title: Potential linkage between compound microsatellites and recombination in geminiviruses: Evidence from comparative analysis.
abstract: The compound microsatellites consist of two or more individual microsatellites, originate from mutation or imperfection in simple repeat sequences. The reports on systematic analysis of the occurrence, size and density of compound microsatellite (cSSR) types are very rare. Our study indicates that cSSRs are clustered at specific regions in the begomovirus genomes. cSSRs were overrepresented in majority of begomovirus genomes indicating that they might have some functional significance. Further, non-random distribution pattern of cSSR in begomovirus genomes was significantly correlated with the recombination breakpoint positions in the genome. The analysis of cSSR regions in the viral genome indicates the presence of stem loop (hairpin) secondary structure. The significance of these findings in biology of geminiviruses is discussed based on our present understanding of recombination and repetitive DNA. To our knowledge, this is the first analysis suggesting the possible association between recombination and microsatellites in any viral genome.
authors: Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
authors: B
authors: B
authors: George
authors: Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
authors: Ch Mashhood
authors: ChM
authors: Alam
authors: Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
authors: R Vinoth
authors: RV
authors: Kumar
authors: Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
authors: Prabu
authors: P
authors: Gnanasekaran
authors: Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India. Electronic address: supriyachakrasls@yahoo.com.
authors: S
authors: S
authors: Chakraborty
mesh_terms: D017791:Geminiviridae / Q000145:classification* / Q000235:genetics*; D014644:Genetic Variation; D016679:Genome, Viral; D018895:Microsatellite Repeats; D009690:Nucleic Acid Conformation; D011995:Recombination, Genetic
keywords: Geminivirus; Hotspot; IMEx; Recombination; Relative abundance; Relative density; cSSR%; dMAX