Shi Yongqiang

Frequency and distribution of genome-based microsatellites in Verticillium dahliae

A total of 5,418 simple sequence repeats (SSRs) were identified in the 33.8 Mb genomic DNA sequence of Verticillium dahliae. SSR loci were classified by repeat types and frequency in different genomic regions. The results show that the SSRs in different repeat units exhibited differential or non-random distribution in different genomic locations. Whole genome analyses showed that the tri-nucleotide (nt) repeat was the most abundant microsatellite type. The number of tri-nt SSRs was 1,677 comprising 31.0% of the total number of SSRs, followed by hexa-nt, mono-nt, di-nt SSRs, tetra-nt and pentra-nt SSRs in that order. In the exonic regions of the genome, the tri-nt SSRs occurred more frequently than the other SSR types. A total of 1, 037 (61.8%) tri-nt SSRs were distributed in the exonic regions, an approximately two-fold higher number than in the intergenic regions (66.1 per Mb versus 32.3 per Mb respectively). Nearly half the hexa-nt SSRs were also distributed in the coding region while most of the mono-nt, di-nt, tetra-nt and penta-nt SSRs were predominantly present in the intronic and intergenic regions. The biased distribution of the SSRs may reveal the functional significance of SSRs in the V. dahliae genome.