Analysis of Transcriptome and Alternative Splicing Landscape in Pineapple

Wai, Ching Man; Powell, Brian; Ming, Ray; Min, Xiang Jia

doi:10.1007/978-3-030-00614-3_14

Cited by 2 publications

(1 citation statement)

References 38 publications

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“…The assembled transcripts and AS events identified in this study along with the predicted gene models, along with the data reported previously in our group including Brachypodium distachyon (Sablok et al, 2011; Walters et al, 2013), pineapple (Wai et al, 2016), and sacred lotus ( Nelumbo nucifera ) (VanBuren et al, 2013), are available from plant alternative splicing database 7 (Walters et al, 2013; VanBuren et al, 2013; Min et al, 2015; Wai et al, 2016, 2018; Sablok et al, 2017; Min, 2017, 2018). BLAST search is also available for searching the transcripts.…”

Section: Methodsmentioning

confidence: 80%

Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato

Clark

et al. 2019

Front. Plant Sci.

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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 ).

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