In present work, we have studied the effect of mutations in ABP genes–coding and regulatory–and the effects of expression of these genes on flower color variation. Our results demonstrate the importance of both structural and regulatory changes during ABP evolution in Ruellia. We identified 12 candidate ABP structural genes plus 9 candidate transcriptional regulators, including 4 MYBs, 2 WDRs, and 3 bHLHs among the 10 investigated species. Through co-expression network analyses, we found evidence for strong correlated expression among most ABP structural genes as well as between most of these genes and one candidate regulatory MYB.
Phylogenetic relationships among the 10 species here investigated yield a hypothesis of four potential flower color transitions within the group: purple to red, red to yellow, red to purple, and purple to yellow (Fig. 1A). These four flower color transitions are consistent with patterns documented in a study with much more extensive phylogenetic sampling (Tripp and Manos 2008) and implicate both gain and loss of function mutations during flower color evolution in Ruellia. Prior studies on ABP have yielded evidence that four classes of mutations contribute importantly to color shifts across angiosperms: (1) mutations in ABP structural genes that cause either loss of function or changes to enzyme binding affinity, (2) mutations in cis-regulatory regions of ABP structural genes, and (3) mutations in coding regions or (4) cis-regions of ABP regulatory genes that impact expression of structural genes (Quattrocchio et al., 1999; Schwab et al., 2006; Whittal et al., 2006; Yakushiji et al., 2006; Chiu et al., 2010; Lin-Wang et al., 2010; Heppel et al., 2013; Shin et al., 2013; Medina-Puche et al., 2014; Yuan et al., 2014; Zhang et al., 2014). The purple to red color transition that occurred between the R. breedlovei lineage and the clade containing R. fulgida likely involved a loss of function mutation in the F3'5'H gene in the latter: our data showed that all essential ABP structural genes including F3'5'H itself were expressed at detectable levels (Fig. 2), but sequence analysis of F3'5'H revealed a premature stop codon caused by a C to T point mutation at positon 373 in R. fulgida (Figure S8). By contrast, both our de novo and reference-based approaches failed to assemble F3'5'H in the red flower species R. brevifolia, which belongs to the same clade as R. fulgida, and expression analysis indicated F3'5'H was expressed at extremely low levels (Fig. 2). These data suggest a regulatory mutation was likely involved in this purple to red color transition. In the yellow-flowered species R. bourgaei, R. speciosa, and R. lutea, we observed down-regulation of multiple structural genes, including down-regulation of F3H in the closely related R. bourgaei and R. speciosa as well as down-regulation of ANS in all three species (Fig. 2). These results suggest either independent loss of functions in the cis-regulatory elements of these structural genes in the two clades or, more likely, mutations in shared regulatory genes given that expression of F3H and ANS is strongly coordinately regulated (Fig. 4). Finally, the shift from red to purple flowers that occurred between Ruellia elegans and R. hirsuto-glandulosa likely involved reactivation of the F3'5'H pathway branch. Although restoration of pathway function is expected to be more difficult than degradation of function (Rausher, 2008, Sobel and Streisfeld, 2013), putative gains in floral anthocyanins have been documented (Armbruster, 2002; Kay et al., 2005). In R. elegans, malvidin–a derivative of delphinidin–was detected in leaf tissues albeit in low concentrations, indicating functionality of the F3'5'H pathway in this species (Data S2). Restoration of the F3'5'H pathway in petals of R. hirsuto-glandulosa may have been achieved by mutation in the cis-regulatory region of this enzyme, leading to decreased binding affinity of transcription inhibitors or increased binding affinity of transcription activators.
