ArticleProceedings of the National Academy of Sciences of the United States of America2012
Long identical multispecies elements in plant and animal genomes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 51 citations in OpenAlex.
- Accurate, Scalable Structural Variant Genotyping in Complex Genomes at Population Scales.Molecular biology and evolution · 2025Article
- Benchmarking, detection, and genotyping of structural variants in a population of whole-genome assemblies using the SVGAP pipeline.bioRxiv : the preprint server for biology · 2025Article
- The Evolution of Ultraconserved Elements in Vertebrates.Molecular biology and evolution · 2024Article
- Characterization of Two Transposable Elements and an Ultra-Conserved Element Isolated in the Genome ofLife (Basel, Switzerland) · 2023Article
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- Ice ages and butterflyfishes: Phylogenomics elucidates the ecological and evolutionary history of reef fishes in an endemism hotspot.Ecology and evolution · 2018Article
- Comparison of taxon-specific versus general locus sets for targeted sequence capture in plant phylogenomics.Applications in plant sciences · 2018Article
- Molecular Cytogenetics ofBioMed research international · 2018Article
- HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees.Evolutionary bioinformatics online · 2018Article
- Review
- Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics.Systematic biology · 2017Article
- A method for identification of highly conserved elements and evolutionary analysis of superphylum Alveolata.BMC bioinformatics · 2016Article
- Combinatorial Gene Regulatory Functions Underlie Ultraconserved Elements in Drosophila.Molecular biology and evolution · 2016Article
- Article
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- How evolution of genomes is reflected in exact DNA sequence match statistics.Molecular biology and evolution · 2015Article
- Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics.Applications in plant sciences · 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
- A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.Applications in plant sciences · 2014Article
- Hyper conserved elements in vertebrate mRNA 3'-UTRs reveal a translational network of RNA-binding proteins controlled by HuR.Nucleic acids research · 2013Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ultraconserved elements (UCEs) are DNA sequences that are 100% identical (no base substitutions, insertions, or deletions) and located in syntenic positions in at least two genomes. Although hundreds of UCEs have been found in animal genomes, little is known about the incidence of ultraconservation in plant genomes. Using an alignment-free information-retrieval approach, we have comprehensively identified all long identical multispecies elements (LIMEs), which include both syntenic and nonsyntenic regions, of at least 100 identical base pairs shared by at least two genomes. Among six animal genomes, we found the previously known syntenic UCEs as well as previously undescribed nonsyntenic elements. In contrast, among six plant genomes, we only found nonsyntenic LIMEs. LIMEs can also be classified as either simple (repetitive) or complex (nonrepetitive), they may occur in multiple copies in a genome, and they are often spread across multiple chromosomes. Although complex LIMEs were found in both animal and plant genomes, they differed significantly in their composition and copy number. Further analyses of plant LIMEs revealed their functional diversity, encompassing elements found near rRNA and enzyme-coding genes, as well as those found in transposons and noncoding DNA. We conclude that despite the common presence of LIMEs in both animal and plant lineages, the evolutionary processes involved in the creation and maintenance of these elements differ in the two groups and are likely attributable to several mechanisms, including transfer of genetic material from organellar to nuclear genomes, de novo sequence manufacturing, and purifying selection.
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