Skip to main content
Dryad logo

Data from: Genomics of Compositae crops: reference transcriptome assemblies, and evidence of hybridization with wild relatives

Citation

Hodgins, Kathryn A. et al. (2013), Data from: Genomics of Compositae crops: reference transcriptome assemblies, and evidence of hybridization with wild relatives, Dryad, Dataset, https://doi.org/10.5061/dryad.cp723

Abstract

Although the Compositae harbours only two major food crops, sunflower and lettuce, many 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 15 reference transcriptome assemblies for Compositae crops or their wild relatives. These data allow us to gain insight into the evolutionary and genomic consequences of plant domestication. Specifically, we performed Illumina sequencing of Cichorium endivia, Cichorium intybus, Echinacea angustifolia, Iva annua, Helianthus tuberosus, Dahlia hybrida, Leontodon taraxacoides and Glebionis segetum, as well 454 sequencing of Guizotia scabra, Stevia rebaudiana, Parthenium argentatum and Smallanthus sonchifolius. 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) and recovered most of these genes (88-98%). We found a correlation between contig length and read length for the 454 assemblies, and greater contig lengths for the 454 compared to the Illumina assemblies. This suggests that longer reads can aid in the assembly of more complete transcripts. Finally, we compared the divergence of orthologs at synonymous sites (Ks) between Compositae crops and their wild relatives and found greater divergence when the progenitors were self-incompatible. We also found greater divergence between pairs of taxa that had some evidence of post-zygotic isolation. For several more distantly related congeners, such as chicory and endive, we identified a signature of introgression in the distribution of Ks values.

Usage Notes

Location

Pakistan
Garden origin West Coast Seeds B.C. Canada
Jimma. Ethiopia. 5km from Jimma on the way to Bonga 1775m evolution. Latitude 7.626 Longitude 36.760
Ohio United States Hwy. 81W 16.8km west of Ada Allen County. Latitude 40.733 Longitude -84.017
Krasnodar Russian Federation (latitude 45.033 longitude 35.977)
Cleden-cap-Sizun Finistere France Porto Portugal (Between Lordelo do Ouro and Porto Douro Litoral Province Latitude 41.15 Longitude -8.633)
Granite City IL Latitude 38.804 Longitude 90.114
Oregon Benton Cty OSU campus vacant lot at corner of SW 11th St and Washington
Oklahoma United States Section 24 T19N R2W Logan County 36.1 -97.367
Peru
Germany