- Research article
- Open Access
Genome-wide characterization and expression analysis of the heat shock transcription factor family in pumpkin (Cucurbita moschata)
BMC Plant Biology volume 20, Article number: 471 (2020)
Crop quality and yield are affected by abiotic and biotic stresses, and heat shock transcription factors (Hsfs) are considered to play important roles in regulating plant tolerance under various stresses. To investigate the response of Cucurbita moschata to abiotic stress, we analyzed the genome of C. moschata.
In this research, a total of 36 C. moschata Hsf (CmHsf) members were identified and classified into three subfamilies (I, II, and III) according to their amino acid sequence identity. The Hsfs of the same subfamily usually exhibit a similar gene structure (intron-exon distribution) and conserved domains (DNA-binding and other functional domains). Chromosome localization analysis showed that the 36 CmHsfs were unevenly distributed on 18 of the 21 chromosomes (except for Cm_Chr00, Cm_Chr08 and Cm_Chr20), among which 18 genes formed 9 duplicated gene pairs that have undergone segmental duplication events. The Ka/Ks ratio showed that the duplicated CmHsfs have mainly experienced strong purifying selection. High-level synteny was observed between C. moschata and other Cucurbitaceae species.
The expression profile of CmHsfs in the roots, stems, cotyledons and true leaves revealed that the CmHsfs exhibit tissue specificity. The analysis of cis-acting elements and quantitative real-time polymerase chain reaction (qRT-PCR) revealed that some key CmHsfs were activated by cold stress, heat stress, hormones and salicylic acid. This study lays the foundation for revealing the role of CmHsfs in resistance to various stresses, which is of great significance for the selection of stress-tolerant C. moschata.
Plants are constantly subjected to all kinds of adverse environmental pressures during growth and development stages, thus, they have developed special mechanisms to cope with adverse conditions [1, 2]. Transcription factors usually play an important role in the regulation of stress responses . Heat shock transcription factors (Hsfs) are the most important transcription regulators . They are the terminal components of signal transduction chains and can mediate the activation of genes that respond to various abiotic pressures (drought stress, heat stress and a large number of chemical stress factors) .
The first Hsf gene was cloned from yeast [5, 6], followed by some mammals [7,8,9,10]. The first plant Hsf gene was cloned from tomato . With the sequencing of the Oryza sativa and Arabidopsis thaliana genomes, Hsf genes have also been identified in O. sativa and A. thaliana [12, 13]. Subsequently, researchers identified 31, 25, 21, 26, 35, 29, 27, 19 and 35 Hsf genes in the Populus trichocarpa , Zea mays , Cucumis sativa , Glycine max , Brassica rapa ssp. pekinensis , Pyrus bretschneideri , Solanum tuberosum , Vitis vinifera  and Brassica oleracea  genomes, respectively.
A typical Hsf usually contains four conserved domains: a DNA-binding domain (DBD) at the N-terminus, a hydrophobic oligomerization domain (HR-A/B or OD), a nuclear localization signal (NLS), and a nuclear export signal (NES) . The DBD is the most conserved domain structure in Hsfs and is mainly responsible for binding to the heat shock elements (HSEs) of the target gene promoter, while the HR-A/B domain is a hydrophobic heptad repeat forming a spiral coil structure, which is a prerequisite for transcription . The NLS is rich in Arg (R) and Lys (K) residues, while the NES is rich in Leu (L). NLS is recognized by the corresponding NES, which interacts with nucleoporins to help protein containing nuclear localization signal reach the nucleus through the nuclear pore [24,25,26]. There is a flexible link between the DBD and the HR-A/B domain. Based on the structural characteristics of the conserved DBD and HR-A/B domain, the Hsfs have been divided into three groups (A, B and C). The main differences between the three groups are as follows: group B proteins exhibit 7 amino acid residues in their HR-A/B domain, while group A has 28 amino acid residues in the relevant domain and group C had 14 amino acid residues in the same domain. In addition, the transcription activation domain (AHA) at the C-terminus is characteristic of group A, which guarantees the normal transcription of the Hsfs by binding to some basic transcription protein complexes. However, the Hsfs of group B and group C cannot maintain their activation activity due to the lack of an AHA motif [26, 27]. The repression domain (RD) is a peptide containing conserved amino acids (LFGV) at the C-terminus and mainly exists in group B .
