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Phylogenetic Relationships of Cucurbitaceae Estimated by Astral Using Six Gene Sets. Bootstrap values of backbone nodes are denoted with solid circles or a diamond. Nodes showing consistent relationships in all six trees are marked with solid circles with three colors, indicating different levels of BS support: maximum support (100%) in at least five trees (red), maximum support in fewer than five trees and >90% support in all six trees (blue), and all other types of support (black). Other types of BS values (black circles) are presented (legend continued on next page) Molecular Plant 13, 1117-1133, August 3 2020 ª The Author 2020. 1119
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The ability of climbing plants to grow upward along others to reach canopy for photosynthesis is hypothesized as a key innovation in flowering plants. Cucurbitaceae, a family containing ∼1000 species and many important crops, are mostly climbers and have characteristic tendrils and pepo fruits. Here, we present 127 newly sequenced transcriptomes an...
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... reconstruct the Cucurbitaceae phylogeny, we used six sets of nuclear genes (referred to here as orthogroups [OGs]) with 1503, 1181, 942, 737, 460, and 258 OGs, respectively, selected using a multi-step procedure with consideration for species coverage, length of aligned matrices, and other factors (see Methods and Supplemental Figure 1 for details). Phylogenetic analysis of the Cucurbitaceae was conducted by using a coalescent method with single nuclear gene trees from each of the aforementioned six sets of OGs (Supplemental Figures 2-7). ...
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... analysis of the Cucurbitaceae was conducted by using a coalescent method with single nuclear gene trees from each of the aforementioned six sets of OGs (Supplemental Figures 2-7). The resulting phylogenies are overwhelmingly congruent with strongly supported monophyly and relationships as summarized in Figure 1. Specifically, the Cucurbitaceae family is monophyletic with maximal support (bootstrap support [BS] = 100%), with high support (BS R 99%) for monophyly of each of the 13 tribes represented by two or more species (with Indofevilleeae being monotypic and Siraitieae represented by one species), consistent with previous phylogenetic studies (Supplemental Figure 8) (Zhang et al., 2006;Kocyan et al., 2007;Schaefer et al., 2009;Schaefer and Renner, 2011a;Renner and Schaefer, 2016). ...
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... addition, the highly supported phylogeny provides resolution of relationships at the tribe level for the first time with eight successive major clades (Clade I to Clade VIII). The earliest diverging lineage (Clade I) consists of tribes Actinostemmateae and Gomphogyneae as sisters with BS R 90% in three trees and BS between 75% and 90% in three other trees (Figure 1 and Supplemental Figures 2-7). The next lineage to diverge is Clade II containing tribes Zanonieae and Triceratieae with maximum support in all trees. ...
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... four trees (from analyses using 1503, 1181, 942, and 737 OGs, respectively) with weak support (BS < 70%), Indofevilleeae and Thladiantheae are successive sisters to a large clade of the other nine tribe (Supplemental Figures 2-5 and 9). In two trees (460 and 258 OGs, respectively) with strong support (BS R 95%; Supplemental Figures 6, 7, and 9), Indofevilleeae and Thladiantheae cluster as sisters forming Clade III in our phylogenetic model (Figure 1). In previous studies, the monotypic Indofevilleeae was either reported as a branch next to the clade of the other ten tribes ( Kocyan et al., 2007) or as sister to Actinostemmateae (Schaefer and Renner, 2011a), although both topologies were reconstructed using a few markers and had low support (Supplemental Figure 8). ...
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... relationships among the 52 genera included here are also largely resolved with high support, with monophyly observed for 28 of the 29 genera with two or more taxa sampled (Figure 1). Among the 15 Cucurbitaceae tribes, six have three or more genera represented here, providing an opportunity to examine their relationships. ...
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... these New World genera form two small clades: one with the pair Marah and Echinocystis, and the other containing three genera ((Sicyos, Echinopepon), Cycylanthera). In the tribe Cucurbiteae, Cayaponia and Sicana are successive sisters to Cucurbita, which is monophyletic for the eight taxa here with strong support (Figure 1). In the tribe Coniandreae, among the nine genera sampled here, Trochomeriopsis and Seyrigia form a branch separated from the remaining seven genera, which each diverge from the others successively. ...
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... chose eight fossils (Supplemental Table 2) as calibration points in our analysis. As illustrated in our chronogram ( Figure 2 and Supplemental Figure 10), the origin of the crown group of Cucurbitaceae dates to $80 million years ago (Ma) with a 95% credibility interval (CI) ranging from 69.9 to 90. Shortly after the origin of Cucurbitaceae came the emergence of the crown group of Clade I ($76.7 Ma, 95% CI: 66-87) and the divergence of Clade II from the remainder of cucurbits ($77.7 Ma, 95% CI: 67.8-87.7). ...
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... improve our understanding of the evolutionary history of cucurbit genomes, we searched for gene duplications (GDs) as evidence for potential WGD events. We used a phylogenomic approach to identify homologs and compare gene trees of the identified gene families with our phylogenetic model (Figure 1) as performed previously for other groups of angiosperms ( Jiao et al., 2012Jiao et al., , 2014Yang et al., 2015;Huang et al., 2016b;Ren et al., 2018;Yang et al., 2018). After examining 20 023 gene trees (see Methods), we found strong evidence for four WGD events (referred to as CucWGD1 to CucWGD4) with relatively large numbers and proportions of gene trees exhibiting duplication events (>500 and >5%, respectively, a relatively cautious cutoff in comparison with that used in recent literature) (Figure 3 and Supplemental Figure 11). ...
