, 15,248, 15,311, and 15,208 bp in size, respectively. All four mitogenomes are comprised of 37 encoded genes and a control region. All 13 protein-coding genes (PCGs) initiate with ATN and terminate with TAN, with the exception of cox1 that starts with CGA, and cox1, cox2, and nad5 that terminate with an incomplete codon T. All transfer RNA genes (tRNAs) present the typical clover-leaf secondary structure except for the trnS1 (AGN) gene. There are some conserved structural elements in the control region. Our analyses indicate that nad6 and atp6 exhibit higher evolution rates compared to other PCGs. Phylogenetic analyses based on mitogenomes using both maximum likelihood (ML) and Bayesian inference (BI) methods revealed the relationship (O. palustralis + (O. penitalis + (O. zealis + (O. furnacalis + (O. nubilalis + O. scapulalis))))) within Ostrinia.
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Affiliation(s)
- Nan Zhou
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Northwest A&F University, Yangling 712100, China
- Entomological Museum, College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Yanling Dong
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Northwest A&F University, Yangling 712100, China
- Entomological Museum, College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Pingping Qiao
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Northwest A&F University, Yangling 712100, China
- Entomological Museum, College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Zhaofu Yang
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Northwest A&F University, Yangling 712100, China
- Entomological Museum, College of Plant Protection, Northwest A&F University, Yangling 712100, China
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16
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Zhou Y, Liang Z, Wang S, Zhong H, Wang N, Liang B. A mitogenomic phylogeny of satyrid butterflies and complete mitochondrial genome of Oeneis urda (Lepidoptera: Nymphalidae: Satyrinae). Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1735272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Yan Zhou
- Co-Innovation Center for Sustainable Forestry in Southern China/College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Zhuoying Liang
- Co-Innovation Center for Sustainable Forestry in Southern China/College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Shaoquan Wang
- Co-Innovation Center for Sustainable Forestry in Southern China/College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Huahan Zhong
- Co-Innovation Center for Sustainable Forestry in Southern China/College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Ning Wang
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
| | - Bin Liang
- Hainan Academy of Forestry, Haikou, China
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17
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Wang S, Jiao N, Zhao L, Zhang M, Zhou P, Huang X, Hu F, Yang C, Shu Y, Li W, Zhang C, Tao M, Chen B, Ma M, Liu S. Evidence for the paternal mitochondrial DNA in the crucian carp-like fish lineage with hybrid origin. SCIENCE CHINA. LIFE SCIENCES 2020; 63:102-115. [PMID: 31728830 DOI: 10.1007/s11427-019-9528-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 08/11/2019] [Indexed: 01/05/2023]
Abstract
In terms of taxonomic status, common carp (Cyprinus carpio, Cyprininae) and crucian carp (Carassius auratus, Cyprininae) are different species; however, in this study, a newborn homodiploid crucian carp-like fish (2n=100) (2nNCRC) lineage (F1-F3) was established from the interspecific hybridization of female common carp (2n=100)×male blunt snout bream (Megalobrama amblycephala, Cultrinae, 2n=48). The phenotypes and genotypes of 2nNCRC differed from those of its parents but were closely related to those of the existing diploid crucian carp. We further sequenced the whole mitochondrial (mt) genomes of the 2nNCRC lineage from F1 to F3. The paternal mtDNA fragments were stably embedded in the mt-genomes of F1-F3 generations of 2nNCRC to form chimeric DNA fragments. Along with this chimeric process, numerous base sites of F1-F3 generations of 2nNCRC underwent mutations. Most of these mutation sites were consistent with the existing diploid crucian carp. Moreover, the mtDNA organization and nucleotide composition of 2nNCRC were more similar to those of the existing diploid crucian carp than those of the parents. The inheritable chimeric DNA fragments and mutant loci in the mt-genomes of different generations of 2nNCRC provided important evidence of the mtDNA change process in the newborn lineage derived from hybridization of different species. Our findings demonstrated for the first time that the paternal mtDNA were transmitted into the mt-genomes of homodiploid lineage, which provided new insights into the existence of paternal mtDNA in the mtDNA inheritance.
