ArticlePlant molecular biology2008
Characterization and comparison of intron structure and alternative splicing between Medicago truncatula, Populus trichocarpa, Arabidopsis and rice.
Article in Plant molecular biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 57 citations in OpenAlex.
- Regulation of Flowering Time and Other Developmental Plasticities by 3' Splicing Factor-Mediated Alternative Splicing inPlants (Basel, Switzerland) · 2023Review
- 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
- Genome-Wide Identification and Characterization of the Trehalose-6-phosphate Synthetase (TPS) Gene Family in Watermelon (International journal of molecular sciences · 2021Article
- PSDX: A Comprehensive Multi-Omics Association Database ofFrontiers in plant science · 2021Article
- Genome-wide profiling of alternative splicing genes in hybrid poplar (P.alba×P.glandulosa cv.84K) leaves.PloS one · 2020Article
- Genome-wide identification and comparative analysis of alternative splicing across four legume species.Planta · 2019Article
- Evolution of Alternative Splicing in Eudicots.Frontiers in plant science · 2019Article
- Identification and characterization of evolutionarily conserved alternative splicing events in a mangrove genus Sonneratia.Scientific reports · 2018Article
- The origin of exon 3 skipping of paternal GLOBOSA pre-mRNA in some Nicotiana tabacum lines correlates with a point mutation of the very last nucleotide of the exon.Molecular genetics and genomics : MGG · 2016Article
- Article
- Genome-wide cataloging and analysis of alternatively spliced genes in cereal crops.BMC genomics · 2015Article
- Cauliflower mosaic virus Transcriptome Reveals a Complex Alternative Splicing Pattern.PloS one · 2015Article
- Genome-wide identification of evolutionarily conserved alternative splicing events in flowering plants.Frontiers in bioengineering and biotechnology · 2015Article
- Genome-wide analysis of alternative splicing in Volvox carteri.BMC genomics · 2014Article
- Genome-wide survey of Alternative Splicing in Sorghum Bicolor.Physiology and molecular biology of plants : an international journal of functional plant biology · 2014Article
- The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana.Nucleic acids research · 2014Article
- The extent of Ds1 transposon to enrich transcriptomes and proteomes by exonization.Botanical studies · 2013Article
- Comprehensive analysis of RNA-seq data reveals the complexity of the transcriptome in Brassica rapa.BMC genomics · 2013Article
- Complexity of the alternative splicing landscape in plants.The Plant cell · 2013Review
- The developing xylem transcriptome and genome-wide analysis of alternative splicing in Populus trichocarpa (black cottonwood) populations.BMC genomics · 2013Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alignment of transcripts and genome sequences yielded a set of alternatively spliced transcripts in four angiosperm genomes: three dicotyledon species Medicago truncatula (Medicago), Populus trichocarpa (poplar) and Arabidopsis thaliana (Arabidopsis), and the monocotyledon Oryzae sativa (rice). Intron retention was the predominant mode of alternative splicing (AS) in each species, consistent with previous reports for Arabidopsis and rice. We analyzed the structure of 5'-splice junctions and observed commonalities between species. There was dependency of base composition between sites flanking the 5'-splice junction, with the potential to create a subset of splice sites that interact more weakly or strongly than average with U1 snRNA. Such altered nucleotide composition was correlated with splicing fidelity in all four species. For Medicago, poplar and Arabidopsis, but not in rice, alternative splicing was most prevalent for introns with decreased UA content, consistent with lower UA content for monocot introns and potentially reflecting evolved differences in splicing mechanisms. Similarly, the occurrence of AS between transcript Gene Ontology categories was positively correlated between Arabidopsis and Medicago, with no correlation between dicots and rice. Analysis of within-species paralogs and between-species reciprocal best-hit homologs yielded rare cases of potentially conserved AS events. Reverse transcriptase PCR and amplicon sequencing were used to confirm a subset of the in silico-predicted AS events within Medicago, as well as to characterize conserved AS events between Medicago and Arabidopsis.
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