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... used a phylogenomic approach to identify homologs and compare gene trees of the identified gene families with our phylogenetic model (Figure 1) as performed previously for other groups of angiosperms ( Jiao et al., 2012Jiao et al., , 2014Yang et al., 2015;Huang et al., 2016b;Ren et al., 2018;Yang et al., 2018). After examining 20 023 gene trees (see Methods), we found strong evidence for four WGD events (referred to as CucWGD1 to CucWGD4) with relatively large numbers and proportions of gene trees exhibiting duplication events (>500 and >5%, respectively, a relatively cautious cutoff in comparison with that used in recent literature) (Figure 3 and Supplemental Figure 11). We identified an early large-scale duplication event at the origin of the family (CucWGD1: 1053 GDs, 19.59%). ...
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... obtain additional support for some of the WGD events, we investigated the genomic location of gene duplicates identified as being derived from CucWGDs in eight publicly available genomes (see Methods) that are proposed to have experienced CucWGD1 and/or CucWGD2; however, there was no genome available to conduct this investigation for the CucWGD3 event in Sicyoeae and CucWGD4 in Gomphogyneae. We detected genomic evidence for CucWGD1 in the form of collinear gene order (synteny) between genomic regions in the genomes of tribes Benincaseae ( Figure 4A) and Momordiceae (Supplemental Figure 12A). In addition, gene duplicates supporting CucWGD2 shared by members of the tribe Cucurbiteae were also found in syntenic regions in the Cucurbita genomes ( Figure 4B). ...
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... members uncovered syntenic regions that are distinct from those corresponding to CucWGD2 and contain gene duplicates derived from CucWGD1 (Supplemental Figure 12B). Additional support for CucWGD2 was also revealed by the analysis of the genomic location of TEN (see below). ...
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... the ancestor of Cucurbitaceae probably was a polyploid, and Cucurbiteae, some Sicyoeae, and Hemsleya of Gomphogyneae each separately experienced a second round of large-scale duplications. We further examined the gene ontology (GO) annotations of retained gene duplicates derived from each of the four CucWGDs and found that the duplicates from the proposed WGDs are enriched for several GO categories ( Figure 5 and Supplemental Figure 13), relative to the genome-wide frequency, such as cell division and movement (including endosome and cytoskeleton) and carbohydrate/ secondary metabolic processes. The enrichment of the same GO categories in retained duplicates from two or more WGDs suggests that potential functional innovations associated with cell division and metabolism might have benefited cucurbits at multiple times during evolution. ...
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... investigate the species diversification dynamics in Cucurbitaceae, we used MEDUSA ( Alfaro et al., 2009) and BAMM (Bayesian analysis of macro-evolutionary mixtures; Rabosky et al., 2014) to estimate diversification rates and the shifts in diversification rates using our time-calibrated phylogeny (Figure 2 and Supplemental Figure 10). We identified two instances of rate acceleration using BAMM and two using MEDUSA, totaling four rate shifts as shown in Figure 3. Two such shifts in diversification rates were observed along the Cucurbitaceae phylogenetic backbone, both having occurred during climate upheavals. ...
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... x axis shows the four CucWGDs proposed here, and the y axis lists the categories in plant GO slim terms. A version with detailed GO terms is presented in Supplemental Figure 13. ...
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... on our resolved Cucurbitaceae phylogeny with branch lengths, we traced the ancestral states of 15 morphological characters (Supplemental Tables 4 and 5). For eight characters, namely habit, stem, leaf, fruit size, seed appendage, sexual system, floral symmetry, and stigma number, there were no detected transitions along the backbone of the cucurbit phylogeny (Supplemental Figures 14-21). Both herbaceous and woody stems had equal probability of being the ancestral character in the early history of cucurbits. ...
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... herbaceous and woody stems had equal probability of being the ancestral character in the early history of cucurbits. The predominance of herbaceous stems was traced back to the ancestors of both the crown of Clade I and that of Clade VII to Clade VIII (Supplemental Figure 15). The morphological states of three traits (stamen number, pollen size, and style number; Supplemental Figures 22-24) transformed once along the phylogenetic backbone at the MRCA of Clades V to VIII. ...
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... A chronogram at the genus level obtained by collapsing tips into genera was used to trace ancestral character states under the maximum parsimony criterion in Mesquite (see Methods). Generic names are listed between trees, with different background colors delimiting the major clades identified in this study (also see Figure 1). Ages for nodes and branches correspond to the scale at the bottom. ...
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... the ancestral cucurbit tendrils were branched with a coiling basal part ( Figure 6A), followed by a trend of simplification that included an initial reduction of the coiling base in the MRCA of Clades V to VIII and a further change to simple, branchless tendrils in some derived clades in Clade VIII. Also, cucurbit stems tended to evolve from woody to herbaceous (Supplemental Figure 15), with the latter form growing rapidly and providing relatively easy access to upper spaces and sunlight for photosynthesis. Simplified tendrils permit plants to redistribute their resources, such as to produce more tendrils along the fast-growing stems to increase the clinging area. ...
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... reduction of stamen number (Supplemental Figure 22) and the enlargement of pollen size (Supplemental Figure 23) seem to simplify the structure of flowers, allowing the plants to reallocate the energy and resources to other purposes, such as increasing ovule production ( Sicard and Lenhard, 2011). The sexual strategy of monoecy in half of extant cucurbits is derived from ancestral dioecy (Supplemental Figure 19), consistent with the little heterosis known in this family (Gusmini and Wehner, 2008;Schaefer and Renner, 2011b). The evolution of monoecy allowed self-pollination while still facilitating crosspollination ( Sicard and Lenhard, 2011). ...
