Lettuce Genome Assembly, Structure and Annotation.

The genome of cultivated lettuce (L. sativa) has been sequenced in collaboration with BGI and a consortium of ten breeding companies. The assembly currently consists of 21,500 scaffolds for a total of 2.38 Gb representing 88% of the 2.7 Gb lettuce genome.    Lettuce’s wild relative L. serriola has also been sequenced. The L. serriola assembly currently contains 45,020 scaffolds combined into 1.99 Gb (74% of lettuce genome). Comparison between L. sativa and L. serriola assemblies has identified conserved and highly divergent genomic regions between the two genomes. More than 11 million high quality SNPs have also been identified.  Using these SNPs a genetic map was constructed on a RIL population between L. sativa and L. serriola. Segregation of scaffold haplotypes on the RIL families has been used to validate the assembly and to identify chimeric scaffolds as well as locate over 90% of the assembled genome into chromosomal linkage groups. Genome annotation of the assembled genome using three prediction pipelines postulated a set of 94,556 non-redundant gene models. From those, 41,000 high confidence gene models were identified using an overlapping weighted evidence gene model scoring method (OWEG score) that combines transcriptomic and prediction evidence. This set represents 94% of all NCBI ESTs from lettuce aligned to the genome. The genome is now being characterized for genes of agricultural importance.