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• W2947549081 abstract "Tomato (Solanum lycopersicum) is an important vegetable and fruit crop. Its genome was completely sequenced and there are also a large amount of available expressed sequence tags (ESTs) and short reads generated by RNA sequencing (RNA-seq) technologies. Mapping transcripts including mRNA sequences, ESTs, and RNA-seq reads to the genome allows identifying pre-mRNA alternative splicing (AS), a post-transcriptional process generating two or more RNA isoforms from one pre-mRNA transcript. We comprehensively analyzed the AS landscape in tomato by integrating genome mapping information of all available mRNA and ESTs with mapping information of RNA-seq reads which were collected from 27 published projects. A total of 369,911 AS events were identified from 34,419 genomic loci involving 161,913 transcripts. Within the basic AS events, intron retention is the prevalent type (18.9%), followed by alternative acceptor site (12.9%) and alternative donor site (7.3%), with exon skipping as the least type (6.0%). Complex AS types having two or more basic event accounted for 54.9% of total AS events. Within 35,768 annotated protein-coding gene models, 23,233 gene models were found having pre-mRNAs generating AS isoform transcripts. Thus the estimated AS rate was 65.0% in tomato. The list of identified AS genes with their corresponding transcript isoforms serves as a catalog for further detailed examination of gene functions in tomato biology. The post-transcriptional information is also expected to be useful in improving the predicted gene models in tomato. The sequence and annotation information can be accessed at plant alternative splicing database (http://proteomics.ysu.edu/altsplice)." @default.
• W2947549081 created "2019-06-07" @default.
• W2947549081 creator A5013142829 @default.
• W2947549081 creator A5014310703 @default.
• W2947549081 creator A5042486252 @default.
• W2947549081 creator A5062158926 @default.
• W2947549081 date "2019-05-28" @default.
• W2947549081 modified "2023-10-10" @default.
• W2947549081 title "Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato" @default.
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• W2947549081 doi "https://doi.org/10.3389/fpls.2019.00689" @default.
• W2947549081 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/6546887" @default.

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