Genomics of Compositae Crops: EST Libraries, and Evidence of Hybridization with Wild Relatives

Although the Compositae harbours only two major food crops, sunflower and lettuce, several other species in this family are utilized by humans and have experienced various levels of domestication. Here we have used next generation sequencing technology to develop 14 reference transcriptome assemblies for Compositae crops or their wild relatives. These data will allow us to gain insight into the evolutionary and genomic consequences of plant domestication. Specifically we performed Illumina sequencing of Cichorium endivia (chicory, wild and cultivar), Cichorium intybus (endive, wild and cultivar), Echinacea angustifolia, Iva annua, Helianthus tuberosus (Jerusalem artichoke), Dahlia sp., Leontodon taraxacoides and Glebionis segetum, as well 454 sequencing of Guizotia scabra, Stevia rebaudiana, Parthenium argentatum (guayule) and, Smallanthus sonchifolius (yacón). Illumina reads were assembled using Trinity, and 454 reads were assembled using MIRA and CAP3. We evaluated the coverage of the transcriptomes using BLASTX analysis of a set of ultra conserved orthologs (UCOs). We examined other assembly metrics, including unigene length and the quality of paralog assembly. We assigned gene ontology (GO) terms to unigenes based on BLASTX to the TAIR protein database. Finally, we compared the divergence of orthologs at synonymous sites between Compositae crops and their wild relatives to determine if there was evidence for introgression and examined the over-representation of GO terms in these sets of putatively introgressed genes.