Hsfs can specifically regulate the transcription of heat shock protein (Hsp) genes by specifically binding to the HSE in the promoter of an Hsp gene, and the Hsp, in turn, protect cells from stress and participate in protein folding [29, 30]. Some studies have confirmed that Hsfs are involved in the heat stress response. For example, the silencing of HsfA1a in tomato reduces the synthesis of heat stress-induced chaperone and HsfA1a proteins, thereby increasing the sensitivity of HsfA1a-silenced tomato plants to heat stress . At 37 °C, A. thaliana HsfA2-mutant plants are more sensitive to heat stress than wild-type plants, which can be reversed by introducing the HsfA2 gene . The OsHsfA4d-mutant shows a phenotype of necrotic damage under high-temperature stress . The expression of OsHsfA2e enhances high temperature and salt tolerance in A. thaliana . In addition to heat stress, Hsfs are involved in plant growth and other biotic and abiotic stress responses. It is found that HsfA9 is involved in embryo development and seed maturation in A. thaliana and Helianthus annuus . Four Hsf genes (HsfA1e, HsfA3, HsfA4a, HsfB2a and HsfC1) in A. thaliana are strongly induced by salt, cold and osmotic stress [35,36,37]. The HsfA2 in A. thaliana is involved in the response to oxidative stress . The HsfA4a in A. thaliana can be used as an H2O2 sensor [35, 39]. The OsHsfA4a in O. sativa is associated with cadmium tolerance . To date, there have been no reports of the cloning and functional analysis of Cucurbita moschata Hsfs.
C. moschata is rich in a variety of amino acids, vitamins, polysaccharides, pectin, and minerals and contains trigonelline, carotenoids and other biologically active substances and nutrients . According to the Food and Agriculture Organization of the United Nations (http://www.fao.org/home/en/), pumpkin ranks the ninth in the output value of different vegetable crops in the world, with an annual sales value of 4 billion US dollars. China and India are the two main pumpkin producing countries in the world. China’s cultivation area ranks second in the world, and its total output ranks first in the world . During growth and development, unfavorable stress often causes great harm to the growth of pumpkin, resulting in a decline in pumpkin yield and quality . Therefore, research on pumpkin resistance-related genes is increasingly important for pumpkin breeding and production. Because the C. moschata (Rifu) genome has been published , the Hsf family in C. moschata can now be subjected to systematic and comprehensive analysis. In this study, we provide information about the gene structural characteristics, gene duplications, chromosomal locations, evolutionary divergence and phylogenetic relationships of 36 C. moschata Hsf genes. Furthermore, we analyze the digital expression profiles of 36 CmHsfs in response to numerous stresses. This study emphasizes the function of the Hsfs in various stress conditions and improves our understanding of the effects of polyploidization events on the evolution of the Hsf family.
Identification of Hsf genes in C. moschata and their physical and chemical characteristics
A total of 36 CmHsf genes were identified after the removal of false positives and the same genes (Table 1), and they were designated CmHsf1 to CmHsf36 according to the starting positions of these genes on the chromosomes (from Cmo_Chr00 to Cmo_Chr20, from top to bottom). The physicochemical parameters of each CmHsf were generated, and the predicted open reading frames (ORFs) ranged from 543 bp (CmHsf32) to 4380 bp (CmHsf13), with predicted proteins of 179–1458 amino acids. The physical and chemical parameters of these genes are similar to those seen in A. thaliana and O. sativa . Furthermore, the molecular weights (MW) of these CmHsfs ranged from 20.5642 to 161.5554 kDa (kDa) (Table 1). Although the deduced heat shock transcription factors presented diversity in terms of the parameters mentioned above, most of the CmHsfs exhibited low isoelectric points (pI) (average 6.3) (Table 1). Subcellular localization prediction indicated that only 2 heat shock transcription factors (CmHsf12 and CmHsf17) were predicted to be localized to the cell membrane, cytoplasm and nucleus, while the remaining CmHsfs were predicted to be localized to the nucleus.
Classification and conserved domain analysis of 36 CmHsfs
To identify the phylogenetic relationships of the 36 CmHsfs, an unrooted phylogenetic tree was produced. These CmHsfs can be divided into three subfamilies (subfamily I, subfamily II and subfamily III; Fig. 1a) according to the amino acid sequence identity. Subfamily I (containing 21 members) was the largest group, and subfamily III included 13 members, while subfamily II presented the fewest members (2 members) (Fig. 1a). Furthermore, based on the structural characteristics of the conserved DBDs and HR-A/B domains, we can divide the 36 CmHsfs into three groups (A, B, and C) (Table 2). All CmHsfs contained a DBD and an HR-A/B domain (Table 2), and the DBD was composed of approximately 100 conserved amino acids (Additional file 2: Fig. S1). In addition, except for CmHsf27 and CmHsf32, all of the CmHsfs contained an NLS. The CmHsfs in group A contained an AHA domain, while the CmHsfs in groups B and C did not contain an AHA domain, and only the proteins in Group B contained an RD (Table 2). To further reveal conserved domains, all CmHsfs were submitted to MEME, and 10 different motifs were identified (Fig. 1b; Additional file 2: Fig. S2). Overall, the CmHsfs exhibited 4–9 motifs, and motifs 1, 2 and 4 were present in all CmHsf proteins. Motif 3 was present in all proteins except for CmHsf20 and CmHsf5. In addition, we found that motif 5 existed only in subfamily I, while motif 9 appeared only in subfamily III (Fig. 1b). The CmHsfs from the same clade usually present conserved domains or similar motif compositions, suggesting functional similarities among these proteins.
