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Article

Unraveling the Nectar Secretion Pathway and Floral-Specific Expression of SWEET and CWIV Genes in Five Dandelion Species Through RNA Sequencing

by
Sivagami-Jean Claude
1,
Sunmi Park
2,
Seong-Jun Park
2 and
SeonJoo Park
2,*
1
Department of Life Sciences, Gachon University, 1342, Seongnamdaero, Seongnam-si 13120, Republic of Korea
2
Department of Life Sciences, Yeungnam University, Gyeongsan 38541, Republic of Korea
*
Author to whom correspondence should be addressed.
Plants 2025, 14(11), 1718; https://doi.org/10.3390/plants14111718
Submission received: 7 April 2025 / Revised: 23 May 2025 / Accepted: 27 May 2025 / Published: 5 June 2025
(This article belongs to the Section Plant Genetics, Genomics and Biotechnology)
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Abstract

Taraxacum, a genus in the Asteraceae family, is widely distributed across temperate regions and plays a vital ecological role by providing nectar and pollen to pollinators during the early flowering season. Floral nectar is a key reward that plants use to attract pollinators, and its production is tightly regulated by genes such as SWEET sugar transporters and CELL WALL INVERTASE (CWIN), which govern sugar efflux and hydrolysis. Despite their ecological importance, the molecular mechanisms underlying nectar secretion in Taraxacum remain poorly understood. In this study, we performed RNA sequencing of flower tissues from five Taraxacum species—T. coreanum, T. monogolicum, T. ohwianum, T. hallaisanense, and T. officinale—to investigate the expression of nectar-related genes. De novo transcriptome assembly revealed that T. coreanum had the highest unigene count (74,689), followed by T. monogolicum (69,234), T. ohwianum (64,296), T. hallaisanense (59,599), and T. officinale (58,924). Functional annotation and phylogenetic analyses identified 17 putative SWEET and 18 CWIN genes across the five species. Differential gene expression analysis highlighted tarSWEET9 and tarCWIN4 as consistently up-regulated during the flowering stage. Quantitative PCR in T. officinale further validated that tarSWEET9, tarCWIN4, tarCWIN6, and tarSPAS2 show significant expression during floral development but are down-regulated after pollination. These genes are likely central to the regulation of nectar secretion in response to pollination cues. Our findings suggest that T. officinale may have evolved to have an efficient, pollinator-responsive nectar secretion system, contributing to its global adaptability. This study sheds light on how pollinator interactions influence gene expression patterns and may drive evolutionary divergence among Taraxacum species.

1. Introduction

Floral nectar (FN) and pollen have evolved in plants as rewards to attract pollinators [1,2,3,4,5]. Pollen, the male gametophyte of land plants, is produced in cones in gymnosperms and in anthers within the stamens in angiosperms. For successful reproduction in flowers, pollen is initially dispersed by insects or wind [6]. Nectar contains sugars and amino acids (AAs) and is associated with specific responses to pollinators [7,8]. It is primarily composed of a sucrose-rich aqueous solution, with lesser amounts of glucose, fructose, amino acids, and enzymes. These components vary among species and are collectively referred to as a hexose solution [9,10]. During nectary development and nectar secretion, starch grains accumulate and subsequently break down in most plants. To establish a mutually beneficial relationship with insects, plants offer floral nectar (FN) through nectaries located at the base of the floral thalamus, between the androecium and gynoecium [11,12]. Most angiosperm nectaries consist of three primary components: the epidermis, specific parenchyma cells, and vascular bundles [13,14].
Nectaries have been analyzed across various angiosperm species, exhibiting structural diversity within the epidermis, hypodermis, and trichomes. Studies indicate that 94% of angiosperms are animal-pollinated [15,16,17]. Nectar synthesis primarily occurs through sucrose biosynthesis and is facilitated by specific transporters, which serve as candidate genes for nectar production in Arabidopsis [18]. Pollinator visits often increase nectar flow; however, nectar production ceases post-pollination, and any remaining nectar is reabsorbed [19]. Nectar production is regulated by two distinct secretion processes: eccrine and granulocrine secretion, which vary among plant species [20,21,22]. The SWEET gene family encodes sugar transporters responsible for regulating the movement of sugars across the cytoplasm, particularly in conditions of low sugar demand [23,24]. These SWEET transporters can facilitate the absorption and release of sugar molecules within cells without relying on energy-dependent uniporters [25]. Nectar diffusion occurs through three different mechanisms: sugar movement from the apoplasm, cytoplasmic sugar transport via symplasms, and diffusion from the phloem [21,26,27]. The morphology, production, and biological significance of floral nectaries have been studied across multiple angiosperm lineages, including Arabidopsis, Borago, Euonymus, Lamprocapnos, Pisum, Parnassia, Opuntia, and Cucurbita species [21,22,28,29].
Genome-wide analyses have identified SWEET and CWIN genes in a wide range of land plants, including representative dicotyledonous species such as Arabidopsis thaliana [30], Vitis vinifera [31], Solanum lycopersicum [32], and Glycine max [33], and monocotyledonous species like Oryza sativa [34] and Triticum aestivum [35]. These genes play key roles in the nectar secretion pathway by regulating sugar transport and hydrolysis. Notably, SWEET9 and CWINV4 have been shown to be essential for nectar production in Arabidopsis, where their knockout results in significantly reduced nectar secretion [30]. Overexpression of SWEET genes in Oryza and Solanum has also been linked to changes in sugar distribution and floral development [32,34]. Similarly, silencing of CWIN genes in tomato disrupted sucrose metabolism and reproductive development [36,37]. Together, these findings highlight the conserved functional roles of SWEET and CWIN genes in floral organ physiology and nectar production.
Taraxacum (dandelion) is a perennial herb belonging to the family Asteraceae. It is an apomictic species that reproduces asexually by dispersing seeds through wind. Dandelions are widely distributed throughout the Northern Hemisphere, with over 2500 species reported [38,39,40,41,42]. Taraxacum is a taxonomically complex genus comprising both diploid and polyploid species, with polyploidy being especially prevalent. Diploid Taraxacum species typically reproduce sexually, while most polyploids reproduce through apomixis (asexual seed formation). The ploidy levels can range from diploid (2n = 2x = 16) to triploid and higher, with triploids (3x = 24) being the most common among apomictic dandelions [43,44]. Dandelions, also referred to as monofloral honey plants, serve as an essential food source for many insects due to their early flowering and abundant supply of pollen and nectar [45,46]. Notably, nectar production in dandelions is highly dependent on the flowering stage. Taraxacum species have been shown to exhibit significant variation in nectar quantity and sugar content under natural conditions, highlighting their ecological relevance and supporting the need to investigate the genetic basis of nectar secretion through transcriptomic approaches [47,48]. In this study, we selected flowers from five Taraxacum species to investigate genes involved in nectar biosynthesis and their secretion mechanisms using single-RNA sequencing. Although Taraxacum species are considered prolific nectar producers [39], the relationship between nectary modifications and variations in nectar secretion among species has not yet been explored at the genetic level. Furthermore, the identification and characterization of SWEET and CWIN genes at a transcriptome-wide level remain unexplored in the Asteraceae family. This study provides fundamental insights into the potential functional roles of SWEET and CWIN gene discoveries in Taraxacum. We identified and characterized 16 tarSWEET and 18 tarCWIN genes, analyzing their differential expression patterns across five Taraxacum species. High-throughput RNA sequencing was employed to characterize genes associated with nectar secretion and related metabolic pathways. Additionally, quantitative RT-PCR was performed to examine the expression of nectar-related sugar metabolism and male-sterility genes in Taraxacum flowers at distinct stages of development. Understanding the nectar secretion pathway in Taraxacum may provide insights into how these species have evolved to utilize both apomixis and cross-pollination strategies while attracting pollinators through nectar production.
This study offers a comprehensive analysis of differential gene expression patterns associated with the nectar secretion pathway, shedding light on the functional roles of tarSWEET and tarCWIN gene families. Our findings contribute valuable information for further exploration of SWEET and CWIN gene functions in Taraxacum. Moreover, this study provides novel insights into the nectar secretion mechanisms, specifically through the merocrine or eccrine model, in five different Taraxacum species using next-generation sequencing.

