Next Article in Journal
The PPARα Regulation of the Gut Physiology in Regard to Interaction with Microbiota, Intestinal Immunity, Metabolism, and Permeability
Next Article in Special Issue
Fine Mapping and Identification of a Candidate Gene of Downy Mildew Resistance, RPF2, in Spinach (Spinacia oleracea L.)
Previous Article in Journal
Retinal Cyclic Nucleotide-Gated Channel Regulation by Calmodulin
Previous Article in Special Issue
Molecular and Genetic Events Determining the Softening of Fleshy Fruits: A Comprehensive Review
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
IJMS
Volume 23
Issue 22
10.3390/ijms232214153
ijms-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles thumb_up
...
Endorse textsms
...
Comment
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Genome-Wide Identification and Characterization of the SBP Gene Family in Passion Fruit (Passiflora edulis Sims)

by
Yanhui Liu
1,†,
Jieyu Yuan
1,†,
Dan Zhang
1,
Kao Deng
1,
Gaifeng Chai
1,
Youmei Huang
1,
Suzhuo Ma
1,
Yuan Qin
1,2,* and
Lulu Wang
2,*
1
Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Pingtan Institute of Science and Technology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
2
Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Int. J. Mol. Sci. 2022, 23(22), 14153; https://doi.org/10.3390/ijms232214153
Submission received: 10 October 2022 / Revised: 13 November 2022 / Accepted: 14 November 2022 / Published: 16 November 2022
(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)
Browse Figures
Versions Notes

Abstract

:
The SQUAMOSA promoter binding proteins (SBPs) gene family plays important roles in plant growth and development. The SBP gene family has been identified and reported in many species, but it has not been well studied in passion fruit. In this study, a total of 14 SBP genes were identified in passion fruit and named from PeSBP1 to PeSBP14 based on their chromosomal distribution. The phylogenetic tree, gene structure, conserved motifs, collinearity analysis, and expression patterns of the identified SBP members were analyzed. We classified the PeSBP genes into eight groups (I to VIII) according to the phylogenetic tree, gene structure, and conserved motifs. Synteny analysis found that 5 homologous gene pairs existed in PeSBP genes and 11 orthologous gene pairs existed between passion fruit and Arabidopsis. Synonymous nucleotide substitution analysis showed that the PeSBP genes were under strong negative selection. The expression pattern of PeSBP genes in seed, root, leaf, and flower showed that nine of the PeSBP genes displayed high expression in the leaf and the flower. The expression patterns of PeSBP3/6/8/9/10 were further detected by qRT-PCR. In addition, differences in the expression levels occurred for each gene in the different flower organs and at the different developmental stages. There were large differences among SBPs based on transcriptional levels under cold, heat, salt, and osmotic stress conditions. Altogether, this study provides an overview of SBP genes in passion fruit and lays the foundation for further functional analysis.