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Affiliation(s)
- Shi Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, China.,College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China
| | - Ni Jiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Lu Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Meiwen Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Pei Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Xuexue Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Fangzhou Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, China.,College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China
| | - Conghui Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yuqin Shu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Wuhui Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, China.,Key Laboratory of Tropical and Subtropical Fisheries Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Bo Chen
- College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China
| | - Ming Ma
- College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China. .,College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
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18
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Wang Q, Tang D, Guo H, Wang J, Xu X, Wang Z. Comparative mitochondrial genomic analysis of Macrophthalmus pacificus and insights into the phylogeny of the Ocypodoidea & Grapsoidea. Genomics 2020; 112:82-91. [DOI: 10.1016/j.ygeno.2019.12.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/12/2019] [Accepted: 12/17/2019] [Indexed: 01/24/2023]
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19
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Wang W, Huang Y, Bartlett CR, Zhou F, Meng R, Qin D. Characterization of the complete mitochondrial genomes of two species of the genus Aphaena Guérin-Méneville (Hemiptera: Fulgoridae) and its phylogenetic implications. Int J Biol Macromol 2019; 141:29-40. [PMID: 31470055 DOI: 10.1016/j.ijbiomac.2019.08.222] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/19/2019] [Accepted: 08/26/2019] [Indexed: 12/27/2022]
Abstract
The complete mitochondrial genomes (mitogenomes) of Aphaena (Callidepsa) amabilis and Aphaena (Aphaena) discolor nigrotibiata were sequenced. The mitogenomes of these two species are 16,237 bp and 16,116 bp in length with an A + T content of 77.9% and 77.0%, respectively. Each contains 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a control region (A + T-rich region). All PCGs initiate with the standard start codon of ATN and terminate with the complete stop codon of TAA or TAG except for atp6, where nad1 ends with an incomplete T codon. All tRNAs have the typical clover-leaf structure except for trnS1 and trnV which have a reduced DHU arm. Moreover, these two mitogenomes have trnL2, trnR and trnT with an unpaired base in the acceptor stem. The putative A + T-rich region includes multiple types of tandem repeat regions. These phylogenetic analyses are reconstructed based on 13 protein-coding genes of 25 auchenorrhynchan mitogenomes, with both maximum likelihood and Bayesian analyses yielding robust identical phylogenetic trees. These results support a monophyletic Auchenorrhyncha and the relationship (Pyrops + (Lycorma + Aphaena)) within Fulgoridae.
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Affiliation(s)
- Wenqian Wang
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yixin Huang
- Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Charles R Bartlett
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, DE 19716, USA
| | - Fanmei Zhou
- Wuzhishan National Nature Reserve, Zhou Fanmei Photographic Art Gallery, Wuzhishan, Hainan 572200, China
| | - Rui Meng
- Post-Entry Quarantine Station for Tropical Plant, Haikou Customs District, Haikou, Hainan 570105, China
| | - Daozheng Qin
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi 712100, China.
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20
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Wang T, Zhang S, Pei T, Yu Z, Liu J. The Complete Mitochondrial Genome and Expression Profile of Mitochondrial Protein-Coding Genes in the Bisexual and Parthenogenetic Haemaphysalis longicornis. Front Physiol 2019; 10:982. [PMID: 31417433 PMCID: PMC6682753 DOI: 10.3389/fphys.2019.00982] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/15/2019] [Indexed: 11/13/2022] Open
Abstract
The tick Haemaphysalis longicornis is widely distributed in eastern Asia, New Zealand and Australia, and is well-known as a vector of multiple zoonotic pathogens. This species exhibits two reproductive strategies, bisexual and obligate parthenogenetic reproduction. Hence, in the current study, the complete mitochondrial genomes of the bisexual and parthenogenetic populations were assembled and analyzed, and the expression of the mitochondrial protein-coding genes was evaluated and compared between the two reproductive populations. The results indicated that the length of the mitochondrial genomes of the two reproductive populations is 14,694 and 14,693 bp in the bisexual and parthenogenetic populations, respectively. The AT content in the mitochondrial genome of the bisexual and obligate parthenogenetic population reached 77.22 and 77.34%, respectively. The phylogenetic tree was constructed combining 13 protein-coding genes, which showed that the genetic distance between the bisexual and parthenogenetic populations was less than that between the subspecies. The expression of the mitochondrial protein-coding genes was quantitatively analyzed at different feeding status for the bisexual and parthenogenetic populations, and the results showed significant differences in the expression patterns of these genes, suggesting that they might trigger specific energy utilization mechanisms due to their different reproductive strategies and environmental pressures.
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Affiliation(s)
- Tianhong Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Shiqi Zhang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Tingwei Pei
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Zhijun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
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21
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Qin J, Li J, Gao Q, Wilson JJ, Zhang AB. Mitochondrial phylogeny and comparative mitogenomics of closely related pine moth pests (Lepidoptera: Dendrolimus). PeerJ 2019; 7:e7317. [PMID: 31372319 PMCID: PMC6659665 DOI: 10.7717/peerj.7317] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/18/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Pine moths, Dendrolimus spp. (Lasiocampidae), are serious economic pests of conifer forests. Six closely related species (Dendrolimus punctatus, D. tabulaeformis, D. spectabilis, D. superans, D. houi, and D. kikuchii) occur in China and cause serious damage to coniferophyte. The complete mito genomes of Dendrolimus genus are significant to resolve the phylogenetic relationship and provide theoretical support in pest control. METHODS The complete mitogenomes of three species (D. superans, D. houi, and D. kikuchii) were sequenced based on PCR-amplified with universal primers, which were used to amplify initial fragments. Phylogenetic analyses were carried out with 78 complete mitogenomes of lepidopteran species from 10 superfamilies. RESULTS The complete mitochondrial genomes of these three species were 15,417, 15,381, and 15,377 bp in length, separately. The phylogenetic analyses produced consistent results for six Dendrolimus species based on complete mitogenomes, two major clades were formed, one containing D. spectabilis clustered with D. punctatus + D. tabulaeformis, and D. superans as the sister group to this three-taxon clade, the other containing D. kikuchii and D. houi. Comparative analyses of the congeneric mitochondrial genomes were performed, which showed that non-coding regions were more variable than the A+T rich region. The mitochondrial nucleotide diversity was more variable when compared within than among genus, and the concatenated tRNA region was the most conserved and the nd6 genes was the most variable.
