ArticleFrontiers in bioengineering and biotechnology2015
Genome-wide identification of evolutionarily conserved alternative splicing events in flowering plants.
Article in Frontiers in bioengineering and biotechnology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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Who cites it
71 citing papers in PubMed, 121 citations in OpenAlex.
- Domain compositions of Arabidopsis Toll/Interleukin-1 Receptor/Resistance domain-containing TX14 proteins affect localization and induction of the hypersensitive response.Journal of experimental botany · 2026Article
- The Role of Small Segmental Duplications in Generating Identical Isoforms Through Alternative Splicing Sites.Biochemical genetics · 2026Article
- Pathogen Effector-Mediated Reprogramming of Plant Alternative Splicing: From Immune Regulation to Crop Disease Resistance.Plants (Basel, Switzerland) · 2026Review
- An ultraconserved pseudo 5' splice site fine-tunes development by regulating alternative splicing within TOR-related pathways.Nature communications · 2026Article
- Pre-mRNA splicing and its regulation in microalgae and cyanobacteria.Advanced biotechnology · 2025Review
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- Conservation and Remodeling of Alternative Splicing Landscapes in the Evolution ofPlants (Basel, Switzerland) · 2025Article
- The genome of the vining fernProceedings of the National Academy of Sciences of the United States of America · 2025Article
- At-RS31 orchestrates hierarchical cross-regulation of splicing factors and integrates alternative splicing with TOR-ABA pathways.The New phytologist · 2025Article
- Whole-Genome Survey Analyses of Five Goby Species Provide Insights into Their Genetic Evolution and Invasion-Related Genes.International journal of molecular sciences · 2024Article
- Splicing and expression dynamics of SR genes in hot pepper (Frontiers in plant science · 2024Article
- Evolution ofFrontiers in plant science · 2024Article
- Conserved and divergent signals in 5' splice site sequences across fungi, metazoa and plants.PLoS computational biology · 2023Article
- MkcDBGAS: a reference-free approach to identify comprehensive alternative splicing events in a transcriptome.Briefings in bioinformatics · 2023Article
- Catsnap: a user-friendly algorithm for determining the conservation of protein variants reveals extensive parallelisms in the evolution of alternative splicing.The New phytologist · 2023Article
- Plant Intron-Splicing Efficiency Database (PISE): exploring splicing of ∼1,650,000 introns in Arabidopsis, maize, rice, and soybean from ∼57,000 public RNA-seq libraries.Science China. Life sciences · 2023Article
- Design, execution, and interpretation of plant RNA-seq analyses.Frontiers in plant science · 2023Review
- Integrated Genomic and Transcriptomic Elucidation of Flowering in Garlic.International journal of molecular sciences · 2022Article
- Evolution of isoform-level gene expression patterns across tissues during lotus species divergence.The Plant journal : for cell and molecular biology · 2022Article
11 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative splicing (AS) plays important roles in many plant functions, but its conservation across the plant kingdom is not known. We describe a methodology to identify AS events and identify conserved AS events across large phylogenetic distances using RNA-Seq datasets. We applied this methodology to transcriptome data from nine angiosperms including Amborella, the single sister species to all other extant flowering plants. AS events within 40-70% of the expressed multi-exonic genes per species were found, 27,120 of which are conserved among two or more of the taxa studied. While many events are species specific, many others are shared across long evolutionary distances suggesting they have functional significance. Conservation of AS event data provides an estimate of the number of ancestral AS events present at each node of the tree representing the nine species studied. Furthermore, the presence or absence of AS isoforms between species with different whole genome duplication (WGD) histories provides the opportunity to examine the impact of WDG on AS potential. Examining AS in gene families identifies those with high rates of AS, and conservation can distinguish ancient events vs. recent or species specific adaptations. The MADS-box and SR protein families are found to represent families with low and high occurrences of AS, respectively, yet their AS events were likely present in the MRCA of angiosperms.
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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.