With exception of a few mutations in F3'H2 and DFR3 (Fig. 6) and two mutations yielding premature stop codons in F3'5'H (Figure S8), sequence comparisons and protein predictions of ABP structural genes among species with different flower colors indicated that the majority of amino acid mutations likely had neutral or minimally different functional effects, thus unlikely to result in enzyme dysfunction (Data S3). Thus, much of the observed variation in flower colors and anthocyanin accumulation in Ruellia is more likely to be the result of mutations impacting the expression of ABP structural genes (Fig. 2). Regulatory mutations are considered to be among the most important factors in driving morphological evolution (Barrier et al., 2001; Whittall et al., 2006) given that such changes can potentially lead to modification in expression of entire pathways. Through co-expression analysis, we found that expression of one of the R2R3 MYBs identified in our study–MYB10L1, which is homologous to the known ABP regulator MdMYB10 in apples (Malus × domestica; Wang et al., 2010)–was highly associated with several structural genes including CHS, F3H, DFR1, DFR2, and ANS (Fig. 4). Thus, mutations that affect MYB10L1, be they regulatory or coding, may potentially impact all five of these candidate structural genes. However, sequence comparison of MYB10L1 across all species of Ruellia sampled here recovered no lethal mutations (Fig. 5, Data S3), suggesting MYB10L1 itself is likely regulated by a higher order of regulators.
Notably, based on patterns of expression correlation with MYB10L1, the regulation of candidate ABP structural genes in our dataset can be separated into two distinct regulatory blocks (Fig. 4). Group 1 contains genes whose expression are likely under the control of MYB10L1: CHS, F3H, F3'5'H (significantly correlated with DFR2, r = 0.65, weakly associated with MYB10L1, r = 0.56), DFR1, DFR2, and ANS. Group 2 contains genes whose expression is independent of MYB10L1, among which CHI and DFR3 seem to be regulated in a coordinated manner (Fig. 4). In contrast to these two blocks, each copy of F3'H and the single copy UF3GT are regulated independently. While independent regulation of F3'H has been observed in other studies (Jeremy et al., 2015), co-expression of UF3GT with CHS or F3H in Arabidopsis has been reported in the past (Shin et al., 2013; Ali and McNear, 2014). Thus, the observed expression pattern of UF3GT in the present study seems to be a unique feature of our dataset.
Prior research has demonstrated lower rates of non-synonymous mutations among genes upstream in the ABP pathway compared to downstream genes (Rausher et al., 1999), likely as a function of relaxed evolutionary constraint on downstream (vs. upstream) genes (Lu and Rausher, 2003) or high rates of positive selection on downstream genes, potentially playing a role in adaptive floral color evolution (Huang et al., 2016). This pattern is expected given that upstream enzymes function in a much broader set of biosynthetic pathways (e.g., lignin and other flavonoids) than downstream enzymes, which are largely specific to anthocyanin production (Figure S9). Data from Ruellia suggest similar patterns of rate evolution of ABP genes compared to prior studies. Specifically, two of the lowest dn/ds substitution rates were documented for CHS and CHI (Table 2), consistent with a hypothesis that these two genes are undergoing stronger purifying selection. Furthermore, across all candidate ABP loci, loss of expression was observed only in instances of genes downstream from CHS and CHI (Fig. 2), likely reflecting the essential role of these two enzymes in other metabolic pathways besides the ABP (Winkel-Shirley, 2001).
Flower color often reflects adaptation to pollinators (Bradshaw and Schemske, 2003). For example, floral anthocyanin content has a direct effect on pollinator behavior (Schemske and Bradshaw, 1999) and plant fitness (Schemske and Bierzychudek, 1999; Bradshaw and Schemske, 2003). That all candidate structural genes identified in present study are under purifying selection adds to evidence that selection acts to maintain overall primary protein function of ABP genes. However, our data also yielded evidence that selection may drive diversification of ABP products in some lineages; specifically, we found signatures of positive selection in DFR and F3H across species (Fig. 6), and some of these sites are located in or nearby protein binding regions (PBR). This is especially the case for DFR3, in which five out of seven sites under positive selection are located within predicted PBS. Mutations occurring at these sites are more likely to impact substrate binding affinities of the corresponding enzyme resulting in new specific interactions (Reva et al., 2011). In this study, we found multiple, orthologous copies of both F3H and DFR to be present and here hypothesizes that duplication of these genes may have facilitated functional diversification of the ABP in Ruellia (Huang et al., 2016).
