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Title: De novo assembly of a draft genome for Cucumis hystrix, the closest relative of cucumber

item THAMMAPICKAI, P - University Of Wisconsin
item Weng, Yiqun

Submitted to: Plant and Animal Genome
Publication Type: Abstract Only
Publication Acceptance Date: 11/3/2015
Publication Date: 1/8/2016
Citation: Thammapickai, P., Weng, Y. 2016. De novo assembly of a draft genome for Cucumis hystrix, the closest relative of cucumber [abstract]. Plant and Animal Genome. Paper No. 1162.

Interpretive Summary:

Technical Abstract: Cucumis hystrix (2n = 2x = 24, HH) 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 through development of introgression library, we sequenced two accessions, TH1 and CN1, of the C. hystrix genome with both Illumina Hi-Seq 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 for C. hystrix was 447.0 Mbp. The resulting assembly contained 16,865 scaffolds (~78× genome 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 Mb. The assembly contains 88,371 contigs with N50 contig size of 4.0 kb. The scaffold assembly for CN1 was 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 the cucumber and melon genomes, as well as mining of molecular markers. For SNP calling, DNA sequence 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 TH1 and CN1 accessions. We also identified > 4.5 million 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.