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Zhang D, Chen X, Yang J, Yi W, Xie Q, Yang H, Sweet MH, Bu W, Li T. Phylogenetic placement and comparative analysis of the mitochondrial genomes of Idiostoloidea (Hemiptera: Heteroptera). Ecol Evol 2024; 14:e11328. [PMID: 38698924 PMCID: PMC11063732 DOI: 10.1002/ece3.11328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 04/06/2024] [Accepted: 04/10/2024] [Indexed: 05/05/2024] Open
Abstract
The classification system and the higher level phylogenetic relationships of Pentatomomorpha, the second largest infraorder of Heteroptera (Insecta: Hemiptera), have been debated and remain controversial over decades. In particular, the placement and phylogenetic relationship of Idiostoloidea are not well resolved, which hampers a better understanding of the evolutionary history of Pentatomomorpha. In this study, for the first time, we reported the complete mitochondrial genome for two narrowly distributed families of Idiostoloidea (including Idiostolidae and Henicocoridae), respectively. The length of the mitochondrial genome of Monteithocoris hirsutus and Henicocoris sp. is 16,632 and 16,013 bp, respectively. The content of AT is ranging from 75.15% to 80.48%. The mitogenomic structure of Idiostoloidea is highly conservative and there are no gene arrangements. By using the Bayesian inference, maximum likelihood, and Bayesian site-heterogeneous mixture model, we inferred the phylogenetic relationships within Pentatomomorpha and estimated their divergence times based on concatenated mitogenomes and nuclear ribosomal genes. Our results support the classification system of six superfamilies within Pentatomomorpha and confirm the monophyletic groups of each superfamily, with the following phylogenetic relationships: (Aradoidea + (Pentatomoidea + (Idiostoloidea + (Coreoidea + (Pyrrhocoroidea + Lygaeoidea))))). Furthermore, estimated divergence times revealed that most pentatomomorphan superfamilies and families diverged during the Late Jurassic to Early Cretaceous, which coincides with the explosive radiation of angiosperms.
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Affiliation(s)
- Danli Zhang
- College of Biological Sciences and TechnologyTaiyuan Normal UniversityJinzhongChina
| | - XiaoYan Chen
- College of Biological Sciences and TechnologyTaiyuan Normal UniversityJinzhongChina
| | - Jingjing Yang
- College of Biological Sciences and TechnologyTaiyuan Normal UniversityJinzhongChina
| | - Wenbo Yi
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Qiang Xie
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - HuanHuan Yang
- School of BioengineeringQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Merrill H. Sweet
- Department of Entomology, Plant Pathology, and Weed ScienceNew Mexico State UniversityLas CrucesNew MexicoUSA
| | - Wenjun Bu
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Teng Li
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
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Zhang N, Wang J, Pu T, Li C, Song Y. Two new species of Erythroneurini (Hemiptera, Cicadellidae, Typhlocybinae) from southern China based on morphology and complete mitogenomes. PeerJ 2024; 12:e16853. [PMID: 38344292 PMCID: PMC10859084 DOI: 10.7717/peerj.16853] [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: 09/14/2023] [Accepted: 01/08/2024] [Indexed: 02/15/2024] Open
Abstract
Erythroneurine leafhoppers (Hemiptera, Cicadellidae, Typhlocybinae, Erythroneurini) are utilized to resolve the relationship between the four erythroneurine leafhopper (Hemiptera, Cicadellidae, Typhlocybinae, Erythroneurini): Arboridia (Arboridia) rongchangensis sp. nov., Thaia (Thaia) jiulongensis sp. nov., Mitjaevia bifurcata Luo, Song & Song, 2021 and Mitjaevia diana Luo, Song & Song, 2021, the two new species are described and illustrated. The mitochondrial gene sequences of these four species were determined to update the mitochondrial genome database of Erythroneurini. The mitochondrial genomes of four species shared high parallelism in nucleotide composition, base composition and gene order, comprising 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs) and an AT control region, which was consistent with majority of species in Cicadellidae; all genes revealed common trait of a positive AT skew and negative GC skew. The mitogenomes of four species were ultra-conservative in structure, and which isanalogous to that of others in size and A + T content. Phylogenetic trees based on the mitogenome data of these species and another 24 species were built employing the maximum likelihood and Bayesian inference methods. The results indicated that the four species belong to the tribe Erythroneurini, M. diana is the sister-group relationship of M. protuberanta + M. bifurcata. The two species Arboridia (Arboridia) rongchangensis sp. nov. and Thaia (Thaia) jiulongensis sp. nov. also have a relatively close genetic relationship with the genus Mitjaevia.
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Affiliation(s)
- Ni Zhang
- School of Karst Science, Guizhou Normal University, Guiyang, China
- State Engineering Technology Institute for Karst Desertification Control, Guizhou Normal University, Guiyang, China
| | - Jinqiu Wang
- School of Karst Science, Guizhou Normal University, Guiyang, China
- State Engineering Technology Institute for Karst Desertification Control, Guizhou Normal University, Guiyang, China
| | - Tianyi Pu
- School of Karst Science, Guizhou Normal University, Guiyang, China
- State Engineering Technology Institute for Karst Desertification Control, Guizhou Normal University, Guiyang, China
| | - Can Li
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region/Guizhou Provincial Engineering Research Center for Biological Resources Protection and Efficient Utilization of the Mountainous Region, Guiyang University, Guiyang, China
| | - Yuehua Song
- School of Karst Science, Guizhou Normal University, Guiyang, China
- State Engineering Technology Institute for Karst Desertification Control, Guizhou Normal University, Guiyang, China
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Zhang M, Chen Z, Zhou J, Zhao X, Chen Y, Sun Y, Liu Z, Gu W, Luo C, Fu X, Zhao X. An imported human case with the SARS-CoV-2 Omicron subvariant BA.2.75 in Yunnan Province, China. BIOSAFETY AND HEALTH 2022; 4:406-409. [PMID: 36320663 PMCID: PMC9613801 DOI: 10.1016/j.bsheal.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/17/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
The Omicron variants spread rapidly worldwide after being initially detected in South Africa in November 2021. It showed increased transmissibility and immune evasion with far more amino acid mutations in the spike (S) protein than the previously circulating variants of concern (VOCs). Notably, on 15 July 2022, we monitored the first VOC / Omicron subvariant BA.2.75 in China from an imported case. Moreover, nowadays, this subvariant still is predominant in India. It has nine additional mutations in the S protein compared to BA.2, three of which (W152R, G446S, and R493Q reversion) might contribute to higher transmissibility and immune escape. This subvariant could cause wider spread and pose a threat to the global situation. Our timely reporting and continuous genomic analysis are essential to fully elucidate the characteristics of the subvariant BA.2.75 in the future.
