Dovetail/in Vitro Proximity Ligation Data Facilitates Analysis of an Ancient Whole Genome Triplication Event in Lactuca sativa

Increases in ploidy level are widespread phenomena in plant genome evolution. Most crops have undergone polyploidization events, some recent and some ancient. A paleoploidization event resulting in a whole genome duplication has been suggested to be basal to all the members of the Compositae (Asteraceae) family based on analysis of duplicated genes. We have investigated this event using a high quality genome assembly and annotation of cultivated lettuce, Lactuca sativa.  The HiRise program developed by Dovetail Genomics was used to improve the assembly using reads from multiple Chicago libraries, which were generated with an in vitro proximity ligation technique.  This greatly increased the contiguity and quality of the L. sativa genome assembly; the improved assembly was validated genetically.  Combined with the curated gene set, this produced a high quality resource for syntenic analysis.  Intragenomic syntenic analysis of the L. sativa genome and syntenic comparisons with other Asterid species revealed multiple paleoploidization events that occurred basal to the Compositae family. Syntenic segments are often present in triplicate indicative sequential genome duplications rather than the originally proposed single duplication event. Analysis of large segments of the genome allowed precise definition of paralogous groups of genes and analysis of their evolution subsequent to the whole genome duplication events.