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Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inference.
Tae-Sung Kim1, James G Booth, Hugh G Gauch
1Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853 USA. tk227@cornell.edu
BMC Genomics
|January 25, 2008
Summary
Simple sequence repeats (SSRs) in Neurospora crassa show varied genomic distribution and size variation, offering stable molecular markers for genetic studies and insights into protein evolution.
Area of Science:
- Genomics
- Evolutionary Biology
- Molecular Genetics
Background:
- Simple sequence repeats (SSRs) are valuable tools for genetic and evolutionary research in eukaryotes.
- The model organism Neurospora crassa provides an excellent system for studying SSR evolution and function.
Purpose of the Study:
- To identify and characterize SSRs in the N. crassa genome.
- To analyze SSR distribution, size variation, and utility as molecular markers.
Main Methods:
- Genome-wide identification and characterization of SSRs.
- Statistical analysis (Poisson log-linear model, PIC, ANOVA) of SSR distribution and variation.
- Construction of linkage maps using polymorphic SSRs from line-cross populations.
Main Results:
- 2749 SSRs of 963 types were identified in the N. crassa genome.
- Tri-nucleotide SSRs were the most common and showed biased distribution in exons.
- Significant genome-wide, chromosome-dependent, and local variations in SSR size were observed.
- Linkage maps were successfully constructed using polymorphic SSRs.
Conclusions:
- SSR distribution in the N. crassa genome varies systematically across chromosomes and SSR types.
- Exon-located tri-nucleotide SSR size variation may drive functional protein diversity.
- SSRs are stable molecular markers suitable for genetic studies in N. crassa.
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