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Gene duplication and relaxation from selective constraints of GCYC genes correlated with various floral symmetry patterns in Asiatic Gesneriaceae tribe Trichosporeae

  • Kuan-Ting Hsin ,

    Contributed equally to this work with: Kuan-Ting Hsin, Jing-Yi Lu

    Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Resources, Software, Validation, Visualization, Writing – original draft, Writing – review & editing

    Affiliation Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan

  • Jing-Yi Lu ,

    Contributed equally to this work with: Kuan-Ting Hsin, Jing-Yi Lu

    Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Resources, Software, Validation, Visualization, Writing – original draft, Writing – review & editing

    Affiliation Department of Life Science, National Taiwan University, Taipei, Taiwan

  • Michael Möller,

    Roles Conceptualization, Resources, Writing – review & editing

    Affiliation Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom

  • Chun-Neng Wang

    Roles Conceptualization, Funding acquisition, Project administration, Resources, Supervision, Visualization, Writing – review & editing

    leafy@ntu.edu.tw

    Affiliations Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan, Department of Life Science, National Taiwan University, Taipei, Taiwan

Gene duplication and relaxation from selective constraints of GCYC genes correlated with various floral symmetry patterns in Asiatic Gesneriaceae tribe Trichosporeae

  • Kuan-Ting Hsin, 
  • Jing-Yi Lu, 
  • Michael Möller, 
  • Chun-Neng Wang
PLOS
x

Abstract

Floral bilateral symmetry is one of the most important acquisitions in flower shape evolution in angiosperms. Members of Gesneriaceae possess predominantly zygomorphic flowers yet natural reversal to actinomorphy have independently evolved multiple times. The development of floral bilateral symmetry relies greatly on the gene CYCLOIDEA (CYC). Our reconstructed GCYC phylogeny indicated at least five GCYC duplication events occurred over the evolutionary history of Gesneriaceae. However, the patterns of GCYC expression following the duplications and the role of natural selection on GCYC copies in relation to floral symmetry remained largely unstudied. The Asiatic tribe Trichosporeae contains most reversals to actinomorphy. We thus investigated shifts in GCYC gene expression among selected zygomorphic species (Hemiboea bicornuta and Lysionotus pauciflorus) and species with reversals to actinomorphy (Conandron ramondioides) by RT-PCR. In the actinomorphic C. ramondioides, none of the three copies of GCYC was found expressed in petals implying that the reversal was a loss-of-function event. On the other hand, both zygomorphic species retained one GCYC1 copy that was expressed in the dorsal petals but each species utilized a different copy (GCYC1C for H. bicornuta and GCYC1D for L. pauciflorus). Together with previously published data, it appeared that GCYC1C and GCYC1D copies diversified their expression in a distinct species-specific pattern. To detect whether the selection signal (ω) changed before and after the duplication of GCYC1 in Asiatic Trichosporeae, we reconstructed a GCYC phylogeny using maximum likelihood and Bayesian inference algorithms and examined selection signals using PAML. The PAML analysis detected relaxation from selection right after the GCYC1 duplication (ωpre-duplication = 0.2819, ωpost-duplication = 0.3985) among Asiatic Trichosporeae species. We propose that the selection relaxation after the GCYC1 duplication created an "evolutionary window of flexibility" in which multiple copies were retained with randomly diverged roles for dorsal-specific expressions in association with floral symmetry changes.

Introduction

Floral symmetry has long been thought to be one of the most extensively researched characters of trait evolution since the studies of Darwin in 1868 [1, 2, 3]. Among the various types of floral symmetry identified, zygomorphy and actinomorphy are the two major types across angiosperms. Zygomorphy, or bilateral symmetry, is characterized by a single plane of symmetry that separates flowers into two mirror images. By contrast, actinomorphy, or radial symmetry, is characterized by multiple planes of symmetry. Evolutionary reconstruction of floral symmetry states reveals that actinomorphy is the ancestral state yet multiple transitions to zygomorphy occurred across the angiosperm phylogeny [4, 5]. Zygomorphy is considered to be a key innovation, promoting specific ecological and evolutionary interactions between pollinators and floral shape [2, 3, 6, 7]. However, events of reversals from zygomorphy back to actinomorphy are also observed in several angiosperm lineages. Some of these reversions have been regarded as adaptations to rare pollinator and/or low pollination efficiency conditions such as high mountains or deep forests [8, 9].

Gesneriaceae is one of the families showing repeated shifts in floral symmetry in their evolutionary history. It is a family with over 3,500 species [10] in the order Lamiales with predominantly zygomorphic flowers, with more than half a dozen species showing actinomorphic flowers [10, 11, 12, 13, 14]. In an early classification Wang & al. [15] assigned the actinomorphic taxa Ramonda Rich., Conandron Siebold & Zucc, Tengia Chun, Bournea Oliv., Thamnocharis W.T. Wang, to a single tribe, Ramondeae, and considered this tribe also to be the most primitive in subfamily Cyrtandroideae (now Didymocarpoideae, see [10]), therefore, regarding actinomorphic taxa to represent a single ancestral lineage in Gesneriaceae. Burtt [16], based on the predominance of zygomorphic species and the scattered distribution of actinomorphic species in the taxonomic system, stated that taxa with actinomorphic flowers were probably reversal from the zygomorphic state and could not be regarded as ancestral. This was supported by molecular phylogenetic studies that indicated the family has a high number of species with reversals to actinomorphy [11, 13, 14, 17]. The most recent classification placed the five Old World actinomorphic genera, Bournea, Conandron, Ramonda, Tengia, Thamnocharis in the tribe Trichosporeae of subfamily Didymocarpoideae, and here in different subtribes: R. myconii (subtribe Ramondinae) and the other four in subtribe Didymocarpinae [10, 13, 14]. The subtribe Didymocarpinae includes the highest number of reversals to actinomorphy, with one event in Conandron [9], one in Tengia (now Petrocodon, see [18]), one in Thamnocharis (now Oreocharis, see [19]) and two in Bournea (now Oreocharis, see [19]) [13, 14, 17, 19]. The multiple reversals to actinomorphy in Trichosporeae make this tribe suitable for studying shifts of floral symmetry correlating to gene expression pattern between closely related zygomorphic and actinomorphic species. In addition, the actinomorphic flowers of species of two New World genera also evolved independently in different tribes within subfamily Gesnerioideae, Bellonia in tribe Gesnerieae and Napeanthus in tribe Napeantheae.

The genetics underlying floral symmetry was revealed by studies conducted on CYCLOIDEA (CYC) in Antirrhinum majus [20] in Plantaginaceae, a family in Lamiales closely related to Gesneriaceae [21]. In core Eudicots, CYC and all its homologues belong to the ECE-CYC2 clade of the CYC/TB1 subfamily in which the dorsal-specific expression evolved in their ancestor [22]. Extensive studies regarding the phylogeny and expression of ECE-CYC2 genes among angiosperm lineages have demonstrated that multiple copies of CYC2-like genes from putative duplication events tend to be retained in both zygomorphic and actinomorphic lineages [22, 23, 24, 25, 26]. However, it is unclear why CYC2-like genes tend to retain multiple copies and whether these multiple CYC2-like copies exhibit diverse expression patterns in association with floral morphology and floral symmetry transitions.

Within Gesneriaceae, previous studies suggested at least four GCYC duplication events [23, 24] and these GCYC duplicates all belonged to ECE-CYC2 clade [27, 28]. These duplications occurred at the subfamily to genus level. The first event occurred during the early diversification of the family, generating GCYC1 and GCYC2. GCYC2 is apparently lost in subfamily Gesnerioideae and perhaps Sanangoideae. Within tribe Trichosporeae, perhaps two additional independent GCYC1 duplication events were identified. One duplication was detected across the tribe except for European species, forming two subclades, namely GCYC1C and GCYC1D, the other occurred solely for the African genus Streptocarpus [29] generating GCYC1A and GCYC1B [23, 27, 28, 30, 31, 32]. Together with the fact that Trichosporeae species have the highest number of reversals to actinomorphy, the high number of GCYC1 duplications may imply that GCYC duplication correlates with the frequent floral symmetry transitions.