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Affiliation(s)
- Meiling Zhang
- Yunnan Center for Disease Control and Prevention, Kunming 650022, China,Corresponding authors: Yunnan Center for Disease Control and Prevention, Kunming 650022, China (M. Zhang and X. Fu); National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China (X. Zhao)
| | - Zhixiao Chen
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jienan Zhou
- Yunnan Center for Disease Control and Prevention, Kunming 650022, China
| | - Xiaonan Zhao
- Yunnan Center for Disease Control and Prevention, Kunming 650022, China
| | - Yaoyao Chen
- Yunnan Center for Disease Control and Prevention, Kunming 650022, China
| | - Yanhong Sun
- Yunnan Center for Disease Control and Prevention, Kunming 650022, China
| | - Zhaosheng Liu
- Yunnan Center for Disease Control and Prevention, Kunming 650022, China
| | - Wenpeng Gu
- Yunnan Center for Disease Control and Prevention, Kunming 650022, China
| | - Chunrui Luo
- Yunnan Center for Disease Control and Prevention, Kunming 650022, China
| | - Xiaoqing Fu
- Yunnan Center for Disease Control and Prevention, Kunming 650022, China,Corresponding authors: Yunnan Center for Disease Control and Prevention, Kunming 650022, China (M. Zhang and X. Fu); National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China (X. Zhao)
| | - Xiang Zhao
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China,Corresponding authors: Yunnan Center for Disease Control and Prevention, Kunming 650022, China (M. Zhang and X. Fu); National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China (X. Zhao)
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Chen X, Li C, Song Y. The complete mitochondrial genomes of two erythroneurine leafhoppers (Hemiptera, Cicadellidae, Typhlocybinae, Erythroneurini) with assessment of the phylogenetic status and relationships of tribes of Typhlocybinae. Zookeys 2021; 1037:137-159. [PMID: 34054318 PMCID: PMC8144164 DOI: 10.3897/zookeys.1037.63671] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/28/2021] [Indexed: 11/12/2022] Open
Abstract
The number and classification of tribes in the leafhopper subfamily Typhlocybinae are not yet fully clear, and molecular data has recently been used to help resolve the problem. In this study, the mitochondrial genomes of Mitjaeviashibingensis Chen, Song & Webb, 2020 and M.dworakowskae Chen, Song & Webb, 2020 of the tribe Erythroneurini (Cicadellidae, Typhlocybinae) were sequenced. Most protein-coding genes (PCGs) start with ATN and end with TAA or TAG, and the AT content of these three codons were found differ from previous results that show that the first codon has the highest incidence. Two rRNA genes are highly conserved, and the AT content in 16S is higher than that of 12S. The nucleotide diversity and genetic distance among 13 PCGs of the four tribes from Typhlocybinae show that Empoascini nucleotide diversity is significantly less than in the other three tribes, and have the largest distance from the others, while Typhlocybini and Zyginellini have the smallest distance, indicating that the relationship between the two is the closest. The nad2, nad4, nad4L, and nad5 genes have greater nucleotide diversity, showing potential for use as the main markers for species identification. The phylogenetic analysis yielded a well-supported topology with most branches receiving maximum support and a few branches pertaining to relationships within Zyginellini and Typhlocybini receiving lower support. The species of these two tribes are intertwined, and it was impossible to resolve them into separate branches. In addition, the tribes Empoascini and Erythroneurini were recovered as monophyletic, and Alebrini was placed at the base of the tree as the most primitive. These results are broadly in line with other molecular phylogenetical studies which differ from traditional morphological classification.
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Affiliation(s)
- Xiaoxiao Chen
- School of Karst Science, Guizhou Normal University/ State Key Laboratory Cultivation Base for Guizhou Karst Mountain Ecology Environment of China, Guiyang, Guizhou 550001, China Guizhou Normal University Guiyang China
| | - Can Li
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Guiyang University, Guiyang, Guizhou 550001, China Guiyang University Guiyang China
| | - Yuehua Song
- School of Karst Science, Guizhou Normal University/ State Key Laboratory Cultivation Base for Guizhou Karst Mountain Ecology Environment of China, Guiyang, Guizhou 550001, China Guizhou Normal University Guiyang China
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Chen X, Yuan Z, Li C, Dietrich CH, Song Y. Structural features and phylogenetic implications of Cicadellidae subfamily and two new mitogenomes leafhoppers. PLoS One 2021; 16:e0251207. [PMID: 33989310 PMCID: PMC8121325 DOI: 10.1371/journal.pone.0251207] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/21/2021] [Indexed: 11/19/2022] Open
Abstract
Complete mitochondrial genome sequences facilitate species identification and analyses of phylogenetic relationships. However, the available data are limited to the diverse and widespread insect family Cicadellidae. This study analyzes and summarizes the complete mitochondrial genome structure characteristics of 11 leafhopper subfamilies and two newly sequenced Typhlocybinae species, Empoascanara wengangensis and E. gracilis. Moreover, using 13PCGs and rRNA data to analyze the nucleotide diversity, evolution rate, and the phylogenetic relationship between the subfamilies of 56 species, verifying the taxonomic status analysis of E. wengangensis and E. gracilis. The analysis results show that the genome structures of the subfamilies and the newly sequenced two species are very similar, and the size of the CR region is significantly related to the repeat unit. However, in the entire AT-skews and CG-skews, the AT-skews of other subfamilies are all positive, and CG-skews are negative, while Empoascini of Typhlocybinae and Ledrinae are the opposite. Furthermore, among 13PCGs, the AT-skews of 13 species are all negative while CG-skews are positive, which from Empoascini in Typhlocybinae, Idiocerinae, Cicadellinae, Ledrinae, and Evacanthinae. Phylogenetic analysis shows that ML and PB analysis produce almost consistent topologies between different data sets and models, and some relationships are highly supported and remain unchanged. Mileewinae is a monophyletic group and is a sister group with Typhlocybinae, and the sister group of Evacanthinae is Ledrinae + Cicadellinae. Phylogenetic analysis grouped the two newly sequenced species with other species of Typhlocybinae, which was separated from other subfamilies, and all Erythroneurini insects gathered together. However, E. gracilis grouped into a single group, not grouped with species of the same genus (Empoascanara). This result does not match the traditional classification, and other nuclear genes or transcriptome genes may be needed to verify the result. Nucleotide diversity analysis shows that nad4 and nad5 may be evaluated as potential DNA markers defining the Cicadellidae insect species.
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Affiliation(s)
- Xiaoxiao Chen
- School of Karst Science, Guizhou Normal University/State Key Laboratory Cultivation Base for Guizhou Karst Mountain Ecology Environment of China, Guiyang, China
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Guiyang University, Guiyang, China
| | - Zhouwei Yuan
- School of Karst Science, Guizhou Normal University/State Key Laboratory Cultivation Base for Guizhou Karst Mountain Ecology Environment of China, Guiyang, China
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Guiyang University, Guiyang, China
| | - Can Li
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Guiyang University, Guiyang, China
| | - Christopher H. Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Illinois, Champaign, United States of America
| | - Yuehua Song
- School of Karst Science, Guizhou Normal University/State Key Laboratory Cultivation Base for Guizhou Karst Mountain Ecology Environment of China, Guiyang, China
- * E-mail:
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6
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Jiang J, Chen X, Li C, Song Y. Mitogenome and phylogenetic analysis of typhlocybine leafhoppers (Hemiptera: Cicadellidae). Sci Rep 2021; 11:10053. [PMID: 33980923 PMCID: PMC8115509 DOI: 10.1038/s41598-021-89525-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/26/2021] [Indexed: 11/09/2022] Open
Abstract
Mitogenomes have been widely used to estimate phylogenetic relationships among insects and provide data useful for augmenting traditional morphological characters in delimiting species. Here, complete mitogenome sequences of two closely related typhlocybine leafhoppers, Cassianeuracassiae (Ahmed, 1970) and C. bimaculata Dworakowska, 1984, were obtained and found to be 15,423 bp and 14,597 bp in length, respectively. The gene order was found to be similar to other published leafhopper mitogenomes, but the control region of C.bimaculata is the shortest among known leafhoppers and lacks tandem repeats. Phylogenetic analysis of 13 protein-coding genes (PCGs), the first and second codons of 13 PCGs, 13 PCGs and two rRNAs formed three well-supported tree topologies. The topologies of phylogenetic trees inferred from three datasets were almost identical, which was consistent with previous molecular phylogenies of this group. Comparative morphological study of the ovipositors revealed several characters potentially useful for diagnosing genera and resolving their phylogenetic relationships. Phylogenetic analysis of these and other morphological characters yielded a tree that is mostly consistent with the tree obtained from analysis of mitogenome sequences. In both molecular and morphological phylogenenies, Typhlocybini and Zyginellini clustered into one clade, but neither was recovered as monophyletic.
