Sequencing and Assembly of the Genome of an American Watermelon Ecotype, Charleston Gray

Watermelon is an important and valuable vegetable crop throughout the world. It is known to have numerous health benefits and is an excellent source of many antioxidants such as lycopene and beta-carotene. The two largest groups of modern cultivated watermelons are East Asian ecotype and American ecotype.  The genome of an East Asian watermelon ecotype, 97103, has been sequenced and assembled. Here we report the sequencing and assembly of the genome of an  American watermelon ecotype, Charleston Gray, which has elongated fruit, light green gray rind and pink flesh. We generated a total of 95.5 Gb high-quality cleaned reads which represent approximately 225X coverage of the Charleston Gray genome using the Illumina sequencing technology, among which around 55X were from mate-pair libraries with large inserts (5 Kb, 10 Kb and 20 Kb). De novo assembly yielded a draft genome of 396.5 Mb, representing about 93.3% of the watermelon genome. The assembly has an N50 scaffold size of 7.47 Mb and N90 of 1.61 Mb, and 90% of the genome draft was assembled in only 59 scaffolds. Furthermore, we have performed deep transctiptome sequencing of fruits of Charleston Gray at four different developmental stages and obtained more than 100 million read pairs. Annotating the genome using the RNA-seq reads and comparative analysis of Charleston Gray and 97103 genomes are currently underway.