Exon-intron analysis of 36 Hsfs in C. moschata
An exon-intron organization map of the 36 CmHsf genes was also produced (Fig. 2). Different numbers of exons (from 2 to 26) were found in the 36 CmHsf genes, suggesting that CmHsfs are quite diverse. In subfamily III, except for CmHsf1, CmHsf10 and CmHsf35, which contained 9, 8 and 3 exons, respectively, the other CmHsf genes all contained 2 exons. CmHsf genes on the same branch usually presented similar intron-exon distributions, such as CmHsf26_CmHsf9. Some genes in the same family exhibited significantly different intron-exon distributions. For example, CmHsf12 contained 26 exons, which was different from the other CmHsfs, indicating that CmHsf12 may have a special function.
Chromosomal distribution and gene duplication of Hsf genes in C. moschata
Chromosomal distribution analysis in the genome revealed that the 36 CmHsf genes were unevenly distributed on 19 of the 21 chromosomes (Fig. 3). The chromosome Cm_Chr06 exhibited the most CmHsf genes, with 5 genes, followed by chromosome Cm_Chr05, with 4 genes. A total of 3 genes were present on each of chromosomes Cm_Chr03, Cm_Chr07 and Cm_Chr14, and 2 genes were present on each of chromosomes Cm_Chr02, Cm_Chr04, Cm_Chr10, Cm_Chr11 and Cm_Chr16, while no genes were distributed on chromosomes Cm_Chr00, Cm_Chr08 and Cm_Chr20.
Two genes, whose putative amino acid identity is > 85% and gene alignment coverage is > 0.75, were defined here as a recently duplicated gene pair [45, 46]. A total of 18 duplicated genes were identified and divided into nine groups, each of which contained two duplicated genes. Eight duplicated gene pairs were distributed on different chromosomes (Fig. 3), which demonstrated that segmental duplication events were involved in the expansion of the CmHsf genes. CmHsf10 and CmHsf12 were separated by a region of more than 100 kb, indicating that all duplicated gene pairs had undergone segmental duplication events. The Ka and Ks ratios were less than 1.0, which suggested that the pairs had evolved mainly under functional constraints with negative or purifying selection (Table 3). We also calculated evolutionary times and divergence times of the duplicated C. moschata Hsf gene pairs ranging from 10.17 to 65.74 million years ago (Mya), averaging 21.11 Mya (Table 3).
Phylogenetic relationship of Hsfs in C. moschata, C. sativa and A. thaliana
To better evaluate the molecular evolution and phylogenetic relationship of plant Hsf, a phylogenetic tree of 79 Hsf proteins in C. moschata, C. sativa and A. thaliana was established. Based on the previous classification of C. moschata Hsf proteins (Fig. 1a), they were divided into 9 clades (Clade Ia-b, Clade II and Clade IIIa-e) (Fig. 4). Subfamily I was divided into Clade Ia and Clade Ib, and subfamily III was divided into Clade IIIa-e. This classification was consistent with the phylogenetic classification of AtHsf proteins . In general, genes from subfamily I (Clade Ia and Clade Ib) (including 51 Hsfs) constituted the largest branch and accounted for 65% of the total Hsfs. Subfamily II contained 2 proteins. The remaining Hsfs belong to subfamily III and contain a total of 26 Hsf proteins. From the perspective of phylogenetic branch, the homology of Hsfs between C. moschata and C. sativa was higher than that between C. moschata and A. thaliana, which was consistent with the evolutionary rules of the three species.