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Affiliation(s)
- Jie Qin
- College of Life Sciences, Capital Normal University, Beijing, P. R. China
| | - Jing Li
- College of Life Sciences, Capital Normal University, Beijing, P. R. China
| | - Qiang Gao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, P. R. China
| | - John-James Wilson
- International College Beijing, China Agricultural University, Beijing, P. R. China
| | - Ai-bing Zhang
- College of Life Sciences, Capital Normal University, Beijing, P. R. China
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22
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He B, Su T, Niu Z, Zhou Z, Gu Z, Huang D. Characterization of mitochondrial genomes of three Andrena bees (Apoidea: Andrenidae) and insights into the phylogenetics. Int J Biol Macromol 2019; 127:118-125. [PMID: 30639593 DOI: 10.1016/j.ijbiomac.2019.01.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 01/08/2019] [Accepted: 01/08/2019] [Indexed: 10/27/2022]
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Su T, He B, Li K, Liang A. Comparative analysis of the mitochondrial genomes of oriental spittlebug trible Cosmoscartini: insights into the relationships among closely related taxa. BMC Genomics 2018; 19:961. [PMID: 30587118 PMCID: PMC6307326 DOI: 10.1186/s12864-018-5365-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 12/12/2018] [Indexed: 11/29/2022] Open
Abstract
Background Cosmoscartini (Hemiptera: Cercopoidea: Cercopidae) is a large and brightly colored Old World tropical tribe, currently containing over 310 phytophagous species (including some economically important pests of eucalyptus in China) in approximately 17 genera. However, very limited information of Cosmoscartini is available except for some scattered taxonomic studies. Even less is known about its phylogenetic relationship, especially among closely related genera or species. In this study, the detailed comparative genomic and phylogenetic analyses were performed on nine newly sequenced mitochondrial genomes (mitogenomes) of Cosmoscartini, with the purpose of exploring the taxonomic status of the previously defined genus Okiscarta and some closely related species within the genus Cosmoscarta. Results Mitogenomes of Cosmoscartini display similar genomic characters in terms of gene arrangement, nucleotide composition, codon usage and overlapping regions. However, there are also many differences in intergenic spacers, mismatches of tRNAs, and the control region. Additionally, the secondary structures of rRNAs within Cercopidae are inferred for the first time. Based on comparative genomic (especially for the substitution pattern of tRNA secondary structure) and phylogenetic analyses, the representative species of Okiscarta uchidae possesses similar structures with other Cosmoscarta species and is placed consistently in Cosmoscarta. Although Cosmoscarta bimacula is difficult to be distinguished from Cosmoscarta bispecularis by traditional morphological methods, evidence from mitogenomes highly support the relationships of (C. bimacula + Cosmoscarta rubroscutellata) + (C. bispecularis + Cosmoscarta sp.). Conclusions This study presents mitogenomes of nine Cosmoscartini species and represents the first detailed comparative genomic and phylogenetic analyses within Cercopidae. It is indicated that knowledge of mitogenomes can be effectively used to resolve phylogenetic relationships at low taxonomic levels. Sequencing more mitogenomes at various taxonomic levels will also improve our understanding of mitogenomic evolution and phylogeny in Cercopidae. Electronic supplementary material The online version of this article (10.1186/s12864-018-5365-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tianjuan Su
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bo He
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Kui Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Aiping Liang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Su T, Liang A. Comparative analysis of seven mitochondrial genomes of Phymatostetha (Hemiptera: Cercopidae) and phylogenetic implications. Int J Biol Macromol 2018; 125:1112-1117. [PMID: 30578900 DOI: 10.1016/j.ijbiomac.2018.12.174] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/18/2018] [Accepted: 12/19/2018] [Indexed: 11/25/2022]
Abstract
In this study, we present seven mitochondrial genomes (mitogenomes) of Phymatostetha. Each mitogenome contains the entire set of 37 genes, which arranged in the same order as the putative ancestral pattern of insects. The nucleotide composition of Phymatostetha mitogenomes is biased toward A/T, with rRNAs and PCG12 (i.e. the first and second codon positions of PCGs) exhibit the highest and lowest A + T content, respectively. Relative synonymous codon usage of PCGs also show that degenerate codons are biased to use more A/T than G/C. All tRNAs exhibit typical clover-leaf structure, with the exception of trnS1. Additionally, unpaired nucleotides are detected in trnS1 anticodon stem and trnR acceptor stem. Phylogenetic relationships, based on the dataset of 13 PCGs, 22tRNAs, and two rRNAs, are analyzed using both the Bayesian and maximum likelihood methods. Our results clearly revealed the systematic status of Phymatostetha species and robustly supported the monophyly of this genus, in which Phymatostetha semele is sister to other Phymatostetha species. It was demonstrated that mitogenome was an effective molecular marker to adequately resolve phylogeny at low taxonomic levels.
