title: Nucleotide diversity analysis highlights functionally important genomic regions.
abstract: 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.
authors: Center for Personalized Medicine and Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA.|Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation.
authors: Tatiana V
authors: TV
authors: Tatarinova
authors: Vavilov Institute of General Genetics, Moscow, Russia.
authors: Evgeny
authors: E
authors: Chekalin
authors: Vavilov Institute of General Genetics, Moscow, Russia.|F1 Genomics, San Diego, CA, USA.|School of Systems Biology, George Mason University, VA, USA.
authors: Yuri
authors: Y
authors: Nikolsky
authors: Vavilov Institute of General Genetics, Moscow, Russia.
authors: Sergey
authors: S
authors: Bruskin
authors: International Rice Research Institute, Los Baños, Laguna 4031, Philippines.
authors: Dmitry
authors: D
authors: Chebotarov
authors: International Rice Research Institute, Los Baños, Laguna 4031, Philippines.
authors: Kenneth L
authors: KL
authors: McNally
authors: International Rice Research Institute, Los Baños, Laguna 4031, Philippines.
authors: Nickolai
authors: N
authors: Alexandrov
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D018388:Codon, Terminator / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics*; D053263:Gene Regulatory Networks; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics / Q000379:methods; D009711:Nucleotides / Q000235:genetics*; D012275:Oryza / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D020413:3' Untranslated Regions; D018388:Codon, Terminator; D021901:DNA, Intergenic; D009711:Nucleotides