title: Genome wide survey and analysis of small repetitive sequences in caulimoviruses.
abstract: Microsatellites are known to exhibit ubiquitous presence across all kingdoms of life including viruses. Members of the Caulimoviridae family severely affect growth of vegetable and fruit plants and reduce economic yield in diverse cropping systems worldwide. Here, we analyzed the nature and distribution of both simple and complex microsatellites present in complete genome of 44 species of Caulimoviridae. Our results showed, in all analyzed genomes, genome size and GC content had a weak influence on number, relative abundance and relative density of microsatellites, respectively. For each genome, mono- and dinucleotide repeats were found to be highly predominant and are overrepresented in genome of majority of caulimoviruses. AT/TA and GAA/AAG/AGA was the most abundant di- and trinucleotide repeat motif, respectively. Repeats larger than trinucleotide were rarely found in these genomes. Comparative study of occurrence, abundance and density of microsatellite among available RNA and DNA viral genomes indicated that simple repeats were least abundant in genomes of caulimoviruses. Polymorphic repeats even though rare were observed in the large intergenic region of the genome, indicating strand slippage and/or unequal recombination processes do occur in caulimoviruses. To our knowledge, this is the first analysis of microsatellites occurring in any dsDNA viral genome. Characterization of such variations in repeat sequences would be important in deciphering the origin, mutational processes, and role of repeat sequences in viral genomes.
authors.affiliation: Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
authors.forename: Biju
authors.initials: B
authors.lastname: George
authors.affiliation: Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
authors.forename: Prabu
authors.initials: P
authors.lastname: Gnanasekaran
authors.affiliation: Department of Biotechnology, Jamia Hamdard University, New Delhi, Delhi 110062, India.
authors.forename: S K
authors.initials: SK
authors.lastname: Jain
authors.affiliation: Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India. Electronic address: supriyachakrasls@yahoo.com.
authors.forename: Supriya
authors.initials: S
authors.lastname: Chakraborty
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D017796:Caulimovirus / Q000235:genetics*; D059646:Genome Size; D016679:Genome, Viral; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D059372:Nucleotide Motifs; D011110:Polymorphism, Genetic; D016415:Sequence Alignment; D059467:Transcriptome
keywords: Caulimoviridae; Compound microsatellite; Relative abundance; Relative density; SSRs