Gene duplication is generally required as precursor of functional divergence [33, 34, 35, 36, 37]. Model prediction and experimental data suggested that following gene duplication, the duplicated copies may have undergone functional divergence through neo-functionalization (shift to new gene expression domain) or sub-functionalization (modified expression domain partially overlapping with ancestral positions) or may have accumulated deleterious mutations and became non-functionalization (cease to express) [33, 36]. It has been proposed for CYC and other positively selected genes that after gene duplication, natural selection favors the fixation of mutations in one or more copies that adapt to divergent functions, and subsequently, sequential purifying selection acts to maintain new functions [34, 35, 36, 38, 39]. In other words, genetic constraints are temporarily lifted after duplication events (i.e. dN/dS deviated from 0), and this relaxation provides the opportunity for duplicated genes to adopt divergent functions [37, 40]. For instance, in Helianthus, shifting strengths of positive selection (dN/dS >1) have acted on three CYC2-like gene copies (CYC2a, b, and c) and functional divergence among them was inferred [41]. This was supported by their divergent expression patterns across the copies in which those of one clade were expressed in all floral tissues, another restricted to rays and disk florets, and the other limited to ray florets only, suggesting a case of sub- or neo-functionalization. In addition to functional divergence, loss of function in one copy, non-functionalization, is another possible fate for gene copies [33, 35, 36]. In wind-pollinated radially symmetrical flowers among six Plantago species, the loss of showy petals was correlated with a loss or non-expression of A-clade CYC2-like copies, a signature of non-functionalization [42]. Together, it is likely that natural selection can act on duplicated CYC2-like genes and subsequently their functions diverge, as inferred from shifts of their expression pattern and associated changes in flower morphology.

Only a few studies have examined the correlation between floral symmetry transition in Gesneriaceae and shifts in GCYC expression. Two studies were conducted on actinomorphic reversals in subtribe Didymocarpinae of tribe Trichosporeae, namely Bournea leiophylla (now Oreocharis leiophylla, see [19]) and Tengia scopulorum (now Petrocodon scopulorum, see [18]). Distinctive expression patterns between GCYC copies were detected in association with a transition to actinomorphy [31, 43]. In O. leiophylla, BlCYC1 was found transiently expressed at the floral meristem initiation stage and then quickly vanished at later developmental stages. Thus, the loss of the ECE-CYC2-like gene expression in later flowering stage seems to correlate with the actinomorphy resulting in mature flowers [31]. In P. scopulorum and DA cultivar of African Violets, on the contrary, GCYC duplicated copies were detected across all petals and stamens, correlating with the development of dorsalized actinomorphy [32; 43]. These expression shifts of GCYC copies emphasize the possible associations of expression pattern change and resulting floral symmetry transition. Among zygomorphic Gesneriaceae species, such as Chirita heterotricha (now Primulina heterotricha, see [44]) and Opithandra dinghushanensis (now Oreocharis dinghushanensis, see [19]), it was found that the expression of duplicated GCYC1 copies was mainly confined to the floral dorsal region, even though the expression pattern between copies usually differed and had expanded [27, 28, 45]. Overall, the expression pattern of GCYC duplications seemed to be correlated with their diversified expression patterns not only in actinomophic but also in zygomorphic species. This raises the possibility that potential expression pattern changes, thus functional divergence, has evolved frequently among GCYC duplicates. However, thus far, no integrated study has combined the evolutionary history, patterns of selective pressure, and expression patterns of GCYC copies to provide an overall interpretation to explain the reason why retention of multiple copies seemed to be preferred. Moreover, their association to floral symmetry remains to be studied.

The aim of this study was to investigate the patterns of gene expression and selective pressure of GCYC copies among species of tribe Trichosporeae in Gesneriaceae that contain species with zygomorphic and with actinomorphic flowers. In specific, we addressed (1) whether the expression patterns of these copies vary among zygomorphic and actinomorphy species, by studying two zygomorphic species H. bicornuta and Lysionotus pauciflorus, and one actinomorphic species C. ramondioides; and (2) whether the rate between nonsynonymous and synonymous substitutions (ω = dN/dS) between different copies changes after GCYC duplication events. Our results will reveal whether the expression pattern of GCYC varies from species to species in general, or whether copy-specific relaxation signals can be detected after gene duplication. The latter might suggest that evolutionary flexibility plays an important role in maintaining the diversity of flower morphology and floral symmetry transitions, underpinned by the retention of multiple GCYC duplicates in angiosperms.

Materials and methods

Ethics statement

Collection permission was granted by Yangmingshan National Park [Permission number: 20151155] for collecting plant species (Hemiboea bicornuta and Lysionotus pauciflorus).

Species sampling and plant materials

In total, 57 Gesneriaceae species representing all major lineages, including 54 zygomorphic and 3 actinomorphic species (Conandron ramondioides, Oreocharis leiophylla, Ramonda myconi) covering two subfamilies Didymocarpoideae (Old World) and Gesnerioideae (New World) were selected to investigate the genealogy of CYC-like genes across Gesneriaceae (S1 Table). Forty-four GCYC copies from 27 species were isolated in this study by PCR with Gesneriaceae specific GCYC primers [46] (S1 Table). An additional 49 GCYC copies from 30 species were downloaded from GenBank, representing all publicly available GCYC sequences. A smaller dataset composing of 17 species of tribe Trichosporeae was used for analyses of the detection of selective pressure among GCYC1C and GCYC1D (excluding GCYC1A and GCYC1B) copies.

To detect whether the GCYC expression pattern of target species showed chronological changes through developmental stages, flower buds of C. ramondioides, H. bicornuta, and L. pauciflorus were collected in the field and fixed in RNAlater (Ambion, USA) for locus-specific reverse transcription-polymerase chain reaction (RT-PCR). Flower buds of these three species were collected at three stages (see Fig 1): early stage (sepals closed with an erect and elongated peduncle), middle stage (sepals open, petal length longer than sepal length), and late stage (flower fully open with mature anthers). To locate organ specific expression of GCYC, early-stage floral buds were dissected. In this process, because of the floral organ differences between zygomorphic and actinomorphic species, we adopted two different processing steps. For the actinomorphic species, C. ramondioides, early-stage buds were dissected into seven regions: five single petals, stamens, and gynoecium. For the zygomorphic species, H. bicornuta and L. pauciflorus, early-stage buds were dissected into six categories: dorsal petals, lateral petals, ventral petal, stamens, staminodes, and gynoecium.

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Fig 1. Flower morphology and developmental stages of Conandron ramondioides, Hemiboea bicornuta, and Lysionotus pauciflorus.