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... used a Bayesian method to estimate divergence times of Cucurbitaceae with MCMCTREE in the PAML package (Yang, 2007), using as the input tree that from ML reconstruction with the concatenated 258 OGs while assigning the topology as shown in Figure 1. We selected eight fossils and a secondary calibration point for dating analyses (Supplemental Table 2). ...
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... reconstruct the Cucurbitaceae phylogeny, we used six sets of nuclear genes (referred to here as orthogroups [OGs]) with 1503, 1181, 942, 737, 460, and 258 OGs, respectively, selected using a multi-step procedure with consideration for species coverage, length of aligned matrices, and other factors (see Methods and Supplemental Figure 1 for details). Phylogenetic analysis of the Cucurbitaceae was conducted by using a coalescent method with single nuclear gene trees from each of the aforementioned six sets of OGs (Supplemental Figures 2-7). ...
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... analysis of the Cucurbitaceae was conducted by using a coalescent method with single nuclear gene trees from each of the aforementioned six sets of OGs (Supplemental Figures 2-7). The resulting phylogenies are overwhelmingly congruent with strongly supported monophyly and relationships as summarized in Figure 1. Specifically, the Cucurbitaceae family is monophyletic with maximal support (bootstrap support [BS] = 100%), with high support (BS R 99%) for monophyly of each of the 13 tribes represented by two or more species (with Indofevilleeae being monotypic and Siraitieae represented by one species), consistent with previous phylogenetic studies (Supplemental Figure 8) (Zhang et al., 2006;Kocyan et al., 2007;Schaefer et al., 2009;Schaefer and Renner, 2011a;Renner and Schaefer, 2016). ...
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... addition, the highly supported phylogeny provides resolution of relationships at the tribe level for the first time with eight successive major clades (Clade I to Clade VIII). The earliest diverging lineage (Clade I) consists of tribes Actinostemmateae and Gomphogyneae as sisters with BS R 90% in three trees and BS between 75% and 90% in three other trees (Figure 1 and Supplemental Figures 2-7). The next lineage to diverge is Clade II containing tribes Zanonieae and Triceratieae with maximum support in all trees. ...
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... four trees (from analyses using 1503, 1181, 942, and 737 OGs, respectively) with weak support (BS < 70%), Indofevilleeae and Thladiantheae are successive sisters to a large clade of the other nine tribe (Supplemental Figures 2-5 and 9). In two trees (460 and 258 OGs, respectively) with strong support (BS R 95%; Supplemental Figures 6, 7, and 9), Indofevilleeae and Thladiantheae cluster as sisters forming Clade III in our phylogenetic model (Figure 1). In previous studies, the monotypic Indofevilleeae was either reported as a branch next to the clade of the other ten tribes ( Kocyan et al., 2007) or as sister to Actinostemmateae (Schaefer and Renner, 2011a), although both topologies were reconstructed using a few markers and had low support (Supplemental Figure 8). ...
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... relationships among the 52 genera included here are also largely resolved with high support, with monophyly observed for 28 of the 29 genera with two or more taxa sampled (Figure 1). Among the 15 Cucurbitaceae tribes, six have three or more genera represented here, providing an opportunity to examine their relationships. ...
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... these New World genera form two small clades: one with the pair Marah and Echinocystis, and the other containing three genera ((Sicyos, Echinopepon), Cycylanthera). In the tribe Cucurbiteae, Cayaponia and Sicana are successive sisters to Cucurbita, which is monophyletic for the eight taxa here with strong support (Figure 1). In the tribe Coniandreae, among the nine genera sampled here, Trochomeriopsis and Seyrigia form a branch separated from the remaining seven genera, which each diverge from the others successively. ...
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... chose eight fossils (Supplemental Table 2) as calibration points in our analysis. As illustrated in our chronogram ( Figure 2 and Supplemental Figure 10), the origin of the crown group of Cucurbitaceae dates to $80 million years ago (Ma) with a 95% credibility interval (CI) ranging from 69.9 to 90. Shortly after the origin of Cucurbitaceae came the emergence of the crown group of Clade I ($76.7 Ma, 95% CI: 66-87) and the divergence of Clade II from the remainder of cucurbits ($77.7 Ma, 95% CI: 67.8-87.7). ...
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... improve our understanding of the evolutionary history of cucurbit genomes, we searched for gene duplications (GDs) as evidence for potential WGD events. We used a phylogenomic approach to identify homologs and compare gene trees of the identified gene families with our phylogenetic model (Figure 1) as performed previously for other groups of angiosperms ( Jiao et al., 2012Jiao et al., , 2014Yang et al., 2015;Huang et al., 2016b;Ren et al., 2018;Yang et al., 2018). After examining 20 023 gene trees (see Methods), we found strong evidence for four WGD events (referred to as CucWGD1 to CucWGD4) with relatively large numbers and proportions of gene trees exhibiting duplication events (>500 and >5%, respectively, a relatively cautious cutoff in comparison with that used in recent literature) (Figure 3 and Supplemental Figure 11). ...
