Possible Emergence of New Geminiviruses by Frequent Recombination

Padidam, Malla; Sawyer, Stanley; Fauquet, Claude

doi:10.1006/viro.1999.0056

Cited by 1,386 publications

(993 citation statements)

References 39 publications

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“…Interspecies recombination has played a major role in the evolution of members of ssDNA virus family Geminiviridae [24], whereas, in positive sense ssRNA viruses, it has been reported in the Potyviridae [25] and Luteoviridae [26]. Interspecies recombination analysis in the current study revealed the lack of extensive exchange of genetic material from other Carlavirus species to GarCLV, but still, provided an evidence for interspecies recombination events in the CP gene of 22 Carlavirus species (Suppl.…”

mentioning

confidence: 47%

Molecular characterization of coat protein gene of Garlic common latent virus isolates from India: an evidence for distinct phylogeny and recombination

Pramesh

2013

Virus Genes

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The coat protein (CP) gene of five Indian Garlic common latent virus (GarCLV) isolates was sequenced and it was 960 bp long in all the five isolates, encoding a protein of 319 amino acids. Comparative nucleotide sequence analysis revealed diversity of 4.3 % among the Indian isolates and of 11.9 % among all isolates worldwide. Amino acid sequence comparison showed a significant variability in the N-terminal of CP of GarCLV. Various protein analysis tools identified thirteen conserved domains and motifs including Carlavirus and Potexvirusspecific Flexi CP and Flexi N CP. Phylogenetic analysis clustered GarCLV isolates in the subgroup II with isolates from Australia, Brazil, Japan, and South Korea. Intraspecies recombination study revealed that only one of the Indian isolates was a recombinant. Interspecies recombination study suggested the absence of genetic exchange from Carlavirus species to GarCLV; conversely, GarCLV was identified as a putative donor for at least two other Carlavirus species. This is the first report of molecular variability and recombination in GarCLV isolates.

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mentioning

confidence: 47%

Molecular characterization of coat protein gene of Garlic common latent virus isolates from India: an evidence for distinct phylogeny and recombination

Pramesh

2013

Virus Genes

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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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“…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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Possible Emergence of New Geminiviruses by Frequent Recombination

Cited by 1,386 publications

References 39 publications

Molecular characterization of coat protein gene of Garlic common latent virus isolates from India: an evidence for distinct phylogeny and recombination

Molecular characterization of coat protein gene of Garlic common latent virus isolates from India: an evidence for distinct phylogeny and recombination

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

Comparative study of the P2X gene family in animals and plants

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