title: Frequency and distribution of simple and compound microsatellites in forty-eight Human papillomavirus (HPV) genomes.
abstract: Simple sequence repeats (SSRs) are tandem-repeated sequences ubiquitously present but differentially distributed across genomes. Present study is a systematic analysis for incidence, composition and complexity of different microsatellites in 48 representative Human papillomavirus (HPV) genomes. The analysis revealed a total of 1868 SSRs and 120 cSSRs. However, four genomes (HPV-60, HPV-92, HPV-112 and HPV-136) lacked any cSSR content; while HPV-31 accounted for a maximum of 10 cSSRs. An overall increase in cSSR% with higher dMAX was observed. The SSRs and cSSRs were prevalent in coding regions. Poly(A/T) repeats were significantly more abundant than poly(G/C) repeats possibly due to high (A/T) content of the HPV genomes. Further, higher prevalence of di-nucleotide repeats over tri-nucleotide repeats may be attributed to instability of former because of higher slippage rate. An in-depth study of the satellite sequences would provide an insight into the imperfections and evolution of microsatellites.
authors.affiliation: Department of Biomedical Sciences, SRCASW, University of Delhi, Vasundhara Enclave, New Delhi 110096, India.
authors.forename: Avadhesh Kumar
authors.initials: AK
authors.lastname: Singh
authors.affiliation: Department of Botany, Patna University, Bihar 800005, India.
authors.forename: Chaudhary Mashhood
authors.initials: CM
authors.lastname: Alam
authors.affiliation: Department of Botany, Patna University, Bihar 800005, India.
authors.forename: Choudhary
authors.initials: C
authors.lastname: Sharfuddin
authors.affiliation: Department of Biomedical Sciences, SRCASW, University of Delhi, Vasundhara Enclave, New Delhi 110096, India. Electronic address: safdar_mgl@live.in.
authors.forename: Safdar
authors.initials: S
authors.lastname: Ali
mesh_terms: D018900:Dinucleotide Repeats / Q000235:genetics; D005787:Gene Frequency; D006801:Humans; D018895:Microsatellite Repeats / Q000235:genetics*; D027383:Papillomaviridae / Q000145:classification* / Q000235:genetics*; D030361:Papillomavirus Infections; D011061:Poly A / Q000235:genetics; D011066:Poly C / Q000235:genetics; D011068:Poly G / Q000235:genetics; D011071:Poly T / Q000235:genetics; D018911:Trinucleotide Repeats / Q000235:genetics
chemical_list: D011061:Poly A; D011071:Poly T; D011068:Poly G; C008961:poly G-poly C; C008950:poly A-T; D011066:Poly C
keywords: Compound microsatellites; Human papillomavirus; Microsatellites; Simple sequence repeats