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... used a phylogenomic approach to identify homologs and compare gene trees of the identified gene families with our phylogenetic model (Figure 1) as performed previously for other groups of angiosperms ( Jiao et al., 2012Jiao et al., , 2014Yang et al., 2015;Huang et al., 2016b;Ren et al., 2018;Yang et al., 2018). After examining 20 023 gene trees (see Methods), we found strong evidence for four WGD events (referred to as CucWGD1 to CucWGD4) with relatively large numbers and proportions of gene trees exhibiting duplication events (>500 and >5%, respectively, a relatively cautious cutoff in comparison with that used in recent literature) (Figure 3 and Supplemental Figure 11). We identified an early large-scale duplication event at the origin of the family (CucWGD1: 1053 GDs, 19.59%). ...
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... obtain additional support for some of the WGD events, we investigated the genomic location of gene duplicates identified as being derived from CucWGDs in eight publicly available genomes (see Methods) that are proposed to have experienced CucWGD1 and/or CucWGD2; however, there was no genome available to conduct this investigation for the CucWGD3 event in Sicyoeae and CucWGD4 in Gomphogyneae. We detected genomic evidence for CucWGD1 in the form of collinear gene order (synteny) between genomic regions in the genomes of tribes Benincaseae ( Figure 4A) and Momordiceae (Supplemental Figure 12A). In addition, gene duplicates supporting CucWGD2 shared by members of the tribe Cucurbiteae were also found in syntenic regions in the Cucurbita genomes ( Figure 4B). ...
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... members uncovered syntenic regions that are distinct from those corresponding to CucWGD2 and contain gene duplicates derived from CucWGD1 (Supplemental Figure 12B). Additional support for CucWGD2 was also revealed by the analysis of the genomic location of TEN (see below). ...
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... the ancestor of Cucurbitaceae probably was a polyploid, and Cucurbiteae, some Sicyoeae, and Hemsleya of Gomphogyneae each separately experienced a second round of large-scale duplications. We further examined the gene ontology (GO) annotations of retained gene duplicates derived from each of the four CucWGDs and found that the duplicates from the proposed WGDs are enriched for several GO categories ( Figure 5 and Supplemental Figure 13), relative to the genome-wide frequency, such as cell division and movement (including endosome and cytoskeleton) and carbohydrate/ secondary metabolic processes. The enrichment of the same GO categories in retained duplicates from two or more WGDs suggests that potential functional innovations associated with cell division and metabolism might have benefited cucurbits at multiple times during evolution. ...
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... investigate the species diversification dynamics in Cucurbitaceae, we used MEDUSA ( Alfaro et al., 2009) and BAMM (Bayesian analysis of macro-evolutionary mixtures; Rabosky et al., 2014) to estimate diversification rates and the shifts in diversification rates using our time-calibrated phylogeny (Figure 2 and Supplemental Figure 10). We identified two instances of rate acceleration using BAMM and two using MEDUSA, totaling four rate shifts as shown in Figure 3. Two such shifts in diversification rates were observed along the Cucurbitaceae phylogenetic backbone, both having occurred during climate upheavals. ...
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... x axis shows the four CucWGDs proposed here, and the y axis lists the categories in plant GO slim terms. A version with detailed GO terms is presented in Supplemental Figure 13. ...
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... on our resolved Cucurbitaceae phylogeny with branch lengths, we traced the ancestral states of 15 morphological characters (Supplemental Tables 4 and 5). For eight characters, namely habit, stem, leaf, fruit size, seed appendage, sexual system, floral symmetry, and stigma number, there were no detected transitions along the backbone of the cucurbit phylogeny (Supplemental Figures 14-21). Both herbaceous and woody stems had equal probability of being the ancestral character in the early history of cucurbits. ...
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... herbaceous and woody stems had equal probability of being the ancestral character in the early history of cucurbits. The predominance of herbaceous stems was traced back to the ancestors of both the crown of Clade I and that of Clade VII to Clade VIII (Supplemental Figure 15). The morphological states of three traits (stamen number, pollen size, and style number; Supplemental Figures 22-24) transformed once along the phylogenetic backbone at the MRCA of Clades V to VIII. ...
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... A chronogram at the genus level obtained by collapsing tips into genera was used to trace ancestral character states under the maximum parsimony criterion in Mesquite (see Methods). Generic names are listed between trees, with different background colors delimiting the major clades identified in this study (also see Figure 1). Ages for nodes and branches correspond to the scale at the bottom. ...
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... the ancestral cucurbit tendrils were branched with a coiling basal part ( Figure 6A), followed by a trend of simplification that included an initial reduction of the coiling base in the MRCA of Clades V to VIII and a further change to simple, branchless tendrils in some derived clades in Clade VIII. Also, cucurbit stems tended to evolve from woody to herbaceous (Supplemental Figure 15), with the latter form growing rapidly and providing relatively easy access to upper spaces and sunlight for photosynthesis. Simplified tendrils permit plants to redistribute their resources, such as to produce more tendrils along the fast-growing stems to increase the clinging area. ...
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... reduction of stamen number (Supplemental Figure 22) and the enlargement of pollen size (Supplemental Figure 23) seem to simplify the structure of flowers, allowing the plants to reallocate the energy and resources to other purposes, such as increasing ovule production ( Sicard and Lenhard, 2011). The sexual strategy of monoecy in half of extant cucurbits is derived from ancestral dioecy (Supplemental Figure 19), consistent with the little heterosis known in this family (Gusmini and Wehner, 2008;Schaefer and Renner, 2011b). The evolution of monoecy allowed self-pollination while still facilitating crosspollination ( Sicard and Lenhard, 2011). ...
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... used a Bayesian method to estimate divergence times of Cucurbitaceae with MCMCTREE in the PAML package (Yang, 2007), using as the input tree that from ML reconstruction with the concatenated 258 OGs while assigning the topology as shown in Figure 1. We selected eight fossils and a secondary calibration point for dating analyses (Supplemental Table 2). ...