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Affiliation(s)
- Jia Jiang
- School of Karst Science, State Key Laboratory Cultivation Base for Guizhou Karst Mountain Ecology Environment of China, Guizhou Normal University, Guiyang, 550001, Guizhou, China.,Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region/Guizhou Provincial Engineering Research Center for Biological Resources Protection and Efficient Utilization of the Mountainous Region, Guiyang University, Guiyang, 550005, Guizhou, China
| | - Xiaoxiao Chen
- School of Karst Science, State Key Laboratory Cultivation Base for Guizhou Karst Mountain Ecology Environment of China, Guizhou Normal University, Guiyang, 550001, Guizhou, China.,Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region/Guizhou Provincial Engineering Research Center for Biological Resources Protection and Efficient Utilization of the Mountainous Region, Guiyang University, Guiyang, 550005, Guizhou, China
| | - Can Li
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region/Guizhou Provincial Engineering Research Center for Biological Resources Protection and Efficient Utilization of the Mountainous Region, Guiyang University, Guiyang, 550005, Guizhou, China
| | - Yuehua Song
- School of Karst Science, State Key Laboratory Cultivation Base for Guizhou Karst Mountain Ecology Environment of China, Guizhou Normal University, Guiyang, 550001, Guizhou, 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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Zhao XN, Zhang HJ, Li D, Zhou JN, Chen YY, Sun YH, Adeola AC, Fu XQ, Shao Y, Zhang ML. Whole-genome sequencing reveals origin and evolution of influenza A(H1N1)pdm09 viruses in Lincang, China, from 2014 to 2018. PLoS One 2020; 15:e0234869. [PMID: 32579578 PMCID: PMC7314029 DOI: 10.1371/journal.pone.0234869] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 06/03/2020] [Indexed: 11/18/2022] Open
Abstract
The continuous variation of the seasonal influenza viruses, particularly A(H1N1)pdm09, persistently threatens human life and health around the world. In local areas of southwest china, the large time-scale genomic research on A(H1N1)pdm09 is still insufficient. Here, we sequenced 45 whole-genome sequences of influenza A(H1N1)pdm09 viruses in Lincang, China, from 2014 to 2018, by next-generation sequencing technology to characterize molecular mechanisms of their origin and evolution. Our phylogenetic analyses suggest that the A(H1N1)pdm09 strains circulating in Lincang belong to clade 6B and the subclade 6B.1A predominates in 2018. Further, the strains in 2018 possess elevated evolutionary rate as compared to strains in other years. Several newly emerged mutations for HA (hemagglutinin) in 2018 are revealed (i.e., S183P and R221K). Intriguingly, the substitution R221K falls into the RBS (receptor binding site) of HA protein, which could affect antigenic properties of influenza A(H1N1)pdm09 viruses, and another substitution S183P near to RBS with a high covering frequency (11/14 strains) in 2018 is exactly located at the epitope B. Notably, the NA (neuraminidase) protein harbors a new mutation I23T, potentially involved in N-glycosylation. Based on the background with a higher evolutionary rate in 2018 strains, we deeply evaluate the potential vaccine efficacy against Lincang strains and discover a substantive decline of the vaccine efficacy in 2018. Our analyses reaffirm that the real-time molecular surveillance and timely updated vaccine strains for prevention and control of influenza A(H1N1)pdm09 are crucial in the future.
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Affiliation(s)
- Xiao-Nan Zhao
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Han-Ju Zhang
- Lincang Center for Disease Control and Prevention, Lincang, Yunnan, China
| | - Duo Li
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Jie-Nan Zhou
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Yao-Yao Chen
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Yan-Hong Sun
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Adeniyi C. Adeola
- State Key Laboratory of Genetic Resources and Evolution, Chinese Academy of Sciences, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - Xiao-Qing Fu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Chinese Academy of Sciences, Kunming Institute of Zoology, Kunming, Yunnan, China
- * E-mail: (MLZ); (YS)
| | - Mei-Ling Zhang
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Center for Disease Control and Prevention, Kunming, Yunnan, China
- * E-mail: (MLZ); (YS)
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9
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Ye Z, Damgaard J, Yang H, Hebsgaard MB, Weir T, Bu W. Phylogeny and diversification of the true water bugs (Insecta: Hemiptera: Heteroptera: Nepomorpha). Cladistics 2020; 36:72-87. [PMID: 34618947 DOI: 10.1111/cla.12383] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2019] [Indexed: 01/29/2023] Open
Abstract
Climate fluctuations and tectonic reconfigurations associated with environmental changes play large roles in determining patterns of adaptation and diversification, but studies documenting how such drivers have shaped the evolutionary history and diversification dynamics of limnic organisms during the Mesozoic are scarce. Members of the heteropteran infraorder Nepomorpha, or aquatic bugs, are ideal for testing the effects of these determinants on their diversification pulses because most species are confined to aquatic environments during their entire life. The group has a relatively mature taxonomy and is well represented in the fossil record. We investigated the evolution of Nepomorpha based on phylogenetic analyses of morphological and molecular characters sampled from 115 taxa representing all 13 families and approximately 40% of recognized genera. Our results were largely congruent with the phylogenetic relationships inferred from morphology. A divergence dating analysis indicated that Nepomorpha began to diversify in the late Permian (approximately 263 Ma), and diversification analyses suggested that palaeoecological opportunities probably promoted lineage diversification in this group.
