Abstract
BackgroundSimple 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.ResultsWe 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.ConclusionTaking 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.
Highlights
Simple sequence repeats (SSRs) have been successfully used for various genetic and evolutionary studies in eukaryotic systems
Genome-wide distribution of SSRs by the SSR unit size In order to systematically characterize the distribution of SSRs, we surveyed all of the SSRs in the N. crassa genome
Potential role of amino acid repeats (AAR) encoded by tri-nt SSRs Our results suggest that AAR encoded by tri-nt SSRs have undergone positive and negative selections, depending on their sequence types: three AAR (Gln, Glutamic acid (Glu) and Ser) were over-represented and three AAR (Leu, Cys and Val) were under-represented in the genome (Fig. 3)
Summary
Simple sequence repeats (SSRs) have been successfully used for various genetic and evolutionary studies in eukaryotic systems. Two alternative hypotheses were suggested to explain the genesis of SSRs. Two alternative hypotheses were suggested to explain the genesis of SSRs These hypotheses propose that SSRs originate either spontaneously from/ within unique sequences (de novo genesis) or that they are brought about in a primal form into a receptive genomic location by mobile elements (adoptive genesis). These two hypotheses are both adequate for explaining the ubiquitous distribution of SSRs. there remains much to be understood to elucidate which one is right and how the non-random distribution of SSRs has emerged in the eukaryotic genome [1,9,10,11]. We reasoned that characterizing the SSR distribution in the N. crassa genome would provide a unique opportunity to explore the non-random distribution of SSRs shaped by the de novo genesis in the eukaryotic genome
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