De Novo Assembly of A Draft Genome for Cucumis hystrix, the Closest Relative of Cucumber

Cucumis hystrix (2n = 2x = 24) is the only known species that is cross-compatible with cucumber and has a great potential for cucumber improvement. To facilitate introgression of C. hystrix chromatins into cucumber genetic background, we sequenced two accessions, TH1 and CN1, of the C. hystrix genome with Illumina HiSeq 2000 and Roche/454 platforms and conducted de novo draft genome assembly. With the Newbler (v2.8) software package, 225 out of 378 million reads (60%) were assembled for TH1. The estimated genome size was 447.0 Mbp. The resulting assembly contained 16,865 scaffolds (~78× coverage) with the largest scaffold being 467 kb and N50 scaffold size of 23.8 kb. For the CN1 accession, 72.4 out of 117 million reads (61.9%) were assembled with 24× coverage and an estimated genome size of 478.8 Mbp. The assembly contains 88,371 contigs with N50 contig size of 4.0 kb. Scaffolds for CN1 were not obtained due to low quality of 454 sequencing reads. We determined that both assemblies were of good quality and with sufficient coverage for comparative analysis with cucumber and melon genomes, as well as mining of molecular markers. For SNP calling, DNA repeats within both assemblies were filtered out using the Viridiplantae repeat database and RepeatMasker program. Over 554,000 SNPs and 58,000 indels were identified between two accessions. We also identified >4.5x10⁶ SNPs between C. hystrix TH1 and cucumber inbred line 9930. A subset of SNPs and indels are being validated and will be used in developing a linkage map for C. hystrix.