(A) Three developmental stages (early, middle, and late) of C. ramondioides—Early Stage: petal length < sepal length; Middle Stage: petal length > sepal length; Late Stage: flower at anthesis. (B) Floral diagram: Five sepals (sep, black); five petals (from p1 to p5, blue); five stamens (st, yellow); gynoecium (gyn, red). (C) Three developmental stages of H. bicornuta—Early Stage: petal length < sepal length; Middle Stage: petal length > sepal size; Late Stage: flower at anthesis. (D) Floral diagram: sepals (sep, black); dorsal petals (dp, blue); lateral petals (lp, yellow); ventral petal (vp, orange); staminodes (sta, blue); ventral stamens (vst, orange); gynoecium (gyn, light blue). (E) Three development stages of L. pauciflorus—Early Stage: petal length < sepal length; Middle Stage: petal length > sepal size; Late Stage: flower at anthesis. (F) Floral diagram: sepals (sep, black); dorsal petals (dp, blue); lateral petals (lp, yellow); ventral petal (vp, orange); staminodes (sta, blue); ventral stamens (vst, orange); gynoecium (gyn, light blue).

https://doi.org/10.1371/journal.pone.0210054.g001

Molecular cloning and sequence analysis

Total genomic DNA was extracted from fresh leaves or leaf material dried by silica gel following a CTAB protocol [47]. Partial sequences of GCYC of the 27 target species were amplified using a degenerate primer pair previously designed for CYC2-like genes in Gesneriaceae: GCYCFs and GCYCR [46]. Amplifications were performed on a DNA Programmable Thermal Cycler (ABI2700, USA) using the following conditions: initial denaturation at 94°C for 3 min; followed by 35 cycles at 94°C for 30 s, annealing at 55°C for 30 s, 72°C for 50 s; and a subsequent final extension at 72°C for 10 min. The PCR mixture (25 μL) contained 13 μL of premixture (Ampliqon, Denmark), 8.5 μL ddH2O, 1.25 μL of each primer, and 1μL of template DNA (20 ng). The PCR products were then cloned using the pGEM-T Easy Vector kit (Promega, USA), according to the manufacturer’s protocol. Plasmids containing the PCR products were further screened using colony PCR and purified with a Viogene kit (Taipei, Taiwan). For each PCR product, 8 clones were sequenced for checking the numbers of GCYC homologues. For sequencing, the T7 forward and reverse primers were used. All sequences were visually rechecked from the chromatograms. To evaluate the homology, sequences were aligned with all available GCYC sequences from GenBank and a phylogenetic tree reconstructed and GCYC clades and duplication events assigned (see below). All sequences were deposited in the National Center for Biotechnology Information (NCBI) nucleotide sequence database under the accession numbers provided in S1 Table.

Locus-specific RT-PCR

Total RNA was extracted from the buds and dissected tissues of H. bicornuta, L. pauciflorus, and C. ramondioides using the Trizol (Invitrogen, USA) protocol. The quantity and quality of total RNA were determined using a Nanodrop Lite spectrophotometer (ThermoFisher Scientific, USA) and visualized by gel electrophoresis. Prior to cDNA synthesis, all RNA samples were treated with RQ1 DNase kit (Promega, USA) to eliminate possible genomic DNA contaminations. Each sample was checked for DNA contamination prior to RT-PCR (S2 Fig). Then, first-strand cDNAs were synthesized from total RNA with Superscript IV Rnase H–Reverse Transcriptase (Invitrogen, USA). The oligonucleotide sequences for primer pairs used to detect the expression pattern of target species are listed in supplementary file S1 Table. Expression levels of the CYC-like genes in floral buds and dissected floral parts were semi-quantified by comparing the intensity of the RT-PCR amplified bands on gels. RT-PCR products from each tissue were compared at 25, 30, 35 and 40 cycles to check for PCR saturation (S3 and S4 Figs). All products were examined via electrophoresis under a UV-light system (Omics Bio, Taipei, Taiwan). The RT-PCR conditions for amplifying the GCYC copies were as follows: denaturing at 94°C for 3 min, followed by 25–40 cycles (see above) of denaturation at 94°C for 30 s, annealing at gene specific settings (for C. ramondioides CrCYC1C and CrCYC1D at 53°C for 35 s; for H. bicornuta HbCYC1C and HbCYC1D at 55°C for 30 s; and for L. pauciflorus LpCYC1C and LpCYC1D at 53°C for 30 s), and extension at 72°C for 30 s, with a final extension step at 72°C for 10 min. 18S rRNA was used as an internal control to calibrate the amount of RNA in all RT-PCR reactions. All RT-PCRs were conducted with at least two biological replicates and two technical replicates for each developmental bud stage/floral organ to check the reproducibility of the results. The PCR products were examined under a UV-light system (see S3 and S4 Figs).

Phylogeny reconstruction

The two homologs of CYC2-like genes of Calceolaria arachnoidea, CaaCYC1 and CaaCYC2, were used as outgroup considering the close phylogenetic relationship of C. arachnoidea to Gesneriaceae [21, 24]. All CYC-like sequences were automatically aligned using MUSCLE [48] in MEGA v.6 [49], and the resulting alignment matrix visually refined based on amino acid translations (S1 File). Substitution model parameters were estimated in jModelTest2 [50]. The HKY+G model was selected as the best-fitting model based on the Bayesian Information criteria (BIC) [51]. Phylogenetic trees were reconstructed using Bayesian inference (BI) and maximum likelihood (ML) methods. Bayesian phylogenetic analyses were performed using MrBayes v.3.2.6 [52]. Two runs of four Markov chain Monte Carlo (MCMC) chains were run in parallel for 10 million generations, with a burn-in of 25% and sample frequency of every 1000th generation. Convergence was assessed using the potential scale reduction factor (PSRF = 1.0) and the average standard deviation of split frequencies (<0.01). Additionally, the effective sampling size (ESS > 200) for all parameters and the traces of likelihoods were examined in Tracer v.1.6 [53]. A majority-rule consensus tree was reconstructed from the remaining trees and posterior probabilities determined in MrBayes using “sump” and “sumt” commands.

The ML phylogenetic analyses were performed using the PhyML 3.0 on-line web interface [54]. The HKY+G model derived from jModelTest2 was applied. Statistical support for nodes was assessed by an approximate likelihood ratio test (aLRT) [55] and conventional ML bootstrap algorithm (ML bootstrap) with 1000 replicates.

Estimation of functional divergence of GCYC sequences between 1C and 1D clades

At the species level, coefficients of type I and II functional divergences (θI and θII) were applied to assess selection on amino acid sites that are responsible for the functional divergence between duplicated GCYC clades, based on an ML approach implemented in DIVERGE v.3.0 [56]. Type I functional divergence aims to detect whether evolutionary rates vary between duplicate genes after gene duplication occurred, whereas type II functional divergence aims to detect the presence of radical changes in amino acid properties between duplicate genes (e.g. charge, hydrophobic, etc.) [57]. The type I and II methods calculate the parameter θ, where a θ value significantly greater than zero indicates functional divergence between the GCYC1C and GCYC1D clades.

Detection of molecular evolutionary patterns of GCYC genes

GCYC sequences among clades at the species level were tested for detecting adaptive evolution after gene duplication by using the alternative and null branch model comparison of CODEML implemented in PAML v.4.0 [58]. A smaller subset including only GCYC1 sequences of tribe Trichosporeae (excluding GCYC1A and GCYC1B) was used in the detection of selective pressure alterations after GCYC1C-GCYC1D duplication. For this, we realigned partial length (see S2 File) GCYC1C and GCYC1D sequences (including those of CaaCYC1, RdCYC1, PsCYC1 and European GCYC1) and gaps were treated as missing data. A Bayesian phylogeny of this dataset was reconstructed based on the same program settings as above. To keep as many site information as possible, we set clean data = 0 in the PAML control file. The setting (clean data = 0) allows PAML to perform pairwise deletion of sites containing only missing data.

