Facilitating candidate gene discovery in an emerging model plant lineage: Transcriptomic and genomic resources for Thalictrum (Ranunculaceae)

The plant genus Thalictrum is a representative of the order Ranunculales (a sister lineage to all other Eudicots) with diverse floral morphologies, encompassing four sexual systems and two pollination modes. Previous studies suggest multiple transitions from insect to wind pollination within this genus, in association with polyploidy and unisexual flowers, but the underlying genes remain unknown. We generated a draft reference genome for Thalictrum thalictroides, a representative of a clade with ancestral floral traits (diploidy, hermaphroditism, and insect pollination) and a model for functional studies. To facilitate candidate gene discovery in flowers with different sexual and pollination systems we also generated floral transcriptomes of T. thalictroides and of wind-pollinated, andromonoecious (staminate and hermaphroditic flowers on the same plant) T. hernandezii. The T. thalictroides draft genome assembly consisted of 44,860 contigs (N50=12,761 bp. and 243 Mbp. total length) and contained 84.5% conserved embryophyte single-copy genes. Floral transcriptomes from Illumina sequencing and de novo assembly contained representatives of most eukaryotic core genes (approximately 80%), with most of their genes falling into common orthologous groups (orthogroups). Simple Sequence Repeat (SSR) motifs were also identified, which together with the single-copy genes constitute a resource for population-level or phylogenetic studies. Finally, to validate the utility of these resources, putative candidate genes were identified for the different floral morphologies using stepwise dataset comparisons. In conclusion, we present genomic and transcriptomic resources for Thalictrum, including the first genome of T. thalictroides and potential candidate genes for flowers with distinct sexual and pollination systems.