Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning

Lemey, Philippe; Lott, Martin; Martin, Darren P.; Moulton, Vincent

doi:10.1186/1471-2105-10-126

Cited by 57 publications

(40 citation statements)

References 51 publications

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“…RDP using 9 recombination analysis methods, RDP 29 , GENECONV 30 , BOOTSCAN 31 , MAXIMUM CHI SQUARE 32 , CHIMAERA 33 , SISCAN 34 , 3SEQ 35 , PHYLPRO 36 , LARD 37 and VisRD 38 for possible recombination breakpoints within query sequences. Recombination events identified by multiple recombination methods with high p-values and good phylogeny were considered potential targets for recombination.…”

Section: Methodsmentioning

confidence: 99%

Multiple begomoviruses found associated with cotton leaf curl disease in Pakistan in early 1990 are back in cultivated cotton

Zubair

Zaidi

Shakir

et al. 2017

Sci Rep

100

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The first epidemic of cotton leaf curl disease (CLCuD) in early 1990’s in the Indian subcontinent was associated with several distinct begomoviruses along with a disease-specific betasatellite. Resistant cotton varieties were introduced in late 1990’s but soon resistance was broken and was associated with a single recombinant begomovirus named Burewala strain of Cotton leaf curl Kokhran virus that lacks a full complement of a gene encoding a transcription activator protein (TrAP). In order to understand the ongoing changes in CLCuD complex in Pakistan, CLCuD affected plants from cotton fields at Vehari were collected. Illumina sequencing was used to assess the diversity of CLCuD complex. At least three distinct begomoviruses characterized from the first epidemic; Cotton leaf curl Multan virus, Cotton leaf curl Kokhran virus and Cotton leaf curl Alabad virus, several distinct species of alphasatellites and cotton leaf curl Multan betasatellite were found associated with CLCuD. These viruses were also cloned and sequenced through Sanger sequencing to confirm the identity of the begomoviruses and that all clones possessed a full complement of the TrAP gene. A new strain of betasatellite was identified here and named CLCuMuBVeh. The implications of these findings in efforts to control CLCuD are discussed.

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Section: Methodsmentioning

confidence: 99%

Multiple begomoviruses found associated with cotton leaf curl disease in Pakistan in early 1990 are back in cultivated cotton

Zubair

Zaidi

Shakir

et al. 2017

Sci Rep

100

View full text Add to dashboard Cite

show abstract

“…The parental and recombinant sequences were determined using the VisRD method [61], modified version of PHYLPRO [62], and EEEP [63] also implemented in RDP3 (default settings).…”

Section: Methodsmentioning

confidence: 99%

Mitochondrial DNA Variation and Introgression in Siberian Taimen Hucho taimen

Balakirev

Романов

Mikheev³

et al. 2013

PLoS ONE

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Siberian taimen Hucho taimen is the largest representative of the family Salmonidae inhabiting rivers of northern Eurasia. The species is under intensive aquaculture activity. To monitor natural taimen populations we have sequenced a portion (8,141 bp) of the mitochondrial (mt) genome in 28 specimens of H. taimen from six localities in the Amur River basin. Nucleotide variability is low (π = 0.0010), but structured in two divergent haplotype groups. A comparison of the data with the GenBank H. taimen mt genome (HQ897271) reveals significant differences between them in spite of the fact that the fish specimens come from neighboring geographical areas. The distribution of divergence is non-uniform with two highly pronounced divergent regions centered on two genes, ND3 and ND6. To clarify the pattern of divergence we sequenced the corresponding portion of the mt genome of lenok Brachymystax tumensis and analyzed the GenBank complete mt genomes of related species. We have found that the first and second divergent regions are identical between the GenBank H. taimen and two lenok subspecies, B. lenok and B. lenok tsinlingensis, respectively. Consequently, both divergent regions represent introgressed mtDNA resulting from intergeneric hybridization between the two lenok subspecies and H. taimen. Introgression is, however, not detected in our specimens. This plus the precise identity of the introgressed fragments between the donor and the recipient GenBank sequence suggests that the introgression is local and very recent, probably due to artificial manipulations involving taimen – lenok intergeneric hybridization. Human-mediated hybridization may become a major threat to aquatic biodiversity. Consequently we suggest that due attention needs to be given to this threat by means of responsible breeding program management, so as to prevent a potential spread of hybrid fishes that could jeopardize the resilience of locally adapted gene pools of the native H. taimen populations.

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“…TYLCV has therefore only recently come into contact and had the opportunity to exchange genetic material with numerous begomovirus species that are indigenous to the environments it has invaded. It is therefore an excellent model with which to study the occurrence and impact of recombination during the geographical range expansion of viruses [6], [7]. Moreover, the small DNA genomes of begomoviruses can be manipulated with relative ease under laboratory conditions, facilitating their use for testing fundamental questions on viral recombination in multicellular hosts [8].…”

Section: Introductionmentioning

confidence: 99%

Within-Host Dynamics of the Emergence of Tomato Yellow Leaf Curl Virus Recombinants

et al. 2013

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Tomato yellow leaf curl virus (TYLCV) is a highly damaging begomovirus native to the Middle East. TYLCV has recently spread worldwide, recombining with other begomoviruses. Recent analysis of mixed infections between TYLCV and Tomato leaf curl Comoros begomovirus (ToLCKMV) has shown that, although natural selection preserves certain co-evolved intra-genomic interactions, numerous and diverse recombinants are produced at 120 days post-inoculation (dpi), and recombinant populations from different tomato plants are very divergent. Here, we investigate the population dynamics that lead to such patterns in tomato plants co-infected with TYLCV and ToLCKMV either by agro-inoculation or using the natural whitefly vector Bemisia tabaci. We monitored the frequency of parental and recombinant genotypes independently in 35 plants between 18 and 330 dpi and identified 177 recombinants isolated at different times. Recombinants were detected from 18 dpi and their frequency increased over time to reach about 50% at 150 dpi regardless of the inoculation method. The distribution of breakpoints detected on 96 fully sequenced recombinants was consistent with a continuous generation of new recombinants as well as random and deterministic effects in their maintenance. A severe population bottleneck of around 10 genomes was estimated during early systemic infection–a phenomenon that could account partially for the heterogeneity in recombinant patterns observed among plants. The detection of the same recombinant genome in six of the thirteen plants analysed beyond 30 dpi supported the influence of selection on observed recombination patterns. Moreover, a highly virulent recombinant genotype dominating virus populations within one plant has, apparently, the potential to be maintained in the natural population according to its infectivity, within-host accumulation, and transmission efficiency - all of which were similar or intermediate to those of the parent genotypes. Our results anticipate the outcomes of natural encounters between TYLCV and ToLCKMV.

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Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning

Cited by 57 publications

References 51 publications

Multiple begomoviruses found associated with cotton leaf curl disease in Pakistan in early 1990 are back in cultivated cotton

Multiple begomoviruses found associated with cotton leaf curl disease in Pakistan in early 1990 are back in cultivated cotton

Mitochondrial DNA Variation and Introgression in Siberian Taimen Hucho taimen

Within-Host Dynamics of the Emergence of Tomato Yellow Leaf Curl Virus Recombinants

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