Synteny analysis of Hsf genes in C. moschata
According to the synteny analysis of Hsfs in C. moschata and 5 other species (A. thaliana; Lagenaria siceraria; Cucumis sativus; Cucurbita maxima; Citrullus lanatus), we found that C. lanatus exhibited the most Hsf homologous genes (56), followed by L. siceraria (52), C. maxima (51) and C. sativus (51). A. thaliana presented the fewest (18) homologous genes (Fig. 5). Furthermore, the syntenic genes of the CmHsfs could be found on all chromosomes of A. thaliana, L. siceraria, C. sativus, C. maxima, and C. lanatus, indicating that the CmHsfs have remained closely related to those of these five species during the process of evolution. In addition, we found that certain CmHsf genes on chromosomes Cm_Chr02, Cm_Chr06, Cm_Chr08, and Cm_Chr016 corresponded to two or more Hsf genes in A. thaliana. This phenomenon was more fully reflected in the collinear diagram of C. moschata with L. siceraria, C. sativus, C. maxima and C. lanatus. In general, the collinear relationship between C. moschata and L. siceraria, C. sativus, C. maxima or C. lanatus) was closer than that for A. thaliana, suggesting that these species may have originated from the same ancestor. The collinear analysis showed that C. moschata and L. siceraria, C. sativus, C. maxima, and C. lanatus had frequent collinearity (Fig. 5), indicating that genes with collinear relationship may have similar functions.
Expression pattern of Hsf genes in C. moschata
To understand the physiological role of CmHsfs, we analysed the expression patterns of 36 heat shock transcription factors in the roots, stems, cotyledons and true leaves of C. moschata via quantitative real-time PCR. The transcriptional abundance of 36 C. moschata heat shock transcription factors can be obtained from at least one of the four tissues (Fig. 6; Additional file 1: Table S1). Heat map and cluster analyses showed that 21 CmHsfs were highly expressed in cotyledons and true leaves, such as CmHsf4, CmHsf32, CmHsf35, CmHsf19 and CmHsf15. Two genes (CmHsf9 and CmHsf10) were expressed more highly in the roots and stem than in the cotyledons and true leaves. Some genes were highly expressed only in one tissue. For example, CmHsf23 was mainly expressed in the roots, and its relative expression level was 100–258 times that in other tissues. Based on the above analysis, 36 heat shock transcription factors showed tissue specificity.
Cis-acting element analysis of Hsf genes in C. moschata
To explore the potential function of Hsfs, the cis-elements in the promoters (2 kb before the start codon) of the 36 Hsf genes in C. moschata were predicted. A total of 429 cis-elements were found among all CmHsfs. They were involved in 9 abiotic stresses, including showing salicylic acid responsiveness, defence and stress responsiveness, low-temperature responsiveness, abscisic acid responsiveness, gibberellin responsiveness, MeJA responsiveness, auxin responsiveness, drought inducibility and wound responsiveness (Fig. 7a; Additional file 1: Table S2). A total of 31% of the 429 cis-acting elements were involved in abscisic acid responsiveness, which existed in 32 of the 36 CmHsfs (Fig. 7b, c). In addition, 27 and 45% of the cis-acting elements were MeJA response elements (harboring CGTCA and TGACG motifs) and auxin response elements, respectively (Fig. 7b). Among the 36 heat shock transcription factors, 28 genes were involved in the MeJA response, and 22 genes were involved in the auxin response. A total of 14 heat shock transcription factors exhibited low-temperature response elements. Since the Hsf genes involved in abscisic acid responsiveness, low-temperature responsiveness, MeJA responsiveness and auxin responsiveness account for a high proportion of these genes, we speculated that these genes might play important roles in these stresses.
By analyzing the cis-acting elements of individual genes, we found that both CmHsf34 and CmHsf27 contained 12 abscisic acid response elements (Additional file 1: Table S2). In addition, CmHsf17, CmHsf26, CmHsf9 and CmHsf35 contained 8 MeJA response elements, and CmHsf23 and CmHsf35 contained the greatest number (3) of low-temperature response elements, which indicates that these key CmHsfs may play an important role in the corresponding stress response.
The response of CmHsf genes to temperature stress
To explore the response of CmHsfs to temperature stress, we cultured C. moschata seedlings at 4 °C and 38 °C. Under cold treatment, 44% of the CmHsfs (16 genes) were significantly upregulated, and 27% of the CmHsfs (10 genes) were significantly downregulated (Fig. 8; Additional file 1: Table S3). For instance, CmHsf3, CmHsf5, CmHsf23, CmHsf24, CmHsf27, CmHsf35 and CmHsf36 were highly expressed under cold stress. In addition, the CmHsf4, CmHsf15, CmHsf31 and CmHsf32 genes exhibited low expression levels under cold stress. At the same time, two genes (CmHsf28 and CmHsf30) were not expressed under cold stress, indicating that the expression of these genes may be limited under cold stress. Under heat treatment, 24 genes were significantly upregulated, and 12 genes were significantly downregulated (Fig. 8; Additional file 1: Table S3). The expression levels of CmHsf9 and CmHsf31 under heat stress were 128.38 and 66.39 times those in the control plants, respectively, suggesting that these two genes may play important roles under heat stress. Some genes presented low expression levels under heat treatment, such as CmHsf17, CmHsf11, CmHsf21, CmHsf22, CmHsf23 and CmHsf35. Considering the expression levels of the CmHsf genes under cold and heat stress together, we found that CmHsf9, CmHsf11, CmHsf21, CmHsf23, CmHsf31, CmHsf34 and CmHsf35 showed opposite trends under the two stresses, so we speculate that these genes may play important roles in temperature stress.
