ArticleScientific reports2016
Nucleotide diversity analysis highlights functionally important genomic regions.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 67 citations in OpenAlex.
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- Clinical applications of and molecular insights from RNA sequencing in a rare disease cohort.Genome medicine · 2025Article
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- Elucidating the functional roles of prokaryotic proteins using big data and artificial intelligence.FEMS microbiology reviews · 2023Review
- Characterization of nuclear DNA diversity in an individualFrontiers in plant science · 2023Article
- Deep learning-assisted genome-wide characterization of massively parallel reporter assays.Nucleic acids research · 2022Article
- BLSSpeller to discover novel regulatory motifs in maize.DNA research : an international journal for rapid publication of reports on genes and genomes · 2022Article
- Genome-Wide Prediction of Transcription Start Sites in Conifers.International journal of molecular sciences · 2022Article
- Functional Haplotypes and Evolutionary Insight into the Granule-Bound Starch Synthase II (Foods (Basel, Switzerland) · 2021Article
- Genomic partitioning of inbreeding depression in humans.American journal of human genetics · 2021Article
- Zea mays RNA-seq estimated transcript abundances are strongly affected by read mapping bias.BMC genomics · 2021Article
- Explore the genetics of weedy traits using rice 3K database.Botanical studies · 2021Article
- Single nucleotide polymorphisms (SNPs) in prostate cancer: its implications in diagnostics and therapeutics.American journal of translational research · 2021Review
- Prediction of Rice Transcription Start Sites Using TransPrise: A Novel Machine Learning Approach.Methods in molecular biology (Clifton, N.J.) · 2021Article
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- DNA methylation changes in clonally propagated oil palm.Plant cell reports · 2020Article
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- Rice 3D chromatin structure correlates with sequence variation and meiotic recombination rate.Communications biology · 2020Article
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Authors and funding
7 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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