To detect selection pressure changes along duplication events of GCYC1C and GCYC1D, we compared the ω value differences between pre-duplication, post-duplication but before divergence, and post divergence (Fig 2A). For model comparison, the null model (one-ratio model, Fig 2B) assumes a constant ω ratio for all GCYC branches, whereas the alternative model was constructed under the assumption that selective constraints changed following duplication events, similar to the strategy in [40]. In the modified model set, the first alternative model is a two-ratio model, which assumes two independent ω ratios: one ratio is before the duplication of GCYC1C and GCYC1D and the second ratio is after the duplication of GCYC1C and GCYC1D (Fig 2C). The second alternative model is a three-ratio model: the first ratio was assigned to all branches before the GCYC1C and GCYC1D duplication event, the second ratio was assigned to the two branches immediately after the duplication event, and the third ratio was assigned with equal values to all descendant branches after the divergence of GCYC1C and GCYC1D (Fig 2D). To test whether positive selection acted separately on GCYC1C or GCYC1D immediately after the duplication event, one additional three-ratio model was designed with the first ratio assigned to all branches before the duplication. But the second ratio was assigned to the branch leading to GCYC1C and all its descendant while the third ratio was assigned to GCYC1D and all its descendant branches. The four-ratio model separate the third ratio (along the divergence of GCYC1C and that of GCYC1D) in the three-ratio model into two clade-specific selective signals, namely GCYC1C or GCYC1D (Fig 2E). These models were tested against their inferior models (i.e. 4-ratio vs. 3-ratio) with 1 degree of freedom difference to examine the statistical support. Furthermore, in order to consider the selective pressure on specific sites or domains, branch-site models were used to increase the detectability and validate the results of branch models. Branch-site model A was built upon the assumption of a two-ratio branch model. The lineages before the duplication of GCYC1C and GCYC1D (second ratio) was assigned as foreground and the others as background (first ratio) to verify whether the ω value of foreground branches show relaxation (ω deviates from 0) or positive selection (ω greater than 1). This Branch-site model A was compared with a null model with fixed ω values of both foreground and background branches to 1 to assess any statistical support for positive selection [59]. Moreover, two separate branch-site model A with either GCYC1C or GCYC1D assigned as foreground were also applied in an attempt to discover hidden selective pressure on specific sites/domains in certain clades of these GCYC duplicates. Finally, clade model C, which allows more than one foreground clade, was used to examine whether ω values among foreground branches are different to those of background branches. Two models, one with post-duplication lineages as foreground and the other with GCYC1C and GCYC1D as different foregrounds, were used to examine the possibility of clade-specific selective pressures. The first clade model C (post-duplications as foreground) was tested against the null model m2a_rel [60] and the second clade model C (GCYC1C and GCYC1D as different foreground) was tested against the first clade model C. All alternative models were compared with their corresponding null models and tested using the likelihood ratio test (LRT) statistics [61].

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Fig 2. Branch models used in PAML analyses.

(A) Schematic representation of the tree used in PAML. Arrowheads indicate the duplication event. Post duplication denotes all branches arising after the duplication event. Before divergence denotes the first branches following immediately the duplication event and post divergence denotes all subsequent branches. (B) One-ratio model, assumes equal ω across the tree. (C) Two-ratio model, assumes that ω changes pre- and post- duplication of GCYC1C and GCYC1D. Light blue line denotes same ω on branches post-duplication. (D) Three-ratio model, assumes ω varies before divergence (light blue lines), post divergence (dark blue lines) and outgroups (black lines). (E) Four-ratio model, assumes ω varies among branches before divergence (light blue lines), branches in GCYC1C clade (dark blue lines), branches in GCYC1D clade (dark blue triangle) and outgoups (black line).

https://doi.org/10.1371/journal.pone.0210054.g002

Results

Evolutionary history of GCYC genes

In total, 98 homologs of 57 Gesneriaceae species were isolated in the present study or acquired from GenBank (S1 Table). The aligned sequence dataset was 840 bp in length. All GCYC genes contained partial conserved TCP, ECE, and R domains. Among the different copies, a GCYC1D specific 12 amino acid insertion located at about ten amino acid downstream the R domain was also found (see S1 Fig) The numbers of copies varied among the clades in the phylogenetic tree across the family (Fig 3). All subfamily Gesnerioideae (New World) species had only one copy, namely GCYC1. For several subfamily Didymocarpoideae species, at least two copies of GCYC were identified, GCYC1 and GCYC2.

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Fig 3. Genealogy and duplication events of GCYC in Gesneriaceae.

Phylogram derived from a Maximum Likelihood (ML) analysis showing average branch lengths. Numbers along branches are BI, ML approximate likelihood value (aLRT), and ML bootstrap values. (--) indicates branch support value lower than 0.7 either in either BI, aLRT or ML bootstrap. GCYC copies of species used for expression studies are colored: Conandron ramondioides (light green); Hemiboea bicornuta (orange); Lysionotus pauciflorus (light blue). Dup1 to Dup5 indicate inferred duplication events.

https://doi.org/10.1371/journal.pone.0210054.g003

To infer duplication events of GCYC genes, we reconstructed the evolutionary history of GCYC genes using both Bayesian Inference (BI) and Maximum Likelihood (ML) algorithms. Only nodes with BI or ML probability value over 0.7 (BI > 0.7 or aLRT > 0.7 or ML bootstrap > 0.7) were regarded as a reliable clade. According to our criteria, five duplication events can be inferred across the phylogeny (Fig 3). The first duplication appeared at the basal part of the tree and gave rise to two well-supported clades (Fig 3, Dup1; BI: 1, aLRT: 0.98, ML bootstrap: 0.98): GCYC1 (BI: 0.7, aLRT: 0.78) and GCYC2 (BI: 1, aLRT: 1, ML bootstrap: 0.75). Most of the subfamily Didymocarpoideae species (Old World) had both GCYC1 and GCYC2 copies but all subfamily Gesnerioideae species (New World) retained only GCYC1 copies. From the tree topology in Fig 3, the split between GCYC1 and GCYC2 was an ancestral duplication in the common ancestor of Gesneriaceae, yet Gesnerioideae species appeared to have lost their GCYC2 copy or it has not yet been found. Within GCYC2, there was one further duplication (Fig 3, Dup2; BI: 1, aLRT: 1, ML bootstrap: 0.75) perhaps occurring in the common ancestor of Old World tribe Trichosporeae species as species of several subtribes across the tribe contained both GCYC2A and GCYC2B. Within GCYC1, there were three further independent lineage-specific duplication events. One duplication (Fig 3, Dup3; aLRT: 0.76, ML bootstrap: 0.71) perhaps occurred in the common ancestor of New World tribes Coronanthereae and Napeantheae thus GCYC1 in these species further duplicated into GCYC1E (BI: 0.7, aLRT: 0.7, ML bootstrap: 0.7) and GCYC1F (aLRT: 0.81). Among Old World tribe Trichosporeae species, a second GCYC1 duplication event (Fig 3, Dup4; BI: 0.97, ML bootstrap: 0.7) gave rise to GCYC1C (BI: 1, aLRT: 0.92, ML bootstrap: 0.94) and GCYC1D (BI: 1, aLRT: 0.95, ML bootstrap: 0.97) and seemed to occur in the common ancestor of the Asiatic and Malesian subtribe Didymocarpinae species and African and Madagascan subtribe Streptocarpinae species, since species of subtribes Ramondinae, Leptoboeinae and Loxocarpinae species possessed only one GCYC1 copy (Fig 3). The African and Madagascan species of subtribe Streptocarpinae seemed to have lost their GCYC1D copy. On the other hand, within subtribe Streptocarpinae species a further gene duplication event had occurred (Fig 3, Dup5; BI: 1, aLRT: 1, ML bootstrap: 0.99), resulting in GCYC1A (BI: 1, aLRT: 0.91, ML bootstrap: 0.93) and GCYC1B (BI: 1, aLRT: 0.94, ML bootstrap: 0.98).