1. Introduction

Transcriptional regulation is an important part of eukaryotic gene expression regulation, and transcription factors (TFs) play pivotal roles in plant growth and development processes [1]. TFs, including DNA binding domains, transcriptional activation domains, nuclear localization signals, and oligomerization sites [2], function by binding to corresponding gene promoters, thus activating or inhibiting the transcription of target genes [3]. TFs can be divided into different families based on their DNA binding domains [4]. In plants, 64 TF families have been identified [5].
The SQUAMOSA promoter binding (like) proteins (SBPs/SPLs) gene family is part of a class of important transcription factor families that regulates the growth and the development of green plants under stress. The SBP TFs have a conserved SBP domain containing about 79 amino acid residues that are highly conserved [6]. The SBP domain includes two typical zinc-binding sites (Cys-Cys-Cys-His, Zn1 and Cys-Cys-His-Cys, Zn2) and a highly conserved nuclear localization signal (NLS) at the C-terminal partially overlapping with the Zn2 zinc finger structural sequence [7]. The SBP protein localizes in the nucleus with the nuclear localization signal serving as a guide to regulate the transcriptional expression of downstream genes [8]. The first SBP gene was discovered in inflorescences of Antirrhinum majus L. in 1995 [9]. Since then, SBP genes have been found in a variety of plants, such as Arabidopsis [10], rice [6], soybean [11], grape [8], sorghum [12], Populus [13], pepper [14], maize [15], and tomato, amongst others [16]. SBP is a unique transcription factor in green plants which plays a very important role in a series of plant development processes. In Arabidopsis, the first SBP gene has been identified as ATSPL3, which regulates flowering under long photoperiod [10,17]. ATSPL8 is a local regulator involved in the regulation of microsporogenesis and megasporogenesis [18]. TaSPL20 and TaSPL21 were highly expressed in the panicle of early wheat, and the ectopic expression of TaSPL20 and TaSPL21 in rice has similar functions in promoting panicle development [19]. Inhibition of the expression of SlSPL13 in tomato increases the number of inflorescences on vegetative branches and side branches, reduced the number of flowers and fruits, and reduced fruit size and yield. SlSPL13 directly binds to the promoter region of the tomato inflorescence-related SFT gene and positively regulates its expression, thereby controlling the development of inflorescence [20]. The high expression of OsSPL14 in the reproductive stage of rice promotes the increase of panicle branch and thus the yield [21], and OsSPL16 promotes the cell division of rice and changes the size and shape of grain [22]. NaCl stress can induce the expression of BpSPL9 in birch roots and leaves, and enhanced expression of BpSPL9 promotes reactive oxygen scavenging under stress [23]. These studies have shown that SBP genes play an important role in plant microsporogenesis, flowering, yield, and stress resistance. Therefore, identifying important genes in the SBP gene family is of great importance for identifying candidate genes for the genetic improvement of economic species.
Passion fruit (Passiflora edulis Sims) belongs to the Passifloraceae family and the Malpighiales order with more than 520 species in the world. It is one of the most economically important genera in the Passifloraceae family [24,25]. Passion fruit is native to subtropical regions of North and South America [26]. It is widely cultivated in tropical and subtropical regions because of its value as an easy-to-manage edible, medicinal, and ornamental crop [27]. The genome sequence of passion fruit has been published recently [28,29] which enables us to study the function and characteristics of passion fruit genes.
SBP genes play a critical role in plant growth and development. However, genome-wide characterization and functional analysis of SBP transcription factors in passion fruit have not yet been carried out. In this study, a total of 14 SBP genes were identified in the passion fruit genome and divided into eight groups. The gene structure, conserved motifs, synteny analysis, and expression analyses were presented. In addition, the expression patterns of PeSBP genes in various stress responses were studied. The systematic analysis provided a foundation for further functional characterization of SBP genes in passion fruit.

2. Results

2.1. Identification and Characterization of SBP Genes in Passion Fruit

To identify PeSBP genes in passion fruit, HMMER software and CDD online tools were used. A total of 14 SBP gene sequences were identified and named from PeSBP1 to PeSBP14 according to the location of the genes on the chromosomes (Supplementary Materials Table S1). Sequence alignment was performed with 14 SBP proteins in passion fruit to predict the SBP domain. The results showed that all PeSBP proteins had typical characteristics of the SBP domain, including two zinc domains (Zn1 and Zn2) and a nuclear localization signal (NLS) (Figure 1). With CDS ranging from 552 to 2943 bp, the full length of the 14 PeSBP proteins varied from 183 (PeSBP2) to 981 (PeSBP7) amino acid residues, with the molecular mass ranging from 20.57 (PeSBP4) to 108.28 (PeSBP5) kDa and isoelectric points ranging from 5.93 (PeSBP5) to 9.64 (PeSBP4). The total average hydrophilicity (GRAVY) values were all negative, indicating that all PeSBPs are hydrophilic. The subcellular localization results showed that thirteen of the fourteen PeSBP proteins were located in the nucleus (Supplementary Materials Table S1), while the PeSBP12 was located in the chloroplast. That may be because the nuclear localization sequence of chloroplast localization proteins will be removed after the protein enters the chloroplast. So, the protein will not move to the nucleus from the chloroplast. Furthermore, we identified the orthologous gene of PeSBPs in Arabidopsis. The orthologous gene and the function in Arabidopsis are shown in Supplementary Materials Table S1.

