Coevolution Between Simple Sequence Repeats (SSRs) and Virus Genome Size

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2012 Aug 31

PMID 22931422

Citations 27

Authors

Xiangyan Zhao

Yonglei Tian

Ronghua Yang

Haiping Feng

Qingjian Ouyang

You Tian

Zhongyang Tan

Mingfu Li

Yile Niu

Jianhui Jiang

Guoli Shen

Ruqin Yu

Affiliations

Soon will be listed here.

Abstract

Background: Relationship between the level of repetitiveness in genomic sequence and genome size has been investigated by making use of complete prokaryotic and eukaryotic genomes, but relevant studies have been rarely made in virus genomes.

Results: In this study, a total of 257 viruses were examined, which cover 90% of genera. The results showed that simple sequence repeats (SSRs) is strongly, positively and significantly correlated with genome size. Certain repeat class is distributed in a certain range of genome sequence length. Mono-, di- and tri- repeats are widely distributed in all virus genomes, tetra- SSRs as a common component consist in genomes which more than 100 kb in size; in the range of genome < 100 kb, genomes containing penta- and hexa- SSRs are not more than 50%. Principal components analysis (PCA) indicated that dinucleotide repeat affects the differences of SSRs most strongly among virus genomes. Results showed that SSRs tend to accumulate in larger virus genomes; and the longer genome sequence, the longer repeat units.

Conclusions: We conducted this research standing on the height of the whole virus. We concluded that genome size is an important factor in affecting the occurrence of SSRs; hosts are also responsible for the variances of SSRs content to a certain degree.

Citing Articles

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