Extensive alternative splicing (AS) of precursor mRNAs (pre-
mRNAs) in multicellular eukaryotes increases the protein-coding
capacity of a genome and allows novel ways to regulate gene
expression. In flowering plants, up to 48% of intron-containing
genes exhibit AS. However, the full extent of AS in plants is
not yet known, as only a few high-throughput RNA-Seq studies
have been performed. As the cost of obtaining RNA-Seq reads
continues to fall, it is anticipated that huge amounts of plant
sequence data will accumulate and help in obtaining a more
complete picture of AS in plants. Although it is not an onerous
task to obtain hundreds of millions of reads using high-
throughput sequencing technologies, computational tools to
accurately predict and visualize AS are still being developed
and refined. This review discusses the tools to predict and
visualize transcriptome-wide AS in plants using short-reads and
highlight their limitations. Comparative studies of AS events
between plants and animals have revealed th