Expression pattern and variation among GCYC copies

The expression patterns of GCYC copies varied from species to species (Fig 4). For the actinomorphic C. ramondioides, three copies namely CrCYC1C, CrCYC1D and CrCYC2 were identified. Both CrCYC1C and CrCYC1D were detected during the early (E) and mid (M) flower developmental stages (Fig 4). In dissected floral organs, both CrCYC1C and CrCYC1D were not detected in single petals (P1, P2, P3, P4, P5), pooled petals (P1 to P5), pooled stamens (st), or the gynoecium, but were detected in pooled sepals (sep). CrCYC2 was not detected throughout the flower developmental stages. This implies that the actinomorphy of C. ramondioides perhaps resulted from the entire loss of GCYC expression in the petal whorl. In the zygomorphic H. bicornuta, four copies of GCYC were isolated, namely HbCYC1C, HbCYC1D, HbCYC2A and HbCYC2B (Fig 3). Only HbCYC1C was found expressed in early flower buds (E), whereas HbCYC1D was not expressed in flowers (Fig 4). Organ specific expression of HbCYC1C was detected in dorsal petals (dp), staminodes (sta) which are situated in the dorsal part of the flower, ventral stamens (vst), and gynoecium (gyn). For the zygomorphic L. pauciflorus, also four copies of GCYC were isolated, namely LpCYC1C, LpCYC1D, LpCYC2A and LpCYC2B (Fig 3). In contrast to Hemiboea, LpCYC1D, instead of LpCYC1C, was expressed in all floral bud stages in L. pauciflorus (Fig 4). Similarly, LpCYC1D had an organ specific expression in the dorsal petals (dp), staminodes (sta), stamens (st), and the gynoecium (gyn). GCYC2 was also not expressed in both zygomorphic species. Dorsal petal and staminode specific expression of GCYC was detected in both zygomorphic species. But in H. bicornuta, GCYC1C (HbCYC1C) was the more prominently expressed copy while in L. pauciflorus, GCYC1D (LpCYC1D) was the more strongly expressed copy.

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Fig 4. Expression pattern of GCYC in floral parts of Conandron ramondioides, Hemiboea bicornuta, and Lysionotus pauciflorus.

(A) Conandron ramondioides. (B) Hemiboea bicornuta. (C) Lysionotus pauciflorus. E: Early Stage flower bud, M: Middle Stage flower bud, L: flower bud at anthesis; n denotes no-template control; dp: dorsal petals, lp: lateral petals vp: ventral petal; p1 to p5: pooled C. ramondioides petals; st: pooled stamens (C. ramondioides); vst: ventral stamens, sta: staminodes (H. bicornuta, L. pauciflorus); gyn: gynoecium; sep: pooled sepals (C. ramondioides). A very faint band appears sometimes in no-template controls in C. ramondioides and represent primer dimer artefacts (see S5 Fig).

https://doi.org/10.1371/journal.pone.0210054.g004

Patterns of molecular evolution in Trichosporeae GCYC1C and GCYC1D sequences

The smaller GCYC sequence subset used for detecting patterns of selection was 744 bp in length and had 383 variable sites. The BI and ML tree topologies were congruent but fully resolved in comparison to the large analysis (Figs 3 and 5). Our two-ratio branch model of the selection analysis revealed that ω significantly increased from before duplication (pre-duplication) (ω0 = 0.2819) to duplication into GCYC1C and GCYC1Dpost-duplication = 0.3985*) (Model A1, Table 1, Fig 2C), suggesting a relaxation from genetic constraints. This was further confirmed by the results for the clade model C (Model C1, Table 1), which detected a relaxation signal of selective pressure after the GCYC1C/1D duplication (post-duplication) (ω0 = 0.0469, ωpost-duplication = 0.1968*, p-value <0.05). Furthermore, the three-ratio branch model (Model A2-1, Table 1) was statistically supported to be superior to the two-ratio model (Model A1), suggesting that a selection pressure was maintained on both GCYC1C and GCYC1D lineages right after duplication (ωbefore divergence = 0.1344), but eventually relaxed after divergence of the GCYC1C/1D lineages (ωafter divergence = 0.431*, Table 1, Fig 2D). The four-ratio branch model (Model A3, Table 1) compared if selective pressures were different between GCYC1C and GCYC1D, but its likelihood was not significantly better than the three ratio model (Model A2-1, Table 1, Fig 2E), indicating the selective pressure was the same in GCYC1C and GCYC1D. Similarly, the clade model C2 (Table 1), which assigned GCYC1C and GCYC1D as separated foregrounds, was not different from the null model C0, therefore failing to detect GCYC1C/1D clade-specific positive selection changes. These results suggested that the relaxation signal observed after GCYC1C/1D duplication was most likely caused by relaxation rather than a positive selection difference acting on either GCYC1C or GCYC1D after their divergence. However, branch site model A, the attempts to detect whether certain sequence regions are under selection, failed to find any site or specific lineage subject to natural selection or relax from selection (S3 Table). Attempts to uncover Type I and Type II functional divergences between GCYC1C and GCYC1D with DIVERGE however, failed to find certain sites which underwent functional divergence (S4 Table).

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Fig 5. GCYC1 phylogenetic tree with summarized GCYC1C and GCYC1D expression pattern in tribe Trichosporeae species.

BI cladogram based on GCYC1 sequences of species in tribe Trichosporeae. Numbers above branches and below branches are approximate likelihood and posterior probability values obtaining from ML and BI analyses respectively. GCYC1 expression patterns are shown in color by organ: D: dorsal petal, L: lateral petal, V: ventral petal; red squares represent presence and white squares absence of gene expression in the respective flower part; square with ‘?’ denote unknown expression. Expression pattern were compiled from this work and previous studies ([27, 28, 31]). GCYC genes isolated from actinomorphy species in boxes. Light green font: Conandron ramondioides, dark green font: Oreocharis dinghushanensis, light blue font: Lysionotus pauciflorus, Orange font: Hemiboea bicornuta, Brown font: Primulina heterotricha, Black font: Oreocharis leiophylla.

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Table 1. Parameter estimates under branch and branch-site models of GCYC1C and GCYC1D in tribe Trichosporeae.

https://doi.org/10.1371/journal.pone.0210054.t001

Discussion

Lineage specific duplications and losses of GCYC in Gesneriaceae

With extensive samplings of 96 GCYC sequences from 57 representative Gesneriaceae species, we reconstructed a comprehensive GCYC phylogeny which allowed the inference of at least five duplication events and two gene loss events across the family during the evolution history of GCYC. The monophyly of GCYC1 and GCYC2 across the Gesneriaceae confirmed hypotheses from previous studies that the two paralogs originated in the most recent common ancestor of Gesneriaceae after its split from Calceolariaceae and subsequently experienced lineage-specific duplications within Gesneriaceae [23, 24]. This GCYC1/2 duplication was first identified from a small set of Gesneriaceae species [23] that suggested that GCYC duplications may be involved in the evolution of floral symmetry. Consistent with previous studies, only GCYC1 is present in the New World species [24, 62]. It is interesting to note that GCYC2 appears to have been immediately lost in the New World clade (i.e. subfamily Gesnerioideae) after the initial GCYC duplication. Lineage-wide losses appear to have played a significant part in the GCYC evolution in Gesneriaceae as indicated by the loss of GCYC1D for subtribe Streptocarpinae (Fig 3; [23]).

Within the GCYC1 clade, the independent duplications in the Old World tribe Trichosporeae (GCYC1C/1D) and New World tribe Coronanthereae (GCYC1E/ 1F) implied they arose from different mechanisms. It is quite likely that a whole genome duplication was involved in the duplication of GCYC in Coronanthereae since cytological data revealed that many of the species in this tribe are polyploid [63, 64]. In tribe Trichosporeae, however, no such mechanism can be invoked since the duplication into GCYC1C/1D at the tribe level and GCYC1C into GCYC1A/1B duplication at subtribal level species with similar chromosome numbers are involved [63, 64]. It is as yet unclear why there are more duplications of GCYC events occurring particularly in Trichosporeae species, but retaining multiple CYC copies would probably allow these to acquire diversified function as discussed below.

