Abstract
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. dahliaegenome. Key words: Verticillium dahliae, genome, simple sequence repeats, distribution.
Highlights
Verticillium dahliae Kleb. is the causal agent of vascular wilt diseases on plants worldwide, resulting in enormous economic losses
The results show that simple sequence repeats (SSR) were abundant in the V. dahliae genome with about one SSR
The tri-nt SSRs were the most abundant in terms of unit numbers being 31.0% of the total number of SSRs in the genome (1,677 of the 5,418) (Table 2). 1,037 (61.8%) of the tri-nt SSRs were distributed in the exonic regions, 552 were in the intergenic regions, and only 88 were found in the intronic regions
Summary
Verticillium dahliae Kleb. is the causal agent of vascular wilt diseases on plants worldwide, resulting in enormous economic losses. Is the causal agent of vascular wilt diseases on plants worldwide, resulting in enormous economic losses. It attacks a wide range of plant hosts, including agriculturally important crops such as alfalfa, tomato, cotton, potato, eggplant, pepper, ornamental flowers, fruit trees, and shrubs (Pegg and Brady, 2002; Fradin and Thomma, 2006; Klosterman et al, 2009). In the Verticillium genus, it was usually only the isolates that produce microsclerotia that were classified as V. dahliae (Barbara and Clewes, 2003), sometimes the host specificity and its pathogenicity varies in different. Mycelial-type V. dahliae isolates without microsclerotia were included (Song et al, 1997). It is well documented that V. dahliae exhibits great phenotypic diversity and genetic plasticity
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