2.2. Phylogenetic Analysis of Passion Fruit SBP Gene Family

To analyze the phylogeny of the SBP gene family, a total of 301 SBP homologs were selected from 18 representative plants from seven green plant families. Among these plants, the soybean had the maximum number of SBP genes, with 46 members. However, only one SBP gene in group I was found in Ostrecocus lucimarinus and Ostrecocus sp. rcc809 (Figure 2). To further understand the phylogenetic relationship of the PeSBP gene family, a phylogenetic tree was constructed using SBP proteins of passion fruit, Arabidopsis, grape, sorghum, and rice. Among them, passion fruit, Arabidopsis, and grape belong to eudicots, while sorghum and rice belong to monocots. According to the unrooted phylogenetic tree, 14 PeSBPs could be divided into 8 groups (I to VIII). Four PeSBPs belonged to group II, while none belonged to group III. There was only one member of PeSBP in groups I, V, and VIII. The homology between the PeSBPs gene and the VvSBPs was relatively high, and the similarity between their protein sequences indicates that the SBP gene of these two species may have similar biological functions (Figure 3).

2.3. Gene Structure and Conserved Motif Analysis of SBP Genes in Passion Fruit

The structure of each gene, especially the number and distribution of exon and intron, may be closely related to evolution. To better understand the diversity of PeSBP gene structure, the coding sequence of each gene was compared with its corresponding genomic sequence. The number of exons varied from 2 to 12. The number of introns in group II was the maximum, while all PeSBP genes in group VI only contained 1 intron, which was the lowest number. Group VII contained two to five introns, and group V contained 4 introns (Figure 4). In group II, PeSBP5, PeSBP7, PeSBP 11, and PeSBP14 in the evolutionary tree may have been cleaved and polymerized during the evolutionary process. The results showed that the number of exons and introns was highly variable in different groups, while the number of exons was nearly consistent in the same group.
The number and types of conserved motifs contained in each protein sequence are different, which may reveal the different functions of each gene. A total of 10 motifs were identified in the PeSBP proteins and named motifs 1 to 10 (Supplementary Materials Figure S1). The results showed that all SBP members contained Motif 1 and Motif 2, suggesting that Motif 1 and Motif 2 constituted the conserved SBP domain (Supplementary Materials Table S2). PeSBP members in group II contained the maximum number of conservative motifs. PeSBP proteins clustered in the same group tended to have similar motif numbers. In contrast, some motifs were specific in some groups of PeSBP proteins—Motif 8, Motif 10, Motif 6, Motif 5, Motif 9, and Motif 7 were only found in group II, and Motif 4 was only found in PeSBP10, suggesting that some proteins may have specific biological functions under specific conditions (Figure 5). The majority within the same group exhibited similarity in motif compositions. Besides, the exon–intron structure of SBP proteins supported the phylogenetic analysis of SBP family genes, and the differences among the different groups indicate their diverse functions.