Association between expression pattern shifts and floral symmetry after GCYC duplications

Shifts of gene expression patterns among duplicated copies are usually an implication for functional divergence. Frequent duplications of ECE-CYC2 together with the evolution of diverse expression patterns among these copies have played a major role in their functional divergence [65]. In A. majus [25] and other Eudicots species, the process of frequent CYC duplications and subsequent functional divergences upon selection can be summarized into three stages: 1) duplication; 2) relaxed from purifying selection immediately after the duplication, this allowed both duplicated copies have equal activities (e.g. same expression levels) as their ancestral gene; and 3) their excess cumulative activities enables one copy to become less constraint than its original function by drift, thus facilitating the accumulation of more deleterious mutations (3a. non-functionalization), or shift into a new expression pattern (3b. neo-functionalization), or both copies could retain the ancestral function by gradually reducing their excess activities/expressions to be cumulatively equal to the level of the ancestral copy (3c. functionally redundancy), or one copy partially overlap its expression/activity to the other with complementary roles (3d, sub-functionalization, one major/one helper). For example, the duplication of CYC in A. majus and the stronger phenotype of cyc relative to dich mutants suggest that they diverged into one major (i.e. CYC) / the other helper (i.e. DICH) function on floral morphology. This is also evident from their expression level differences in that both CYC and DICH were found to be expressed in the adaxial flower region, but CYC showed a broader and stronger expression on the dorsal side than DICH [20, 66, 67].

The duplication of CYC2-like genes among zygomorphic species in Dipsacales has resulted in a shift in expression out of the ventral part of the corolla (dorsal and lateral lobes) of both duplicates, DipsCYC2B and DipsCYC2A [68]. But in derived species, DipsCYC2A became limited in expression to just two dorsal lobes while DipsCYC2B maintained its expression in the dorsal and lateral lobes. In species with actinomorphic reversals, both CYC2-like copies shifted to expand their expression to either lateral lobes (DipsCYC2A, dorsal + lateral) or further to the ventral lobe (DipsCYC2B, dorsal + lateral + ventral). This supports the view that duplications may promote shifts of gene expression patterns among duplicates. Because DipsCYC2A and DipsCYC2B partly overlap in their expression to each other in Dipsacales species, this consequence of the duplication can be viewed as a sub-functionalization process.

The loss of association between plant and oil bee pollinator was found repeatedly in several unrelated Malpighiaceae lineages, and in each case these loss was associated with changes in floral symmetry (corresponding to shifts of CYC2A expression) and the loss of CYC2B expression in flower buds. This may indicate non-functionalization of one of the duplicates, CYC2B, helps to alter flower morphology [69, 70]. The rise of heterogeneous gene expression patterns after gene duplication events is therefore a common feature for the evolution of CYC2-like genes in Eudicot species. In the present study, the expression pattern shifts of duplicated GCYC1 copies became even more diversified compared to these above examples (see below).

GCYC1 duplications generate diversified expression patterns correlating with floral symmetry in a species-specific manner

The expression of GCYC1C and GCYC1D copies post duplication seemed to exhibit a species-specific expression pattern among Trichosporeae species as observed from our data and previous results (Fig 5, Fig 6). As summarized in Fig 6, the duplication of GCYC1 into GCYC1C and GCYC1D, as well as GCYC1C duplicated into GCYC1A and GCYC1B, resulted in diversified expression patterns among these copies in Trichosporeae species and they varied species by species.

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Fig 6. Reconstructed ECE-CYC2 evolution emphasizing shifts of GCYC expression pattern after gene duplication in correlation to floral symmetry transitions among selected Asiatic Trichosporeae species.

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The hollow-branch phylogeny indicates the phylogenetic relationships among selected Trichosporeae species based on [13]. The superimposed solid-line phylogenies depict GCYC genealogy and duplication events. Black lines: ancestral ECE-CYC2 lineages in the outgroup Antirrhinum majus and the New World representing sister species, Sinningia speciosa. GCYC1 paralogs originated in the common ancestor of New World and Old World Gesneriaceae species. Because CYC/DICH are dorsal petal specifically expressed, it is hypothesized that GCYC1 expression at the most recent common ancestor (MRCA) of Gesneriaceae is also dorsal specific. After GCYC1 duplication into GCYC1C (green lines) and GCYC1D (purple lines) in the MRCA of Trichosporeae species, their expression patterns greatly diversified and differentiated into “species-specific” expression patterns (see discussion). GCYC1C underwent one further duplication among the genus Streptocarpus species into GCYC1A (brown line) and GCYC1B (orange line) [23]. Stars denote the three independently evolved reversals to actinomorphic lineages. The corolla (petal) cartoons indicate expression of ECE-CYC2 including GCYC1 copies. Red color indicates expression domains of GCYC1 copies within petals. Pink indicates a relatively weak expression of DICH and GCYC1B, the helper copy for CYC in Antirrhinum majus and that for GCYC1B in Streptocarpus ionanthus, respectively. The dotted outlines indicate the potential loss of expression of a certain gene copy.

Because in the sister clade of tribe Trichosporeae, such as the New World tribe Gesnerieae represented by Sinningia speciosa, GCYC1 is dorsally expressed, as in Antirrhinum majus, GCYC1 expression in the MRCA of Trichosporeae is probably dorsal specific (Fig 6). However, upon the duplication of GCYC1 into GCYC1C and GCYC1D copies, their expression patterns became much diversified but these expression shifts correlated to their floral symmetry forms. Among three independently evolved actinomorphic species (braches marked with star in Fig 6), in C. ramondioides, both CrCYC1C and CrCYC1D were found to have completely lost their expression in all five petals (Fig 4). But both CrCYC1C and CrCYC1D were still expressed in floral buds, particularly in the sepals. Thus, the reversal to actinomorphy in C. ramondioides is not a CYC loss of function mutation, instead, it is due to the expression shifts of GCYC1 away from the petal whorl into sepals. This shifted expression pattern suggests that CrCYC1C and CrCYC1D had acquired a neo-functionalization for flower development due to an expressions shift to sepals (Fig 6). In another reversal to actinomorphy case, Petrocodon scopulorum (Tengia), however, both GCYC1C and GCYC1D are ubiquitously expressed in all five petals to result in a dorsalized actinomorphic flower [43]. This expression pattern shifts from the ancestrally dorsal-specific pattern can also be regarded as neo-functionalization, yet it was independently evolved in different lineage to C. ramondioides (Fig 6). In one other actinomorphic reversal case, Oreocharis leiophylla (Bournea), GCYC1C (BlCYC1) although transiently expressed in the dorsal region of the flower, the expression did not persist to later stages and thus the flower developed radially symmetry [31]. The other duplicated copy GCYC1D was likely lost in O. leiophylla because PCR was failed to amplify this copy even primers designed from conserved domain were used [31]. Non-functionalization of GCYC1C and GCYC1D is a plausible consequence after their duplication from GCYC1.

For zygomorphic species, as revealed in this study, non-functionalization of randomly selected GCYC1C or GCYC1D paralogs was found, such as in Lysionotus pauciflorus (loss of GCYC1C expression but retaining GCYC1D dorsal expression) and Hemiboea bicornuta (loss of GCYC1D expression but retaining GCYC1C instead) (Figs 5 and 6). A similar randomly selected non-functionalization case can be inferred from one other zygomorphic lineage such as Oreocharis benthamii where GCYC1C expression is retained dorsally but GCYC1D expression is likely lost (Fig 6) [30]. Therefore, the recruitment of dorsal specific expression of GCYC1C or GCYC1D is likely not predetermined among Trichosporeae species, rather, these copies are randomly fixed from species to species.

