Data from: Genome of ‘Charleston Gray’, the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection

Years of selection for desirable fruit quality traits in dessert watermelon (Citrullus lanatus) has resulted in a narrow genetic base in modern cultivars. Development of novel genomic and genetic resources offers great potential to expand genetic diversity and improve important traits in watermelon. Here, we report a high‐quality genome sequence of watermelon cultivar ‘Charleston Gray’, a principal American dessert watermelon, to complement the existing reference genome from ‘97103’, an East Asian cultivar. Comparative analyses between genomes of ‘Charleston Gray’ and ‘97103’ revealed genomic variants that may underlie phenotypic differences between the two cultivars. We then genotyped 1365 watermelon plant introduction (PI) lines maintained at the U.S. National Plant Germplasm System using genotyping‐by‐sequencing (GBS). These PI lines were collected throughout the world and belong to three Citrullus species, C. lanatus, C. mucosospermus and C. amarus. Approximately 25 000 high‐quality single nucleotide polymorphisms (SNPs) were derived from the GBS data using the ‘Charleston Gray’ genome as the reference. Population genomic analyses using these SNPs discovered a close relationship between C. lanatus and C. mucosospermus and identified four major groups in these two species correlated to their geographic locations. Citrullus amarus was found to have a distinct genetic makeup compared to C. lanatus and C. mucosospermus. The SNPs also enabled identification of genomic regions associated with important fruit quality and disease resistance traits through genome‐wide association studies. The high‐quality ‘Charleston Gray’ genome and the genotyping data of this large collection of watermelon accessions provide valuable resources for facilitating watermelon research, breeding and improvement.

• Resource Title: Supplementary Data - Tables S1 to S13 (xlsx).

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  Table S1: Summary of ‘Charleston Gray’ genome sequencing data.

  Table S2: Statistics of ‘Charleston Gray’ pseudomolecules.

  Table S3: Mapping of RNA‐Seq reads and ESTs to the ‘Charleston Gray’ genome.

  Table S4: Assessment of ‘Charleston Gray’ genome assembly completeness by BUSCO.

  Table S5: Summary of repeat sequences in the ‘Charleston Gray’ genome.

  Table S6: Summary of SNPs and small indels between ‘Charleston Gray’ and ‘97103’.

  Table S7: Structural variations between ‘Charleston Gray’ and ‘97103’.

  Table S8: Structural variations between ‘Charleston Gray’ and ‘97103’ overlapping with known QTLs.

  Table S9: List of the 1365 watermelon accessions from the NPGS collection.

  Table S10: Weighted pairwise FST values between C. mucosospermus and C. lanatus accessions from different geographic regions.

  Table S11: Phenotypic data for GWAS.

  Table S12: SNPs significantly associated with agronomic traits identified through GWAS.

  Table S13: Evaluation of the SNP imputation using KNN under the optimal parameters ‘w = 50, k = 7, p = ‐9, r = 0.8’.