ArticleThe Plant cell2003
Conserved noncoding sequences among cultivated cereal genomes identify candidate regulatory sequence elements and patterns of promoter evolution.
Article in The Plant cell, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed, 106 citations in OpenAlex.
- Genetic diversity, GWAS, and candidate genes identification for plant architecture traits in maize (Zea mays L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- A single-cell rice atlas integrates multi-species data to reveal cis-regulatory evolution.Nature plants · 2025Article
- A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants.The plant genome · 2022Article
- Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize.Genome research · 2021Article
- TheNAR genomics and bioinformatics · 2020Article
- An inferred fitness consequence map of the rice genome.Nature plants · 2020Article
- Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan Sorghum Core collection.BMC genomics · 2020Article
- Conserved non-coding elements: developmental gene regulation meets genome organization.Nucleic acids research · 2017Review
- GC Content Heterogeneity Transition of Conserved Noncoding Sequences Occurred at the Emergence of Vertebrates.Genome biology and evolution · 2016Article
- A Collection of Conserved Noncoding Sequences to Study Gene Regulation in Flowering Plants.Plant physiology · 2016Article
- CNMS: The preferred genic markers for comparative genomic, molecular phylogenetic, functional genetic diversity and differential gene regulatory expression analyses in chickpea.Journal of biosciences · 2015Article
- Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea.Journal of experimental botany · 2015Article
- Upstream regulatory architecture of rice genes: summarizing the baseline towards genus-wide comparative analysis of regulatory networks and allele mining.Rice (New York, N.Y.) · 2015Article
- Lineage-specific conserved noncoding sequences of plant genomes: their possible role in nucleosome positioning.Genome biology and evolution · 2014Article
- Inference of transcriptional networks in Arabidopsis through conserved noncoding sequence analysis.The Plant cell · 2014Article
- The most deeply conserved noncoding sequences in plants serve similar functions to those in vertebrates despite large differences in evolutionary rates.The Plant cell · 2014Article
- An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions.Nature genetics · 2013Article
- Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes.Genome research · 2012Article
- Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants.The Plant cell · 2012Article
- New cis-regulatory elements in the Rht-D1b locus region of wheat.Functional & integrative genomics · 2012Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Surveys for conserved noncoding sequences (CNS) among genes from monocot cereal species were conducted to assess the general properties of CNS in grass genomes and their correlation with known promoter regulatory elements. Initial comparisons of 11 orthologous maize-rice gene pairs found that previously defined regulatory motifs could be identified within short CNS but could not be distinguished reliably from random sequence matches. Among the different phylogenetic footprinting algorithms tested, the VISTA tool yielded the most informative alignments of noncoding sequence. VISTA was used to survey for CNS among all publicly available genomic sequences from maize, rice, wheat, barley, and sorghum, representing >300 gene comparisons. Comparisons of orthologous maize-rice and maize-sorghum gene pairs identified 20 bp as a minimal length criterion for a significant CNS among grass genes, with few such CNS found to be conserved across rice, maize, sorghum, and barley. The frequency and length of cereal CNS as well as nucleotide substitution rates within CNS were consistent with the known phylogenetic distances among the species compared. The implications of these findings for the evolution of cereal gene promoter sequences and the utility of using the nearly completed rice genome sequence to predict candidate regulatory elements in other cereal genes by phylogenetic footprinting are discussed.
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