Landscape and Fruit Developmental Regulation of Alternative Splicing in Tomato by Genome-Wide Analysis

In eukaryotes, alternative splicing (AS) is one of the posttranscriptional regulatory mechanisms that play important roles by generating transcriptome diversity. To obtain a global view of AS and its dynamics during tomato fruit development, we analyzed the AS events using a large amount of transcriptome datasets. Same with other plant species, about half of the expressed multiexonic genes were alternatively spliced in tomato. Besides that, our further analyzation of RNA-seq datasets of ovule and pericarp at early fruit developmental stages reveals that the dynamic alteration of AS events occurred in specific tissues and AS was regulated spatially and temporally during early fruit development in tomato. By investigating the sequence variations at splice sites causing differential AS events between tomato cultivar ‘Moneymaker’ and wild species Solanum pimpinellifolium PI365967, we uncover that AS may play the regulatory roles during domestication of tomato. Taken together, our results provided the global AS pattern in tomato and highlighted the importance of AS during tomato fruit development and domestication.