The response of CmHsf genes to hormones and salicylic acid
According to the prediction of cis-acting elements in the CmHsfs promoter, a total of 28, 32, and 19 CmHsf genes were found to be involved in the MeJA response, abscisic acid responsiveness and salicylic acid responsiveness, respectively (Fig. 7; Additional file 1: Table S2). Therefore, we analysed the responses of these genes to MeJA, ABA, and SA. The results of qRT-PCR analysis showed that 31 CmHsfs responded to MeJA to varying degrees, and the expression of CmHsf20 was 5.1 times that in the control (Fig. 9; Additional file 1: Table S4). Under ABA treatment, 21 CmHsfs were significantly upregulated, and 15 genes were significantly downregulated. The expression levels of CmHsf3, CmHsf4, CmHsf5, CmHsf6, CmHsf7, CmHsf8, CmHsf12, CmHsf25, CmHsf29 and CmHsf31 under ABA stress were 20 ~ 86 times those of the control plants, indicating that these genes play important roles under ABA stress. All CmHsfs responded to SA, among which CmHsf25, CmHsf27, CmHsf29 and CmHsf32 were significantly increased under SA treatment, while CmHsf1, CmHsf2, CmHsf23 and CmHsf28 were significantly decreased under SA treatment. Based on the above analysis, we conclude that CmHsf family genes are involved in multiple stresses and may play different roles in these stresses.
Heat shock transcription factors are broadly present in all plants and are considered to be important regulators of abiotic stress. The Hsf family has been comprehensively and systematically analyzed in G. max , B. rapa , P. bretschneideri , S. tuberosum , V. vinifera  and B. oleracea . However, the Hsf family has not been extensively studied in C. moschata.
In our study, we identified 36 Hsf genes in C. moschata via genome-wide analysis (Table 1). The analysis of the physical and chemical properties of the gene family can show the diversity of each member in the process of evolution . Our results showed that the MW and the number of amino acids of 36 CmHsfs vary widely (Table 1), which indicates that C. moschata changes in the process of evolution. Most of the CmHsfs exhibited low isoelectric points (pI) (average 6.3), this result is similar to the report of Hsf in C. sativa . Regardless of the size and domain composition of proteins, the characteristics of low pI are preserved, indicating that CmHsf proteins should be negatively charged at physiological pH. Through predictive analysis of subcellular location, it was found that most of the CmHsfs were predicted to be localized to the nucleus (Table 1), which indicated that their functions were indeed as transcription factors. But CmHsf12 and CmHsf17, from the same subfamily, were predicted to be localized to cell membrane, cytoplasm and nucleus, indicate that CmHsf members in the same subfamily do not necessarily correspond to the same subcellular location, and they might have other special function.
The phylogenetic tree divided 36 CmHsfs into 3 subfamilies (Subfamily I, Subfamily II and Subfamily III), most of the genes within the same subfamily shared similar gene structures in terms of either exon length or intron number (Fig. 2). Therefore, we speculated that the CmHsfs in one branch may have similar functions, and this feature was similar to that previously reported in other species [16, 18]. The structural characteristics of some CmHsfs in the same branch are different from those of other CmHsf genes, indicating that these genes may have functional diversity. In addition, The CmHsfs were also divided into three groups (groups A, B and C) based on the conserved structural characteristics of the DBD and the HR-A/B domain (Table 2). Subfamily II corresponded to group C and subfamily III corresponds to group B, subgroup I contained not only group A genes but also group C genes. Due to the close homology of the genes on the same branch, we speculate that the evolutionary path of the CmHsfs has been changing.
The conserved motifs of CmHsfs protein were also predicted and analyzed (Fig. 1). It was found that motifs 1, 2 and 4 exist in all CmHsf proteins (Fig. 1). According to the comprehensive analysis of the motif position and conserved domain position of 36 CmHsf protein, we found that motif 1, motif 2 and motif 3 together formed the DBD, and motif 4 formed the HR-A/B domain (Fig. 1; Table 2). The result is consistent with the previous reports in Z. mays , C. sativa , B. rapa ssp. pekinensis , S. tuberosum , which indicates that CmHsfs may have similar functional characteristics.