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Affiliation(s)
- Tianjuan Su
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Aiping Liang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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Su T, Liang A. Characterization of the complete mitochondrial genome of Phymatostetha huangshanensis (Hemiptera: Cercopidae) and phylogenetic analysis. Int J Biol Macromol 2018; 119:60-69. [DOI: 10.1016/j.ijbiomac.2018.07.135] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 07/17/2018] [Accepted: 07/20/2018] [Indexed: 11/25/2022]
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Li J, Zhu JL, Lou SD, Wang P, Zhang YS, Wang L, Yin RC, Zhang PP. The Complete Mitochondrial Genome of Coptotermes 'suzhouensis' (syn. Coptotermes formosanus) (Isoptera: Rhinotermitidae) and Molecular Phylogeny Analysis. JOURNAL OF INSECT SCIENCE (ONLINE) 2018; 18:4926003. [PMID: 29718488 PMCID: PMC5846291 DOI: 10.1093/jisesa/iey018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Indexed: 06/08/2023]
Abstract
Coptotermes suzhouensis (Isoptera: Rhinotermitidae) is a significant subterranean termite pest of wooden structures and is widely distributed in southeastern China. The complete mitochondrial DNA sequence of C. suzhouensis was analyzed in this study. The mitogenome was a circular molecule of 15,764 bp in length, which contained 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and an A+T-rich region with a gene arrangement typical of Isoptera mitogenomes. All PCGs were initiated by ATN codons and terminated by complete termination codons (TAA), except COX2, ND5, and Cytb, which ended with an incomplete termination codon T. All tRNAs displayed a typical clover-leaf structure, except for tRNASer(AGN), which did not contain the stem-loop structure in the DHU arm. The A+T content (69.23%) of the A+T-rich region (949 bp) was higher than that of the entire mitogenome (65.60%), and two different sets of repeat units (A+B) were distributed in this region. Comparison of complete mitogenome sequences with those of Coptotermes formosanus indicated that the two taxa have very high genetic similarity. Forty-one representative termite species were used to construct phylogenetic trees by maximum likelihood, maximum parsimony, and Bayesian inference methods. The phylogenetic analyses also strongly supported (BPP, MLBP, and MPBP = 100%) that all C. suzhouensis and C. formosanus samples gathered into one clade with genetic distances between 0.000 and 0.002. This study provides molecular evidence for a more robust phylogenetic position of C. suzhouensis and inferrs that C. suzhouensis was the synonymy of C. formosanus.
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Affiliation(s)
- Juan Li
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Jin-long Zhu
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Shi-di Lou
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Ping Wang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - You-sen Zhang
- Hefei Termite Control Institute, Hefei, Anhui, China
| | - Lin Wang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Ruo-chun Yin
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Ping-ping Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
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27
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Kim MJ, Jeong JS, Kim JS, Jeong SY, Kim I. Complete mitochondrial genome of the lappet moth, Kunugia undans (Lepidoptera: Lasiocampidae): genomic comparisons among macroheteroceran superfamilies. Genet Mol Biol 2017; 40:717-723. [PMID: 28767123 PMCID: PMC5596373 DOI: 10.1590/1678-4685-gmb-2016-0298] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 02/25/2017] [Indexed: 11/21/2022] Open
Abstract
The mitochondrial genome (mitogenome) characteristics of the monotypic Lasiocampoidea are largely unknown, because only limited number of mitogenomes is available from this superfamily. In this study, we sequenced the complete mitogenome of the lappet moth, Kunugia undans (Lepidoptera: Lasiocampidae) and compared it to those of Lasiocampoidea and macroheteroceran superfamilies (59 species in six superfamilies). The 15,570-bp K. undans genome had one additional trnR that was located between trnA and trnN loci and this feature was unique in Macroheterocera, including Lasiocampoidea. Considering that the two trnR copies are located in tandem with proper secondary structures and identical anticodons, a gene duplication event might be responsible for the presence of the two tRNAs. Nearly all macroheteroceran species, excluding Lasiocampoidea, have a spacer sequence (1-34 bp) at the trnS2 and ND1 junction, but most lasiocampid species, including K. undans, have an overlap at the trnS2 and ND1 junction, which represents a different genomic feature in Lasiocampoidea. Nevertheless, a TTAGTAT motif, which is typically detected in Macroheterocera at the trnS2 and ND1 junction, was also detected in all Lasiocampoidea. In summary, the general mitogenome characteristics of Lasiocampoidea did not differ greatly from the remaining macroheteroceran superfamilies, but it did exhibit some unique features.