2.4. Synteny Analysis of PeSBP Genes

The distribution analysis of PeSBP genes on the chromosomes indicated that 13 PeSBP genes map to seven chromosomes, except LG2 and LG8, while PeSBP14 was located on P_eduliaContig 140022932.g. Since the passion fruit chromosome assembly and anchoring rate was only 96.07%, the PeSBP14 (P_ eduliaContig140022932.g) was not anchored to any chromosome but was assembled to Contig14. Among them, LG1 had the maximum number of PeSBP genes, including 5 PeSBP members. LG4 and LG5 chromosomes contain 2 PeSBP genes. The remaining four chromosomes had only 1 PeSBP gene (Figure 6). MCScanX software was used to analyze the collinearity of SBP genes between passion fruit and Arabidopsis. The blue line represents the collinearity of SBP genes between passion fruit and Arabidopsis, and the red line represents the synteny gene pairs of SBP genes between different chromosomes of passion fruit. A total of 16 pairs of collinear genes were identified, including 5 pairs of collinear genes within passion fruit and 11 pairs of synteny gene pairs between passion fruit and Arabidopsis. It can also be seen from the chromosome distribution diagram that there is still a collinearity relationship between PeSBP14 and other genes on chromosomes. However, PeSBP14 was located on the contig rather than the chromosome (Figure 6). It indicated that segmental duplication events might play a more important role in the evolution of the passion fruit SBP gene family. To further understand the evolutionary relationship of the SBP genes, we calculated Ka and Ks values to predict selection pressure for synteny gene pairs. Ka/Ks = 1 indicates neutral selection for homologous genes, Ka/Ks > 1 indicates that these genes evolved under positive selection, and Ka/Ks < 1 indicates that these genes had purification selection [30]. The results showed that the Ka/Ks values of all the SBP homogenous gene pairs within passion fruit and between passion fruit and Arabidopsis were less than 1, indicating that they may play a role in purification selection in the evolutionary process (Supplementary Materials Table S3).

2.5. Expression Profiles of PeSBP Genes in Different Tissues

Recent studies in various species have indicated that the SBP gene plays an important regulatory role in processes associated with plant flowering and inflorescence development [31]. To investigate the tissue-specific expression pattern of PeSBP genes in passion fruit flower development, we analyzed RNA-sequencing data from NGCB to determine the tissue-specific expression patterns of different passion fruit flower tissues (including the mixed flower, bract, sepal, petal, corona filament, stamen, stigma, and ovule at different development processes) and vegetative tissues (including the seed, root, and leaf).
According to their expression patterns, we found that the PeSBP genes showed a tissue-specific expression pattern. For instance, PeSBP13 had high expression during pollen development, while PeSBP9 had specifically high expression in the stigma, and PeSBP4 had increased expression in the sepal and early stigma stages (Figure 7A, Supplementary Materials Table S4). The expression level of PeSBP6, PeSBP8, and PeSBP13 genes were higher in flowers and leaves but lower in seeds and roots (Figure 7B, Supplementary Materials Table S4), suggesting that these three genes may play an important role in passion fruit flower and leaf development. The expression levels of PeSBP7, PeSBP10, PeSBP11, and PeSBP12 were high in all tissues, indicating that they might be involved in various physiological processes of passion fruit flower development. Strangely, the expression levels of PeSBP3 in all tissues were significantly lower than in other genes. These results suggest that diverse PeSBPs might be involved in the different floral tissues of passion fruit.
Furthermore, to validate the expression patterns of the PeSBP genes in the root, leaf, seed, and flower tissues, five PeSBP genes (PeSBP3, PeSBP6, PeSBP8, PeSBP9, and PeSBP10) were randomly selected to test their expression level in these four tissues by qRT-PCR. The qRT-PCR results were consistent with our RNA-sequencing results (Figure 7C), suggesting that all the PeSBP gene expression patterns in different tissues are reliable.

