Analysis of dinucleotide signatures in HIV-1 subtype B genomes

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• 作者：ARIDAMAN PANDIT (1) (3)
  JYOTHIRMAYI VADLAMUDI (1)
  SOMDATTA SINHA (2)
  
• 关键词：genome signature ; DRAP ; HIV ; 1 ; chaos game representation
• 刊名：Journal of Genetics
• 出版年：2013
• 出版时间：December 2013
• 年：2013
• 卷：92
• 期：3
• 页码：403-412
• 全文大小：1,467 KB
• 作者单位：ARIDAMAN PANDIT (1) (3)
  JYOTHIRMAYI VADLAMUDI (1)
  SOMDATTA SINHA (2)
  
  1. Centre for Cellular and Molecular Biology (CSIR), Hyderabad, 500 007, India
  3. Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, Utrecht, 3584, CH, The Netherlands
  2. Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli, 140 306, India
  
• ISSN：0973-7731

文摘

Dinucleotide usage is known to vary in the genomes of organisms. The dinucleotide usage profiles or genome signatures are similar for sequence samples taken from the same genome, but are different for taxonomically distant species. This concept of genome signatures has been used to study several organisms including viruses, to elucidate the signatures of evolutionary processes at the genome level. Genome signatures assume greater importance in the case of host–pathogen interactions, where molecular interactions between the two species take place continuously, and can influence their genomic composition. In this study, analyses of whole genome sequences of the HIV-1 subtype B, a retrovirus that caused global pandemic of AIDS, have been carried out to analyse the variation in genome signatures of the virus from 1983 to 2007. We show statistically significant temporal variations in some dinucleotide patterns highlighting the selective evolution of the dinucleotide profiles of HIV-1 subtype B, possibly a consequence of host specific selection.