Expression shifts inferring sub-functionalization (expression domains of one duplicated copy expanded/reduced but still overlapping with the other copy with ancestral expression pattern) among GCYC1 duplicates can also be inferred from two other zygomorphic Trichosporeae lineages. In Primulina heterotricha, GCYC1C (ChCYC1C) expression was found extended to the lateral petals from dorsal petals, while GCYC1D (ChCYC1D) expression remained restricted to the dorsal petals (Figs 5 and 6) [28]. While in Oreocharis dinghushanensis, GCYC1C (OpdCYC1C) expression further extended to all petals but GCYC1D (OpdCYC1D) remained expressed in the dorsal petals only (Fig 6) [27]. In Saintpaulia ionanthus (now Streptocarpus ionanthus, see [29]), one additional duplication of GCYC1C resulted in one major copy, GCYC1A, strongly expressed in dorsal petals, and the other copy, GCYC1B, weakly expressed there [32] (Fig 6). Similar to the case for CYC and DICH, this GCYC1A / GCYC1B duplication indicated a functionally redundant duplication in which perhaps one major and one helper function evolved. Alternatively, in the absence of empirical functional data, GCYC1B may be on a trajectory to non-functionalization. This is the evolutionarily the most recent duplication (Fig 3) and copy GCYC1B maybe at present redundant and may eventually become lost, or attains a new function.

It is clear that multiple GCYC1 duplications (GCYC1C / GCYC1D and GCYC1A / GCYC1B) and their resulting diversified expression patterns correlate well with zygomorphic and actinomorphic development in Trichosporeae species, and these patterns evolved randomly in different copies in a “species-specific” manner.

Relaxation signals detected after duplication of GCYC1C and GCYC1D

Given the fact that GCYC1 duplications in the Trichosporeae species have evolved species-specific gene expression pattern, we investigated whether differential selective pressures were apparent among the GCYC copies (Table 1, Fig 2). The divergence of both GCYC1C and GCYC1D copies show a signature of relaxation from purifying selection among the GCYC1 duplicates. Furthermore, the post duplication relaxation signal persisted throughout their divergence. Our two-ratio branch and clade C model results (two-ratio model) both revealed a relaxation signal immediately after the GCYC1 duplication (post-duplication) (model A1: ω0 = 0.2819, ωpost-duplication = 0.3985*, model C1: ω0 = 0.0469, ωpost-duplication = 0.1968*, Table 1, Fig 2c). However, there was no indication of positive selection acting specifically on either the GCYC1C or GCYC1D clade (model A3 and C2, no statistic support for natural selection on GCYC1C or GCYC1D as foreground, Table 1). This seems to suggest that the duplication of GCYC1 into GCYC1C or GCYC1D resulted in relaxation of both copies among Asiatic Trichosporeae species with one copy randomly shifting into a new expression pattern (see Fig 6). However, our results for the three-ratio branch model further indicated that the relaxation signal was still detectable throughout the divergence of these GCYC1C and GCYC1D copies after the duplication (model A2-1: ω0 = 0.2834, ωpost divergence = 0.4310*, Table 1, Fig 2D), and its likelihood was significantly better than for the two-ratio model above. This implies that the GCYC1 relaxation signal was not only maintained immediately after the duplication but also throughout the divergence of GCYC1C and GCYC1D, a phenomenon similar to the balancing selection whereby all duplicated copies tended to be retained because no selective constraint acted on a specific copy. In this way, their functions were randomly fixed in each species, as revealed by their species-specific expression pattern.

This species-specific GCYC1C and GCYC1D expression pattern among Trichosporeae species following GCYC1 duplication is therefore unique within Gesneriaceae. A similar conclusion was reached for Ranunculaceae zygomorphic species (tribe Delphinieae species) in which all CYC2-like paralogs were expressed in a species-specific pattern in correlation to their distinct perianth architecture [38]. But the selection analysis failed to detect any positive selection and relaxation from purifying selection signals among the copies, except for one duplicate, RANACYL1a, that experienced a higher level of functional constraint for maintaining zygomorphy (ω value close to 0) [38].

Extensive duplications of CYC2-like genes have been reported for species in Lamiales, to which Gesneriaceae belong to, Eudicots and monocot species. However, very few studies investigated what selective regime favored the retention of multiple copies post duplication, and different conclusions were drawn. In Plantaginaceae tribe Antirrhineae, immediately after CYC/DICH duplication, relaxation from purifying selection was detected only in the functional domain along the lineage leading to DICH, but not for the CYC lineage [25]. However, we found that both GCYC1C and GCYC1D copies experienced relaxation post duplication. Perhaps due to this finding the expression patterns of both GCYC1C and GCYC1D copies were able to diversify resulting in the species-specific patterns found here.

Several studies focused on the retention of CYC2-like copies in a range of plants such as Zingiberales, sunflower (Asteraceae) and Lupinus densiflorus (Fabaceae), and reported that one paralog post duplication experienced positive selection or had deviated expression patterns thus allowing for functional divergence [41, 71, 72]. In fact, a “selection mosaic” hypothesis, in which episodic positive selection, purifying selection and relaxed purifying selection have been suggested to act parallel or in tandem to account for the high rates of duplication and diversification in CYC2-like genes [71]. Recent findings on the evolution of CYC2-like genes from Lamiales and Anacyclus (Asteracaeae) provide support for this view [39, 65]. Our results of persistent relaxation after duplications of GCYC1 copies, however, adds a new facet to explain why CYC2-like genes are retained in multiple copies.

On the other hand, we cannot rule out the possibility that the relaxation signal was actually resulting from a mixture of global and copy specific selection signals. Our conclusions here are preliminary and could be substantiated by adding more samples from Trichosporeae species, although it is unlikely that this would result in less variation in GCYC expression. In fact, in CYC2-like duplication-selection analysis among species of Lamiales, Zhong and Kellog [65] did not find any relaxation or positive selection signal among Gesneriaceae CYC2-like copies because of their limited sampling size. The reason why our analysis, on the contrary, found continuous relaxation signals among GCYC1 duplicated copies, is probably due to the more extensive species sampling.

One possible explanation for the retaining of multiple GCYC copies is to generate diverse flower morphology that may have resulted from a functional-morphological adaptation for Trichosporeae species to cope with potential pollinator shifts [8, 9, 69, 70]. Positive selection on CYC2-like copies has been found associated with larger lateral petals (wings) and narrower dorsal petals in Lupinus densiflorus, that play a putative role to attract pollinators for outcrossing [71]. Furthermore, maintaining multiple GCYC1 copies is also a prerequisite for evolutionary flexibility (see below).

Potential role of evolutionary flexibility since the duplication of GCYC1

Duplicated genes provide opportunities to acquire evolutionary flexibility and can be recruited for divergent functions, such as Hox genes in animals [73]. Traditionally, the fate of duplicated genes was believed to be consistent within single duplicates by either functional divergence or random fixation at the copy level [40, 74]. We argue that GCYC1 also acquired this flexibility similar to the concept of a toolbox of genes for generating diverse functions. By plotting the available expression data of Trichosporeae to the GCYC1 phylogeny, we observed a unique and diversified species-specific GCYC expression patterns that evolved after duplication into GCYC1C/1D and GCYC1A/1B copies (Fig 6). This indicated that no specific GCYC1 copy was exclusively correlated with the establishment and/or maintenance of either zygomorphy or actinomorphy in Trichosporeae species. Particularly for zygomorphic species, these GCYC copies seemed to be randomly fixed with one retaining dorsally specific expression but the other deviated to a new expression pattern. Thus, we propose that random fixation occurred at each species generating a possible “evolutionary flexibility” among GCYC1C/1D duplicates in Trichosporeae. Moreover, the PAML result suggest that those GCYC1C/1D duplicates were maintained by relaxed purifying selection. This might allow these GCYC1 copies to co-exist or co-function throughout their divergence without immediately being selected against, providing rooms for evolutionary flexibility (Table 1, Fig 6). Thus, in contrast to other cases of CYC2-like gene duplications [38, 65], the fate of each GCYC1C/1D copy in Trichosporeae species is not pre-determined but randomly fixed into a species-specific pattern.