2. Results

2.1. Assembly and Functional Annotation

The de novo assembly of individual Taraxacum species yielded the highest number of transcripts in T. coreanum (74,689 unigenes), while T. officinale exhibited the lowest count (Table 1). The combined de novo assembly of all five species resulted in a total of 197,473 unigenes from Taraxacum flower sequencing. The quality of transcriptome assembly was assessed using BUSCO, with the combined assembly achieving a completeness score of 91.6%. Among individual species, T. mongolicum showed the highest completeness (93.6%), followed by T. officinale (93.5%), T. ohwianum (93.0%), T. coreanum (92.6%), and T. hallaisanense (82.2%) (Supplementary Figure S2). Functional annotation using BLAST against the TAIR database revealed unigene assignments of 44.34% (T. coreanum), 33.07% (T. mongolicum), 26.78% (T. officinale), 30.02% (T. hallaisanense), and 25.55% (T. ohwianum). Similarly, alignment against the Swiss-Prot database identified 47.36% of unigenes in T. coreanum, 38.90% in T. ohwianum, 37.59% in T. mongolicum, 34.59% in T. hallaisanense, and 29.78% in T. officinale. KEGG pathway annotation further categorized unigenes into functional pathways, with distributions consistent with TAIR-based annotation (Table 1).

2.2. Gene Ontology (GO) Terms Associated with Sucrose Biosynthesis in Taraxacum

GO analysis of functionally annotated transcripts related to sucrose metabolism was performed using the TAIR database (Figure S3A, Supplementary Table S1). A total of 8238 transcripts were associated with biological processes and cellular components. Of these, 2408 genes were annotated to localization processes, including secretion, nectar secretion, and transport (Supplementary Figure S3A). Carbohydrate metabolic processes accounted for 308 unigenes, including disaccharide metabolism (70), oligosaccharide metabolism (80), and sucrose metabolism (46).
In the category of organic transport, 1001 unigenes were identified, with 63 related to carbohydrate transport, 20 to disaccharide transport, 21 to oligosaccharide transport, and 20 to sucrose transport in Taraxacum flowers. Additionally, 1643 unigenes were assigned to responses to organic substances, including responses to carbohydrates (153), cellular responses to oxygen-containing compounds (518), monosaccharide stimuli (72), hexose (68), and hexose-mediated signaling (7).
For monosaccharide metabolism, 128 unigenes were identified and categorized as hexose metabolism (87), fructose metabolism (13), and fructose response (15). Further GO terms included metabolic starch processes (64 unigenes), glucose responses (63), and glucose metabolism (42), which were classified under biological processes. Additionally, genes associated with reproductive structure development included 738 unigenes involved in seed development and 765 in fruit development (Supplementary Figure S3A).
Molecular function analysis revealed that 40.38% of genes were associated with carbohydrate transmembrane processes and transport activity. Sugar transmembrane transport activity was specifically represented by 28.85% of the genes (Supplementary Figure S3B). Cellular component analysis indicated that 30.57% of genes were associated with cellular and anatomical entities, 21.40% were classified under membrane-related functions, and 28.85% were linked to intrinsic and integral membrane components (Supplementary Figure S3C).

