Duplications inCYC‐like Genes from Dipsacales Correlate with Floral Form

Abstract

Flower symmetry is of special interest in understanding the evolution and ecology of angiosperms. Evidence from the Antirrhineae (within the lamiid clade of Asteridae) indicates that several TCP gene family transcription factors, especially CYCLOIDEA (CYC), play a role in specifying dorsal identity in the corolla and androecium of monosymmetric (bilateral) flowers. We examine the evolution of this gene family in Dipsacales, representing the campanulid clade of Asteridae, in relation to evolutionary shifts in floral symmetry and stamen abortion. We identify three major forms of CYC-like genes in Dipsacales. We identify the position of additional gene duplications by comparing each of the three gene trees to a well-supported Dipsacales phylogeny. We infer duplications in two of the major gene lineages along the line leading to the Caprifoliaceae correlated with the origin of monosymmetric flowers. There are no duplications or losses associated with major shifts in stamen number. However, there are several additional duplications within the Caprifoliaceae, especially in the Morinaceae, possibly related to calyx monosymmetry and/or stamen reduction. Within the protein-coding sequences, we identify a new conserved region-the ECE region-that appears to be present across known angiosperm sequences. There are major changes in length and in the presence or absence of the ECE region in the Dipsacales, indicating changes in gene function. These studies expand our understanding of the evolution of CYC-like genes in angiosperms and provide a new system for studying the role of this gene family in determining floral form.

Phylogenetic analysis of the “ECE” (CYC/TB1) clade reveals duplications predating the core eudicots

“…Our rooting with Aquilegia places the first split between CYC1 and CYC2 plus CYC3. Also, members of the CYC1 clade differ the most from the other two copies in sequence divergence, and, unlike CYC2 and CYC3, no duplications have been found within CYC1, here or in previous studies (27,30,31,35).…”

“…Duplications within the CYC3 clade are similar to those within CYC2. For instance, in Dipsacales, it seems that duplications in CYC2 and CYC3 occur in the same places in the phylogeny of Caprifoliaceae, and additional parallel duplications occur within Morinaceae (27). Our data also indicate a duplication in Scaevola (Asterales) in both CYC2 and CYC3.…”

“…Additionally, our recent work on the angiosperm clade Dipsacales (27) demonstrated that three major copies of CYC-like genes (Dips-CYC1, -2, and -3) were present in the ancestor of that group, and that several additional duplication events then occurred within this clade (Fig. 1B).…”

“…1), includes both TB1 and CYC͞DICH (as well as TCP1, -12, and -18 from Arabidopsis) and is the clade we focus on in this study. ECE refers to a conserved short motif (glutamic acid-cysteine-glutamic acid) between the TCP and R domains that we have found in most members of this clade (27). The remaining members of the TCP gene family are either suspected to function outside of the flower or do not function in dorsal͞ventral patterning (8,26).…”

Phylogeny and Phylogenetic Nomenclature of the Campanulidae based on an Expanded Sample of Genes and Taxa

“…For instance, one potential use is mining the data sets for candidate low-copy nuclear genes of interest in nonmodel organisms to use in phylogeny reconstruction or downstream evo-devo experiments (Straub et al, 2011(Straub et al, , 2012Blischak et al, 2014;Ripma et al, 2014). The inclusion of nuclear genes in phylogenetic reconstruction often relies on genes with at least two conserved domains from distantly related taxa and the use of degenerate primers (e.g., ADH, GAPDH, CYCLOIDEA [Strand et al, 1997;Hileman, 2003]), which limits the amount of known coding sequence (see Howarth and Donoghue, 2005) and does not include upstream or downstream regulatory elements. Here we present an approach to obtain lowcopy nuclear genes that could be used for detailed evo-devo experiments.…”