Potential linkage between compound microsatellites and recombination in geminiviruses: Evidence from comparative analysis

George, Binu; Alam, Ch. Mashhood; Kumar, Ravinder; Gnanasekaran, Prabu; Chakraborty, Supriya

doi:10.1016/j.virol.2015.03.003

Cited by 32 publications

(19 citation statements)

References 81 publications

(93 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A detailed insight into various betasatellites associated with chilli leaf curl disease causing begomoviruses [6] indicates a likelihood of ToLCuPaB helping the non-cognate CLCuMuV (DNA-A) to cause infection in the host. The GC content analysis also suggests the presence of below average GC content (the lowest) at the coat-protein region (AV1) in DNA-A molecule and the region spanning the A-rich region in betasatellite molecule, which further supports the possibility of viral genome to undergo recombination [37]. The low GC region has also been reported to be potential recombination site in human adenovirus which may facilitate the evolution [38].…”

Section: Discussionmentioning

confidence: 72%

Occurrence of Cotton leaf curl Multan virus and associated betasatellites with leaf curl disease of Bhut-Jolokia chillies (Capsicum chinense Jacq.) in India

et al. 2021

View full text Add to dashboard Cite

Geminiviridae comprises the largest family of plant viruses which causes severe crop losses in India. The highest pungency chilli Bhut-Jolokia or ghost pepper (Capsicum chinense Jaqc.) hails from North-East region of India and is used in many dishes to add flavors and also for its medicinal value. However, this chilli variety is also affected by viruses leading to crop and economic losses. The present study reports the identification of begomoviruses in the infected chilli Bhut-Jolokia leaf samples collected from eight different places of North-East region (Manipur) of India. The infected leaf samples were screened for the presence of viral genome by rolling circle amplification (RCA) followed by PCR using degenerate primer pairs. The subsequent analyses using restriction fragment length polymorphism and sequencing revealed the presence of Cotton leaf curl Multan virus (CLCuMuV), and Tomato leaf curl Patna betasatellite (ToLCPaB). The findings focus on the phylogenetic relatedness, probable recombinational hot-spots and evolutionary divergence of the viral DNA sequences with the current reported begomoviral genome. To the best of our knowledge, this is the first report showing the presence of CLCuMuV, and associated non-cognate ToLCPaB with leaf curl disease of Bhut-Jolokia chillies. The study reveals potential recombination sites on both viral genome and betsatellite which, during the course of evolution, may have aided the virus to progress and successfully establish infection in chilli plants. Taken together, our results suggest a possible spread of CLCuMuV to the hitherto non-host crop in the North-East region of India.

show abstract

Section: Discussionmentioning

confidence: 72%

Occurrence of Cotton leaf curl Multan virus and associated betasatellites with leaf curl disease of Bhut-Jolokia chillies (Capsicum chinense Jacq.) in India

et al. 2021

View full text Add to dashboard Cite

show abstract

“…However, in the current analysis, low complexity of cSSR was observed in both coding and non-coding regions. In a recent study on Geminivirus, cSSRs was reported as site of recombination (29), thus ascertaining their role in evolution of viruses.…”

Section: Ssrs/cssrs In Coding Regionsmentioning

confidence: 99%

Microsatellite Diversity and Complexity in Eighteen Staphylococcus Phage Genomes

Alam

Iqbal²,

Tripathi

et al. 2017

Gene Cell Tissue

View full text Add to dashboard Cite

The present study focused on Staphylococcus phage genomes, which have been classified to 3 categories on the basis of their size. Overall, 18 classes of II Staphylococcus phage genomes with genome size around 40 kbp were investigated to elucidate the presence, distribution, and complexity of SSRs therein. The full length genome sequences from NCBI were analyzed using the IMEx software. A total of 3656 simple sequence repeats (SSRs) and 213 compound SSRs (cSSR) were present in the studied genomes. The incident frequency of SSR and cSSR per genome ranged from 183 to 308 and 8 to 19, respectively. The SSRs distribution across genomes was non-linear and so was its conversion to cSSR (the range of cSSR percentage was from 4.15 to 9.13) implicating a non-uniform incidence and clustering in genomes. The AT rich content of genomes was reflected in the prevalence of repeats with A, AT/TA, and AAG/GAA being the highest represented mono-, di-, and tri-nucleotide repeat motifs, respectively. An increase in dMAX was accompanied by greater cSSRs in the genomes yet the increase was neither uniform across genomes nor linear. The SSRs and cSSRs are predominantly localized on the coding region. The non-coding region accounts for~19% in SSR and~30% in cSSR while a hypothetical protein accounted for~30% in SSRs as well as cSSR. The relative frequencies and distribution of different classes of simple and compound microsatellites within and across genomes are suggestive of these sequences being involved in genome evolution and adaptation.

show abstract

“…The hairpins formed by the compound microsatellites consisting of two or more individual microsatellites are considered to be hot-spots for recombination in plant viruses [15]. Stable secondary hairpin structures resulting in trinucleotide repeat expansion causing DNA polymerase slippage and trinucleotide expansion are removed by special helicases aimed at resolving theses hairpins [16].…”

Section: Dna Secondary Structurementioning

confidence: 99%

Structural and functional significance of microsatellites

2016

View full text Add to dashboard Cite

Here we review literature data on impact of microsatellite repeats on DNA and chromatin structure and the results of studies on association between the length of microsatellite repeats and predisposition to pathologies. The DNA secondary structure is modified in microsatellite sites, the repeats favour formation of Z-DNA, hairpins, triplexes and quadruplexes. The chromatin structure and chromatin loop organization are also modified in microsatellite sites. The data of association studies are classified according to the localization of the microsatellite: in the gene promoter, in exon 1 part coding the signal sequence, in the gene introns, coding area s and 3'-UTRs.

show abstract

Potential linkage between compound microsatellites and recombination in geminiviruses: Evidence from comparative analysis

Cited by 32 publications

References 81 publications

Occurrence of Cotton leaf curl Multan virus and associated betasatellites with leaf curl disease of Bhut-Jolokia chillies (Capsicum chinense Jacq.) in India

Occurrence of Cotton leaf curl Multan virus and associated betasatellites with leaf curl disease of Bhut-Jolokia chillies (Capsicum chinense Jacq.) in India

Microsatellite Diversity and Complexity in Eighteen Staphylococcus Phage Genomes

Structural and functional significance of microsatellites

Contact Info

Product

Resources

About