2.3. KEGG Annotation

KEGG pathway analysis was performed on the assembled unigenes of five Taraxacum species (Table 1, Supplementary Figure S4). A total of 397,344 transcripts from the combined assembly were submitted for KEGG annotation, of which 109,162 (27.55%) were assigned to various metabolic pathways. Among the annotated pathways, the highest proportion of unigenes were associated with protein families involved in protein families genetic information processing (20.24%), followed by general genetic information processing (16.37%), signaling and cellular processes (8.46%), carbohydrate metabolism (8.32%), secondary metabolism (6.88%), amino acid metabolism (2.87%), and terpenoid and polyketide metabolism (1.64%) (Supplementary Figure S4A). Additionally, genes involved in nectar secretion pathways were identified, including those associated with amino acid biosynthesis (111 unigenes), starch and sucrose metabolism (40), amino sugar and nucleotide sugar metabolism (54), fatty acid metabolism (46), and fructose and mannose metabolism (22) (Supplementary Figure S4B).

2.4. SWEET/CWIN/MS Genes and Their Phylogeny

A phylogenetic analysis was conducted using SWEET and CWIN genes identified in Taraxacum flowers, along with 16 AtSWEET and 4 AtCWIN genes from Arabidopsis thaliana (Figure 1).
SWEET proteins exhibited a highly conserved amino acid length ranging from 171 to 227 residues, with two characteristic PQ (Pro and Gln) loop repeat domains. The identified TarSWEET genes were classified into four clades:
  • Clade I (SWEET1–3) and Clade II (SWEET4–8) were associated with glucose transport.
  • Clade III (SWEET9–15) participated in sucrose transport.
  • Clade IV (SWEET16) was linked to fructose transport.
A total of 17 SWEET genes were discovered in Taraxacum, corresponding to similar groupings found in Arabidopsis. Additionally, two pseudogenes with incomplete Gln motifs were identified but excluded from phylogenetic analysis (Figure 1). Using four AtCWIN sequences as queries, 18 INV genes were identified in Taraxacum (Figure 1). CWIN proteins exhibited a conserved amino acid length of 415 to 665 bp. Among the 18 Taraxacum CWIN genes, 2 copies were closely related to AtCWIN, and the remaining genes were distributed into three major clades, with 14 belonging to a distinct Taraxacum flower-specific CWIN cluster. Furthermore, two MS genes were identified, but only two homologs to Arabidopsis were confirmed. To re-examine CWIN and other INVERTASE genes in Taraxacum, sequence alignments were performed to identify conserved motifs of CWIN and vacuolar invertases (vINVs) (Figure 2). A total of twelve genes were classified as CWIN, and six were classified as vINV. All Taraxacum flower SWEET, CWIN, and MS gene sequences were submitted to NCBI GenBank under accession numbers ON351066–ON351241.

2.5. DEG Analysis of SWEET/CWIN/MS Genes in Taraxacum Flowers

We identified 130,294 differentially expressed unigenes (DEGs) at a log2 fold change threshold across five Taraxacum species, based on a complete set of 655,076 transcripts. Relative expression values were obtained using the NOISeq and Trinity-RSEM pipeline (Supplementary Figure S3). The DEG correlation matrix indicated that T. coreanum and T. mongolicum are closely related, while T. officinale forms a sister clade with T. ohwianum and T. hallaisanense (Supplementary Figure S4). The highest number of up-regulated genes was observed in T. mongolicum (34,405), whereas T. officinale exhibited the lowest number (25,644). Similarly, T. officinale had the highest number of down-regulated genes, while T. hallaisanense had the lowest (Supplementary Figure S3A). A total of 16 SWEET genes, represented by 42 transcripts, were identified. Among them, seven were up-regulated, and nine were down-regulated in T. coreanum, T. ohwianum, and T. mongolicum. In T. officinale, nine unigenes were up-regulated, and seven were down-regulated. Additionally, two SWEET genes were uniquely present in T. officinale. T. hallaisanense exhibited the lowest number of up-regulated (six) and down-regulated (ten) genes (Figure 3, Supplementary Table S3).
The CWIN expression heatmap revealed that 17 genes were shared among Taraxacum flowers. Of these, eleven genes were up-regulated, and six were down-regulated in T. coreanum, T. ohwianum, T. mongolicum, and T. hallaisanense. In T. officinale, thirteen unigenes were up-regulated, while four were down-regulated. Furthermore, apart from the seventeen DEGs, one additional CWIN gene was detected in T. officinale (Figure 3, Supplementary Table S4). Interestingly, both copies of MS genes were up-regulated in T. coreanum and T. mongolicum only. In contrast, in T. hallaisanense, T. ohwianum, and T. officinale, only one copy of MS was up-regulated, and the other was down-regulated (Supplementary Table S5).

