Transcriptomic analysis of alternative splicing associated with crassulacean acid metabolism in pineapple (Ananas comosus)

Abstract Crassulacean acid metabolism photosynthesis pathway highlights the possible of sustainable production on margin agricultural land and crop improvement with higher water use efficiency by engineering CAM into C3 crops. A comprehensive view of the regulatory network of CAM photosynthesis is prerequisite for utilization CAM pathway. Diverse factors were involved in the regulation but many of them remain unexplained. Alternative splicing (AS) is a common and crucial posttranscriptional mechanism which get deep involved in responding to biotic and abiotic stresses. Using all the available RNA-seq data of pineapple, which is the most economic valuable CAM crops with abundant omics resource, we re-assembled a reference transcriptome and used to perform alternative splicing analysis associated with crassulacean acid metabolism. The results shown that AS events were prevalent in pineapple. CAM core genes, circadian clock genes, stomatal movement and starch metabolism related genes were found to be significantly differentially alternative spliced between photosynthesis and non-photosynthesis tissues across time course. Isoform switch events were found in many DAS genes, which indicated the sensitivity of AS across the CAM processes in pineapple. The dataset described here also contributed to identify promising candidate genes such as nAco00160 involved in CAM photosynthesis. Our results suggested that AS play an important regulatory role in CAM photosynthesis in pineapple and would help to gain a more systematic understanding about the regulatory networks of CAM photosynthesis.