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Affiliation(s)
- Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Jakob Damgaard
- Natural History Museum of Denmark, Zoological Museum, Universitetsparken 15, Kobenhavn, 2100 Ø, Denmark
| | - Huanhuan Yang
- School of Life Sciences, Ludong University, 264025, Yantai, Shandong, China
| | - Martin B Hebsgaard
- Natural History Museum of Denmark, Zoological Museum, Universitetsparken 15, Kobenhavn, 2100 Ø, Denmark
| | - Tom Weir
- CSIRO Entomology, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
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Zhao L, Wei J, Lu Y, Wang B, Hao S, Zhao Q. The complete mitochondrial genome of Menida violacea (Hemiptera: Pentatomidae) and its phylogenetic implication. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1617055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Ling Zhao
- Department of Entomology, Shanxi Agricultural University, Taigu, China
| | - Jiufeng Wei
- Department of Entomology, Shanxi Agricultural University, Taigu, China
| | - Yunyun Lu
- Department of Entomology, Shanxi Agricultural University, Taigu, China
| | - Bingwei Wang
- Department of Entomology, Shanxi Agricultural University, Taigu, China
| | - Shangji Hao
- Department of Entomology, Shanxi Agricultural University, Taigu, China
| | - Qing Zhao
- Department of Entomology, Shanxi Agricultural University, Taigu, China
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11
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Alurralde G, de Aranzamendi MC, Taverna A, Maggioni T, Tatián M. Not as clear as expected: what genetic data tell about Southern Hemisphere corellids (Ascidiacea: Phlebobranchia). J NAT HIST 2018. [DOI: 10.1080/00222933.2018.1553250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Gastón Alurralde
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, Ecología Marina, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Diversidad y Ecología Animal (IDEA), Córdoba, Argentina
| | - María Carla de Aranzamendi
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, Ecología Marina, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Diversidad y Ecología Animal (IDEA), Córdoba, Argentina
| | - Anabela Taverna
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, Ecología Marina, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Diversidad y Ecología Animal (IDEA), Córdoba, Argentina
| | - Tamara Maggioni
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, Ecología Marina, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Diversidad y Ecología Animal (IDEA), Córdoba, Argentina
| | - Marcos Tatián
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, Ecología Marina, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Diversidad y Ecología Animal (IDEA), Córdoba, Argentina
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12
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Yang H, Li T, Dang K, Bu W. Compositional and mutational rate heterogeneity in mitochondrial genomes and its effect on the phylogenetic inferences of Cimicomorpha (Hemiptera: Heteroptera). BMC Genomics 2018; 19:264. [PMID: 29669515 PMCID: PMC5907366 DOI: 10.1186/s12864-018-4650-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 04/08/2018] [Indexed: 01/24/2023] Open
Abstract
Background Mitochondrial genome (mt-genome) data can potentially return artefactual relationships in the higher-level phylogenetic inference of insects due to the biases of accelerated substitution rates and compositional heterogeneity. Previous studies based on mt-genome data alone showed a paraphyly of Cimicomorpha (Insecta, Hemiptera) due to the positions of the families Tingidae and Reduviidae rather than the monophyly that was supported based on morphological characters, morphological and molecular combined data and large scale molecular datasets. Various strategies have been proposed to ameliorate the effects of potential mt-genome biases, including dense taxon sampling, removal of third codon positions or purine-pyrimidine coding and the use of site-heterogeneous models. In this study, we sequenced the mt-genomes of five additional Tingidae species and discussed the compositional and mutational rate heterogeneity in mt-genomes and its effect on the phylogenetic inferences of Cimicomorpha by implementing the bias-reduction strategies mentioned above. Results Heterogeneity in nucleotide composition and mutational biases were found in mt protein-coding genes, and the third codon exhibited high levels of saturation. Dense taxon sampling of Tingidae and Reduviidae and the other common strategies mentioned above were insufficient to recover the monophyly of the well-established group Cimicomorpha. When the sites with weak phylogenetic signals in the dataset were removed, the remaining dataset of mt-genomes can support the monophyly of Cimicomorpha; this support demonstrates that mt-genomes possess strong phylogenetic signals for the inference of higher-level phylogeny of this group. Comparison of the ratio of the removal of amino acids for each PCG showed that ATP8 has the highest ratio while CO1 has the lowest. This pattern is largely congruent with the evolutionary rate of 13 PCGs that ATP8 represents the highest evolutionary rate, whereas CO1 appears to be the lowest. Notably, the value of Ka/Ks ratios of all PCGs is less than 1, indicating that these genes are likely evolving under purifying selection. Conclusions Our results demonstrate that mt-genomes have sites with strong phylogenetic signals for the inference of higher-level phylogeny of Cimicomorpha. Consequently, bioinformatic approaches to removing sites with weak phylogenetic signals in mt-genome without relying on an a priori tree topology would greatly improve this field. Electronic supplementary material The online version of this article (10.1186/s12864-018-4650-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Huanhuan Yang
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Teng Li
- Institute of Zoology and Developmental Biology, College of Life Sciences, Lanzhou University, 222 Tianshui South Road, Lanzhou, 730000, China.
| | - Kai Dang
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
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13
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Chen C, Wei J, Ji W, Zhao Q. The first complete mitochondrial genome from the subfamily Phyllocephalinae (Heteroptera: Pentatomidae) and its phylogenetic analysis. Mitochondrial DNA B Resour 2017; 2:938-939. [PMID: 33474045 PMCID: PMC7799901 DOI: 10.1080/23802359.2017.1413313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 12/01/2017] [Indexed: 11/30/2022] Open
Abstract
The true bug, Gonopsis affinis, is an important pest in China. Here, we determined the complete mitogenome of G. affinis, which is the first for the subfamily Phyllocephalinae. This 16,011-basepair (bp) mitogenome comprises of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes, and an A + T-rich region. The gene order and the orientation are similar to those of other sequenced Hemipteran species. All PCGs start with ATN codons, except COI, and end with TAA. The 22 tRNAs have a typical cloverleaf secondary structure except trnS-Ser (AGN), which lacks a dihydrouridine (DHU) arm. Phylogenetic analyses highly supported the monophyly of each family, and confirmed the reasonable placement of G. affinis.
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Affiliation(s)
- Chao Chen
- Department of Environment Science and Engineering, Taiyuan University of Technology, Taiyuan, Shanxi, PR China
| | - Jiufeng Wei
- Department of Entomology, Shanxi Agricultural University, Taigu, PR China
| | - Wei Ji
- College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi, PR China
| | - Qing Zhao
- Department of Entomology, Shanxi Agricultural University, Taigu, PR China
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14
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Zhao Q, Wei J, Zhao W, Cai B, Du X, Zhang H. The first mitochondrial genome for the subfamily Asopinae (Heteroptera: Pentatomidae) and its phylogenetic implications. Mitochondrial DNA B Resour 2017; 2:804-805. [PMID: 33473988 PMCID: PMC7800504 DOI: 10.1080/23802359.2017.1398599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 10/26/2017] [Indexed: 10/28/2022] Open
Abstract
Here, we determined the complete mitogenome of Picromerus griseus, the first for the subfamily Asopinae. This mitochondrial genome contains 16,338 bp, with an A + T content of 71.69%, and contains 37 typical mitochondrial genes (13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a control region). The genome size, gene arrangement, A + T content, codon usage and secondary structures of 22 transfer RNA genes of the P. griseus mitogenome were similar to those of other sequenced pentatomoids. Bayesian analyses performed using the mitogenomes of P. griseus and its relatives, including 14 taxa, confirmed the reasonable placement of P. griseus.
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Affiliation(s)
- Qing Zhao
- Department of Entomology, Shanxi Agricultural University, Taigu, China
| | - Jiufeng Wei
- Department of Entomology, Shanxi Agricultural University, Taigu, China
| | - Wanqing Zhao
- Department of Entomology, Shanxi Agricultural University, Taigu, China
| | - Bo Cai
- Hainan Entry-Exit Inspection and Quarantine Bureau, Haikou, Hainan, China
| | - Xin Du
- Institute of Biomedical Sciences, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Hufang Zhang
- Department of Entomology, Shanxi Agricultural University, Taigu, China
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15
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Thankachan SV, Chockalingam SP, Liu Y, Krishnan A, Aluru S. A greedy alignment-free distance estimator for phylogenetic inference. BMC Bioinformatics 2017; 18:238. [PMID: 28617225 PMCID: PMC5471951 DOI: 10.1186/s12859-017-1658-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Alignment-free sequence comparison approaches have been garnering increasing interest in various data- and compute-intensive applications such as phylogenetic inference for large-scale sequences. While k-mer based methods are predominantly used in real applications, the average common substring (ACS) approach is emerging as one of the prominent alignment-free approaches. This ACS approach has been further generalized by some recent work, either greedily or exactly, by allowing a bounded number of mismatches in the common substrings. RESULTS We present ALFRED-G, a greedy alignment-free distance estimator for phylogenetic tree reconstruction based on the concept of the generalized ACS approach. In this algorithm, we have investigated a new heuristic to efficiently compute the lengths of common strings with mismatches allowed, and have further applied this heuristic to phylogeny reconstruction. Performance evaluation using real sequence datasets shows that our heuristic is able to reconstruct comparable, or even more accurate, phylogenetic tree topologies than the kmacs heuristic algorithm at highly competitive speed. CONCLUSIONS ALFRED-G is an alignment-free heuristic for evolutionary distance estimation between two biological sequences. This algorithm is implemented in C++ and has been incorporated into our open-source ALFRED software package ( http://alurulab.cc.gatech.edu/phylo ).