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Affiliation(s)
- Min Jee Kim
- Department of Applied Biology, College of Agriculture & Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Jun Seong Jeong
- Department of Applied Biology, College of Agriculture & Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Jong Seok Kim
- Department of Applied Biology, College of Agriculture & Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Su Yeon Jeong
- Department of Applied Biology, College of Agriculture & Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Iksoo Kim
- Department of Applied Biology, College of Agriculture & Life Sciences, Chonnam National University, Gwangju, Republic of Korea
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Kapli P, Lutteropp S, Zhang J, Kobert K, Pavlidis P, Stamatakis A, Flouri T. Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinformatics 2017; 33:1630-1638. [PMID: 28108445 PMCID: PMC5447239 DOI: 10.1093/bioinformatics/btx025] [Citation(s) in RCA: 239] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 12/27/2016] [Accepted: 01/17/2017] [Indexed: 11/15/2022] Open
Abstract
MOTIVATION In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced "Poisson Tree Processes" (PTP) method is a phylogeny-aware approach that does not rely on such thresholds. Yet, two weaknesses of PTP impact its accuracy and practicality when applied to large datasets; it does not account for divergent intraspecific variation and is slow for a large number of sequences. RESULTS We introduce the multi-rate PTP (mPTP), an improved method that alleviates the theoretical and technical shortcomings of PTP. It incorporates different levels of intraspecific genetic diversity deriving from differences in either the evolutionary history or sampling of each species. Results on empirical data suggest that mPTP is superior to PTP and popular distance-based methods as it, consistently yields more accurate delimitations with respect to the taxonomy (i.e., identifies more taxonomic species, infers species numbers closer to the taxonomy). Moreover, mPTP does not require any similarity threshold as input. The novel dynamic programming algorithm attains a speedup of at least five orders of magnitude compared to PTP, allowing it to delimit species in large (meta-) barcoding data. In addition, Markov Chain Monte Carlo sampling provides a comprehensive evaluation of the inferred delimitation in just a few seconds for millions of steps, independently of tree size. AVAILABILITY AND IMPLEMENTATION mPTP is implemented in C and is available for download at http://github.com/Pas-Kapli/mptp under the GNU Affero 3 license. A web-service is available at http://mptp.h-its.org . CONTACT : paschalia.kapli@h-its.org or alexandros.stamatakis@h-its.org or tomas.flouri@h-its.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- P Kapli
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - S Lutteropp
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Department of Informatics, Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - J Zhang
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - K Kobert
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - P Pavlidis
- Foundation for Research and Technology, Hellas Institute of Computer Science GR, Heraklion, Crete, Greece
| | - A Stamatakis
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Department of Informatics, Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - T Flouri
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Department of Informatics, Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
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Yang CH, Yang PC, Zhang SF, Shi ZY, Kang L, Zhang AB. Identification, expression pattern, and feature analysis of cuticular protein genes in the pine moth Dendrolimus punctatus (Lepidoptera: Lasiocampidae). INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2017; 83:94-106. [PMID: 28284855 DOI: 10.1016/j.ibmb.2017.03.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 01/19/2017] [Accepted: 03/06/2017] [Indexed: 06/06/2023]
Abstract
Cuticular proteins (CPs) are vital components of the insects' cuticle that support movement and protect insect from adverse environmental conditions. The CPs exist in a large number and diversiform structures, thus, the accurate annotation is the first step to interpreting their roles in insect growth. The rapid development of sequencing technology has simplified the access to the information on protein sequences, especially for non-model species. Dendrolimus punctatus is a Lepidopteran defoliator, and its periodic outbreaks cause severe damage to the coniferous forests. The transcriptome of D. punctatus integrating the whole developmental periods are available for the potential investigation of CPs. In this study, we identified 216 CPs from D. punctatus, including 147 from CPR family, 4 from TWDL family, 3 from CPF/CPFL families, 22 from CPAP families, 8 low complexity proteins, 1 CPCPC and 31 from other CP families. The putative CPs were compared with homologs in other species such as Bombyx mori, Manduca sexta and Drosophila melanogaster. We further identified five co-orthologous groups have highly similar sequences of CRPs in nine lepidopteran species, which exclusively presented in RR-2 subfamily rather than RR-1. We inferred that in Lepidoptera the difference in RR-2 numbers was maintained by homologs in co-orthologous groups, coincided with observation in Drosophila and Anopheles that gene cluster was the model and source for the expansion of RR-2 genes. In combination with the variation of members in each CP family among different species, these results indicated the evolution of CPs was highly correlated to the adaptation of insect to environment. Furthermore, we compared the amino acid composition of the different types CPRs, and examined the expression patterns of CP genes in various developmental stages. The comprehensive overview of CPs from our study provides an insight into their evolution and the association between them and insect development.
