title: Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inference.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853 USA. tk227@cornell.edu
authors.forename: Tae-Sung
authors.initials: TS
authors.lastname: Kim
authors.forename: James G
authors.initials: JG
authors.lastname: Booth
authors.forename: Hugh G
authors.initials: HG
authors.lastname: Gauch
authors.forename: Qi
authors.initials: Q
authors.lastname: Sun
authors.forename: Jongsun
authors.initials: J
authors.lastname: Park
authors.forename: Yong-Hwan
authors.initials: YH
authors.lastname: Lee
authors.forename: Kwangwon
authors.initials: K
authors.lastname: Lee
mesh_terms: D019143:Evolution, Molecular; D020224:Expressed Sequence Tags; D005819:Genetic Markers; D016681:Genome, Fungal; D018895:Microsatellite Repeats; D009492:Neurospora crassa / Q000235:genetics*; D011110:Polymorphism, Genetic
chemical_list: D005819:Genetic Markers