ArticleBMC plant biology2008
Cross-species EST alignments reveal novel and conserved alternative splicing events in legumes.
Article in BMC plant biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed, 61 citations in OpenAlex.
- Pre-mRNA splicing and its regulation in microalgae and cyanobacteria.Advanced biotechnology · 2025Review
- 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
- The Arabidopsis lncRNA ASCO modulates the transcriptome through interaction with splicing factors.EMBO reports · 2020Article
- Quick and efficient approach to develop genomic resources in orphan species: Application in Lavandula angustifolia.PloS one · 2020Article
- Identification and characterization of evolutionarily conserved alternative splicing events in a mangrove genus Sonneratia.Scientific reports · 2018Article
- xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud.The Plant cell · 2016Article
- De novo construction of a "Gene-space" for diploid plant genome rich in repetitive sequences by an iterative Process of Extraction and Assembly of NGS reads (iPEA protocol) with limited computing resources.BMC research notes · 2016Article
- Evolutionary Character of Alternative Splicing in Plants.Bioinformatics and biology insights · 2015Review
- Genome-wide identification of evolutionarily conserved alternative splicing events in flowering plants.Frontiers in bioengineering and biotechnology · 2015Article
- Analysis of pollen-specific alternative splicing in Arabidopsis thaliana via semi-quantitative PCR.PeerJ · 2015Article
- Conservation and functional influence of alternative splicing in wood formation of Populus and Eucalyptus.BMC genomics · 2014Article
- Genome-wide analysis of alternative splicing in Zea mays: landscape and genetic regulation.The Plant cell · 2014Article
- Comprehensive analysis of alternative splicing in Digitalis purpurea by strand-specific RNA-Seq.PloS one · 2014Article
- Expression dynamics of the Medicago truncatula transcriptome during the symbiotic interaction with Sinorhizobium meliloti: which role for nitric oxide?Plant physiology · 2013Article
- Functional analysis of splice variant expression of MADS AFFECTING FLOWERING 2 of Arabidopsis thaliana.Plant molecular biology · 2013Article
- Identification of novel splice variants and exons of human endothelial cell-specific chemotaxic regulator (ECSCR) by bioinformatics analysis.Computational biology and chemistry · 2012Article
- Alternative splicing in plants--coming of age.Trends in plant science · 2012Review
- Deciphering the plant splicing code: experimental and computational approaches for predicting alternative splicing and splicing regulatory elements.Frontiers in plant science · 2012Article
- Article
- Intragenic alternative splicing coordination is essential for Caenorhabditis elegans slo-1 gene function.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAlthough originally thought to be less frequent in plants than in animals, alternative splicing (AS) is now known to be widespread in plants. Here we report the characteristics of AS in legumes, one of the largest and most important plant families, based on EST alignments to the genome sequences of Medicago truncatula (Mt) and Lotus japonicus (Lj).
resultsBased on cognate EST alignments alone, the observed frequency of alternatively spliced genes is lower in Mt (approximately 10%, 1,107 genes) and Lj (approximately 3%, 92 genes) than in Arabidopsis and rice (both around 20%). However, AS frequencies are comparable in all four species if EST levels are normalized. Intron retention is the most common form of AS in all four plant species (~50%), with slightly lower frequency in legumes compared to Arabidopsis and rice. This differs notably from vertebrates, where exon skipping is most common. To uncover additional AS events, we aligned ESTs from other legume species against the Mt genome sequence. In this way, 248 additional Mt genes were predicted to be alternatively spliced. We also identified 22 AS events completely conserved in two or more plant species.
conclusionThis study extends the range of plant taxa shown to have high levels of AS, confirms the importance of intron retention in plants, and demonstrates the utility of using ESTs from related species in order to identify novel and conserved AS events. The results also indicate that the frequency of AS in plants is comparable to that observed in mammals. Finally, our results highlight the importance of normalizing EST levels when estimating the frequency of alternative splicing.
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