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Affiliation(s)
- Cong-Hui Yang
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Peng-Cheng Yang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Su-Fang Zhang
- Key Laboratory of Forest Protection, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, State Forestry Administration, Beijing, 100091, China
| | - Zhi-Yong Shi
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Le Kang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China; State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ai-Bing Zhang
- College of Life Sciences, Capital Normal University, Beijing, 100048, China.
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Kononov A, Ustyantsev K, Wang B, Mastro VC, Fet V, Blinov A, Baranchikov Y. Genetic diversity among eight Dendrolimus species in Eurasia (Lepidoptera: Lasiocampidae) inferred from mitochondrial COI and COII, and nuclear ITS2 markers. BMC Genet 2016; 17:157. [PMID: 28105930 PMCID: PMC5249024 DOI: 10.1186/s12863-016-0463-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2024] Open
Abstract
Background Moths of genus Dendrolimus (Lepidoptera: Lasiocampidae) are among the major pests of coniferous forests worldwide. Taxonomy and nomenclature of this genus are not entirely established, and there are many species with a controversial taxonomic position. We present a comparative evolutionary analysis of the most economically important Dendrolimus species in Eurasia. Results Our analysis was based on the nucleotide sequences of COI and COII mitochondrial genes and ITS2 spacer of nuclear ribosomal genes. All known sequences were extracted from GenBank. Additional 112 new sequences were identified for 28 specimens of D. sibiricus, D. pini, and D. superans from five regions of Siberia and the Russian Far East to be able to compare the disparate data from all previous studies. In total, 528 sequences were used in phylogenetic analysis. Two clusters of closely related species in Dendrolimus were found. The first cluster includes D. pini, D. sibiricus, and D. superans; and the second, D. spectabilis, D. punctatus, and D. tabulaeformis. Species D. houi and D. kikuchii appear to be the most basal in the genus. Conclusion Genetic difference among the second cluster species is very low in contrast to the first cluster species. Phylogenetic position D. tabulaeformis as a subspecies was supported. It was found that D. sibiricus recently separated from D. superans. Integration of D. sibiricus mitochondrial DNA sequences and the spread of this species to the west of Eurasia have been established as the cause of the unjustified allocation of a new species: D. kilmez. Our study further clarifies taxonomic problems in the genus and gives more complete information on the genetic structure of D. pini, D. sibiricus, and D. superans. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0463-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander Kononov
- Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Science, 10 Prospekt Lavrentyeva, Novosibirsk, 630090, Russia.
| | - Kirill Ustyantsev
- Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Science, 10 Prospekt Lavrentyeva, Novosibirsk, 630090, Russia
| | - Baode Wang
- USDA-APHIS-PPQ CPHST, Otis Laboratory, Building 1398, Otis Air National Guard Base, Buzzards Bay, MA, 02542, USA
| | - Victor C Mastro
- USDA-APHIS-PPQ CPHST, Otis Laboratory, Building 1398, Otis Air National Guard Base, Buzzards Bay, MA, 02542, USA
| | - Victor Fet
- Department of Biological Sciences, Marshall University, 1601 5th Avenue, Huntington, WV, 25755, USA
| | - Alexander Blinov
- Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Science, 10 Prospekt Lavrentyeva, Novosibirsk, 630090, Russia
| | - Yuri Baranchikov
- V.N. Sukachev Institute of Forest, the Siberian Branch of the Russian Academy of Science, 50/28 Akademgorodok, Krasnoyarsk, 660036, Russia
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31
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Wu L, Xiong X, Wang X, Xin T, Wang J, Zou Z, Xia B. The complete mitochondrial genome of Trabala vishnou guttata (Lepidoptera: Lasiocampidae) and the related phylogenetic analyses. Genetica 2016; 144:675-688. [PMID: 27770241 DOI: 10.1007/s10709-016-9934-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 10/17/2016] [Indexed: 10/20/2022]
Abstract
The bluish yellow lappet moth, Trabala vishnou guttata is an extraordinarily important pest in China. The complete mitochondrial genome is sequenced and determined firstly, which is based on traditional PCR amplification and primer walking methods with a length of 15,281 bp, including 13 protein-coding (PCG) genes, 22 transfer RNA (rRNA) genes, two ribosomal RNA (tRNA) genes, and an A + T-rich region. The gene order and orientation of the T. vishnou guttata mitogenome were identical to the other sequenced Lasiocampidae species. The overall nucleotide composition of T. vishnou guttata is A (40.27 %), T (40.59 %), C (11.58 %) and G (7.56 %), respectively. All the PCGs initiate with the three orthodox start codons ATN except for coxI with CGA start codon. Three PCGs (coxI, coxII and nad4) used incomplete stop codon T, while the other 10 PCGs terminate with complete stop codon TAA. All tRNA genes have a typical clover-leaf structure except for the absence of a dihydrouridine arm in trnS (AGN). The length of A + T-rich region is 383 bp. Phylogeny is established to reveal the genetic relationship between T. vishnou guttata and other lepidopteran species based on 13 PCGs nucleotide sequences of the sequenced species (32 taxa) by Maximum likelihood and Bayesian methods. Phylogenetic analyses presents that T. vishnou guttata and its closely related species (Dendrolimus taxa) are clustered on Lasiocampidae group. It is a sister clade relationship between Lasiocampidae and other families in Bombycoidea with a bootstrap value of 83 % and a posterior probability of 0.75. This study supports that Lasiocampidae may be independent from Bombycoidea.
