CYCLOIDEA paralogs function redundantly to specify dorsal flower development in Mimulus lewisii (Phrymaceae)

Premise: Duplicated genes (paralogs) are abundant in plant genomes and their retention may influence the function of genetic programs and contribute to evolutionary novelty. How gene duplication affects genetic modules, and the forces that contribute to paralog retention are outstanding questions. The CYCLOIDEA(CYC)-dependent flower symmetry program is a model for understanding the evolution of gene duplication, providing multiple examples of paralog partitioning and novelty. However, a novel CYC gene lineage duplication event near the origin of Higher Core Lamiales (HCL) has received little attention.
Methods: To understand the evolutionary fate of duplicated HCL CYC2 genes, we determined the effects on flower symmetry of suppressing MlCYC2A and MlCYC2B expression using RNA interference (RNAi). We determined flower symmetry phenotypic effects in single and double silenced backgrounds and coupled this with expression surveys of MlCYC2A, MlCYC2B, and a putative downstream RADIALIS (MlRAD..., Methods for generating file: CYC_alignment.txt
Putative M. lewisii CYC orthologs were identified in Sengupta and Hileman (2018): Mimulus_lewisii_CYCLOIDEA_like_2b_sc2324_contig13781 (found on scaffold 2324 of the M. lewisii LF10 genome assembly v1.8 and as contig 13781 in the LF10 transcriptome v1.2, here MlCYC2A) and Mimulus_lewisii_CYCLOIDEA_like_2a_sc424_contig9407 (found on scaffold 424 of the M. lewisii LF10 genome assembly v1.8 and as contig 9407 in the LF10 transcriptome v1.2, here MlCYC2B). We recovered coding sequences for these genes from the M. lewisii LF10 draft genome (www.mimubase.org) and aligned them to known higher core Lamiales (HCL) CYC2A and CYC2B lineage genes (Appendices S1 and S2; see Supplemental Data with this article) in Geneious Prime v.2021.2.2. We manually aligned the coding sequences from start to stop codon with reference to amino acid translations and removed regions of high sequence divergence for which we could not confidently assign homology. We used t..., , # CYCLOIDEA paralogs function redundantly to specify dorsal flower development in Mimulus lewisii (Phrymaceae)

[https://doi.org/10.5061/dryad.qv9s4mwmg](https://doi.org/10.5061/dryad.qv9s4mwmg)

CYC\_alignment.txt
The DNA sequence alignment used to generate the *CYCLOIDEA* gene tree presented in Fig. 3.

Mimulus\_lewisii\_floral\_measurementsB.csv
The floral measurements gathered for comparison of RNAi lines to wild type presented in Figs. 6-8, Appendices S8-11.

## Description of the data and file structure

CYC\_alignment.txt
Fasta formatted alignment; document in .txt format.

Mimulus\_lewisii\_floral\_measurementsB.csv
spreadsheet of raw trait data in comma delimited format (.csv)