Transcription factors (TFs) are key players in regulating flux through secondary metabolic pathways by controlling relative levels of gene expression (Broun, 2005). To further investigate regulation of the ABP in the context of potential interactions with other metabolic pathways, we conducted a phylogenetic study of candidate MYBs as well as co-expression analyses of broader diversity of TFs across all species. We identified nine candidate R2R3 MYBs associated with the ABP identified in Ruellia (Table S3). Among these, orthologs of RsMYB10L1, RsMYB114L (i.e., AtMYB75; Borevitz et al., 2000), RsMYB305L1, and RsMYB305L2 (i.e., NtMYB305; Wang et al., 2014) have been reported to function in regulating anthocyanin accumulation. Our investigation demonstrated that RsMYB10L1 expression is highly correlated with five ABP structural genes (Fig. 4), and phylogenetic analyses demonstrated that RsMYB10L1 belongs to a strongly supported clade that contains AtMYB75 orthologs (Figure S7). This result in combination with sequence analysis and other expression patterns (Fig. 5) suggest specifically that RsMYB10L1 is a very strong candidate regulator of the ABP in Ruellia. Pilot experimentation with virus-induced gene silencing focusing on ABP knockdowns of RsMYB10L1 have yielded additional support for this candidate (Y. Zhuang and E. Tripp, unpub. data; Figure S10). Our phylogenetic analyses placed the remaining Ruellia R2R3 MYBs in clade with Arabidopsis orthologs that function in lignin biosynthesis (e.g., AtMYB4, AtMYB31, and AtMYB46/AtMYB83; Patzlaff et al., 2003; Newman, et al., 2004; Cai et al., 2014; Agarwal et al., 2016; Koshiba et al., 2017). These results support a hypothesis of different functional roles of the R2R3 MYBs recovered in Ruellia–some in ABP production vs. others potentially in lignin production–albeit in pathways that interact via common upstream enzymes (Figure S9; Tohge et al., 2005). Functionally, anthocyanins and lignins are both proposed to protect plants against UV radiation (Mouradov et al., 2014), and redirection of metabolic fluxes between the lignin and flavonoid pathways has been observed in many plant species (Ring et al., 2013). Over-expression of AmMYB308 in transgenic tobacco plants and several of its orthologs belonging to the same clade led to significant repression of lignin biosynthesis and increased total flavonoids (Tamagnone et al., 1998; Ma et al., 2011). Other studies have similarly demonstrated MYBs as negative regulators of lignin content (Agarwal et al., 2016) whereas others likely serve as activators of lignin biosynthesis (Bevan et al., 2003; Zhao and Bartley, 2014; Koshiba et al., 2017). Taken together, data suggest extensive interactions between anthocyanin and lignin biosynthesis through modification of expression of relevant TFs. As such, future attempts to understand regulatory impacts on flower color evolution in Ruellia would optimally incorporate information from other biosynthetic pathways that likely interact with anthocyanin production.
We also identified several TFs that are highly co-expressed with ABP-associated TFs in Ruellia. These include auxin responsive factors (ARFs), abscisic acid signaling genes (ABA), and other TFs, some of which function as activators and others as repressors based on prior studies in other plants (Figure S5; Ulmasov et al., 1999; Okushima et al., 2007; Gutierrez et al., 2009; Wheeler et al., 2009; Daminato et al., 2013;). In present study, we found positive co-expression between two auxin signaling pathway activators ARF6 and ARF19 (Ulmasov et al.,1999; Okushima et al., 2007) and ABP-asscociated TFs in Ruellia. We speculate that this positive association results from the role of auxin in flower development. Specifically, the accumulation of anthocyanins gradually increases during flower development in Ruellia (shown in Fig. 3A). Auxin is required for the initiation of floral primordia and disruption of auxin biosynthesis leads to the failure of flower formation (Cheng et al., 2007). Our hypothesis is further supported by the observed correlation of a group of MADS-box TFs with ABP structural genes, which is exclusively expressed only in petal tissues (Figure S11). Sequence analysis indicated one gene was homologous to AGL6, two genes were homologous to MADS1, and another two genes were homologous to MADS2, all of which impact flower development (Ma, 1994; Schwab et al., 2006). Taken together, our data suggested strong, coordinated regulation between anthocyanin accumulation and flower development.