2.6. In Silico Promoter Analysis and Expression Profiles of PeSBP Genes in Response to Abiotic Stresses

To explore the mechanisms of PeSBPs in response to various stresses, we analyzed cis-elements of PeSBPs promoters. Two kb upstream genomic DNA sequences with transcriptional start site (ATG) from 14 PeSBP genes were analyzed. Four different classes of cis-elements were found in PeSBPs promoter regions, including stress responsiveness, light responsiveness, growth and development, and hormone responsiveness (Figure 8). The distribution of cis-elements in PeSBP genes is different, indicating that the expression of PeSBPs may vary in stressful, developmental, and hormonal contexts. Most PeSBP genes contained regulatory elements ABRE, ERE, CGTCA-motif, MBS, and W-box (Supplementary Materials Table S5). These results indicated that various types of cis-element in the same type of PeSBP genes might have different functions. ABRE is involved in abscisic acid responsiveness [32], while CGTCA-motif is involved in MeJA-responsiveness, and MBS (MYB binding site) is involved in drought inducibility. W-box is an important class of cis-element found in the promoter of plant defence response-related genes [33]. Gene ontology (GO) enrichment analysis of the PeSBPs was performed to understand their possible functions at the molecular level, i.e., molecular function (MF), biological process (BP), cellular component (CC). In MF class, PeSBPs enrichment in DNA binding, transcription regulator activity, nucleic acid binding, and so on (Supplementary Materials Figure S2). Five terms were identified as belonging to the CC class (Supplementary Materials Figure S2). Most promoters of PeSBPs genes were significantly enriched in the binding sites of transcription factors involved in the BP class in terms of regulation of nucleic acid-templated transcription, regulation of DNA-templated transcription, and regulation of gene expression (Supplementary Materials Figure S2). The information regarding the enrichment annotation results of GO terms for MF, CC, and BP is provided in Supplementary Materials Table S6. These results show that SBP gene family members may play an important role in different regulations.
To further confirm whether different abiotic stresses influence the expression of PeSBP genes, qRT-PCR experiments were performed to analyze the SBP gene expression patterns in response to different treatments, including cold, heat, and osmotic stress. As shown in Figure 9, seven SBP genes were selected for transcription-level detection. Under cold treatment, five genes (PeSBP6/7/8/9/10) had similar expression patterns that initially decreased and subsequently increased during the course of the treatment, while the relative expression level PeSBP3/12 first increased and then decreased with the treatment time. During the heat treatment, three genes (PeSBP3/6/8) showed a continuous decrease with the treatment time, and the other four genes (PeSBP7/9/10/12) first decreased and then increased their expression with the treatment time.
The cis-elements in promoter regions are essential for regulating the gene expression of different stress response pathways. As shown above, we found some low-temperature responsiveness elements (LTR) in the promoter of PeSBP6, PeSBP7, and PeSBP8 (Figure 8). Additionally, the qRT-PCR results showed that the LTR regulates the expression of PeSBP6, PeSBP7, and PeSBP8 in response to temperature stress. Similarly, the MYB binding site involved in drought-inducibility was found in the PeSBP3/8/10/12 promoter region. After osmotic stress, the transcription of PeSBP8/12 continuously decreased with the treatment time, while the expression of PeSBP3/10 first showed an increase and then decreased with the treatment time. It indicates that the MBS is important as it participates in regulating the expression of PeSBP3/8/10/12 response to osmotic stress. After salt treatment, the expression level of PeSBP8/9/10 increased gradually, while the expression of PeSBP6/7/12 was repressed, and the expression of PeSBP3 increased within 24 h and then decreased 48 h after treatment. Altogether, different SBP genes display differential expression patterns after stress treatment, indicating that these genes might function in response to abiotic stresses.