In some species, the number of members of a specific gene family is considered to be the result of natural evolution. At the same time, the diversity of gene family members is generally due to genome recombination and amplification . Chromosomal segmental duplications and individual gene duplications are a major driving force in the genome evolution process . Compared with the 25 reported ZmHsfs , 21 CsHsfs  and 31 PtHsfs , we found that the number of Hsf genes in C. moschata is greater than those in Z. mays, C. sativa and P. trichocarpa. Genome sizes vary significantly in these species; for instance, the genome size of C. moschata is 197.83 Mb, and that of Z. mays is 2300 Mb. The maize genome size is 11 times that of C. moschata. However, the number of maize Hsf genes is much lower than the number of Hsf genes in C. moschata. The reason for this difference might be that although two rounds of gene duplication occurred in the Z. mays genome during its evolution [48, 49], the Hsf genes of Z. mays underwent large gene losses. In addition, the genome of C. moschata also underwent a whole-genome duplication (WGD) event during the phylogeny of the species . For C. sativa, the genome size is 350 Mb, but 21 CsHsfs was less than the number of CmHsfs. We speculated that gene duplication promotes the amplification of CmHsf genes  or gene degeneration and mutation promotes the reduction of the number of CsHsf genes , ultimately resulting in the number of CmHsf genes more than that of other plants.
In this study, all CmHsf gene pairs were found to have experienced segmental duplication events, with no tandem duplication events, indicating that segmental duplication has played an important role in the evolution of the C. moschata Hsf gene family (Fig. 3). The Ka and Ks ratios of all duplicated pairs indicated that these gene pairs were under purifying selection. Additionally, the relatively high Ka/Ks ratios for CmHsf12-CmHsf10 suggested that they have experienced rapid evolution (Table 3).
A study proposes three hypotheses to explain the fate of duplicated genes: (1) In the process of plant evolution, sometimes gene degeneration and mutation occur, which often leads to the loss of copy function of some duplicated genes. (2) Due to the diversity and directionality of mutations, one copy of the duplicated gene may mutate and retain its new function during evolution, while the other copy retains its original function. This process is called new functionalization. (3) Two copies of the duplicated gene may mutate to obtain different functions, which is called subfunctionalization . According to the different expression patterns of CmHsf26 and CmHsf9 genes, it can be inferred that there are differences between the duplicated genes. CmHsf26 is highly expressed in cotyledon and true leaf, while CmHsf9 gene is highly expressed in root and stem (Fig. 6). Their gene structure and motif composition are similar, which indicates that the subfunctionalization of duplicated genes in CmHsf gene family may change the gene expression pattern (Fig. 1; Fig. 2). In addition, the duplicated genes CmHsf30 and CmHsf16 have similar intron-exon structure, the same motif component, and the similar tissue expression pattern, but there are obvious differences in temperature stress and hormone treatment (Fig. 2; Fig. 6; Fig. 8; Fig. 9), which indicates that the new functionalization of the duplicated genes in the CmHsf gene family may play a key role. The collinear analysis showed that C. moschata had frequent collinearity with L. siceraria, C. sativus, C. maxima, and C. lanatus (Fig. 5), indicating that genes with collinear relationship may have similar functions.
Cis-acting elements are essential for gene expression, and their numbers are correlated with gene expression intensity [51, 52]. CmHsf23 and CmHsf35 contain three low-temperature response elements (Fig. 7), which mean that CmHsf23 and CmHsf35 may play key roles under low-temperature stress. The qRT-PCR results showed that CmHsf23, CmHsf21, CmHsf11, and CmHsf35 were significantly upregulated under low temperature, and the expression profiles of these genes showed opposite trends under high-temperature stress, which further verified the response of these genes to temperature stress (Fig. 8). However, CmHsf13, CmHsf36, CmHsf3 and CmHsf5 were significantly induced under cold stress and heat stress (Fig. 8), and their responses were more prominent under cold stress, which indicated that these genes were highly sensitive to temperature and might play a key role under temperature stress. The prediction of cis-acting elements showed that the promoters of 28 CmHsf genes contained MeJA response elements (Fig. 7), and qRT-PCR analysis showed that the expression levels of 31 genes changed to varying degrees under MeJA treatment (Fig. 9). However, from the relative expression values, we found that the CmHsfs responded less to MeJA than to ABA and SA (Fig. 9). Therefore, we concluded that C. moschata Hsf family genes were mainly involved in the respond to ABA and SA.
In summary, we identified 36 Hsfs in the Cucurbita moschata genome based on a thorough analysis and provided genetic information such as chromosome locations and exon-intron structures, conserved domains, and duplicated genes. We specifically examined the expression profiles of these CmHsfs in different tissues. At the same time, we examined the responses of CmHsfs to multiple stresses, and several key genes were found to respond to adverse environments.
