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Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inference
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 characteriz...
Autores principales: | , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2008
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2257937/ https://www.ncbi.nlm.nih.gov/pubmed/18215294 http://dx.doi.org/10.1186/1471-2164-9-31 |
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author | Kim, Tae-Sung Booth, James G Gauch, Hugh G Sun, Qi Park, Jongsun Lee, Yong-Hwan Lee, Kwangwon |
author_facet | Kim, Tae-Sung Booth, James G Gauch, Hugh G Sun, Qi Park, Jongsun Lee, Yong-Hwan Lee, Kwangwon |
author_sort | Kim, Tae-Sung |
collection | PubMed |
description | 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. CONCLUSION: 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. |
format | Text |
id | pubmed-2257937 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-22579372008-02-28 Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inference Kim, Tae-Sung Booth, James G Gauch, Hugh G Sun, Qi Park, Jongsun Lee, Yong-Hwan Lee, Kwangwon BMC Genomics Research Article 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. CONCLUSION: 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. BioMed Central 2008-01-23 /pmc/articles/PMC2257937/ /pubmed/18215294 http://dx.doi.org/10.1186/1471-2164-9-31 Text en Copyright © 2008 Kim et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Kim, Tae-Sung Booth, James G Gauch, Hugh G Sun, Qi Park, Jongsun Lee, Yong-Hwan Lee, Kwangwon Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inference |
title | Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inference |
title_full | Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inference |
title_fullStr | Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inference |
title_full_unstemmed | Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inference |
title_short | Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inference |
title_sort | simple sequence repeats in neurospora crassa: distribution, polymorphism and evolutionary inference |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2257937/ https://www.ncbi.nlm.nih.gov/pubmed/18215294 http://dx.doi.org/10.1186/1471-2164-9-31 |
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