3. Discussion

The SBP gene family is a plant-specific transcription factor family widely found in green plants, and it plays a crucial role in plant growth and development, physiological and biochemical activities, and environmental response [34]. Passion fruit is a famous tropical and subtropical crop which has extensive economic value [35]. However, only a few studies on the SBP gene family in passion fruit exist. In this study, a total of 14 SBP genes were identified from the passion fruit genome via the bioinformatics method, which was similar in number to other eudicot plants, like Arabidopsis thaliana (16), Arabidopsis lyrata (15), and Vitis vinifera (17), but fewer in number than Glycine max (46) and Populus trichocarpa (28), suggesting that SBP genes in different eudicot species underwent different gene duplication events [36]. There was only one SBP gene in Ostrecocus lucimarinus and Ostrecocus sp. rcc809 in group I, leading us to speculate that the SBP gene of group I might be their ancestor. We found that the number of SBP genes increased in terrestrial plants, and gene expansion was intensified strongly in angiosperms, which may reflect the flowering plants’ effectiveness in adapting to the different unstable environmental conditions [37]. According to phylogenetic tree analysis, the SBP gene family of passion fruit could be divided into eight groups. This result is consistent with previous SBP gene studies in other plants [30]. No PeSBP gene belonging to group III was identified. Whether these genes were lost in the evolution of passion fruit remains to be explored. Most PeSBP genes were clustered closely with the SBP family genes of grape and Arabidopsis but were far away from the SBP genes of rice. This finding is consistent with the fact that passion fruit, grape, and Arabidopsis are eudicot plants. Compared with the lineage that led to the formation of monocots, it is closer to the divergence in evolution from a common ancestor.
The isoelectric points of PeSBPs were between 5.93–9.64, indicating that most PeSBP proteins are rich in basic amino acids, and they may play a role in an acidic subcellular environment. Genes clustered in an evolutionary clade may have similar genetic structures and functions and often have closer relationships [38]. The gene structure of PeSBPs was relatively simple, and the number of exons ranged from 2 to 12. Most PeSBP genes in the same group shared a similar exon–intron structure. The exon –intron structure varied significantly among different groups, suggesting that the gene structure is closely related to the function. Motif identification is particularly important to explore new members of the gene family. Conserved motif analysis results showed that all PeSBP proteins contained motif 1 and motif 2, suggesting that motif 1 and motif 2 constitute the SBP domain. There were some differences in the number of motifs among different groups, with group II possessing ten motifs and groups V, VI, IV, and VII only having two motifs (motif 1 and motif 2). In general, gene structure and conserved motif analysis can support the grouping of evolutionary trees and are associated with specific biological functions [39].
Gene duplication events (segmental and tandem) are the major driving forces for finding novel genes and gene family expansion which can support the adaptation of organisms to different complex environments [40]. Collinearity analysis mainly evaluates the remaining and lost duplication genes through homology comparison. It can provide an important basis for studying the evolutionary history of genes by comparing the homologous gene sequences of different plant genomes [41]. Colinear analysis revealed the evolutionary relationship between homologous gene pairs within passion fruit and between passion fruit and Arabidopsis. A total of 5 segmental duplication events of collinear genes were found within passion fruit, and 11 duplication synteny gene pairs were found between passion fruit and Arabidopsis, indicating segmental duplication events produced the diversity of PeSBPs. The Ka/Ks values of SBP collinearity gene pairs in all identified homologous gene pairs were less than 1, suggesting that SBP collinearity gene pairs underwent purification selection in the evolution process with no functional change.
Plant SBP transcription factors play an important role in plant development, including flower development [42], fruit development [36], plant hormone signal transduction [43], and vegetative to reproductive phase transition [44,45]. An analysis of cis-acting elements of the PeSBP gene promoters showed that the promoters of SBP genes contained multiple cis-acting regulatory elements, which regulate multiple different growth and development and stress tolerance processes. The regulatory elements of different SBP genes in passion fruit were different, which might be closely related to the functional diversity of SBP genes. In Arabidopsis, AtSPL6 is a positive regulator of defence gene expression [46]. The phylogenetic tree results showed that AtSPL6 are orthologous to PeSBP1 and PeSBP10 in group IV. Interestingly, the cis-element analysis showed that PeSBP1 and PeSBP10 contain multiple defence and stress-responsive elements, such as plant defence response, defence and stress responsiveness, and the MYB binding site involved in drought-inducibility. We speculate that PeSBP1 and PeSBP10 might also be positive regulators of defence gene expression in passion fruit. However, the role of cis-elements in the PeSBP gene promoter regions in stress response requires further investigation. To further understand the possible role of PeSBP genes, we examined the expression levels of 14 SBP genes in different tissues of passion fruit. The results showed tissue-specific SBP gene expression during the growth and development of passion fruit, and the expression levels of the same gene were different in different tissues. In addition, most PeSBP genes were highly expressed in leaf and flower tissues. These results were similar to SBP genes of other species and were highly expressed in the shoot development, apical buds inflorescences, and flower buds [47]. For instance, PeSBP8 in group V was orthologous to AtSPL2, AtSPL10, and AtSPL11 [48] and expressed highly in the passion fruit leaves, suggesting that PeSBP8 plays an important role in the regulation of leaf development. The mutant of AtSPL1 and AtSPL12 inflorescences displayed hypersensitivity to heat stress, whereas the overexpression of AtSPL1 or AtSPL12 enhanced the thermotolerance in Arabidopsis [49]. PeSBP5, PeSBP7, and PeSBP14 were orthologous to AtSPL1 and AtSPL12, expressed highly in the passion fruit ovule and flower stages. The cis-element analysis also showed that PeSBP5, PeSBP7, and PeSBP14 promoters contained many growth, development, and stress response related elements, such as binding sites for transcription factors involved in the regulation of endosperm expression, meristem expression, LTR, and defence and stress responsiveness (Figure 8, Supplementary Materials Table S5). These results may improve the cognition of PeSBPs and furnish potential clues for further studies of SBP family genes in passion fruit.