Sequence retrieval from the Cucurbit genomics database and physicochemical characterization
To identify the heat shock transcription factor family in C. moschata, the genome was downloaded from the Cucurbit genomics database (CuGenDB, http://cucurbitgenomics.org/) . A total of 25 A. thaliana Hsf genes were obtained from the NCBI database by using their gene IDs from A. thaliana references . We used 25 AtHsf proteins as queries to search against the Cucurbit genomics database using BLASTP with an e-value cut-off of 1 × e− 10. To eliminate false positives, sequences were discarded if they constituted < 70% of the corresponding A. thaliana Hsf protein. SMART (http://smart.embl-heidelberg.de/)  and MARCOIL (http://toolkit.tuebingen.mpg.de/marcoil)  were used to predict the DBDs and HR-A/B domains. After the removal of the same genes, the remaining genes were identified as CmHsf genes. The coding sequence and protein sequence information for each of the CmHsfs were shown in Additional file 1: Table S6.
The physical and chemical characteristics of the heat shock transcription factors, including their theoretical molecular weight (MW), theoretical isoelectric point (pI) and the number of amino acids, were analyzed with ExPASy (http://web.expasy.org/tools/) . Information on CmHsf genes including their chromosomal distribution, their start and the end positions on the chromosomes were extracted from the Cucurbit genomics database, and their subcellular locations were predicted with Plant-mPLoc .
Phylogenetic tree construction
To reveal the phylogenetic relationships of Hsf genes in C. moschata, an unrooted phylogenetic tree was constructed with MEGA 5.0  according to the similarity of full-length amino acid sequence of 36 CmHsfs. In addition, the phylogenetic relationship of Hsf protein from C. moschata, C. sativa and A. thaliana was also constructed by MEGA 5.0. The protein sequences of 21 CsHsfs and 22 AtHsfs were obtained based on previous literature [44, 57]. The unrooted Neighbor-Joining (NJ) method was used to construct the phylogenetic tree, and the bootstrap values were obtained using 1000 replicates with the pairwise deletion option.
Analysis of conserved domains and gene structure
The conserved motifs of Hsf in C. moschata were obtained on the Multiple Expectation Maximization or Motif Elicitation (MEME, http://meme-suite.org/)  using the protein sequences, and the LOGOs (Additional file 2: Fig. S2) of the protein motifs were also obtained with MEME. The NLSs and NESs of the heat shock transcription factors were predicted by using cNLS Mapper  and the NetNES 1.1 Server , respectively. The exon-intron structures were obtained from GSDS (Gene Structure Display Server, http: //gsds.cbi. pku.edu.cn/)  by comparing the cDNA sequences and its corresponding genomic DNA sequences of CmHsfs members.
Gene duplication and gene collinearity analysis
The chromosomal locations of the CmHsf genes were mapped and imaged with visualization tools (http://visualization.ritchielab.psu.edu/home/index) based on their initial positional information obtained from C. moschata (CuGenDB, http://cucurbitgenomics.org/). To identify gene duplications, all CDS sequences of C. moschata Hsf genes were subjected to BLAST searches against each other (Identity > 85%, E-value <1e− 10) by using the Local Blast program. Gene alignment coverage was then acquired by pair-wise alignment using the previously calculated method: Gene alignment coverage = (alignment length - mismatches)/length of the longer gene. Pairs were considered duplications when the gene alignment coverage was greater than 0.75. Moreover, two genes that were separated by several genes in a 100-kb were named as tandemly duplicated genes . To estimate the divergence of these duplicated CmHsf genes, we used the KaKs calculator to calculate the synonymous substitution ratio (Ks) according to the method of Gojo-bori and Nei . To avoid the saturation of substitutions, we required that Ks values > 2.0 must be discarded [64, 65]. The divergence time (T) was computed according to the formula (T = Ks/2λ × 10− 6 million years ago (Mya), λ = 1.5 × 10− 8) in the previous literature . The criteria for identifying gene collinearity were based on previous reports , and the synteny relationships between the heat shock transcription factors of C. moschata and those of other species (A. thaliana, C. sativus, C. maxima, C. lanatus, L. siceraria) were constructed using Advanced Circos program in TBtools .
Analysis of cis-acting elements of CmHsf gene promoters
The promoter sequences (2 kb before the start codon) of all CmHsf genes were extracted from the Cucurbit genome database (http://cucurbitgenomics.org/), and we predicted the promoter cis-acting elements of CmHsfs by using PlantCare program (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/)  and visualized by Simple BioSequence Viewer in TBtools .