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Affiliation(s)
- Sharma V. Thankachan
- Department of Computer Science, University of Central Florida, Orlando, 32816 FL USA
| | - Sriram P. Chockalingam
- Institute for Data Engineering and Science, Georgia Institute of Technology, Atlanta, 30332 GA USA
| | - Yongchao Liu
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, 30332 GA USA
| | - Ambujam Krishnan
- School of Electrical Engineering and Computer Science, Louisiana State University, Baton Rouge, 70703 LA USA
| | - Srinivas Aluru
- Institute for Data Engineering and Science, Georgia Institute of Technology, Atlanta, 30332 GA USA
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, 30332 GA USA
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16
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Li T, Yang J, Li Y, Cui Y, Xie Q, Bu W, Hillis DM. A Mitochondrial Genome of Rhyparochromidae (Hemiptera: Heteroptera) and a Comparative Analysis of Related Mitochondrial Genomes. Sci Rep 2016; 6:35175. [PMID: 27756915 PMCID: PMC5069475 DOI: 10.1038/srep35175] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/26/2016] [Indexed: 11/23/2022] Open
Abstract
The Rhyparochromidae, the largest family of Lygaeoidea, encompasses more than 1,850 described species, but no mitochondrial genome has been sequenced to date. Here we describe the first mitochondrial genome for Rhyparochromidae: a complete mitochondrial genome of Panaorus albomaculatus (Scott, 1874). This mitochondrial genome is comprised of 16,345 bp, and contains the expected 37 genes and control region. The majority of the control region is made up of a large tandem-repeat region, which has a novel pattern not previously observed in other insects. The tandem-repeats region of P. albomaculatus consists of 53 tandem duplications (including one partial repeat), which is the largest number of tandem repeats among all the known insect mitochondrial genomes. Slipped-strand mispairing during replication is likely to have generated this novel pattern of tandem repeats. Comparative analysis of tRNA gene families in sequenced Pentatomomorpha and Lygaeoidea species shows that the pattern of nucleotide conservation is markedly higher on the J-strand. Phylogenetic reconstruction based on mitochondrial genomes suggests that Rhyparochromidae is not the sister group to all the remaining Lygaeoidea, and supports the monophyly of Lygaeoidea.
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Affiliation(s)
- Teng Li
- Institute of Zoology and Developmental Biology, College of Life Sciences, Lanzhou University, 222 Tianshui South Road, Lanzhou 730000, China
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Jie Yang
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Yinwan Li
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Ying Cui
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Qiang Xie
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - David M. Hillis
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
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17
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Ling C, Hamada T, Gao J, Zhao G, Sun D, Shi W. MrBayes tgMC 3++: A High Performance and Resource-Efficient GPU-Oriented Phylogenetic Analysis Method. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016; 13:845-854. [PMID: 26529779 DOI: 10.1109/tcbb.2015.2495202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
MrBayes is a widespread phylogenetic inference tool harnessing empirical evolutionary models and Bayesian statistics. However, the computational cost on the likelihood estimation is very expensive, resulting in undesirably long execution time. Although a number of multi-threaded optimizations have been proposed to speed up MrBayes, there are bottlenecks that severely limit the GPU thread-level parallelism of likelihood estimations. This study proposes a high performance and resource-efficient method for GPU-oriented parallelization of likelihood estimations. Instead of having to rely on empirical programming, the proposed novel decomposition storage model implements high performance data transfers implicitly. In terms of performance improvement, a speedup factor of up to 178 can be achieved on the analysis of simulated datasets by four Tesla K40 cards. In comparison to the other publicly available GPU-oriented MrBayes, the tgMC3++ method (proposed herein) outperforms the tgMC3 (v1.0), nMC3 (v2.1.1) and oMC3 (v1.00) methods by speedup factors of up to 1.6, 1.9 and 2.9, respectively. Moreover, tgMC3++ supports more evolutionary models and gamma categories, which previous GPU-oriented methods fail to take into analysis.
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18
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Thankachan SV, Chockalingam SP, Liu Y, Apostolico A, Aluru S. ALFRED: A Practical Method for Alignment-Free Distance Computation. J Comput Biol 2016; 23:452-60. [PMID: 27138275 DOI: 10.1089/cmb.2015.0217] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Alignment-free approaches are gaining persistent interest in many sequence analysis applications such as phylogenetic inference and metagenomic classification/clustering, especially for large-scale sequence datasets. Besides the widely used k-mer methods, the average common substring (ACS) approach has emerged to be one of the well-known alignment-free approaches. Two recent works further generalize this ACS approach by allowing a bounded number k of mismatches in the common substrings, relying on approximation (linear time) and exact computation, respectively. Albeit having a good worst-case time complexity [Formula: see text], the exact approach is complex and unlikely to be efficient in practice. Herein, we present ALFRED, an alignment-free distance computation method, which solves the generalized common substring search problem via exact computation. Compared to the theoretical approach, our algorithm is easier to implement and more practical to use, while still providing highly competitive theoretical performances with an expected run-time of [Formula: see text]. By applying our program to phylogenetic inference as a case study, we find that our program facilitates to exactly reconstruct the topology of the reference phylogenetic tree for a set of 27 primate mitochondrial genomes, at reasonably acceptable speed. ALFRED is implemented in C++ programming language and the source code is freely available online.
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Affiliation(s)
| | - Sriram P Chockalingam
- 2 Department of Computer Science and Engineering, Indian Institute of Technology Bombay , Mumbai, India
| | - Yongchao Liu
- 1 College of Computing, Georgia Institute of Technology , Atlanta, Georgia
| | - Alberto Apostolico
- 1 College of Computing, Georgia Institute of Technology , Atlanta, Georgia
| | - Srinivas Aluru
- 1 College of Computing, Georgia Institute of Technology , Atlanta, Georgia
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19
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Wu YZ, Yu SS, Wang YH, Wu HY, Li XR, Men XY, Zhang YW, Rédei D, Xie Q, Bu WJ. The evolutionary position of Lestoniidae revealed by molecular autapomorphies in the secondary structure of rRNA besides phylogenetic reconstruction (Insecta: Hemiptera: Heteroptera). Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12385] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yan-Zhuo Wu
- Institute of Entomology; College of Life Sciences; Nankai University; Tianjin 300071 China
| | - Sha-Sha Yu
- Institute of Entomology; College of Life Sciences; Nankai University; Tianjin 300071 China
| | - Yan-Hui Wang
- Institute of Entomology; College of Life Sciences; Nankai University; Tianjin 300071 China
| | - Hao-Yang Wu
- Institute of Entomology; College of Life Sciences; Nankai University; Tianjin 300071 China
| | - Xiu-Rong Li
- Institute of Entomology; College of Life Sciences; Nankai University; Tianjin 300071 China
| | - Xin-Yu Men
- Institute of Entomology; College of Life Sciences; Nankai University; Tianjin 300071 China
| | - Yi-Wei Zhang
- Institute of Entomology; College of Life Sciences; Nankai University; Tianjin 300071 China
| | - Dávid Rédei
- Institute of Entomology; College of Life Sciences; Nankai University; Tianjin 300071 China
| | - Qiang Xie
- Institute of Entomology; College of Life Sciences; Nankai University; Tianjin 300071 China
| | - Wen-Jun Bu
- Institute of Entomology; College of Life Sciences; Nankai University; Tianjin 300071 China
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20
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Zhang D, Xie T, Li T, Bu W. The complete mitochondrial genome of Nepa hoffmanni (Hemiptera: Heteroptera: Nepidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3770-1. [PMID: 26403708 DOI: 10.3109/19401736.2015.1079898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome (mt-genome) of Nepa hoffmanni has been reported in this study. This mitochondrial genome is 15 774 bp long, with an A + T content of 72.04%, containing the typical 37 genes (13 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes) and a control region. All genes are arranged in the same gene order as most other known heteropteran mt-genome. This is the second completely sequenced mt-genome from the family Nepidae of Nepomorpha. Bayesian analyses were performed using the mt-genome of Nepa hoffmanni and its relatives, including 17 taxa, showing a reasonable placement of Nepa hoffmanni.
