Comprehensive tissue-specific transcriptome profiling of pineapple (Ananas comosus) and building an eFP-browser for...

Pineapple is one of the most economically important tropical or subtropical fruit trees. However, few studies focus on the development of its unique collective fruit. In this study, we generated a genome-wide developmental transcriptomic profile of 14 different tissues of the collective fruit of the pineapple covering each of the three major fruit developmental stages. In total, 273 tissue-specific and 1,051 constitutively expressed genes were detected. We also performed gene co-expression analysis and 18 gene modules were classified. Among these, we found three interesting gene modules; one was preferentially expressed in bracts and sepals and was likely involved in plant defense; one was highly expressed at the beginning of fruit expansion and faded afterward and was probably involved in endocytosis; Another gene module increased expression level with pineapple fruit development and was involved in terpenoid and polyketide metabolism. In addition, we built a pineapple electronic fluorescent pictograph (eFP) browser to facilitate exploration of gene expression during pineapple fruit development. With this tool, users can visualize expression data in this study in an intuitive way. Together, the transcriptome profile generated in this work and the corresponding eFP browser will facilitate further study of fruit development in pineapple.