Plant material, growth conditions and stress treatment
The C. moschata variety “Tianmi 1” was used as the study material. The seeds were provided by the pumpkin team of School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology. The seeds were sown in a tray containing a vermiculite-matrix (2:1) mixture and grown in a plant growth chamber. The artificial growth conditions were set as light intensity of 350 μmol/m2/sec, 25 °C 16 h light / 16 °C 8 h dark and 65% relative humidity. We sampled and analyzed different tissues (roots, stems, cotyledons and true leaves) of two-month-old seedlings. In addition, some of the seedlings were transferred to 38 °C for 6 h heat treatment, or transferred to 4 °C for 6 h cold treatment. Another portion of the seedlings was cultured in 1/2 Hoagland solution, pH 6.5. After 5 days of adaptation, the plants were cultured with the following treatments: (1) control (untreated plants); (2) 1 mM MeJA; (3) 5 mM salicylic acid (SA); (4) 100 μM abscisic acid (ABA) . Leaf samples were collected at 10 h after the above treatments. Control and stress-treated samples were frozen in liquid nitrogen and stored at − 70 °C for further analysis.
RNA extraction, reverse transcription and qRT-PCR analysis
Total RNA was extracted from the frozen samples according to the instructions of the RNA kit (Tiangen, Beijing). Moreover, the RNA was isolated and then reverse transcribed into cDNA using a Prime Script RT reagent kit (TaKaRa, Dalian, China). Finally, quantitative real-time PCR was performed using the SYBR Premix ExTaq kit (TaKaRa, Dalian). To verify the specificity of gene primers, the target genes and the reference gene (β-Actin) primers (Additional file 1: Table S5) were aligned at the Cucurbit genome database. The qRT-PCR analysis was performed on an ABI7500 Real-Time PCR System (Applied Biosystems) with the following cycling profile: stage 1, 95 °C 20 s; stage 2, 95 °C 3 s, 60 °C 30 s (40 cycles); stage 3, 95 °C 15 s, 60 °C 1 min, 95 °C 15 s. Stage 3 was used to perform a melting curve. Experimental repeats were run for three technical and three biological replicates. The relative gene expression was calculated according to the 2-ΔΔCt method.
Availability of data and materials
The Cucurbita moschata Hsf gene and protein sequences were downloaded from the Cucurbit genomics database (CuGenDB, http://cucurbitgenomics.org/). All of the data and materials supporting our research findings are contained in the methods section of the manuscript. Details are provided in the attached additional files.
- Hsfs :
Heat shock transcription factors
Nuclear localization signal
Nuclear export signal
Heat shock element
Heat shock protein
- Cm :
- pI :
Multiple expectation maximization or motif elicitation
Coding domain sequence
- Ks :
Synonymous substitution ratio
Million years ago
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The data of expression levels of 36 CmHsf genes in root, stem, cotyledon and true leaves. The results were calculated via the 2−ΔΔCt method. Table S2. Statistics for the number of cis-acting elements in the 36 CmHsf gene promoters. Table S3. The data of expression levels of 36 CmHsf genes in leaves under temperature stress. CK referred to the untreated plants at 25 °C. The data represented the expression levels of CmHsf genes at 6 h after cold stress (4 °C) and heat stress (38 °C). The results were calculated via the 2−ΔΔCt method. Table S4. The data of expression profiles of 36 CmHsf genes in true leaves under MeJA, ABA and SA treatments. CK referred to untreated plants in this figure. The data represented the expression levels of CmHsf genes at 10 h after the MeJA, ABA and SA treatments. The results were calculated via the 2−ΔΔCt method. Table S5. List of primer sequences used for the tissue-specific analysis of 36 CmHsf genes. Table S6. The coding sequence and protein sequence information for each of the CmHsfs.
Multiple sequence alignment analysis and the secondary structure elements of DBD in CmHsf proteins. Sequence alignments were performed using Clustal X 2.0. Different background colors indicated different amino acids. “*” meant that the amino acid sequences of different Hsf proteins are highly consistent. The secondary structure elements of DBD (α1-β1-β2-α2-α3-β3-β4) were shown above the alignment. The secondary structure was predicted by SOPMA secondary structure prediction software. Cylindrical tubes represented a-helices or β-sheets. Figure. S2. Detailed information about the 10 motifs identified in CmHsf proteins. The LOGOs of the protein motifs were also obtained with Multiple Expectation Maximization or Motif Elicitation (MEME, http://meme-suite.org/).
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Shen, C., Yuan, J. Genome-wide characterization and expression analysis of the heat shock transcription factor family in pumpkin (Cucurbita moschata). BMC Plant Biol 20, 471 (2020). https://doi.org/10.1186/s12870-020-02683-y
- Cucurbita moschata
- Heat shock transcription factor
- Gene duplication
- Conserved domain
- Cis-acting elements
- Expression pattern