2.6. Analysis of Nectar Secretion Pathway and Associated Gene Expressions in Taraxacum Flowers

Genes associated with hexose solution (nectar) secretion in Taraxacum flowers were analyzed through gene BLAST and DEG analysis (Figure 4). The nectar secretion pathway was identified in Taraxacum flowers, which involves the conversion of D-glucose into D-glucose-6-phosphate by five Sucrose Synthase 1 (tarSUS1) genes that are responsible for converting UDP-D-glucose into sucrose. Two tarSUS1 unigenes were up-regulated, while three were down-regulated in T. hallaisanense and T. mongolicum. In T. ohwianum and T. coreanum, one unigene was up-regulated, while four were down-regulated. Notably, all five tarSUS1 unigenes were up-regulated in T. officinale but exhibited multiple isoform variations (Table S6). The two-way synthesis of sucrose involves the conversion of UDP-D-glucose into Sucrose-6-phosphate, which is catalyzed by SPSA2. Three unigenes were associated with tarSPSA2 in Taraxacum flowers. In T. hallaisanense and T. coreanum, one unigene was up-regulated, while two were down-regulated. In T. ohwianum, T. mongolicum, and T. officinale, two unigenes were up-regulated, and one was down-regulated (Figure 4). Comparative analysis with Arabidopsis revealed that both copies of tarSWEET9 were up-regulated in all Taraxacum species except T. mongolicum. Additionally, 12 unigenes were identified as homologous to the Arabidopsis class CWIN genes, possessing conserved INV-CWIN catalytic motifs (NES and GET). Among these, four CWIN genes were up-regulated, and one was down-regulated in T. officinale and T. hallaisanense. Meanwhile, three tarCWIN4 genes were up-regulated, and two were down-regulated in T. ohwianum, T. coreanum, and T. mongolicum, clustering within Clade III (Supplementary Table S4).
The Taraxacum nectar secretion pathway involved hexokinase 1 and 2 (HXK1 and HXK2). Four transcript variants of tarHXK1 and tarHXK2 were identified. Two tarHXK genes were up-regulated in T. ohwianum and T. officinale, while one copy was up-regulated in T. hallaisanense, T. coreanum, and T. mongolicum. Phosphoglucomutase 2 (tarPGM2) catalyzes the conversion of D-glucose-6-phosphate to D-glucose-1-phosphate. Three copies of tarPGM were identified: two were up-regulated in T. coreanum, T. ohwianum, and T. officinale, while in T. mongolicum and T. hallaisanense, one was up-regulated, and two were down-regulated. The conversion of D-glucose-1-phosphate to UDP-D-glucose is catalyzed by UTP-glucose-1-phosphatase 2 (tarUGP2). This gene was found in five copies: two were up-regulated in T. coreanum, T. ohwianum, and T. hallaisanense, while T. mongolicum exhibited one up-regulated and four down-regulated copies. In T. officinale, three copies were up-regulated, and two were down-regulated, making it the species with the highest copy number of tarUGP genes (Figure 4, Supplementary Table S6).

2.7. Quantification of Genes Involved in the Nectar Secretion Pathway in T. officinale

To validate the involvement of key genes in the nectar secretion pathway, six nectar-associated genes were selected for quantitative analysis. Gene expressions were assessed across different flowering stages to elucidate the roles of these genes in nectar secretion during floral development. qPCR analysis revealed that tarSPAS and tarSUS1 exhibited differential expression patterns across flower developmental stages, suggesting that sucrose transport in T. officinale is primarily mediated by tarSPAS, rather than through sucrose conversion from UDP-glucose by tarSUS1 (Figure 5). Specifically, tarSPAS showed high expression levels before and after flower opening and on day 1, followed by moderate expression on day 5 and at the post-fertilization (after pollination) stage. This pattern suggests that tarSPAS plays a significant role in flower development, whereas tarSUS1 may have a more limited function. Further analysis of tarSWEET9.1 and tarSWEET9.2 revealed that tarSWEET9.2 was more actively involved in sucrose transport than tarSWEET9.1 during flowering. Expression profiling of tarCWIN6 demonstrated significant up-regulation from dawn through day 1 and sustained expression until day 5. In contrast, tarCWIN4 was significantly expressed from flower opening (day 1 to day 5) until after pollination but showed minimal expression before flower opening (Figure 5).

