Comparative Transcriptome Analysis of Watermelon Flesh and Rind During Fruit Development

The flesh and rind of watermelon fruit are fundamentally different, and with the advent of high throughput sequencing, it is possible to determine this difference at the level of gene expression.  Through comparative transcriptome sequencing and analysis of watermelon flesh and rind at four critical stages of fruit development, immature white (10 days after pollination (DAP)), white-pink flesh (18 DAP), red flesh (26 DAP) and over-ripe (34 DAP), we were able to identify a total of 764, 1389, 4305, and 3358 differentially expressed genes between flesh and rind at 10, 18, 26, and 34 DAP, respectively. Further characterization of these differentially expressed genes indicated that functional categories such as responses to various biotic/abiotic stresses and photosynthesis were highly enriched in all four stages, whereas carotene/carotenoid metabolic process and sugar metabolism including hexose catabolic process, glucose catabolic process, and monosaccharide catabolic process were highly enriched in later stages of fruit development. These results supported the major physiological differences including sugar content and fruit color observed between flesh and rind.

My Experience

This internship opportunity has been a great opportunity to look into the field of bioinformatics.  Before this summer, I did not have a good idea what it is like to work in this field.  Now, after working with Dr. Fei and his lab group I have a new appreciation for what it is like to work with very large data sets.  His lab group was very helpful and answered whatever questions I had and pointed me in the right direction when I was confused about what to do next.  As a computational biologist, this was a worthwhile experience because it helps narrow down this broad field that I wish to enter as I start to look for graduate programs.