Citations
... The fruits and seeds of many plant species present distinct surface protrusions, often associated with various types of dispersion [1]. Thus, winged fruits and seeds occur in species of 93 families at least [2][3][4], being frequent in climbers such as the Aristolochiaceae [5] and Cucurbitaceae [6], and absent or not described in the Arecaceae. Seed surface formations may also contribute to zoochory or hydrochory, as the endocarp fibers of Chamaedorea cataractarum Mart. ...
Recently, based on light microscopy images, the tubercle structure on the seed surface of 100 Silene species was quantitatively described, including tubercle width, height, and curvature associated with general morphometric data. Curvature measures the rate of change of the tangent vector in a curve and can be calculated by the following methods described for Arabidopsis roots. Here, we apply curvature measurements to the SEM images of 40 Silene species from Türkiye, demonstrating that a quantitative analysis of tubercles can be made based on SEM images with similar results to optical photographs. The association of morphometric tubercle data allows for classification into six groups, five of them corresponding to described shapes: rugose (two groups), echinate, mammillate, and papillose, and a sixth group of tubercles plane on top. The curvature values vary between 20 and 200 mm−1 and differ among the morphological tubercle types described. The correlation of curvature values with other general measurements and morphological seed characteristics is investigated. Tubercle quantification not only is a useful tool for Silene taxonomy, but also provides the basis for the analysis of the genetic control and developmental effects on tubercle structure and shape in the seed surface.
... Today, plant phylogenetic investigations routinely utilize organellar (plastid and mitochondria) genomic data and transcriptomic data (Wickett et al., 2014;Johnson et al., 2016;Bazinet et al., 2017;Unruh et al., 2018;Jin et al., 2021;Xia et al., 2022;Liu et al., 2023;Perez-Escobar et al., 2024;Zhang et al., 2023). For example, studies have shown that mitochondrial data is suitable for populations with diverse evolutionary rates, i.e., orchids (Ran et al., 2018;Guo et al., 2020;Stull et al., 2020). Although there are concerns that the transcriptomes of different tissues raise biases in phylogenetic inference, recent studies have demonstrated that lineage transcriptomics can be effectively employed for phylogenetic analysis as the results are only slightly affected by tissue type . ...
... Phylogenetic analyses based on plastid and nuclear genomes have advanced our understanding of orchid relationships at the subfamilial and tribal levels (Table 1; Unruh et al., 2018;Fernandez et al., 2019;Li et al., 2019b;Guo et al., 2020;Serna-Sanchez et al., 2021). Phylogenetic reconstructions based on chloroplast coding sequences (ptCDS) and mitochondrial coding sequences (mtCDS) have contrasted with previous studies based on morphology (Dressler and Dodson, 1960;Vermeulen, 1966;Garay, 1972;Dressler, 1981;Burns-Balogh and Funk, 1986;Berg et al., 2000;Chase et al., 2003), repositioning subfamilies Vanilloideae and Cypripedioideae (Li et al., 2019b), as well as designating Thaieae as a sister to the higher epidendroids (Xiang et al., 2012). ...
... Transcriptomic data have emerged as a source of information that can confirm fundamental phylogenetic relationships in Orchidaceae, but perhaps more importantly elucidate the evolution of traits within the family Guo et al., 2020Guo et al., , 2023. For example, studies have used transcription data of 315 single-copy orthologous genes to confirm that Ochidaceae consists of five subfamilies (Deng et al., 2015). ...
... The Cucurbitaceae members (cucurbits) contain many important vegetable and fruit crops, such as cucumber (Cucumis sativus L.), melon (Cucumis melo L.), watermelon (Citrullus lanatus L.), pumpkin (Cucurbita moschata L.), cushaw (Cucurbita argyrosperma L.), zucchini (Cucurbita pepo L.), and winter squash (Cucurbita maxima Duch.), etc. [11]. The flowering time of the cucurbit crops is strongly correlated with early maturity and production, which is of great significance to the global or local economy [12]. ...
The family of phosphatidylethanolamine-binding proteins (PEBPs) participates in various plant biological processes, mainly flowering regulation and seed germination. In cucurbit crops, several PEBP genes have been recognized to be responsible for flowering time. However, the investigation of PEBP family members across the genomes of cucurbit species has not been reported, and their conservation and divergence in structure and function remain largely unclear. Herein, PEBP genes were identified from seven cucurbit crops and were used to perform a comparative genomics analysis. The cucurbit PEBP proteins could be classified into MFT, FT, TFL, and PEBP clades, and further, the TFL clade was divided into BFT-like, CEN-like, and TFL1-like subclades. The MFT-like, FT-like, and TFL-like proteins were clearly distinguished by a critical amino acid residue at the 85th position of the Arabidopsis FT protein. In gene expression analysis, CsaPEBP1 was highly expressed in flowers, and its expression levels in females and males were 70.5 and 89.2 times higher, respectively, than those in leaves. CsaPEBP5, CsaPEBP6, and CsaPEBP7 were specifically expressed in male flowers, with expression levels 58.1, 17.3, and 15.7 times higher, respectively, than those of leaves. At least five CsaPEBP genes exhibited the highest expression during the later stages of corolla opening. Through clustering of time-series-based RNA-seq data, several potential transcription factors (TFs) interacting with four CsaPEBPs were identified during cucumber corolla opening. Because of the tandem repeats of binding sites in promoters, NF-YB (Csa4G037610) and GATA (Csa7G64580) TFs appeared to be better able to regulate the CsaPEBP2 and CsaPEBP5 genes, respectively. This study would provide helpful information for further investigating the roles of PEBP genes and their interacting TFs in growth and development processes, such as flowering time regulation in cucurbit crops.