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Affiliation(s)
- Danli Zhang
- a Institute of Entomology, College of Life Sciences, Nankai University , Tianjin , China and
| | - Tongyin Xie
- a Institute of Entomology, College of Life Sciences, Nankai University , Tianjin , China and
| | - Teng Li
- b Institute of Zoology and Developmental Biology, College of Life Sciences, Lanzhou University , Lanzhou , China
| | - Wenjun Bu
- a Institute of Entomology, College of Life Sciences, Nankai University , Tianjin , China and
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21
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Pang S, Stones RJ, Ren MM, Liu XG, Wang G, Xia HJ, Wu HY, Liu Y, Xie Q. GPU MrBayes V3.1: MrBayes on Graphics Processing Units for Protein Sequence Data. Mol Biol Evol 2015; 32:2496-7. [PMID: 26012905 DOI: 10.1093/molbev/msv129] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We present a modified GPU (graphics processing unit) version of MrBayes, called ta(MC)(3) (GPU MrBayes V3.1), for Bayesian phylogenetic inference on protein data sets. Our main contributions are 1) utilizing 64-bit variables, thereby enabling ta(MC)(3) to process larger data sets than MrBayes; and 2) to use Kahan summation to improve accuracy, convergence rates, and consequently runtime. Versus the current fastest software, we achieve a speedup of up to around 2.5 (and up to around 90 vs. serial MrBayes), and more on multi-GPU hardware. GPU MrBayes V3.1 is available from http://sourceforge.net/projects/mrbayes-gpu/.
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Affiliation(s)
- Shuai Pang
- College of Computer and Control Engineering, Nankai University, Tianjin, China College of Software, Nankai University, Tianjin, China
| | - Rebecca J Stones
- College of Computer and Control Engineering, Nankai University, Tianjin, China College of Software, Nankai University, Tianjin, China
| | - Ming-Ming Ren
- College of Computer and Control Engineering, Nankai University, Tianjin, China College of Software, Nankai University, Tianjin, China
| | - Xiao-Guang Liu
- College of Computer and Control Engineering, Nankai University, Tianjin, China College of Software, Nankai University, Tianjin, China
| | - Gang Wang
- College of Computer and Control Engineering, Nankai University, Tianjin, China College of Software, Nankai University, Tianjin, China
| | - Hong-ju Xia
- College of Computer and Control Engineering, Nankai University, Tianjin, China College of Software, Nankai University, Tianjin, China
| | - Hao-Yang Wu
- College of Life Science, Nankai University, Tianjin, China
| | - Yang Liu
- College of Life Science, Nankai University, Tianjin, China
| | - Qiang Xie
- College of Life Science, Nankai University, Tianjin, China
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22
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The molecular symplesiomorphies shared by the stem groups of metazoan evolution: can sites as few as 1% have a significant impact on recognizing the phylogenetic position of myzostomida? J Mol Evol 2014; 79:63-74. [PMID: 25128981 DOI: 10.1007/s00239-014-9635-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 07/22/2014] [Indexed: 10/24/2022]
Abstract
Although it is clear that taxon sampling, alignments, gene sampling, tree reconstruction methods and the total length of the sequences used are critical to the reconstruction of evolutionary history, weakly supported or misleading nodes exist in phylogenetic studies with no obvious flaw in those aspects. The phylogenetic studies focusing on the basal part of bilaterian evolution are such a case. During the past decade, Myzostomida has appeared in the basal part of Bilateria in several phylogenetic studies of Metazoa. However, most researchers have entertained only two competing hypotheses about the position of Myzostomida-an affinity with Annelida and an affinity with Platyhelminthes. In this study, dozens of symplesiomorphies were discovered by means of ancestral state reconstruction in the complete 18S and 28S rDNAs shared by the stem groups of Metazoa. By contrastive analysis on the datasets with or without such symplesiomorphic sites, we discovered that Myzostomida and other basal groups are basal lineages of Bilateria due to the corresponding symplesiomorphies shared with earlier lineages. As such, symplesiomorphies account for approximately 1-2% of the whole dataset have an essential impact on phylogenetic inference, and this study reminds molecular systematists of the importance of carrying out ancestral state reconstruction at each site in sequence-based phylogenetic studies. In addition, reasons should be explored for the low support of the hypothesis that Myzostomida belongs to Annelida in the results of phylogenomic studies. Future phylogenetic studies concerning Myzostomida should include all of the basal lineages of Bilateria to avoid directly neglecting the stand-alone basal position of Myzostomida as a potential hypothesis.
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23
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Li T, Hua J, Wright AM, Cui Y, Xie Q, Bu W, Hillis DM. Long-branch attraction and the phylogeny of true water bugs (Hemiptera: Nepomorpha) as estimated from mitochondrial genomes. BMC Evol Biol 2014; 14:99. [PMID: 24884699 PMCID: PMC4101842 DOI: 10.1186/1471-2148-14-99] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 04/29/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most previous studies of morphological and molecular data have consistently supported the monophyly of the true water bugs (Hemiptera: Nepomorpha). An exception is a recent study by Hua et al. (BMC Evol Biol 9: 134, 2009) based on nine nepomorphan mitochondrial genomes. In the analysis of Hua et al. (BMC Evol Biol 9: 134, 2009), the water bugs in the group Pleoidea formed the sister group to a clade that consisted of Nepomorpha (the remaining true water bugs) + Leptopodomorpha (shore bugs) + Cimicomorpha (assassin bugs and relatives) + Pentatomomorpha (stink bugs and relatives), thereby suggesting that fully aquatic hemipterans evolved independently at least twice. Based on these results, Hua et al. (BMC Evol Biol 9: 134, 2009) elevated the Pleoidea to a new infraorder, the Plemorpha. RESULTS Our reanalysis suggests that the lack of support for the monophyly of the true water bugs (including Pleoidea) by Hua et al. (BMC Evol Biol 9: 134, 2009) likely resulted from inadequate taxon sampling. In particular, long-branch attraction (LBA) between the distant outgroup taxa and Pleoidea, as well as LBA among taxa in the ingroup, made Nepomorpha appear to be polyphyletic. We used three complementary strategies to test and alleviate the effects of LBA: (1) the removal of distant outgroups from the analysis; (2) the addition of closely related outgroups; and (3) the addition of a mitochondrial genome from a second family of Pleoidea. We also performed likelihood-ratio tests to examine the support for monophyly of Nepomorpha with different combinations of taxa included in the analysis. Furthermore, we found that specimens of Helotrephes sp. were misidentified as Paraplea frontalis (Fieber, 1844) by Hua et al. (BMC Evol Biol 9: 134, 2009). CONCLUSIONS All analyses that included the addition of more taxa significantly and consistently supported the placement of Pleoidea within the Nepomorpha (i.e., supported the monophyly of the traditional true water bugs). Our analyses further support a close relationship between Notonectoidea and Pleoidea within Nepomorpha, and the superfamilies Nepoidea, Ochteroidea, Naucoroidea, and Pleoidea are resolved as monophyletic in all trees with strong support. Our results also confirmed that monophyly of Nepomorpha clearly is not refuted by the mitochondrial genome data.
