Genomic and transcriptomic resources for candidate gene discovery in the Ranunculids

Abstract

Premise: Multiple transitions from insect to wind pollination are associated with polyploidy and unisexual flowers in Thalictrum (Ranunculaceae), yet the underlying genetics remains unknown. We generated a draft genome of Thalictrum thalictroides, a representative of a clade with ancestral floral traits (diploid, hermaphrodite, and insect pollinated) and a model for functional studies. Floral transcriptomes of T. thalictroides and of wind-pollinated, andromonoecious T. hernandezii are presented as a resource to facilitate candidate gene discovery in flowers with different sexual and pollination systems.

Methods: A draft genome of T. thalictroides and two floral transcriptomes of T. thalictroides and T. hernandezii were obtained from HiSeq 2000 Illumina sequencing and de novo assembly.

Results: The T. thalictroides de novo draft genome assembly consisted of 44,860 contigs (N50 = 12,761 bp, 243 Mbp total length) and contained 84.5% conserved embryophyte single-copy genes. Floral transcriptomes contained representatives of most eukaryotic core genes, and most of their genes formed orthogroups.

Discussion: To validate the utility of these resources, potential candidate genes were identified for the different floral morphologies using stepwise data set comparisons. Single-copy gene analysis and simple sequence repeat markers were also generated as a resource for population-level and phylogenetic studies.

Keywords: Ranunculaceae; Thalictrum hernandezii; Thalictrum thalictroides; draft genome; floral transcriptome; pollination syndrome; sexual system.

Figure 1

Floral phenotypes of Thalictrum study species. Inflorescence of hermaphroditic T. thalictroides with hermaphrodite open flowers (A) and andromonoecious T. hernandezii with staminate buds () and hermaphrodite open flowers () occurring together in an inflorescence (B); inset, detail of young staminate flower. Scale bar = 1 cm.

Figure 2

Proportion of Benchmarking Universal Single‐Copy Orthologs (BUSCOs) for the Thalictrum thalictroides genome (total number of BUSCOs = 1440 genes in Embryophyta from OrthoDB version 9.0). Data are shown for the two sequenced accessions (WT964 and WT478) and the consensus.

Figure 3

The relative abundance of different families of transcription‐associated proteins (TAPs) in the floral transcriptomes of Thalictrum thalictroides (Tt) and T. hernandezii (Th_H, hermaphrodite and Th_S, staminate). Transcripts >0.1 TPM (transcripts per million) are included. Statistically significant differences between samples (chi‐square test) are marked with black (P < 0.01) or red (P < 0.05) asterisks. TFF: transcription factor family, OTR: other transcriptional regulator family.

Figure 4

The number of shared and unique orthogroups or transcripts among the Thalictrum data sets in this study, with examples of candidate genes (in red based on Arabidopsis, see text for details). The total number of orthogroups per data set is indicated in parentheses. Representative flower pictures are shown for T. thalictroides (TTHA), insect‐pollinated with hermaphrodite flowers, and T. hernandezii (THER), wind‐pollinated with hermaphrodite (THER_HERM) and staminate (THER_MALE) flowers. (A) Interspecies comparison of floral transcriptomes (TTHA_RNA and THER_RNA) and validation against the T. thalictroides draft genome (TTHA). Area “a” represents T. thalictroides‐exclusive orthogroups found in the draft genome; “b” represents T. hernandezii‐exclusive orthogroups (both floral types combined) found in the draft genome. (B) Intraspecies comparison of transcripts of two floral types in T. hernandezii (male and hermaphrodite). Area “c” represents male flower–specific transcripts; “d” represents hermaphrodite flower–specific transcripts.