Simple sequence repeats in <it>Neurospora crassa</it>: distribution, polymorphism and evolutionary inference
<p>Abstract</p> <p>Background</p> <p>Simple sequence repeats (SSRs) have been successfully used for various genetic and evolutionary studies in eukaryotic systems. The eukaryotic model organism <it>Neurospora crassa </it>is an excellent system to study evolu...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2008-01-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/9/31 |
| _version_ | 1819181012564836352 |
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| author | Park Jongsun Sun Qi Gauch Hugh G Booth James G Kim Tae-Sung Lee Yong-Hwan Lee Kwangwon |
| author_facet | Park Jongsun Sun Qi Gauch Hugh G Booth James G Kim Tae-Sung Lee Yong-Hwan Lee Kwangwon |
| author_sort | Park Jongsun |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Simple sequence repeats (SSRs) have been successfully used for various genetic and evolutionary studies in eukaryotic systems. The eukaryotic model organism <it>Neurospora crassa </it>is an excellent system to study evolution and biological function of SSRs.</p> <p>Results</p> <p>We identified and characterized 2749 SSRs of 963 SSR types in the genome of <it>N. crassa</it>. The distribution of tri-nucleotide (nt) SSRs, the most common SSRs in <it>N. crassa</it>, 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 <it>N. crassa </it>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.</p> <p>Conclusion</p> <p>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 <it>N. crassa</it>, 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 <it>N. crassa</it>.</p> |
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| format | Article |
| id | doaj.art-01605565b8b94be59949a743405682e7 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-22T22:23:28Z |
| publishDate | 2008-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-01605565b8b94be59949a743405682e72022-12-21T18:10:36ZengBMCBMC Genomics1471-21642008-01-01913110.1186/1471-2164-9-31Simple sequence repeats in <it>Neurospora crassa</it>: distribution, polymorphism and evolutionary inferencePark JongsunSun QiGauch Hugh GBooth James GKim Tae-SungLee Yong-HwanLee Kwangwon<p>Abstract</p> <p>Background</p> <p>Simple sequence repeats (SSRs) have been successfully used for various genetic and evolutionary studies in eukaryotic systems. The eukaryotic model organism <it>Neurospora crassa </it>is an excellent system to study evolution and biological function of SSRs.</p> <p>Results</p> <p>We identified and characterized 2749 SSRs of 963 SSR types in the genome of <it>N. crassa</it>. The distribution of tri-nucleotide (nt) SSRs, the most common SSRs in <it>N. crassa</it>, 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 <it>N. crassa </it>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.</p> <p>Conclusion</p> <p>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 <it>N. crassa</it>, 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 <it>N. crassa</it>.</p>http://www.biomedcentral.com/1471-2164/9/31 |
| spellingShingle | Park Jongsun Sun Qi Gauch Hugh G Booth James G Kim Tae-Sung Lee Yong-Hwan Lee Kwangwon Simple sequence repeats in <it>Neurospora crassa</it>: distribution, polymorphism and evolutionary inference BMC Genomics |
| title | Simple sequence repeats in <it>Neurospora crassa</it>: distribution, polymorphism and evolutionary inference |
| title_full | Simple sequence repeats in <it>Neurospora crassa</it>: distribution, polymorphism and evolutionary inference |
| title_fullStr | Simple sequence repeats in <it>Neurospora crassa</it>: distribution, polymorphism and evolutionary inference |
| title_full_unstemmed | Simple sequence repeats in <it>Neurospora crassa</it>: distribution, polymorphism and evolutionary inference |
| title_short | Simple sequence repeats in <it>Neurospora crassa</it>: distribution, polymorphism and evolutionary inference |
| title_sort | simple sequence repeats in it neurospora crassa it distribution polymorphism and evolutionary inference |
| url | http://www.biomedcentral.com/1471-2164/9/31 |
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