Chromosome-Scale Assembly of the Lettuce (Lactuca sativa) Genome Using Genotyping By Shotgun Sequencing (GBSS)

Next Generation Sequencing (NGS)-based assemblies of moderately large genomes [1-3 Gb] often consist of thousands of scaffolds. The combination of NGS and segregation analysis allows the generation of saturated, ultra-high density genetic maps, which can be employed to improve the contiguity of genome assemblies. The genome of the cultivated lettuce, Lactuca sativa, cv. Salinas has been sequenced in collaboration with the BGI supported by a consortium of ten breeding companies. The SOAPdenovo assembly of the L. sativa genome (2.7 Gb) consisted of 21,500 scaffolds covering 2.38 Gb [http://lgr.genomecenter.ucdavis.edu/]. We also sequenced L. serriola, a close relative of L. sativa and its likely progenitor. In addition, 99 Recombinant Inbred Lines (RILs) from a cross between L. sativa x L. serriola genotypes was sequenced at 1x coverage. We then used Genotyping by Shotgun Sequencing (GBSS) to generate a comprehensive map of the Lactuca genome. Comparison of the sequences from L. sativa, L. serriola and the RILs using CLC Genomics Workbench revealed more than 11 million reliable high-quality SNPs. Custom scripts were used to assign haplotypes to scaffolds and to identify chimeric misassemblies. The latter were corrected by breakage at the junction point. GBSS and segregation analysis of the RILs allowed the chromosomal assignment of more than ten thousand scaffolds and their ordering into genetic bins, covering 2.3 Gb of the lettuce genome. The resulting comprehensive chromosome assemblies are facilitating the identification and functional analysis of candidate genes for a broad spectrum of domestication and agriculturally-important phenotypes.