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Affiliation(s)
- Liuyu Wu
- College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Xiao Xiong
- College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Xuming Wang
- Plant Protection Unit, Dayu County, Ganzhou, 341500, China
| | - Tianrong Xin
- College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Jing Wang
- College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Zhiwen Zou
- College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Bin Xia
- College of Life Science, Nanchang University, Nanchang, 330031, China.
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32
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Transcriptome Characterization of Dendrolimus punctatus and Expression Profiles at Different Developmental Stages. PLoS One 2016; 11:e0161667. [PMID: 27560151 PMCID: PMC4999207 DOI: 10.1371/journal.pone.0161667] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 08/09/2016] [Indexed: 11/19/2022] Open
Abstract
The pine moth Dendrolimus punctatus (Walker) is a common insect pest that confers serious damage to conifer forests in south of China. Extensive physiology and ecology studies on D. punctatus have been carried out, but the lack of genetic information has limited our understanding of the molecular mechanisms behind its development and resistance. Using RNA-seq approach, we characterized the transcriptome of this pine moth and investigated its developmental expression profiles during egg, larval, pupal, and adult stages. A total of 107.6 million raw reads were generated that were assembled into 70,664 unigenes. More than 30% unigenes were annotated by searching for homology in protein databases. To better understand the process of metamorphosis, we pairwise compared four developmental phases and obtained 17,624 differential expression genes. Functional enrichment analysis of differentially expressed genes showed positive correlation with specific physiological activities of each stage, and these results were confirmed by qRT-PCR experiments. This study provides a valuable genomic resource of D. punctatus covering all its developmental stages, and will promote future studies on biological processes at the molecular level.
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33
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Zhang SF, Kong XB, Wang HB, Zhou G, Yu JX, Liu F, Zhang Z. Sensory and immune genes identification and analysis in a widely used parasitoid wasp Trichogramma dendrolimi (Hymenoptera: Trichogrammatidae). INSECT SCIENCE 2016; 23:417-429. [PMID: 26940718 DOI: 10.1111/1744-7917.12330] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/21/2016] [Indexed: 06/05/2023]
Abstract
Trichogramma dendrolimi Matsumura (Hymenoptera: Trichogrammatidae) is one of the preponderant egg parasitoids of Dendrolimus spp., which are important defoliators of coniferous forests. This parasitoid wasp has been widely released to control pine caterpillar and other lepidopteran pests, but its control efficiency needs to be improved. Sensory systems are crucial for T. dendrolimi to locate hosts, and immunity is probably involved after egg deposition in the host cavity; however, few reports have focused on the molecular mechanism of olfactory detection and survival of T. dendrolimi. It is necessary to identify these genes before further functional research is conducted. In this study, we assembled and analyzed the transcriptome of T. dendrolimi using next-generation sequencing technology. The sequencing and assembly resulted in 38 565 contigs with N50 of 3422 bp. Sequence comparison indicate that T. dendrolimi sequences are very similar to those of another parasitoid Nasonia vitripennis. Then the olfactory, vision, and immune-related gene families were identified, and phylogenetic analyses were performed with these genes from T. dendrolimi and other model insect species. Furthermore, phylogenetic tree with odorant binding proteins of T. dendrolimi and their host Dendrolimus was constructed to determine whether convergent evolution exists. These genes can be valid targets for further gene function research. The present study may help us to understand host location and survival mechanisms of T. dendrolimi and to use them more efficiently for pest control in the future.