3. Discussion

Nectar is a sugar-rich solution secreted by specific angiosperms to attract pollinators, facilitating pollination [14,49]. It has evolved primarily in female flowers and varies between male and female flowers in higher plants [50]. Additionally, nectar can deter certain species from visiting or engaging in other biological interactions [4]. It contains various components, including sugars, amino acids, alkaloids, glycosides, flavonoids, phenolics, vitamins, ions, proteins, and free fatty acids [8]. Both nectar and pollen have been extensively studied in the context of plant evolution, genetics, physiology, and ecology [3,51]. In this study, we performed RNA sequencing (RNA-Seq) on five Taraxacum species to analyze nectar secretion mechanism-related genes. While Taraxacum species primarily rely on cross-pollination for seed dispersal, they can also undergo self-pollination through triploid or tetraploid pollen when cross-pollination is unsuccessful [52,53].
The SWEET gene family, known for its role in sugar transport, as well as plant seed and pollen development, has been identified in over 27 plant species [54,55,56,57]. It plays a crucial role in plant growth, development, and stress responses [23,57,58]. A study on zucchini nectar and pollen visits revealed that a higher sucrose-to-hexose ratio in nectar attracted more pollinator visits [59]. Comparative genome-wide studies have identified SWEET genes in various plant species: 17 in Arabidopsis [23], 17 in Vitis [31], 21 in Oryza [34], 10 in Averrhoa [60], 27 in Citrus [61], 19 in Hemerocallis [62], 52 in Eucalyptus [63], 28 in Camellia [64], 13 in Poa [65], 20 in octoploid Fragaria X ananassa [66], 108 in Triticum [35], 22 in Citrullus [67], 16 in Litchi [68], 17–26 in Cucumis species [69,70], 60 in Glycine [33,71], 25 in Medicago [72], 36 in Hevea [73], 16 in Brassica [74], 68 in Malus [75], 25 in Musa [76] and 28 in Solanum [32]. Genome-wide studies in Taraxacum kok-saghyz identified 22 SWEET genes, with SWEET1 and SWEET12 specifically implicated in cytoplasmic functions within rubber-producing laticifers, suggesting a role in rubber biosynthesis [77]. In our study, we identified only the tarSWEET1 gene, which was strongly up-regulated in all species except T. mongolicum, suggesting its potential role in latex synthesis across most Taraxacum species.
Phylogenetic analysis of Arabidopsis SWEET genes supports a four-clade division, which is also reflected in Taraxacum: Clade I (three genes), Clade II (six genes), Clade III (seven genes), and Clade IV (one gene) [23]. Clade III of the SWEET family, particularly SWT9, facilitates sucrose transport from the cytoplasm and functions as an efflux transporter [78]. SWEET genes also influence fruit development and ripening [79,80]. We identified 17 SWEET genes in Taraxacum and analyzed their expression through differential expression gene (DEG) analysis. Six unigenes belonged to Clade III, which is responsible for sucrose transport by phloem parenchymal cells [24,81]. DEG analysis revealed that tarSWEET10 genes were up-regulated in T. hallaisanense and T. ohwianum, indicating regional or species-specific bidirectional sucrose transport activity in leaves and shoot apices. In T. officinale, two unique tarSWEET10 and tarSWEET11 genes were up-regulated, suggesting their role in accelerated flowering and sugar transport [82]. SWEET10 has been identified as being expressed in the shoot apex during floral transition, suggesting its role in the transport of gibberellins and sucrose in potato [83]. In contrast, SWEET11 plays a critical role in seed filling and is essential for facilitating sugar efflux from the nucellar epidermis as well as the ovular vascular trace into the apoplast in rice [84,85].
Expression analysis of SWEET gene family Clade III and IV genes revealed that tarSWEET15 was up-regulated exclusively in T. officinale and T. ohwianum, while it was down-regulated in other Taraxacum species. SWEET15 is known to play a key role in two major steps of apoplasmic seed filling, as previously observed in rice and barley [84,85,86]. Similarly, both tarSWEET16/17 were regulated in T. mongolicum while being down-regulated in other species. In Arabidopsis, SWEET15 and SWEET16 are strongly induced during senescence and osmotic stress, suggesting that tarSWEET15 and tarSWEET16 play roles in stress response in Taraxacum flowers [87,88,89]. Whereas the SWEET15/17 gene functions as a vacuolar sugar facilitator and is primarily expressed in vascular parenchyma cells, the overexpression of SWEET16 has been shown to alter sugar accumulation [88]. Under stress conditions, SWEET16 plays roles in cold stress response, nitrogen starvation, enhanced germination under cold conditions, and improved salinity tolerance in Arabidopsis [90].
The sucrose-specific gene SWEET9, located in the cytoplasm, is activated in response to increased sugar concentration [78]. In our study, we identified two genes related to tarSWEET9, one of which was up-regulated in four Taraxacum species but down-regulated in T. mongolicum, suggesting that most of the Taraxacum species are capable of nectar secretion during pollination [24,78]. Quantification of two tarSWEET9 gene copies in T. officinale revealed that tarSWEET9 and other nectar secretion-related genes were highly expressed in closed and open buds [18]. This pattern aligns with a previous report on nectar secretion in Cucurbita, where peak nectar production occurred before and after the opening of the buds, followed by a decline approximately nine hours post-anthesis [91]. We observed that tarSWEET9 expression remained significant in closed and open buds and was maintained at moderate levels from days 1 to 6 in T. officinale, with Clade III SWEET genes being highly expressed in Taraxacum. Interestingly, our quantification assay showed that tarSWEET9, tarCWIN4, and tarSUS1 expression levels declined after pollination, which indicates the previously accepted pattern of nectar secretion before and after pollination.
The enzyme CWIN4, localized in the cell wall, hydrolyzes sucrose into glucose and fructose within the apoplast. This process increases both intra- and extracellular sucrose concentrations, leading to the efflux of water and sugar molecules into the apoplast, forming nectar droplets through epidermal cells during stomatal opening. The glycosylation sites of the CWIN and vINV genes have been previously identified [92]. Additionally, our study identified six vINV-related genes, which may function as hexose transporters, facilitating the mobilization of stored vacuolar sucrose during nectar secretion [93]. These findings provide valuable insights into the differential gene expression patterns in Taraxacum species and their functional implications in sucrose metabolism and regulatory pathways.
In our analysis, we identified 12 copies of CWIN and 6 copies of vINV in Taraxacum flowers, representing a higher copy number of CWIN than that reported in Populus, Arabidopsis, Manihot, or Oryza [30,94,95,96]. The duplication of CWIN genes may indicate the necessity for dual sugar efflux via both merocrine and eccrine secretion models in Taraxacum flowers [20,48]. Unlike the two tarSWEET9 paralogs, tarCWIN4 and tarCWIN6 exhibited elevated expression levels at the bud-opening stage and remained active throughout all flowering stages. During flower pollination, a sugar efflux from the epidermis suggests the preferential secretion of nectar from cells with higher cytoplasmic and apoplastic sugar concentrations, which are regulated by tarSWEET9 in Taraxacum flowers [18,97]. Expression analysis of the SPSA2 gene, which has at least two copies in flowers, showed a twofold increase in expression throughout Taraxacum flowering days, emphasizing its importance in sucrose biosynthesis. The significant expression of SPSA2 enzyme levels suggests that cytoplasmic sucrose secretion is actively involved in nectar production, like findings in Arabidopsis [78]. Differential gene expression analysis further revealed that tarCWIN1, tarCWIN3, tarCWIN7, and tarCWIN8 were up-regulated in T. coreanum, suggesting that Taraxacum species other than T. officinale also produce nectar during flower development. The presence of multiple tarCWIN gene copies in Taraxacum highlights their potential novel functions, arising from gene duplication [30,98].
Additionally, we were interested in identifying MS genes that are essential for anther and pollen development, general plant reproduction, and lipid and carbohydrate metabolism, as well as overall flower function in maize [99,100,101]. MS genes hold particular significance in genetic studies related to hybrid seed production, breeding for vigor, and stress adaptation [102,103,104]. Studies in Arabidopsis and Oryza have revealed their involvement in molecular pathways regulating anther and pollen development [105]. Notably, we identified two MS genes: tarMS1, which was up-regulated and expressed across all Taraxacum species, and tarMS2, which was detected only in T. coreanum and T. mongolicum, suggesting an important role for tarMS genes in flowering and pollination. The species-specific expression of tarMS2 suggests that these species may rely more on pollen, rather than nectar secretion, to attract pollinators. Unlike T. officinale, which is widely distributed, T. coreanum and T. mongolicum are geographically restricted to East Asia, which may indicate an evolutionary adaptation involving nectar- and pollen-based specialization.
The widespread success of dandelions in harsh environments highlights the evolutionary significance of their flower development and pollination mechanisms in enabling resilience and ecological adaptability. This study discovered and predicted the nectar secretion pathway, SWEET, and CWIN gene families using comparative transcriptomic analysis in five Taraxacum flowers. Our results showed that the 17 SWEET gene families were identified in all. Eighteen INVERTASE genes were also identified; twelve belonged to CWIN and six belonged to the vINV class. Our study revealed that the number of SWEET genes in Taraxacum is less than that reported for other Angiosperm species, but at the whole genomic DNA level. However, CWIN genes were highly duplicated and expressed in Taraxacum flowers, indicating that the nectar secretion pathway results in greater sugar solution efflux through eccrine routes in Taraxacum. Finally, we suggest that identifying tarMS genes in Taraxacum (T. coreanum and T. monogynam) might provide a piece of information to study the two independent pollination systems in Taraxacum species. Our findings lay the groundwork for further research into the function and contribution of SWEET and CWIN genes in plant nectar secretion systems and their role during flower development in Taraxacum species.

