Analysis of Transcriptome and Alternative Splicing Landscape in Pineapple

Gene expression profiling and alternative splicing (AS) landscapes were analyzed in pineapple. Among 27,024 protein-coding genes, based on the transcripts to gene models mapping data, a total of 17,308 predicted genes are supported by expressed transcripts. Between leaf and root tissue, 795 genes were upregulated in leaf tissue relative to root tissue, and 1391 genes were upregulated in root tissue relative to leaf tissue. Between young fruit tissue and ripening fruit tissue, 931 genes were upregulated, and 189 genes were downregulated in ripening fruit tissue relative to young fruit tissue. Genes involved in crassulacean acid metabolism (CAM) pathway and in ethylene biosynthesis and responses were identified and further analyzed in details. A total of 10,348 AS events involving 13,449 unique transcripts which were generated from a total of 5146 genes were identified. The identification of differentially expressed genes, assembled transcripts, along with the identified AS isoforms and events, provides a solid foundation for further examination of the gene functions in pineapple metabolism, growth, development, and fruit ripening. The data are available at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/).