... With the advent of phylogenomics, many remaining problems in systematics have gradually been resolved (Xiang & al., 2017;Guo & al., 2020), with large amounts of sequence data acting as a buffer to reduce random errors in phylogenetic reconstruction (Zou & Ge, 2008). For Hydrangea, such a robust reconstruction is possible due to the recent abundance of plastid genomes from the genus that have been sequenced Sakaguchi & al., 2021;Yang & al., 2023). ...
The genus Hydrangea s.l. (Hydrangeaceae), a favorite among gardeners, comprises more than 80 species that are important understory plants in natural temperate and subtropical forests of the Northern Hemisphere. These species are hypervariable in morphology , especially in indumentum and floral characters, warranting a thorough exploration of the complex evolutionary history of morphological characters of the genus. Ideally, this is done within a robust phylogenetic framework with extensive taxon sampling. In this study, we propose a comprehensive taxonomic reassessment of Hydrangea based on a reconstruction of its molecular phylog-eny based mainly on the chloroplast genome (plastome) and the most representative taxon sampling reported to date. Phylogenomic reconstruction yielded five well-resolved major clades and three newly recognized subclades. Inspection of the 28 characters employed in traditional taxonomic revisions revealed homoplasy in many of these traits. Our results show that characters such as growth habit, woody stem type, number of enlarged marginal sepals, style and stamen number, fruit shape, and ovary position are useful for circumscribing infrageneric divisions. Unique synapomorphies are limited. For example, herb and subshrub growth habits are associated with all the species in H. sect. Deinanthe and sect. Cardiandra, respectively. Character state combinations are proposed for distinguishing infrageneric taxa. Based on a robust phylogenetic framework, our findings suggest a complex evolutionary history of Hydrangea morphological characters. Following the criterion of monophyly and considering the morphological consistency and synapomorphy of single and combined characters to diagnose relevant lineages, we update the classification of Hydrangea into 5 sub-genera and 19 sections. Our proposed taxonomic scheme, based on a robust phylogenetic framework and in-depth character study, provides an updated perspective on the infrageneric subdivision of Hydrangea s.l.
... Variations in the WRKY motif can alter the DNA-binding activity, which may help to explain the functional diversity among the WRKY TFs [6]. Earlier research showed that Cucurbitaceae originated approximately 80 million years ago, with at least four whole-genome duplication (WGD) events occurring during the evolution of cucurbits [46]. These WGD events are the main factors that have contributed to the morphological diversity of cucurbit plants; however, the genome size and the number of genes in these species decreased to the corresponding levels before the WGD events [47]. ...
The plant-specific WRKY transcription factor family members have diverse regulatory effects on the genes associated with many plant processes. Although the WRKY proteins in Arabidopsis thaliana and other species have been thoroughly investigated, there has been relatively little research on the WRKY family in Luffa cylindrica, which is one of the most widely grown vegetables in China. In this study, we performed a genome-wide analysis to identify L. cylindrica WRKY genes, which were subsequently classified and examined in terms of their gene structures, chromosomal locations, promoter cis-acting elements, and responses to abiotic stress. A total of 62 LcWRKY genes (471–2238 bp) were identified and divided into three phylogenetic groups (I, II, and III), with group II further divided into five subgroups (IIa, IIb, IIc, IId, and IIe) in accordance with the classification in other plants. The LcWRKY genes were unevenly distributed across 13 chromosomes. The gene structure analysis indicated that the LcWRKY genes contained 0–11 introns (average of 4.4). Moreover, 20 motifs were detected in the LcWRKY proteins with conserved motifs among the different phylogenetic groups. Two subgroup IIc members (LcWRKY16 and LcWRKY31) contained the WRKY sequence variant WRKYGKK. Additionally, nine cis-acting elements related to diverse responses to environmental stimuli were identified in the LcWRKY promoters. The subcellular localization analysis indicated that three LcWRKY proteins (LcWRKY43, LcWRKY7, and LcWRKY23) are localized in the nucleus. The tissue-specific LcWRKY expression profiles reflected the diversity in LcWRKY expression. The RNA-seq data revealed the effects of low-temperature stress on LcWRKY expression. The cold-induced changes in expression were verified via a qRT-PCR analysis of 24 differentially expressed WRKY genes. Both LcWRKY7 and LcWRKY12 were highly responsive to the low-temperature treatment (approximately 110-fold increase in expression). Furthermore, the LcWRKY8, LcWRKY12, and LcWRKY59 expression levels increased by more than 25-fold under cold conditions. Our findings will help clarify the evolution of the luffa WRKY family while also providing valuable insights for future studies on WRKY functions.
... It was suggested to have originated in the late Miocene (ca. 8-6 million-year ago) (de Boer et al., 2012;de Boer et al., 2015;Guo et al., 2020). Trichosanthes pilosa is a perennial, night-flowering, insect-pollinated dioecious vine that reproduces sexually and possesses a pair of heteromorphic sex chromosomes XX/XY (Ming et al., 2011). ...
... To investigate the evolutionary rates of coding sequences, we estimated nonsynonymous substitution (d N ), synonymous substitution (d S ) rates, as well as protein substitution rates (d N /d S , ω), using two branch models from CodeML package in PAML v.4.9h with the F3 × 4 codon frequencies (Codon-Freq = 2) (Yang, 2007). According to the phylogenetic relationships of Trichosanthes (de Boer et al., 2012;Guo et al., 2020), we set up tree structures ((T. anguina, T. pilosa), T. kirilowii, L. cylindrica) in the control file of CodeML. ...
