ArticleNucleic acids research2011
Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- A single-cell rice atlas integrates multi-species data to reveal cis-regulatory evolution.Nature plants · 2025Article
- The role of mobile DNA elements in the dynamics of plant genome plasticity.Journal of experimental botany · 2025Review
- DNA Transposons Favor De Novo Transcript Emergence Through Enrichment of Transcription Factor Binding Motifs.Genome biology and evolution · 2024Article
- Expression of Physaria longchain acyl-CoA synthetases and hydroxy fatty acid accumulation in transgenic Arabidopsis.Journal of plant physiology · 2022Article
- BLSSpeller to discover novel regulatory motifs in maize.DNA research : an international journal for rapid publication of reports on genes and genomes · 2022Article
- Ectopic expression of Triticum polonicum VRT-A2 underlies elongated glumes and grains in hexaploid wheat in a dosage-dependent manner.The Plant cell · 2021Article
- The modular nature of protein evolution: domain rearrangement rates across eukaryotic life.BMC evolutionary biology · 2020Article
- Lineage-Specific Expression Divergence in Grasses Is Associated with Male Reproduction, Host-Pathogen Defense, and Domestication.Genome biology and evolution · 2019Article
- Single-Base Resolution Map of Evolutionary Constraints and Annotation of Conserved Elements across Major Grass Genomes.Genome biology and evolution · 2018Article
- New Insights on Leucine-Rich Repeats Receptor-Like Kinase Orthologous Relationships in Angiosperms.Frontiers in plant science · 2017Article
- BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements.Bioinformatics (Oxford, England) · 2015Article
- 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
- MorTAL Kombat: the story of defense against TAL effectors through loss-of-susceptibility.Frontiers in plant science · 2015Review
- 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
- The fate of Arabidopsis thaliana homeologous CNSs and their motifs in the Paleohexaploid Brassica rapa.Genome biology and evolution · 2013Article
- Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses.Frontiers in plant science · 2013Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The discovery of regulatory motifs embedded in upstream regions of plants is a particularly challenging bioinformatics task. Previous studies have shown that motifs in plants are short compared with those found in vertebrates. Furthermore, plant genomes have undergone several diversification mechanisms such as genome duplication events which impact the evolution of regulatory motifs. In this article, a systematic phylogenomic comparison of upstream regions is conducted to further identify features of the plant regulatory genomes, the component of genomes regulating gene expression, to enable future de novo discoveries. The findings highlight differences in upstream region properties between major plant groups and the effects of divergence times and duplication events. First, clear differences in upstream region evolution can be detected between monocots and dicots, thus suggesting that a separation of these groups should be made when searching for novel regulatory motifs, particularly since universal motifs such as the TATA box are rare. Second, investigating the decay rate of significantly aligned regions suggests that a divergence time of ~100 mya sets a limit for reliable conserved non-coding sequence (CNS) detection. Insights presented here will set a framework to help identify embedded motifs of functional relevance by understanding the limits of bioinformatics detection for CNSs.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.