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Open Access Research article

Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inference

Tae-Sung Kim1, James G Booth2, Hugh G Gauch3, Qi Sun4, Jongsun Park15, Yong-Hwan Lee5 and Kwangwon Lee1*

Author Affiliations

1 Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853 USA

2 Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853 USA

3 Department of Crop and Soil Sciences, Cornell University, Ithaca, NY 14853 USA

4 Computational Biology Service Unit, Cornell University, Ithaca NY 14853 USA

5 Department of Agricultural Biotechnology and Center for Fungal Genetic Resources, Seoul National University, Seoul 151-921, Republic of Korea

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BMC Genomics 2008, 9:31  doi:10.1186/1471-2164-9-31

Published: 23 January 2008



Simple sequence repeats (SSRs) have been successfully used for various genetic and evolutionary studies in eukaryotic systems. The eukaryotic model organism Neurospora crassa is an excellent system to study evolution and biological function of SSRs.


We identified and characterized 2749 SSRs of 963 SSR types in the genome of N. crassa. The distribution of tri-nucleotide (nt) SSRs, the most common SSRs in N. crassa, was significantly biased in exons. We further characterized the distribution of 19 abundant SSR types (AST), which account for 71% of total SSRs in the N. crassa genome, using a Poisson log-linear model. We also characterized the size variation of SSRs among natural accessions using Polymorphic Index Content (PIC) and ANOVA analyses and found that there are genome-wide, chromosome-dependent and local-specific variations. Using polymorphic SSRs, we have built linkage maps from three line-cross populations.


Taking our computational, statistical and experimental data together, we conclude that 1) the distributions of the SSRs in the sequenced N. crassa genome differ systematically between chromosomes as well as between SSR types, 2) the size variation of tri-nt SSRs in exons might be an important mechanism in generating functional variation of proteins in N. crassa, 3) there are different levels of evolutionary forces in variation of amino acid repeats, and 4) SSRs are stable molecular markers for genetic studies in N. crassa.