4. Materials and Methods

4.1. Plant Materials, RNA Sequencing, and Assembly

Five species of the Taraxacum genus—T. coreanum, T. officinale, T. mongolicum, T. hallaisanense, and T. ohwianum—were selected for this study, as they are naturally distributed in South Korea (plant collection locations listed in Supplementary Table S1). Flowers at 12 h post-anthesis were harvested for RNA extraction using the single-step RNA isolation method [106]. The extracted total RNA was used for cDNA library construction with the TruSeq Stranded mRNA kit. High-throughput sequencing was performed using the Illumina HiSeq 2500 platform at the Phyzen Genomics Institute (South Korea), generating paired-end reads. Quality control of the raw reads was assessed using FastQC v0.11.9, and adapter trimming was performed using Trimmomatic v0.40 [107]. A combined dataset of paired-end reads from the five Taraxacum species was assembled de novo using Trinity v2.12.0 [108]. Super-Transcripts, representing unigenes with exon structures while minimizing redundancy, were generated using the Trinity v2.12.0 pipeline [108,109]. The quality of assembled transcripts was evaluated using BUSCO v5.1.2 with the eudicot lineage dataset [110]. The overall methodological workflow of this study is outlined in Supplementary Figure S1.

4.2. Gene Annotation

TransDecoder v5.5.0 (https://github.com/TransDecoder/TransDecoder, 4 February 2022) was used to predict candidate protein-coding regions from the assembled transcripts. Reference sequences for sucrose biosynthesis, pollen development, and nectar synthesis (58 genes) were obtained from the TAIR database [111] (Supplementary Table S2). Additionally, 59 genes related to sugar biosynthesis, including SWEET (SWT) genes, were retrieved from the TAIR and Swiss-Prot databases [112]. BLASTX and BLASTP searches were conducted for functional annotation. KEGG pathway analysis was performed using the longest open reading frames (ORFs) predicted by TransDecoder to categorize unigenes into metabolic pathways, including sucrose biosynthesis [113,114,115]. Candidate Taraxacum cell wall invertase (CWIN) unigenes were identified through BLAST searches against Arabidopsis thaliana CWIN4. Conserved CWIN motifs, active sites, and glycosylation sites were analyzed using MUSCLE alignment in Geneious R11, and a phylogenetic tree was constructed using IQ-TREE v2.2.0 with 10,000 bootstrap replicates [116,117]. Phylogenetic visualization was performed using FigTree v1.4.4 (http://github.com/rambaut/figtree/, accessed on 2 April 2022).

4.3. Differential Gene Expression Analysis

Differential gene expression analysis was conducted using RSEM (RNA-Seq by Expectation Maximization), an accurate quantitative method for estimating transcript abundances [118]. A combined Taraxacum transcriptome was assembled in a single run using the Trinity assembler [108]. Differential expression analysis was performed using a contrast-based approach, where T. officinale served as the reference species for the comparative expression analysis of nectar synthesis-related genes across other Taraxacum species. The EdgeR package was used to identify differentially expressed genes (DEGs) with a false discovery rate (FDR) cut-off of 0.05, log-fold changes (>2 and >10FC), and a dispersion parameter of 0.1 [119]. Visualization of MA and volcano plots was conducted in R Studio (2022.05.08). Additionally, the NOISeq pipeline (https://www.bioconductor.org/packages/release/bioc/html/NOISeq.html, accessed on 18 February 2022) was employed to assess overall DEG patterns using a non-parametric approach for up- and down-regulated gene comparisons among Taraxacum species [120].

4.4. Quantitative PCR Expression Studies

To validate the expression patterns of SWEET, CWIN, and other nectar-related genes, candidate genes were first identified via BLAST searches against the TAIR database [111,114,115]. Complete ORFs and conserved domains (CDs) were confirmed using Geneious R11 (https://www.geneious.com/prime/, accessed on 19 May 2022). The tarSWEET9, tarCWIN4, tarSPAS, and tarSUS genes were selected for primer design, and primer specificity was evaluated using Primer3 (default parameters, melting temperature of 60 °C) in Geneious R11. Quantitative real-time PCR (qRT-PCR) was performed to examine gene expression across different flower development stages (days 1–6), as well as at specific time points: closed buds (3:00 AM) and buds opened (8:00 AM). Total RNA was extracted from T. officinale flowers using the RNeasy Plant Mini Kit (Qiagen Inc., Germany), and cDNA was synthesized using the TOPscript™ cDNA Synthesis Kit (Enzynomics, Daejeon, South Korea). Reverse transcription was conducted in a 10 µL reaction at 70 °C for 5 min using an Oligo (dT) 15 primer. qPCR was performed using the GoTaq® qPCR Master Mix (A6001, Promega) under standard cycling conditions on an Applied Biosystems 7500 Step OnePlus system, with triplicate technical replicates. Actin and elongation factor genes were selected as reference controls based on the complete ORF structure, and primers were designed for normalization analysis (Table S7). Leaf and root tissues of T. officinale were used as comparative controls, with water serving as the negative control. DEGs, including tarSWEET9 and tarCWIN4, were analyzed for expression profiles at different time points to validate their roles in the nectar secretion pathway. Quantitative real-time PCR (qPCR) data were analyzed using one-way analysis of variance (ANOVA) to assess differences in gene expression across floral developmental stages. When the ANOVA indicated significant variation (p < 0.05), Tukey’s Honest Significant Difference (HSD) post hoc test was performed to determine pairwise differences between groups [121]. The significance of gene expression was calculated using a t-test in R (stats package, version 3.6.2, accessed on 30 April 2022).

