RDP: detection of recombination amongst aligned sequences

Martin, Darren P.; Rybicki, Edward P.

doi:10.1093/bioinformatics/16.6.562

Cited by 1,371 publications

(1,005 citation statements)

References 10 publications

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“…A total of seven methods were applied, including GENECONV,46 RDP,47 Chimaera,48 SiScan,49 3Seq,50 MaxChi,51 LARD 52. Recombination had to be confirmed by at least four of the seven methods with p value cut‐off of 0.05.…”

Section: Methodsmentioning

confidence: 99%

Origin, Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Circovirus 3

et al. 2018

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Porcine circovirus 3 (PCV3) is a novel virus associated with acute PDNS (porcine dermatitis and nephropathy syndrome)‐like clinical signs identified by metagenomic sequencing from swine. Its high occurrence may pose a potential threat to the swine industry worldwide. The processes resulting in the emergence and spread of PCV3 remain poorly understood. Herein, the possible origin, genotypes, and evolutionary dynamics of PCV3 based on available genomic sequences are determined. The closest ancestor of PCV3 is found to be within the clade 1 bat CVs. Using different phylogenetic methods, two major genotypes are identified, PCV3a and PCV3b. It is found that the effective population size of PCV3 increased rapidly during late 2013 to early 2014 and this is associated with the diversification of PCV3a and PCV3b. A relatively high effective reproductive number (Re) value and higher evolutionary rate were found compared to other single‐stranded DNA viruses, and positive selection on codons 122 and 320 (24 of ORF2) is identified. It is hypothesized that this, together with the prediction of a potential change of an antigenic epitope at position 320, might have allowed PCV3 to escape from the host immune response. Overall, this study has important implications for understanding the ongoing PCV3 cases worldwide and will guide future efforts to develop effective preventive and control measures.

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Section: Methodsmentioning

confidence: 99%

Origin, Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Circovirus 3

et al. 2018

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“…This analysis sequentially tests every combination of three sequences in an input alignment for evidence that one of the three sequences is a recombinant and the other two are its parents. RDP4 uses a range of methods including the original RDP method (Martin and Rybicki 2000), BOOTSCAN (Salminen et al 1995), MAXCHI (Maynard Smith 1992), CHIMAERA (Posada and Crandall 2001), 3SEQ (Boni, Posada, and Feldman 2007), GENECONV (Padidam, …”

Section: Recombination Analysismentioning

confidence: 99%

New species in the papaya ringspot virus cluster: Insights into the evolution of the PRSV lineage

Desbiez¹,

Wipf-Scheibel²,

Millot³

et al. 2017

Virus Research

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Please cite this article as: Desbiez, C., Wipf-Scheibel, C., Millot, P., Verdin, E., Dafalla, G., Lecoq, H., New species in the papaya ringspot virus cluster: insights into the evolution of the PRSV lineage.Virus Research http://dx.doi.org/10. 1016/j.virusres.2017.06.022 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. SuWMV appeared 10 times more frequent than WMVBV in that country (14.6% vs. 1.5% of the samples tested). The geographic structure and molecular diversity patterns of the putative and acknowledged species suggest that the PRSV-like cluster originated in the Old World about 3600 years ago, with an important diversification in Africa.

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“…Recombination Detection Program (RDP v4.43) [45] was used to identify potential recombination events through different models. In this study, three methods were used to analyze the sequence: RDP [46], GENECONV [47], and MaxChi [48]. The highest acceptable p value is 0.05 with 100 times of permutation and shuffled alignment columns.…”

Section: Detection Of Recombination Events In P2x Genesmentioning

confidence: 99%

“…To understand the evolutionary feature of P2X genes, recombination points were investigated using the RDP software with the RDP [46], Geneconv [47], and MaxChi [48] methods. As shown in Table 3, a total of 116 intragenic recombination events were identified, 64 identified using RDP, 10 using GENECONV, and 42 using MaxChi.…”

Section: Detection Of Intragenic Recombination Events In the Putativementioning

confidence: 99%

Comparative study of the P2X gene family in animals and plants

Hou

Cao

2016

Purinergic Signalling

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P2X receptors are ligand-gated ion channels that can bind with the adenosine triphosphate (ATP) and have diverse functional roles in neuropathic pain, inflammation, special sense, and so on. In this study, 180 putative P2X genes, including 176 members in 32 animal species and 4 members in 3 species of lower plants, were identified. These genes were divided into 13 groups, including 7 groups in vertebrates and 6 groups in invertebrates and lower plants, through phylogenetic analysis. Their gene organization and motif composition are conserved in most predicted P2X members, while groupspecific features were also found. Moreover, synteny relationships of the putative P2X genes in vertebrates are conserved while simultaneously experiencing a series of gene insertion, inversion, and transposition. Recombination signals were detected in almost all of the vertebrates and invertebrates, suggesting that intragenic recombination may play a significant role in the evolution of P2X genes. Selection analysis also identified some positively selected sites that acted on the evolution of most of the predicted P2X proteins. The phenomenon of alternative splicing occurred commonly in the putative P2X genes of vertebrates. This article explored in depth the evolutional relationship among different subtypes of P2X genes in animal and plants and might serve as a solid foundation for deciphering their functions in further studies.

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RDP: detection of recombination amongst aligned sequences

Cited by 1,371 publications

References 10 publications

Origin, Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Circovirus 3

Origin, Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Circovirus 3

New species in the papaya ringspot virus cluster: Insights into the evolution of the PRSV lineage

Comparative study of the P2X gene family in animals and plants

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