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United States Department of Agriculture

Agricultural Research Service

Title: SIMPLE SEQUENCE REPEAT ABUNDANCE AND DISTRIBUTION IN TWO OOMYCETE GENOMES: PHYTOPHTHORA SOJAE AND P. RAMORUM)

Author
item Grunwald, Niklaus - Nik
item Tripathi, Sucheta
item Ivors, Kelly
item Lamour, Kurt
item Tyler, Brett

Submitted to: Fungal Genetics Conference Proceedings
Publication Type: Abstract only
Publication Acceptance Date: 1/15/2005
Publication Date: 3/10/2005
Citation: Grunwald, N.J., Tripathi, S., Ivors, K., Lamour, K.H., Tyler, B.M. 2005. Simple sequence repeat abundance and distribution in two oomycete genomes: phytophthora sojae and p. ramorum. Fungal Genetics Conference Proceedings. p64.

Interpretive Summary:

Technical Abstract: The first whole genome assembly of the two oomycete plant pathogens Phytophthora sojae (95 Mb) and P. ramorum (65 Mb) were examined to determine types, abundance, and distribution of different simple sequence repeats (SSRs) ranging between 2 to 6 bp in motif length. We found 2,128 and 1,000 SSRs in P. sojae and P. ramorum, respectively. In general, the density of SSRs (bp per Mb) in P. sojae is about 1.5 times that of P. ramorum. Whereas AC dinucleotide repeats appear at a higher density in P. ramorum, AG and AT repeats appear at a higher density in P. sojae. Interestingly, density of most trinucleotide repeats was higher in Ps than in Pr. Although P. sojae has a larger genome, the percentage of SSR loci located in coding regions is higher at 17.4% compared to P. ramorum at 14.8%. Compared to other species, including Saccharomyces cerevisiae, repeats of length 4, 5, and 6 bp are considerably underrepresented in both Phytophthora genomes based on density. Whereas in most genomes studied to date dinucleotide repeat stretches tended to be longer than other repeats, in the case of Phytophthora only tetranucleotide repeats were occasionally considerably longer (ACAG, ACAT, and AGAT). As expected frequency of trinucleotide repeats in exons was considerably higher when compared to di, tetra- or pentanucleotide repeats.

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