de novo Genome Assembly and Ultra-Dense Mapping of Artichoke, Chicory and Endive, and Syntenic Comparisons Across the Compositae

The Compositae family is one of the largest and most diverse botanical families.  Its richness of evolutionary histories is being exploited for studying the mechanisms underlying speciation and domestication events. Several species including lettuce, sunflower, globe artichoke, Belgian endive and chicory are economically important.   Genome assemblies of Lactuca sativa and Helianthus annuus are well advanced. In order to develop a wider set of genomic resources within the family and accelerate the application of forward genetics to these horticultural species, we generated high-quality draft genome assemblies for Cynara cardunculus, Cichorium endivia and C. intybus together with de novo prediction of gene models and genetic anchoring of scaffolds through low-coverage genotyping-by-sequencing of segregating progenies and the construction of ultra-dense genetic maps. To accomplish this, a novel algorithm was developed to permit the detection of heterozygous regions with low sequencing depth, especially in phase-unknown, pseudo-test cross populations as for C. cardunculus. The availability of genetically-anchored scaffold sequences allowed us to demonstrate syntenic relationships among these sequenced species, and in particular with respect to L. sativa and H. annuus, where we detected contrasting patterns of conservation resulting from the duplication event which occurred during speciation of the Heliantheae. This information allows mapping of traits across several species leveraging genetic studies that have been carried out in individual species.