ArticleBMC genomics2017
Identification and analysis of alternative splicing events in Phaseolus vulgaris and Glycine max.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Phylogenetic diversity of light-dependent phosphorylation of Thr78 in Rubisco activase.Journal of experimental botany · 2025Article
- Functional Validation of Different Alternative Splicing Variants of theCurrent issues in molecular biology · 2024Article
- Importance of pre-mRNA splicing and its study tools in plants.Advanced biotechnology · 2024Review
- Alternative splicing responses to salt stress inFrontiers in genetics · 2024Article
- Identification of Splice Variants and Isoforms in Transcriptomics and Proteomics.Annual review of biomedical data science · 2023Review
- Potential role of NiScience · 2023Article
- Transcriptome profiling of banana shrimp (Fenneropenaeus merguiensis) ovaries and testes: Insights into FoxL2.PloS one · 2023Article
- Article
- Analysis of Whole-Transcriptome RNA-Seq Data Reveals the Involvement of Alternative Splicing in the Drought Response ofFrontiers in genetics · 2022Article
- Expression Elements Derived From Plant Sequences Provide Effective Gene Expression Regulation and New Opportunities for Plant Biotechnology Traits.Frontiers in plant science · 2021Article
- Article
- Transcriptome Analysis of Alternative Splicing Events Induced by Arbuscular Mycorrhizal Fungi (Plants (Basel, Switzerland) · 2020Article
- Alternative Splicing During theG3 (Bethesda, Md.) · 2020Article
- Genome-wide profiling of alternative splicing genes in hybrid poplar (P.alba×P.glandulosa cv.84K) leaves.PloS one · 2020Article
- Genome-wide analysis of alternative splicing divergences between Brassica hexaploid and its parents.Planta · 2019Article
- Genetics of alternative splicing evolution during sunflower domestication.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Alternative Splicing as a Regulator of Early Plant Development.Frontiers in plant science · 2018Review
- Analysis and Prediction of Exon Skipping Events from RNA-Seq with Sequence Information Using Rotation Forest.International journal of molecular sciences · 2017Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe vast diversification of proteins in eukaryotic cells has been related with multiple transcript isoforms from a single gene that result in alternative splicing (AS) of primary transcripts. Analysis of RNA sequencing data from expressed sequence tags and next generation RNA sequencing has been crucial for AS identification and genome-wide AS studies. For the identification of AS events from the related legume species Phaseolus vulgaris and Glycine max, 157 and 88 publicly available RNA-seq libraries, respectively, were analyzed.
resultsWe identified 85,570 AS events from P. vulgaris in 72% of expressed genes and 134,316 AS events in 70% of expressed genes from G. max. These were categorized in seven AS event types with intron retention being the most abundant followed by alternative acceptor and alternative donor, representing ~75% of all AS events in both plants. Conservation of AS events in homologous genes between the two species was analyzed where an overrepresentation of AS affecting 5'UTR regions was observed for certain types of AS events. The conservation of AS events was experimentally validated for 8 selected genes, through RT-PCR analysis. The different types of AS events also varied by relative position in the genes. The results were consistent in both species.
conclusionsThe identification and analysis of AS events are first steps to understand their biological relevance. The results presented here from two related legume species reveal high conservation, over ~15-20 MY of divergence, and may point to the biological relevance of AS.
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