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Affiliation(s)
- Teng Li
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Jimeng Hua
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - April M Wright
- Department of Integrative Biology, University of Texas at Austin, Austin TX 78712, USA
| | - Ying Cui
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Qiang Xie
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - David M Hillis
- Department of Integrative Biology, University of Texas at Austin, Austin TX 78712, USA
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24
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Chen GK, Guo Y. Discovering epistasis in large scale genetic association studies by exploiting graphics cards. Front Genet 2013; 4:266. [PMID: 24348518 PMCID: PMC3848199 DOI: 10.3389/fgene.2013.00266] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 11/16/2013] [Indexed: 11/13/2022] Open
Abstract
Despite the enormous investments made in collecting DNA samples and generating germline variation data across thousands of individuals in modern genome-wide association studies (GWAS), progress has been frustratingly slow in explaining much of the heritability in common disease. Today's paradigm of testing independent hypotheses on each single nucleotide polymorphism (SNP) marker is unlikely to adequately reflect the complex biological processes in disease risk. Alternatively, modeling risk as an ensemble of SNPs that act in concert in a pathway, and/or interact non-additively on log risk for example, may be a more sensible way to approach gene mapping in modern studies. Implementing such analyzes genome-wide can quickly become intractable due to the fact that even modest size SNP panels on modern genotype arrays (500k markers) pose a combinatorial nightmare, require tens of billions of models to be tested for evidence of interaction. In this article, we provide an in-depth analysis of programs that have been developed to explicitly overcome these enormous computational barriers through the use of processors on graphics cards known as Graphics Processing Units (GPU). We include tutorials on GPU technology, which will convey why they are growing in appeal with today's numerical scientists. One obvious advantage is the impressive density of microprocessor cores that are available on only a single GPU. Whereas high end servers feature up to 24 Intel or AMD CPU cores, the latest GPU offerings from nVidia feature over 2600 cores. Each compute node may be outfitted with up to 4 GPU devices. Success on GPUs varies across problems. However, epistasis screens fare well due to the high degree of parallelism exposed in these problems. Papers that we review routinely report GPU speedups of over two orders of magnitude (>100x) over standard CPU implementations.
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Affiliation(s)
- Gary K Chen
- Division of Biostatics, Department of Preventive Medicine, University of Southern California Los Angeles, CA, USA
| | - Yunfei Guo
- Division of Biostatics, Department of Preventive Medicine, University of Southern California Los Angeles, CA, USA ; Zilkha Neurogenetic Institute, University of Southern California Los Angeles, CA, USA
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25
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Ling C, Hamada T, Bai J, Li X, Chesters D, Zheng W, Shi W. MrBayes tgMC³: a tight GPU implementation of MrBayes. PLoS One 2013; 8:e60667. [PMID: 23593277 PMCID: PMC3621901 DOI: 10.1371/journal.pone.0060667] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 03/01/2013] [Indexed: 11/18/2022] Open
Abstract
MrBayes is model-based phylogenetic inference tool using Bayesian statistics. However, model-based assessment of phylogenetic trees adds to the computational burden of tree-searching, and so poses significant computational challenges. Graphics Processing Units (GPUs) have been proposed as high performance, low cost acceleration platforms and several parallelized versions of the Metropolis Coupled Markov Chain Mote Carlo (MC3) algorithm in MrBayes have been presented that can run on GPUs. However, some bottlenecks decrease the efficiency of these implementations. To address these bottlenecks, we propose a tight GPU MC3 (tgMC3) algorithm. tgMC3 implements a different architecture from the one-to-one acceleration architecture employed in previously proposed methods. It merges multiply discrete GPU kernels according to the data dependency and hence decreases the number of kernels launched and the complexity of data transfer. We implemented tgMC3 and made performance comparisons with an earlier proposed algorithm, nMC3, and also with MrBayes MC3 under serial and multiply concurrent CPU processes. All of the methods were benchmarked on the same computing node from DEGIMA. Experiments indicate that the tgMC3 method outstrips nMC3 (v1.0) with speedup factors from 2.1 to 2.7×. In addition, tgMC3 outperforms the serial MrBayes MC3 by a factor of 6 to 30× when using a single GTX480 card, whereas a speedup factor of around 51× can be achieved by using two GTX 480 cards on relatively long sequences. Moreover, tgMC3 was compared with MrBayes accelerated by BEAGLE, and achieved speedup factors from 3.7 to 5.7×. The reported performance improvement of tgMC3 is significant and appears to scale well with increasing dataset sizes. In addition, the strategy proposed in tgMC3 could benefit the acceleration of other Bayesian-based phylogenetic analysis methods using GPUs.
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Affiliation(s)
- Cheng Ling
- Guangzhou Institute of Advanced Technology, Chinese Academy of Science, Guangzhou, China
- * E-mail: (CL); (WS)
| | - Tsuyoshi Hamada
- Department of Computer and Information Science, Nagasaki University, Nagasaki, Japan
| | - Jianing Bai
- Guangzhou Institute of Advanced Technology, Chinese Academy of Science, Guangzhou, China
| | - Xianbin Li
- Guangzhou Institute of Advanced Technology, Chinese Academy of Science, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Douglas Chesters
- Guangzhou Institute of Advanced Technology, Chinese Academy of Science, Guangzhou, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Weimin Zheng
- Guangzhou Institute of Advanced Technology, Chinese Academy of Science, Guangzhou, China
| | - Weifeng Shi
- School of Basic Medical Sciences, Taishan Medical College, Taian, Shandong, China
- * E-mail: (CL); (WS)
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26
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Abstract
MrBayes, using Metropolis-coupled Markov chain Monte Carlo (MCMCMC or (MC)3), is a popular program for Bayesian inference. As a leading method of using DNA data to infer phylogeny, the (MC)3 Bayesian algorithm and its improved and parallel versions are now not fast enough for biologists to analyze massive real-world DNA data. Recently, graphics processor unit (GPU) has shown its power as a coprocessor (or rather, an accelerator) in many fields. This article describes an efficient implementation a(MC)3 (aMCMCMC) for MrBayes (MC)3 on compute unified device architecture. By dynamically adjusting the task granularity to adapt to input data size and hardware configuration, it makes full use of GPU cores with different data sets. An adaptive method is also developed to split and combine DNA sequences to make full use of a large number of GPU cards. Furthermore, a new “node-by-node” task scheduling strategy is developed to improve concurrency, and several optimizing methods are used to reduce extra overhead. Experimental results show that a(MC)3 achieves up to 63× speedup over serial MrBayes on a single machine with one GPU card, and up to 170× speedup with four GPU cards, and up to 478× speedup with a 32-node GPU cluster. a(MC)3 is dramatically faster than all the previous (MC)3 algorithms and scales well to large GPU clusters.