In MADS-box gene family of angiosperms, multiple gene duplications have provided evolutionary flexibility allowing each copy to be randomly fixed to maintain its original function or acquired new roles to interact with other copies or downstream genes [75, 76]. Indeed, protein interactions exist among the CYC/TB1 gene subfamily of TCP family, demonstrated that combinations of different CYC copies may interact each other to generate novel genetic modules, such as those reported in Arabidopsis and tomato [77, 78]. For example, if CYC expression is extended to other flower parts, it might not interact with its original CYC/TB1 copies but instead interacts with another partners incorporated into new modules. This may help to generate modified flower morphologies particularly in species of Asiatic Trichosporeae that exhibit a wide diversity in flower morphologies, even within a single genus such as Oreocharis [19] or Petrocodon [18].

Supporting information

S1 Table. List of accession numbers of GCYC from NCBI used in this study.

https://doi.org/10.1371/journal.pone.0210054.s001

(DOCX)

S2 Table. Primer pairs used to perform RT-PCR in this study.

https://doi.org/10.1371/journal.pone.0210054.s002

(DOCX)

S3 Table. Parameters estimate under branch-site model A of GCYC1C and GCYC1D in tribe Trichosporeae.

https://doi.org/10.1371/journal.pone.0210054.s003

(DOCX)

S4 Table. No Type I or Type II functional divergence detected between GCYC1C and GCYC1D clades.

https://doi.org/10.1371/journal.pone.0210054.s004

(DOCX)

S1 Fig. Alignments of protein sequences of GCYC1C and GCYC1D genes.

Partial TCP domain, ECE and R domain are outlined. The black hollow square denoted the putative sub-lineage specific motif (PSLM) of GCYC1D genes (see Gao et al., 2008).

https://doi.org/10.1371/journal.pone.0210054.s005

(TIF)

S2 Fig. Using 18S rRNA PCR amplifications on DNase (RQ1) treated RNA samples for checking residual genomic contamination.

As all samples amplified nothing after PCR, this indicates the successful eliminations on genomic DNA in all RNA extractions after RQ1 DNase treatment. These DNase treated RNA samples therefore are free from DNA contaminations before undergoing reverse transcription (RT) reaction.

(a) and (b), the 18S PCR results for two biological repeats of RNA extractions among various bud stages (E, M, L: early, middle and at anthesis late stage flower buds) in C. ramondioides (Cr18S), H. bicornuta (Hb18S) and L. pauciflorus (Lp18S). The “n” denotes non template control.

(c) and (d), the 18S PCR results for two biological repeats of RNA extractions among dissected tissues. For C. ramondioides (Cr18S), p1 to p5 denotes petals of C. ramondioides corresponding to that in Fig 4; sep for sepals, pe for pooled petals, st for pooled 5 stamens, and gyn for gynoecium. For H. bicornuta (Hb18S) and L. pauciflorus (Lp18S), dp denotes dorsal petals; lp: lateral petals, vp: ventral petal, sta: pooled staminodes, st: pooled stamens and gyn: gynoecium. “n” denotes non template control.

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(TIF)

S3 Fig. Electrophoresis results of expression pattern (RT-PCR) of GCYC duplicates through floral developmental stages (biological and technical repeats) of C. ramondioides, H. bicornuta and L. pauciflorus.

(a), (b), (c) and (d) represent two biological repeats each with two technical repeats of GCYC gene expression pattern of floral bud at early (E), middle (M) and late (L) developmental stage of C. ramondioides;

(e), (f), (g) and (h) represent two biological repeats each with two technical repeats of GCYC gene expression pattern of floral bud at early (E), middle (M) and late (L) developmental stage of H. bicornuta;

(i), (j), (k) and (l) represent two biological repeats each with two technical repeats of GCYC gene expression pattern of floral bud at early (E), middle (M) and late (L) developmental stage of L. pauciflorus.

PCR products of each sample were examined at 25, 30, 35 and 40 cycles to ensure whether certain GCYC copy is expressed (presence of band) or not (absence of band).

https://doi.org/10.1371/journal.pone.0210054.s007

(TIF)

S4 Fig. Electrophoresis results of expression pattern (RT-PCR) of GCYC duplicates among dissected floral tissues (biological and technical repeats) of C. ramondioides, H. bicornuta and L. pauciflorus.

(a), (b), (c) and (d) represent two biological repeats each with two technical repeats of GCYC gene expression pattern of dissected tissue of C. ramondioides;

(e), (f), (g) and (h) represent two biological repeats each with two technical repeats of GCYC gene expression pattern of dissected tissue of H. bicornuta;

(i), (j), (k) and (l) represent two biological repeats each with two technical repeats of GCYC gene expression pattern of dissected tissue of L. pauciflorus.

For C. ramondioides, p1 to p5 denotes petals of C. ramondioides corresponding to that in Fig 4; sep for sepals, pe for pooled petals, st for pooled 5 stamens, and gyn for gynoecium. For H. bicornuta and L. pauciflorus, dp denotes dorsal petals; lp: lateral petals, vp: ventral petal, sta: pooled staminodes, st: pooled stamens and gyn: gynoecium. “n” denotes non template control.

PCR products of each sample were examined at 25, 30, 35 and 40 cycles to ensure whether certain GCYC copy is expressed (presence of band) or not (absence of band).

https://doi.org/10.1371/journal.pone.0210054.s008

(TIF)

S5 Fig. Primer dimer identified from gel picture of amplification of CrCYC1C of C. ramondioides.

P1, P2, P3, P4 and P5 corresponds to five petals of C. ramondioides in Fig 2. sep: pooled sepals of C. ramondioides. P1 to p5: pooled C. ramondioides petals; st: pooled stamens of C. ramondioides; gyn: gynoecium of C. ramondioides.

https://doi.org/10.1371/journal.pone.0210054.s009

(TIF)

S1 File. Alignment of all CYC-like genes used in this study.

https://doi.org/10.1371/journal.pone.0210054.s010

(FAS)

S2 File. Alignment of GCYC duplicates used in codeml analysis.

https://doi.org/10.1371/journal.pone.0210054.s011

(FAS)

Acknowledgments

The work was supported by the Ministry of Science and Technology of Taiwan to CNW [Grant number: 106-2621-B-002-002-MY2 and 106-2313-B-002-035-MY3]. The Royal Botanic Garden Edinburgh is supported by the Rural and Environment Science and Analytical Services division (RESAS) in the Scottish Government to MMO. We thank Dr. Hao-Chih Kuo for providing comments on PAML analyses, and Dr. Zhao-Jun Pan for providing suggestions on RNA extraction and writing comments. Thanks to Mr. Hong-Wen Ma for assisting the field collection, and Mr. Yen-Wei Chou for his help for collecting plant materials and isolating GCYC genes. Collection Permission was granted by Yangmingshan National Park [Permission number: 20151155] for collecting plant species (H. bicornuta and L. pauciflorus). This manuscript was edited by Wallace Academic Editing and word usage suggestions by Kenneth Huang. We thank especially the anonymous reviewers and the editor for their careful reading and many insightful comments and suggestions.

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