4. Materials and Methods

4.1. Plant Materials

Two-month-old plants were used for different treatments. Passion fruit cultivar Tainong No. 1 seeds were germinated in the greenhouse at 30 ± 1 °C, with a relative humidity of 70%, and a 16-h light/8-h dark photoperiod. At two true leaves stages, the seedlings were transferred to the growth chamber and grown for an additional two months. The materials were provided by the passion fruit breeding group at Fujian Agriculture and Forestry University.

4.2. Identification and Characterization Analysis of SBP Genes in Passion Fruit

First, SBP protein sequences were downloaded from National Genomics Data Center (NGDC) (accession number GWHAZTM00000000). A hidden Markov model (HMM) map of the SBP gene family (PF03110) was obtained from the Pfam database [50]. SBP genes were identified from the whole genome of passion fruit using HMMER (v3.2.1, http://hmmer.org/ (accessed on 22 November 2021)) software and the BLAST program (v2.12.0, ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.12.0/ (accessed on 22 November 2021)), and the candidate genes were further confirmed by containing SBP domain using CDD (https://www.ncbi.nlm.nih.gov/cdd/, (accessed on 22 November 2021)) and SMART server (http://smart.embl.de/, (accessed on 22 November 2021)) online tools, and sequences without complete SBP domains were deleted. Finally, DNAMAN software (v8, LynnonBiosoft, USA) was used to perform multiple sequence alignments on all candidate genes to ensure that they contained the SBP domain. Meanwhile, ExPASy Server (https://web.expasy.org/protparam/ (accessed on 9 December 2021)) [51] was used to calculate the isoelectric point (pI) and the molecular weight (MW), and the length of the amino acids, introns, exons, and open reading frames (ORF) were also calculated. Subcellular localization of SBP protein was predicted using BaCelLo (Balanced Subcellular Localization Predictor) software (http://gpcr2.biocomp.unibo.it/bacello/index.htm, (accessed on 9 December 2021)) [52].

