Differential distributions of mononucleotide repeat sequences in 256 viral genomes and its potential implications.
Mononucleotide repeats (MNRs) have been systematically investigated in the genomes of eukaryotic and prokaryotic organisms. However, detailed information on the distribution of MNRs in viral genomes is limited. In this study, we examined the distributions of MNRs in 256 fully sequenced virus genomes which showed extensive variations across viral genomes, and is significantly influenced by both genome size and CG content. Furthermore, the ratio of the observed to the expected number of MNRs (O/E ratio) appears to be influenced by both the host range and genome type of a particular virus. Additionally, the densities and frequencies of MNRs in genic regions are lower than in non-coding regions, suggesting that selective pressure acts on viral genomes. We also discuss the potential functional roles that these MNR loci could play in virus genomes. To our knowledge, this is the first analysis focusing on MNRs in viruses, and our study could have potential implications for a deeper understanding of virus genome stability and the co-evolution that occurs between a virus and its host.
State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; College of Biology, State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China.
Lü
L
Qin
State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
Yuxin
Y
Ma
College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China.
Pengbo
P
Liang
State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; College of Biology, State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China. Electronic address: zhongyang@hnu.edu.cn.
Zhongyang
Z
Tan
State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China. Electronic address: sfli@ippcaas.cn.
Shifang
S
Li
D000818:Animals; D001482:Base Composition / Q000235:genetics; D001483:Base Sequence; D002874:Chromosome Mapping; D004279:DNA, Viral / Q000032:analysis / Q000235:genetics*; D014644:Genetic Variation; D059646:Genome Size; D016679:Genome, Viral / Q000235:genetics*; D058507:Host Specificity / Q000235:genetics; D006801:Humans; D018895:Microsatellite Repeats / Q000235:genetics*; D014780:Viruses / Q000235:genetics*
D004279:DNA, Viral
Evolution; Mononucleotide repeats; Virus genomes