Gene Expression Across Ploidy Levels Of Watermelon

Seedless watermelons are the preferred type for the US consumers and currently 95% of watermelons are seedless. We used vegetative and fruit tissues of diploid and its isogenic tetraploid for genome wide transcriptome analysis and identified genes that are up and down regulated differentially among the diploid and tetraploid watermelon types. RNAseq resolved transcriptome differences between CLD1 (Charleston diploid), CLT1 (isogenic tetraploid Charleston) and a non-isogenic diploid (Crimson sweet). The results of qRT-PCR corraborated with the deep sequencing data. A heat map is made involving significantly up and down regulated genes. Further our small RNA library sequencing contained about 5 million small RNA reads for each of the diploid and tetraploid lines and  sequence analysis indicated that the identification of 147 miRNA homologs belonging to 27 conserved miRNA families in diploid and tetraploid libraries. We noted expression abundance using the deep sequencing data and validated expression levels using the qRT PCR and Northern blots. miR 156 and miR164 showed higher expression in the diploid watermelon and Arabidopsis diploid ecotypes when compared with their tetraploid counterparts. Contrastingly, miR168-1and miR166 expressed more in tetraploid lines than the diploids exactly in the same pattern in both the Arabidopsis and watermelon suggesting that these miRNAs regulate differentially across the ploidy levels in plants.