Sex-biased genes offer insights into the evolution of sexual dimorphism. Sex-biased genes, especially those with male bias, show elevated evolutionary rates of protein sequences driven by positive selection and relaxed purifying selection in animals. Although rapid sequence evolution of sex-biased genes and evolutionary forces have been investigated in animals and brown algae, less is known about evolutionary forces in dioecious angiosperms. In this study, we separately compared the expression of sex-biased genes between female and male floral buds and between female and male flowers at anthesis in dioecious Trichosanthes pilosa (Cucurbitaceae). In floral buds, sex-biased gene expression was pervasive, and had significantly different roles in sexual dimorphism such as physiology. We observed higher rates of sequence evolution for male-biased genes in floral buds compared to female-biased and unbiased genes. Male-biased genes under positive selection were mainly associated with functions to abiotic stress and immune responses, suggesting that high evolutionary rates are driven by adaptive evolution. Additionally, relaxed purifying selection may contribute to accelerated evolution in male-biased genes generated by gene duplication. Our findings, for the first time in angiosperms, suggest evident rapid evolution of male-biased genes, advance our understanding of the patterns and forces driving the evolution of sexual dimorphism in dioecious plants.
... A survey of fruit types in a phylogenetic context concluded that specific fruit types were not clustered according to major phylogenetic lineages (Lorts et al., 2008); however, the angiosperm phylogeny has changed dramatically since then and further analyses would be desirable. Recent progress in molecular phylogenetics has provided great opportunities to systematically study fruit evolution at the scale of genera (Lorts et al., 2008), tribes (Areces-Berazain and Ackerman, 2017), families (Huang et al., 2016a;Xiang et al., 2017;Guo et al., 2020), or larger groups (Beaulieu and Donoghue, 2013;Zhang et al., 2020). However, fruit evolution across angiosperms has rarely been reported, probably due to the difficulties associated with convoluted patterns of fruit types. ...
... However, fruit evolution across angiosperms has rarely been reported, probably due to the difficulties associated with convoluted patterns of fruit types. Studies on fruit evolution at smaller scales have led to the proposal that the same fruit type has evolved multiple times (Huang et al., 2016a;Xiang et al., 2017;Guo et al., 2020), possibly contributing to the difficulty in tracing the fruit evolution history. Another obstacle lies in the uncertainties of All lineages are shown, except those within rosids and asterids, which are shown in Figures 2, 3, respectively. ...
Fruit functions in seed protection and dispersal and belongs to many dry and fleshy types, yet their evolutionary pattern remains unclear in part due to uncertainties in the phylogenetic relationships among several orders and families. Thus we used nuclear genes of 502 angiosperm species representing 231 families to reconstruct a well supported phylogeny, with resolved relationships for orders and families with previously uncertain placements. Using this phylogeny as a framework, molecular dating supports a Triassic origin of the crown angiosperms, followed by the emergence of most orders in the Jurassic and Cretaceous and their rise to ecological dominance during the Cretaceous Terrestrial Revolution. The robust phylogeny allowed an examination of the evolutionary pattern of fruit and ovary types, revealing a trend of parallel carpel fusions during early diversifications in eudicots, monocots, and magnoliids. Moreover, taxa in the same order or family with the same ovary type can develop either dry or fleshy fruits with strong correlations between specific types of dry and fleshy fruits; such associations of ovary, dry and fleshy fruits define several ovary‐fruit “modules” each found in multiple families. One of the frequent modules has an ovary containing multiple ovules, capsules and berries, and another with an ovary having one or two ovules, achenes (or other single‐seeded dry fruits) and drupes. This new perspective of relationships among fruit types highlights the closeness of specific dry and fleshy fruit types, such as capsule and berry, that develop from the same ovary type and belong to the same module relative to dry and fleshy fruits of other modules (such as achenes and drupes). Further analyses of gene families containing known genes for ovary and fruit development identified phylogenetic nodes with multiple gene duplications, supporting a possible role of whole‐genome duplications, in combination with climate changes and animal behaviors, in angiosperm fruit and ovary diversification.
... WGD is an intrinsic factor that provides a rich base of genetic material for morphological trait variation and synergistically contributes to the diversification of cucurbit species, with multiple WGD events occurring in the ancestors of Cucurbitaceae [25]. Cucurbitaceae evolved a branch containing nearly 80% of extant species after the WGD event, which coincided with a brief climatic optimum in the middle Eocene, providing suitable environmental conditions for species diversification [25]. ...
... WGD is an intrinsic factor that provides a rich base of genetic material for morphological trait variation and synergistically contributes to the diversification of cucurbit species, with multiple WGD events occurring in the ancestors of Cucurbitaceae [25]. Cucurbitaceae evolved a branch containing nearly 80% of extant species after the WGD event, which coincided with a brief climatic optimum in the middle Eocene, providing suitable environmental conditions for species diversification [25]. A phylogenetic tree was constructed using 19, 17, and 16 TPR protein sequences from C. moschata, C. maxima, and C. pepo, respectively, and the results were divided into four groups ( Figure S2). ...