5. Conclusions

This study provides the first comprehensive transcriptomic and expression-based analysis of nectar secretion-related genes in five Taraxacum species, focusing on the key roles of SWEET and CWIN gene families. Among the 17 SWEET and 18 CWIN genes identified, SWEET9 and CWIN4 were consistently up-regulated during flowering, indicating their central function in nectar secretion across species. qPCR validation in T. officinale further confirmed that SWEET9, CWIN4, CWIN6, and SPAS2 exhibit significant expression during floral development, with marked down-regulation after pollination, suggesting a pollination-responsive regulation mechanism. The relatively high expression of these genes in T. officinale correlates with its dual provision of nectar and pollen and its successful global distribution. In contrast, reduced gene expression after pollination reflects a potential resource-conservation strategy once fertilization is achieved. Together, these results highlight how nectar secretion is finely tuned by genetic regulation and how such regulation may influence pollinator interactions and species divergence. By integrating transcriptomic analysis with gene expression profiling, this study offers new insights into the molecular basis of nectar production and lays a foundation for future research on the evolution of floral traits and pollination strategies in Taraxacum and other members of the Asteraceae family.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/plants14111718/s1, Supplementary Figure S1. Overview of the RNA-Seq analysis pipeline used in this study. Supplementary Figure S2. BUSCO assessment and summary of Taraxacum transcriptome unigene data. Supplementary Figure S3. Gene Ontology (GO) analysis of sugar metabolism-related terms in Taraxacum using TAIR database BLAST analysis: (A) biological process, (B) molecular function, and (C) cellular components. Supplementary Figure S4. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of all Taraxacum unigenes. (B) Nectar compound-related unigenes in the KEGG pathway. Supplementary Figure S5. (A) Differentially expressed gene (DEG) analysis of unigene expression in the Taraxacum genus using NOISeq. (B) Differentially expressed genes in different Taraxacum species compared to T. officinale. tha: T. hallaisanense; tmo: T. mongolicum; toh: T. ohwianum; tof: T. officinale; tco: T. coreanum. Supplementary Figure S6. Heatmap of differential expressions (log10 fold change) in Taraxacum flowers. Supplementary Table S1. List of Taraxacum species, including species collection details and specimen numbers. Supplementary Table S2. TAIR database BLAST results for nectar secretion and sucrose metabolism-related unigenes in Taraxacum flowers. Supplementary Table S3. Differentially expressed tarCWIN unigenes in Taraxacum flowers analyzed using edgeR (log2 fold change). Supplementary Table S4. DEGs of tarCWIN unigenes compared to all Taraxacum flowers using the edgeR tool at log2 fold change. Supplementary Table S5. Differentially expressed tarMS unigenes in Taraxacum flowers analyzed using edgeR (log2 fold change). Supplementary Table S6. Differential expression analysis of all nectar secretion pathway unigenes in Taraxacum flowers using edgeR (log2 fold change). Supplementary Table S7. The primer list used for unigene analysis in the nectar secretion pathway.

Author Contributions

S.-J.C. contributed to the design of the project, performed the experiments, generated datasets and figures, and wrote the manuscript. S.P. (Sunmi Park) and S.-J.P., performed gene annotation and qPCR experiments. S.P. (SeonJoo Park) contributed to project design and read/edited the manuscript. All authors have read and agreed to the published version of the manuscript.

Funding

The National Institute of Biological Resources (NIBR202005101), Seo-gu, Incheon, Republic of Korea, supported this work.

Data Availability Statement

The datasets supporting the results of this article are included in the additional files. Unique-Transcripts sequences are available in GenBank (ON351066-ON351241), and whole transcriptome sequencing data are available in the NCBI-SRA database (SRR32995710-14).

Conflicts of Interest

The authors declare no conflicts of interest.

