Sequencing the Genomes of Cultivated Lactuca sativa and its Wild Progenitor, L. serriola

The genome of Lactuca sativa cv. Salinas has been sequenced in collaboration with the BGI and a consortium of ten breeding companies. This is the first member of the Compositae (Asteraceae) to be sequenced. Approximately 2.5 Gb (93% of the entire genome) was assembled into 13,352 scaffolds over 2 kb with an N50 of 461 kb from ~72x coverage with high quality Illumina reads. A genetic map containing over 11,000 transcript-derived loci was used to assess the quality of the assembly. These loci identified 3200 scaffolds. Of these, 3100 scaffolds, which represent ~60% of the genome, were genetically validated and assigned to nine linkage groups. Additional scaffolds are being assigned to genetic bins on chromosomal linkage groups via mapping by sequencing the gene space of RILs from the reference L. sativa cv. Salinas x L. serriola mapping population. The lettuce genome is made up of 73% repeated sequences, mostly retrotransposons and uncharacterized repeats.  Over 45,000 genes have been predicted using manual and automated annotation pipelines; 79% of these have some level of functional annotation.  Genespace sequencing of L. serriola has been performed to ~10x coverage and whole genome sequencing and assembly of L. serriola is underway. Details of the lettuce genome and analysis tools can be accessed at the Lettuce Genome Resource (https://lgr.genomecenter.ucdavis.edu/). The Lettuce Genome Resource includes several versions of the data displayed in GBrowse and can be used for syntenic comparisons with other plant genomes. In addition, lettuce genes have been assigned to KEGG metabolic pathways.