Lettuce Genome Update

The Compositae Genome Project (http://compgenomics.ucdavis.edu) is a collaborative project to analyze genetic diversity in the Compositae plant family. Lettuce, an economically important member of this family, is being studied to correlate genotype with phenotypic variation in domestication and agriculturally significant traits. Several resources have been generated including lettuce transcriptome, gene-space, and whole genome assemblies. The whole genome of Lactuca sativa cv. Salinas has been sequenced in collaboration with the BGI and a consortium of ten breeding companies. From ~70x coverage with high quality, filtered Illumina reads, 2.5 Gb (93% of the entire genome) was assembled into scaffolds with a N50 of 461,580 bp. Over 11,000 loci from an ultra-dense, transcript-based genetic map was used to assess the quality of the assembly. Over 95% of 3,100 scaffolds that had multiple unigenes were genetically validated and could be ordered in chromosomal linkage groups. The resulting data are displayed using GBrowse. More scaffolds are being assigned to chromosomal linkage groups using genotyping by sequencing of 99 RILs from the reference L. sativa cv. Salinas x L. serriola mapping population. Chromosomal orders are being refined using population and syntenic information. Approximately, 45,000 gene models have been predicted using several automated annotation pipelines. Manual curation of these models is underway to refine the automated annotations. The genome sequence is being used to clone and functionally validate genes for disease resistance and development.