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Figure 1. Phylogenetic analysis of SWEET, Invertase (INV), and Male Sterility (MS) genes in the Taraxacum genus and Arabidopsis. A total of 59 protein sequences (TAIR + Taraxacum unigenes) were used to construct the maximum likelihood (ML) tree with 1000 bootstrap replicates in IQ-TREE. The tree was midpoint-rooted using FigTree. Taraxacum phylogroups are color-coded to represent gene categories: MS (Male Sterility), CWIN (Cell Wall Invertase), vINV (Vacuolar Invertase), and SWEET.
Figure 1. Phylogenetic analysis of SWEET, Invertase (INV), and Male Sterility (MS) genes in the Taraxacum genus and Arabidopsis. A total of 59 protein sequences (TAIR + Taraxacum unigenes) were used to construct the maximum likelihood (ML) tree with 1000 bootstrap replicates in IQ-TREE. The tree was midpoint-rooted using FigTree. Taraxacum phylogroups are color-coded to represent gene categories: MS (Male Sterility), CWIN (Cell Wall Invertase), vINV (Vacuolar Invertase), and SWEET.
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Figure 2. MUSCLE alignment of 18 unigenes of Taraxacum invertase family members. INV-CW protein active sites, beta fructosidase motifs, glycosylation sites of CWIN (NES), and vacuolar INV (vINV) (GET) sites were identified.
Figure 2. MUSCLE alignment of 18 unigenes of Taraxacum invertase family members. INV-CW protein active sites, beta fructosidase motifs, glycosylation sites of CWIN (NES), and vacuolar INV (vINV) (GET) sites were identified.
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Figure 3. Heatmaps of SWEET/CWIN/MS unigenes were produced from DEG analysis. tha: T. hallaisanense; tmo: T. mongolicum; toh: T. ohwianum; tof: T. officinale; tco: T. coreanum.
Figure 3. Heatmaps of SWEET/CWIN/MS unigenes were produced from DEG analysis. tha: T. hallaisanense; tmo: T. mongolicum; toh: T. ohwianum; tof: T. officinale; tco: T. coreanum.
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Figure 4. Differentially expressed genes (DEGs) were identified in the nectar secretion pathway as well as genes involved in sucrose production, transport, and hydrolysis in Taraxacum. The following genes were examined: HXE, hexokinase 1/2; PGM2, phosphoglucomutase 2; UGP, UTP-glucose-1-phosphatase; SPSA2, sucrose phosphate synthase 2; SUS1, sucrose transport1,3,5; CWIN, cell wall invertase 4. The sucrose metabolic pathway was constructed using the Plant Metabolic Network (PMN). Most genes associated with nectar secretion were up-regulated in Taraxacum. Detailed DEG analysis and transcripts of sucrose biosynthesis are provided in Supplementary Table S6. The species examined include tha: T. hallaisanense; tmo: T. mongolicum; toh: T. ohwianum; tof: T. officinale; and tco: T. coreanum.
Figure 4. Differentially expressed genes (DEGs) were identified in the nectar secretion pathway as well as genes involved in sucrose production, transport, and hydrolysis in Taraxacum. The following genes were examined: HXE, hexokinase 1/2; PGM2, phosphoglucomutase 2; UGP, UTP-glucose-1-phosphatase; SPSA2, sucrose phosphate synthase 2; SUS1, sucrose transport1,3,5; CWIN, cell wall invertase 4. The sucrose metabolic pathway was constructed using the Plant Metabolic Network (PMN). Most genes associated with nectar secretion were up-regulated in Taraxacum. Detailed DEG analysis and transcripts of sucrose biosynthesis are provided in Supplementary Table S6. The species examined include tha: T. hallaisanense; tmo: T. mongolicum; toh: T. ohwianum; tof: T. officinale; and tco: T. coreanum.
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Figure 5. Quantification of nectar secretion pathway-related unigenes from day 1 to 5, with bud closed (bc) and bud opened (bo), and during after-pollination (ap), a distinct stage of T. officinale, was analyzed. The error bar indicates the mean ± SD. Significance was assessed using a one-way ANOVA, and non-overlapping letters (a–d) above the bars indicate groups that are statistically different (p < 0.05) according to Tukey’s HSD post hoc test. SWT: SWEET; SPSA2: sucrose phosphate synthase 2; SUS1: sucrose transport 1; CWIN: cell wall invertase 4/6.
Figure 5. Quantification of nectar secretion pathway-related unigenes from day 1 to 5, with bud closed (bc) and bud opened (bo), and during after-pollination (ap), a distinct stage of T. officinale, was analyzed. The error bar indicates the mean ± SD. Significance was assessed using a one-way ANOVA, and non-overlapping letters (a–d) above the bars indicate groups that are statistically different (p < 0.05) according to Tukey’s HSD post hoc test. SWT: SWEET; SPSA2: sucrose phosphate synthase 2; SUS1: sucrose transport 1; CWIN: cell wall invertase 4/6.
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Table 1. Assembly and gene annotation statistics of Taraxacum unigenes.
Table 1. Assembly and gene annotation statistics of Taraxacum unigenes.
S.noSpeciesLongest TranscriptsN50UnigenesCd-Hit-Est
Unigenes		TAIRSwiss-ProtKEGG
1T. ohwianum122,494163564,29627,69116,43147,65935,261
2T. officinale120,911938.7558,92429,51115,78235,78835,165
3T. mongolicum129,4331053.7569,23432,70622,90048,09239,386
4T. coreanum156,377929.8473,69831,31824,67869,37544,722
5T. hallaisanense96,360927.6559,59929,03917,89733,33428,375
6combined397,3441304197,47358,33953,56465,14958,783
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Claude, S.-J.; Park, S.; Park, S.-J.; Park, S. Unraveling the Nectar Secretion Pathway and Floral-Specific Expression of SWEET and CWIV Genes in Five Dandelion Species Through RNA Sequencing. Plants 2025, 14, 1718. https://doi.org/10.3390/plants14111718

AMA Style

Claude S-J, Park S, Park S-J, Park S. Unraveling the Nectar Secretion Pathway and Floral-Specific Expression of SWEET and CWIV Genes in Five Dandelion Species Through RNA Sequencing. Plants. 2025; 14(11):1718. https://doi.org/10.3390/plants14111718

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Claude, Sivagami-Jean, Sunmi Park, Seong-Jun Park, and SeonJoo Park. 2025. "Unraveling the Nectar Secretion Pathway and Floral-Specific Expression of SWEET and CWIV Genes in Five Dandelion Species Through RNA Sequencing" Plants 14, no. 11: 1718. https://doi.org/10.3390/plants14111718

APA Style

Claude, S.-J., Park, S., Park, S.-J., & Park, S. (2025). Unraveling the Nectar Secretion Pathway and Floral-Specific Expression of SWEET and CWIV Genes in Five Dandelion Species Through RNA Sequencing. Plants, 14(11), 1718. https://doi.org/10.3390/plants14111718

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