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Affiliation(s)
- Jie Bao
- College of Information Technical Science, Nankai University, Tianjin, China
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27
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Li T, Gao C, Cui Y, Xie Q, Bu W. The complete mitochondrial genome of the stalk-eyed bug Chauliops fallax Scott, and the monophyly of Malcidae (Hemiptera: Heteroptera). PLoS One 2013; 8:e55381. [PMID: 23390534 PMCID: PMC3563593 DOI: 10.1371/journal.pone.0055381] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 12/21/2012] [Indexed: 11/19/2022] Open
Abstract
Chauliops fallax Scott, 1874 (Hemiptera: Heteroptera: Malcidae: Chauliopinae) is one of the most destructive insect pests of soybean and rice fields in Asia. Here we sequenced the complete mitochondrial genome of this pest. This genome is 15,739 bp long, with an A+T content of 73.7%, containing 37 typical animal mitochondrial genes and a control region. All genes were arranged in the same order as most of other Heteroptera. A remarkable strand bias was found for all nine protein coding genes (PCGs) encoded by the majority strand were positive AT-skew and negative GC-skew, whereas the reverse were found in the remaining four PCGs encoded by the minority strand and two rRNA genes. The models of secondary structures for the two rRNA genes of sequenced true bugs and Lygaeoidea were predicted. 16S rRNA consisted of six domains (domain III is absent as in other known arthropod mitochondrial genomes) and 45 helices, while three domains and 27 helices for 12S rRNA. The control region consists of five subregions: a microsatellite-like region, a tandem repeats region and other three motifs. The unusual intergenic spacer between tRNA-H and ND4 only found in the species of Lygaeoidea, not in other heteropteran species, may be the synapomorphy of this superfamily. Phylogenetic analyses were carried out based on all the 13 PCGs showed that Chauliopinae was the sister group of Malcinae and the monophyly of Lygaeoidea.
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MESH Headings
- Animals
- Base Composition
- Base Sequence
- DNA, Intergenic/genetics
- DNA, Mitochondrial/classification
- DNA, Mitochondrial/genetics
- Evolution, Molecular
- Gene Order
- Genes, Mitochondrial
- Genome, Insect
- Genome, Mitochondrial
- Heteroptera/classification
- Heteroptera/genetics
- Microsatellite Repeats
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phylogeny
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Transfer/genetics
- Sequence Analysis, DNA
- Species Specificity
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Affiliation(s)
- Teng Li
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Cuiqing Gao
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Ying Cui
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Qiang Xie
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
- * E-mail:
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28
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Jin Z, Bakos JD. Extending the BEAGLE library to a multi-FPGA platform. BMC Bioinformatics 2013; 14:25. [PMID: 23331707 PMCID: PMC3599256 DOI: 10.1186/1471-2105-14-25] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 01/04/2013] [Indexed: 11/17/2022] Open
Abstract
Background Maximum Likelihood (ML)-based phylogenetic inference using Felsenstein’s pruning algorithm is a standard method for estimating the evolutionary relationships amongst a set of species based on DNA sequence data, and is used in popular applications such as RAxML, PHYLIP, GARLI, BEAST, and MrBayes. The Phylogenetic Likelihood Function (PLF) and its associated scaling and normalization steps comprise the computational kernel for these tools. These computations are data intensive but contain fine grain parallelism that can be exploited by coprocessor architectures such as FPGAs and GPUs. A general purpose API called BEAGLE has recently been developed that includes optimized implementations of Felsenstein’s pruning algorithm for various data parallel architectures. In this paper, we extend the BEAGLE API to a multiple Field Programmable Gate Array (FPGA)-based platform called the Convey HC-1. Results The core calculation of our implementation, which includes both the phylogenetic likelihood function (PLF) and the tree likelihood calculation, has an arithmetic intensity of 130 floating-point operations per 64 bytes of I/O, or 2.03 ops/byte. Its performance can thus be calculated as a function of the host platform’s peak memory bandwidth and the implementation’s memory efficiency, as 2.03 × peak bandwidth × memory efficiency. Our FPGA-based platform has a peak bandwidth of 76.8 GB/s and our implementation achieves a memory efficiency of approximately 50%, which gives an average throughput of 78 Gflops. This represents a ~40X speedup when compared with BEAGLE’s CPU implementation on a dual Xeon 5520 and 3X speedup versus BEAGLE’s GPU implementation on a Tesla T10 GPU for very large data sizes. The power consumption is 92 W, yielding a power efficiency of 1.7 Gflops per Watt. Conclusions The use of data parallel architectures to achieve high performance for likelihood-based phylogenetic inference requires high memory bandwidth and a design methodology that emphasizes high memory efficiency. To achieve this objective, we integrated 32 pipelined processing elements (PEs) across four FPGAs. For the design of each PE, we developed a specialized synthesis tool to generate a floating-point pipeline with resource and throughput constraints to match the target platform. We have found that using low-latency floating-point operators can significantly reduce FPGA area and still meet timing requirement on the target platform. We found that this design methodology can achieve performance that exceeds that of a GPU-based coprocessor.
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Affiliation(s)
- Zheming Jin
- Department of Computer Science and Engineering, University of South Carolina, Columbia, SC, USA
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29
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Wang Y, Engel MS, Rafael JA, Dang K, Wu H, Wang Y, Xie Q, Bu W. A unique box in 28S rRNA is shared by the enigmatic insect order Zoraptera and Dictyoptera. PLoS One 2013; 8:e53679. [PMID: 23301099 PMCID: PMC3536744 DOI: 10.1371/journal.pone.0053679] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 12/03/2012] [Indexed: 01/30/2023] Open
Abstract
The position of the Zoraptera remains one of the most challenging and uncertain concerns in ordinal-level phylogenies of the insects. Zoraptera have been viewed as having a close relationship with five different groups of Polyneoptera, or as being allied to the Paraneoptera or even Holometabola. Although rDNAs have been widely used in phylogenetic studies of insects, the application of the complete 28S rDNA are still scattered in only a few orders. In this study, a secondary structure model of the complete 28S rRNAs of insects was reconstructed based on all orders of Insecta. It was found that one length-variable region, D3-4, is particularly distinctive. The length and/or sequence of D3-4 is conservative within each order of Polyneoptera, but it can be divided into two types between the different orders of the supercohort, of which the enigmatic order Zoraptera and Dictyoptera share one type, while the remaining orders of Polyneoptera share the other. Additionally, independent evidence from phylogenetic results support the clade (Zoraptera+Dictyoptera) as well. Thus, the similarity of D3-4 between Zoraptera and Dictyoptera can serve as potentially valuable autapomorphy or synapomorphy in phylogeny reconstruction. The clades of (Plecoptera+Dermaptera) and ((Grylloblattodea+Mantophasmatodea)+(Embiodea+Phasmatodea)) were also recovered in the phylogenetic study. In addition, considering the other studies based on rDNAs, this study reached the highest congruence with previous phylogenetic studies of Holometabola based on nuclear protein coding genes or morphology characters. Future comparative studies of secondary structures across deep divergences and additional taxa are likely to reveal conserved patterns, structures and motifs that can provide support for major phylogenetic lineages.
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Affiliation(s)
- Yanhui Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Michael S. Engel
- Division of Entomology (Paleoentomology), Natural History Museum, London, England
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Jose A. Rafael
- Instituto Nacional de Pesquisas da Amazônia, INPA, Manaus, Amazonas, Brazil
| | - Kai Dang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Haoyang Wu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Ying Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Qiang Xie
- 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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30
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Molecular phylogeny of the western South Atlantic Sciaenidae based on mitochondrial and nuclear data. Mol Phylogenet Evol 2013; 66:423-8. [DOI: 10.1016/j.ympev.2012.09.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 09/11/2012] [Accepted: 09/17/2012] [Indexed: 11/18/2022]
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