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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETICS AND GENETIC IMPROVEMENT OF DISEASE RESISTANCE AND QUALITY TRAITS IN WATERMELON, BROCCOLI, AND LEAFY GREEN BRASSICAS

Location: Vegetable Research

Title: Sequencing the Genome of the Heirloom Watermelon Cultivar Charleston Gray

Authors
item LEVI, AMNON
item Hernandez, A -
item Thimmapuram, J -
item Donthu, R -
item Wright, C -
item Ali, C -
item WECHTER, WILLIAM
item Reddy, U -
item Mikel, M -

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: November 10, 2010
Publication Date: January 10, 2011
Citation: Levi, A., Hernandez, A., Thimmapuram, J., Donthu, R., Wright, C., Ali, C., Wechter, W.P., Reddy, U., Mikel, M. 2011. Sequencing the Genome of the Heirloom Watermelon Cultivar Charleston Gray. Plant and Animal Genome Conference. P047.

Technical Abstract: The genome of the watermelon cultivar Charleston Gray, a major heirloom which has been used in breeding programs of many watermelon cultivars, was sequenced. Our strategy involved a hybrid approach using the Illumina and 454/Titanium next-generation sequencing technologies. For Illumina, shotgun genomic libraries with fragment sizes of 500bp and 1,000bp were sequenced from both ends, 100nt from each end. For 454, paired-end libraries with a jump size of 3kb were sequenced with the Titanium chemistry. The sequencing results from Illumina platform produced over 270 million paired-end high quality sequence reads, representing about 120X coverage of the watermelon genome. The sequencing results from GS FLX platform produced about 1.5 million shotgun and 1.5 million 3Kb paired-end reads, representing 2X coverage of the watermelon genome. De novo assembly of these reads resulted in a genome with a total length of 307 Mb, about 72% of the estimated watermelon genome size, represented in scaffolds and contigs of more than 2Kb in length, with a N50 scaffold size of 29Kb and longest scaffold of 457Kb. Another 100Mb of the genome is represented in scaffolds and contigs less than 2Kb in length. Additional sequencing will be done with shotgun and 8kb and 20kb paired-end libraries using the new 454/1kb-Titanium system to improve the assembly. The data in this study elucidate the watermelon genome structure and can be used as a platform for further genome assembly and for development of genetic markers useful in breeding programs aiming to enhance disease or pest resistance in watermelon cultivars.

Last Modified: 9/10/2014