Nucleotide diversity analysis highlights functionally important genomic regions
We analyzed functionality and relative distribution of genetic variants across the complete Oryza sativa genome, using the 40 million single nucleotide polymorphisms (SNPs) dataset from the 3,000 Rice Genomes Project (http://snp-seek.irri.org), the largest and highest density SNP collection for any...
| Main Authors: | , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Springer
2016
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| Online Access: | https://hdl.handle.net/10568/165189 |
| _version_ | 1855533827757178880 |
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| author | Tatarinova, Tatiana V. Chekalin, Evgeny Nikolsky, Yuri Bruskin, Sergey Chebotarov, Dmitry McNally, Kenneth L. Alexandrov, Nickolai |
| author_browse | Alexandrov, Nickolai Bruskin, Sergey Chebotarov, Dmitry Chekalin, Evgeny McNally, Kenneth L. Nikolsky, Yuri Tatarinova, Tatiana V. |
| author_facet | Tatarinova, Tatiana V. Chekalin, Evgeny Nikolsky, Yuri Bruskin, Sergey Chebotarov, Dmitry McNally, Kenneth L. Alexandrov, Nickolai |
| author_sort | Tatarinova, Tatiana V. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | We analyzed functionality and relative distribution of genetic variants across the complete Oryza sativa genome, using the 40 million single nucleotide polymorphisms (SNPs) dataset from the 3,000 Rice Genomes Project (http://snp-seek.irri.org), the largest and highest density SNP collection for any higher plant. We have shown that the DNA-binding transcription factors (TFs) are the most conserved group of genes, whereas kinases and membrane-localized transporters are the most variable ones. TFs may be conserved because they belong to some of the most connected regulatory hubs that modulate transcription of vast downstream gene networks, whereas signaling kinases and transporters need to adapt rapidly to changing environmental conditions. In general, the observed profound patterns of nucleotide variability reveal functionally important genomic regions. As expected, nucleotide diversity is much higher in intergenic regions than within gene bodies (regions spanning gene models), and protein-coding sequences are more conserved than untranslated gene regions. We have observed a sharp decline in nucleotide diversity that begins at about 250 nucleotides upstream of the transcription start and reaches minimal diversity exactly at the transcription start. We found the transcription termination sites to have remarkably symmetrical patterns of SNP density, implying presence of functional sites near transcription termination. Also, nucleotide diversity was significantly lower near 3′ UTRs, the area rich with regulatory regions. |
| format | Journal Article |
| id | CGSpace165189 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2016 |
| publishDateRange | 2016 |
| publishDateSort | 2016 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1651892024-12-19T14:13:10Z Nucleotide diversity analysis highlights functionally important genomic regions Tatarinova, Tatiana V. Chekalin, Evgeny Nikolsky, Yuri Bruskin, Sergey Chebotarov, Dmitry McNally, Kenneth L. Alexandrov, Nickolai We analyzed functionality and relative distribution of genetic variants across the complete Oryza sativa genome, using the 40 million single nucleotide polymorphisms (SNPs) dataset from the 3,000 Rice Genomes Project (http://snp-seek.irri.org), the largest and highest density SNP collection for any higher plant. We have shown that the DNA-binding transcription factors (TFs) are the most conserved group of genes, whereas kinases and membrane-localized transporters are the most variable ones. TFs may be conserved because they belong to some of the most connected regulatory hubs that modulate transcription of vast downstream gene networks, whereas signaling kinases and transporters need to adapt rapidly to changing environmental conditions. In general, the observed profound patterns of nucleotide variability reveal functionally important genomic regions. As expected, nucleotide diversity is much higher in intergenic regions than within gene bodies (regions spanning gene models), and protein-coding sequences are more conserved than untranslated gene regions. We have observed a sharp decline in nucleotide diversity that begins at about 250 nucleotides upstream of the transcription start and reaches minimal diversity exactly at the transcription start. We found the transcription termination sites to have remarkably symmetrical patterns of SNP density, implying presence of functional sites near transcription termination. Also, nucleotide diversity was significantly lower near 3′ UTRs, the area rich with regulatory regions. 2016-10-24 2024-12-19T12:54:49Z 2024-12-19T12:54:49Z Journal Article https://hdl.handle.net/10568/165189 en Open Access Springer Tatarinova, Tatiana V.; Chekalin, Evgeny; Nikolsky, Yuri; Bruskin, Sergey; Chebotarov, Dmitry; McNally, Kenneth L. and Alexandrov, Nickolai. 2016. Nucleotide diversity analysis highlights functionally important genomic regions. Sci Rep, Volume 6, no. 1 |
| spellingShingle | Tatarinova, Tatiana V. Chekalin, Evgeny Nikolsky, Yuri Bruskin, Sergey Chebotarov, Dmitry McNally, Kenneth L. Alexandrov, Nickolai Nucleotide diversity analysis highlights functionally important genomic regions |
| title | Nucleotide diversity analysis highlights functionally important genomic regions |
| title_full | Nucleotide diversity analysis highlights functionally important genomic regions |
| title_fullStr | Nucleotide diversity analysis highlights functionally important genomic regions |
| title_full_unstemmed | Nucleotide diversity analysis highlights functionally important genomic regions |
| title_short | Nucleotide diversity analysis highlights functionally important genomic regions |
| title_sort | nucleotide diversity analysis highlights functionally important genomic regions |
| url | https://hdl.handle.net/10568/165189 |
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