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Affiliation(s)
- Su-Fang Zhang
- Key Laboratory of Forest Protection, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Xiang-Bo Kong
- Key Laboratory of Forest Protection, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Hong-Bin Wang
- Key Laboratory of Forest Protection, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Gang Zhou
- Hunan Academy of Forestry, Changsha, China
| | - Jin-Xiu Yu
- Hunan Academy of Forestry, Changsha, China
| | - Fu Liu
- Key Laboratory of Forest Protection, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Zhen Zhang
- Key Laboratory of Forest Protection, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
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Kim MJ, Kim JS, Kim SS, Kim SR, Kim I. Complete mitochondrial genome of the pine moth Dendrolimus spectabilis (Lepidoptera: Lasiocampidae). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:180-181. [PMID: 33644337 PMCID: PMC7871830 DOI: 10.1080/23802359.2016.1149789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We have sequenced the complete mitochondrial genome (mitogenome) of the pine moth Dendrolimus spectabilis Butler (Lepidoptera: Lasiocampidae), which has been a serious pest for the Japanese red pine (Pinus densiflora S. et Z.) in Korea. The 15 409 bp complete mitochondrial genome (mitogenome) of the species consists of a typical set of genes (13 protein-coding genes, 2 rRNA genes and 22 tRNA genes) and the A + T-rich region, with an arrangement typical of Ditrysia in Lepidoptera. The 320 bp long A + T-rich region of D. spectabilis contains the motif ATAGA near the 5′-end of the srRNA, with a 14 bp-long poly-T stretch – the ATTTA sequence – and a microsatellite-like sequence consisting of (TA)7, but lacks the poly-A stretch often found immediately upstream of tRNAMet in other Lepidoptera. A phylogenetic analysis using 13 protein-coding genes from Bombycoidea and Lasiocampoidea has shown that D. spectabilis was placed as a sister to the congeneric species group, D. tabulaeformis + D. punctatus.
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Affiliation(s)
- Min Jee Kim
- College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Jong Seok Kim
- College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Sung-Soo Kim
- Research Institute for East Asian Environment and Biology, Seoul, Republic of Korea
| | - Seong Ryul Kim
- Department of Agricultural Biology, National Academy of Agricultural Science, RDA, Wanju-gun, Korea
| | - Iksoo Kim
- College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
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35
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Díaz-Jaimes P, Bayona-Vásquez NJ, Adams DH, Uribe-Alcocer M. Complete mitochondrial DNA genome of bonnethead shark, Sphyrna tiburo, and phylogenetic relationships among main superorders of modern elasmobranchs. Meta Gene 2016; 7:48-55. [PMID: 27014583 PMCID: PMC4794228 DOI: 10.1016/j.mgene.2015.11.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 11/30/2022] Open
Abstract
Elasmobranchs are one of the most diverse groups in the marine realm represented by 18 orders, 55 families and about 1200 species reported, but also one of the most vulnerable to exploitation and to climate change. Phylogenetic relationships among main orders have been controversial since the emergence of the Hypnosqualean hypothesis by Shirai (1992) that considered batoids as a sister group of sharks. The use of the complete mitochondrial DNA (mtDNA) may shed light to further validate this hypothesis by increasing the number of informative characters. We report the mtDNA genome of the bonnethead shark Sphyrna tiburo, and compare it with mitogenomes of other 48 species to assess phylogenetic relationships. The mtDNA genome of S. tiburo, is quite similar in size to that of congeneric species but also similar to the reported mtDNA genome of other Carcharhinidae species. Like most vertebrate mitochondrial genomes, it contained 13 protein coding genes, two rRNA genes and 22 tRNA genes and the control region of 1086 bp (D-loop). The Bayesian analysis of the 49 mitogenomes supported the view that sharks and batoids are separate groups.
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Key Words
- ATP, Adenosine triphosphate
- Bonnethead
- CO, Cytochrome oxidase
- Cytb, Cytochrome B
- D-loop, Control region
- Hypnosqualea hypothesis
- ML, Maximum likelihood
- Mitogenome
- ND, Nicotine adenine dehydrogenase
- PCR, Polymerase chain reaction
- Phylogeny
- bp, Base pairs
- mt, Mitochondrial
- myr, Million years
- rRNA, Ribosomal RNA
- tRNA, Transference RNA
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Affiliation(s)
- Píndaro Díaz-Jaimes
- Laboratorio de Genética de Organismos Acuáticos, Instituto de
Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Apdo.
Postal 70-305, México D.F. 04510, Mexico
| | - Natalia J. Bayona-Vásquez
- Laboratorio de Genética de Organismos Acuáticos, Instituto de
Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Apdo.
Postal 70-305, México D.F. 04510, Mexico
| | - Douglas H. Adams
- Florida Fish and Wildlife Conservation Commission, Fish and
Wildlife Research Institute, 1220 Prospect Avenue, Suite 285, Melbourne, FL
32901, USA
| | - Manuel Uribe-Alcocer
- Laboratorio de Genética de Organismos Acuáticos, Instituto de
Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Apdo.
Postal 70-305, México D.F. 04510, Mexico
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