... To further analyze the phylogenetic relationship of the TPR gene family in cucurbit crops, we used the identified 144 TPR in cucurbit crops and 36 TPR proteins in Arabidopsis to construct an unrooted phylogenetic tree, which showed that all the TPR proteins were divided into four groups, consistent with those in the Benincaseae and Cucurbitaceae tribes ( Figure 1). Group I included 99 TPR genes, group II contained 35 TPR genes, and group IV contained the least number of TPR genes, with 5. Most members of the Benincaseae tribe were clustered together, and the TPR proteins from watermelon, bottle gourd, and wax gourd were clustered together on most branches, which is consistent with the evolutionary relationship of the modern cucurbit genome [25,48]. In addition, most TPR members from the tribe Cucurbitaceae gathered preferentially, suggesting that they originated from a common ancestor [33]. ...
Tetratricopeptide repeat (TPR) proteins play numerous roles in plant growth and development by mediating protein–protein interactions in biological systems by binding to peptide ligands. Although genome-wide analyses of the TPR gene family in other species have been performed, its evolution and function in Cucurbitaceae remain unclear. In this study, 144 TPR genes from 11 genomes of eight Cucurbitaceae species with a heterogeneous distribution on the chromosomes were characterized. Based on the homology between Cucurbitaceae and Arabidopsis, the TPR genes were divided into four groups, and the evolutionary relationships of the Benincaceae and Cucurbitaceae tribes were also represented in a phylogenetic tree. Using the ‘DHL92′ genome as a reference, an integrated chromosome map was obtained containing 34 loci, 4 of which were common to the Cucurbitaceae. Cis-regulatory element analysis showed that these elements are essential for melon development and responses to light, phytohormones, and various stresses. CmTPR tissue- and development-specific expression analysis revealed differential expression patterns under normal growth conditions. Furthermore, the CmTPR genes responded to various abiotic stressors. Overall, this study offers insights into the evolutionary history of the TPR gene family in Cucurbitaceae and provides valuable information for elucidating the potential role of CmTPR genes during development and under different stresses in melon.
... The Cucurbitaceae (cucurbits) constitutes an important family of plants including most of 900 species in over 90 genera that are mainly distributed in tropical and subtropical areas (14). Some cucurbits members, that were domesticated and subsequently cultivated for thousands of years, represent agronomical important crops, including cucumber (Cucumis sativus), melon (Cucumis melo), watermelon (Citrullus lanatus), pumpkin and squash (Cucurbita pepo, C. moschata, C. maxima and C. agyrosperma) and bitter gourd (Momordica charantia). ...
... sativus, C. melo, C. lanatus, L. siceraria, C. moschata, C. argyrosperma, C. pepo, C. maxima and M. charantia) comprising 1116 cleaned and strand-specific RNA-seq libraries and 78 RNA-seq projects were included in the subsequent analysis ( Table 1). The nine analized species constitute representative members of three different tribes and five genus in the Cucurbitaceae family (14). Cleaned reads were mapped to the corresponding reference genome and assembled to create a merged transcriptome for each analyzed species ( Figure 1A and "Material and Methods"). ...
Long non-coding RNAs (lncRNAs) constitute a fascinating class of regulatory RNAs, widely distributed in eukaryotes. In plants, they exhibit features such as tissue-specific expression, spatiotemporal regulation, and responsiveness to stress, suggesting their involvement in specific biological processes. Although an increasing number of studies support the regulatory role of lncRNAs in model plants, our knowledge about these transcripts in relevant crops is limited. In this study we employ a custom pipeline on a dataset of over 1,000 RNA-seq studies across nine representative species of the family Cucurbitaceae to predict 91,209 non-redundant lncRNAs. LncRNAs were predicted according to three confidence levels and classified into intergenic, natural antisense, intronic, and sense overlapping. Predicted lncRNAs have lower expression levels compared to protein-coding genes but a more specific behavior when considering plant tissues, developmental stages, and response to stress, emphasizing their potential roles in regulating various aspects of plant-biology. The evolutionary analysis indicates higher positional conservation than sequence conservation, which may be linked to the presence of conserved modular motifs within syntenic lncRNAs. In short, this research provides a comprehensive map of lncRNAs in the agriculturally relevant Cucurbitaceae family, offering a valuable resource for future investigations in crop improvement.
... To investigate the relationship between eIF4E variation and PRSV resistance, we compared the eIF4E of multiple PRSV resistance accessions in the Cucurbit Genomics Database (CuGenDB) (http:// cucur bitge nomics. org/ v2) (Guo et al., 2020). Among the 14 watermelon accessions with the highest resistance to PRSV-W (Strange et al., 2002), 12 resistant accessions were listed in the CuGenDBv2 database. ...
Eukaryotic translation initiation factor 4E (eIF4E), which plays a pivotal role in initiating translation in eukaryotic organisms, is often hijacked by the viral genome‐linked protein to facilitate the infection of potyviruses. In this study, we found that the naturally occurring amino acid substitution D71G in eIF4E is widely present in potyvirus‐resistant watermelon accessions and disrupts the interaction between watermelon eIF4E and viral genome‐linked protein of papaya ringspot virus‐watermelon strain, zucchini yellow mosaic virus or watermelon mosaic virus. Multiple sequence alignment and protein modelling showed that the amino acid residue D ⁷¹ located in the cap‐binding pocket of eIF4E is strictly conserved in many plant species. The mutation D71G in watermelon eIF4E conferred resistance against papaya ringspot virus‐watermelon strain and zucchini yellow mosaic virus, and the equivalent mutation D55G in tobacco eIF4E conferred resistance to potato virus Y. Therefore, our finding provides a potential precise target for breeding plants resistant to multiple potyviruses.