4.3. Sequence Alignments and Phylogenetic Analysis

MUSCLE software was used to compare the amino acid sequences of the SBP gene family. To study the evolutionary relationship of SBP genes, a phylogenetic tree was constructed among passion fruit, Arabidopsis, grape, sorghum, and rice using MEGA (v6.0, Tokyo Metropolitan University, Hachioji, Tokyo, Japan) with the maximum likelihood method. The following parameters were used: JTT model, pairwise deletion, and the bootstrap test, which were replicated 1000 times. The phylogenetic tree was imported into the Interactive tree of life (iTOL, https://itol.embl.de/ (accessed on 12 December 2021)) [53].

4.4. Gene Structure and Conserved Motif Analysis

The Gene Structure Display Server (GSDS, http://gsds.gao-lab.org/https://itol.embl.de/ (accessed on 15 December 2021)) was used to determine the exon–intron structure of passion fruit SBP genes based on their genome DNA sequence and CDS sequence [54]. Then, the protein sequence of the passion fruit SBP gene family was submitted to the MEME online tool (https://meme-suite.org/meme https://itol.embl.de/ (accessed on 15 December 2021)) [55] for conserved motif prediction, and the number of motif discovery was set to 10 with default parameters. TBtools was used to visualize the prediction motif results of the SBP gene family in passion fruit [56].

4.5. Chromosomal Locations and Synteny Analysis

The 14 passion fruit SBP family genes were located on the chromosomes using the information annotated in the passion fruit genome. The physical location of PeSBPs on the chromosomes was visualized using Circos software (v0.69, http://www.circos.ca/ (accessed on 19 December 2021)). A synteny analysis of the SBP gene family in the passion fruit genome was conducted using MCScanX software (http://chibba.pgml.uga.edu/mcscan2 (accessed on 19 December 2021)). Circos software also was used to visually map synteny genes. The easy_Kaks calculation program (https://github.com/tangerzhang/FAFU-cgb/tree/master/easy_KaKs (accessed on 19 December 2021)) was used to calculate the non-synonymous (Ka), synonymous (Ks), and Ka/Ks substitution ratios of the homologous gene pairs of passion fruit and Arabidopsis to estimate the selection and substitution rates.

4.6. Cis-Elements Analysis of PeSBPs Promoters

The promoter sequence of PeSBP genes was 2 kb upstream of the transcriptional start site (ATG). The cis-elements of the promoter of the PeSBP genes were predicted using the Plant Cis-Acting Regulatory Element (PlantCARE, http://bioinformatics.psb.ugent.be/webtools/plantcare/html/ (accessed on 19 December 2021)) [57].

4.7. Expression Patterns Analysis

The RNA-sequencing data of the different floral tissues, including bract, sepal, corona filament, petal, stamen, stigma, and ovule, were obtained from China National GenBank (CNGB) (accession number CNP0002747), and the RNA-sequencing results of the root, flower, leaf, and seed tissues were downloaded from (https://ngdc.cncb.ac.cn/gsa/browse/CRA003773 (accessed on 19 December 2021)). The heatmap was then constructed using the pheatmap package of R software.

4.8. RNA Extraction and Quantitative Real-Time PCR

High-quality RNA was extracted using plant total RNA extraction kits (Omega Bio-Tek, Shanghai, China) and then reverse-transcribed into cDNA using a reverse transcription kit (TaKaRa, Beijing, China). A SYBR Premix Ex Taq kit (TaKaRa, Beijing, China) was used for qRT-PCR to verify the expression levels of each sample. Three replicates were designed for each sample, and the EF1a gene was used as a reference to calculate the relative expression levels of SBP genes in various tissues. Primers were designed to amplify sequences in PrimerQuest tools (Supplementary Materials Table S7).

4.9. PeSBPs Response to the Abiotic Stresses

Two-month-old passion fruit plants (variety in Tainong No. 1) in soil were analyzed in response to the abiotic stress treatment. For cold (4 °C) and heat (45 °C) stress, seedlings in soil were transferred to the incubator at 16/8 h, day/night. For salt and osmotic stress treatment, the passion fruit plants were first grown in the liquid ½MS medium for 7 days and then transferred to fresh liquid ½MS medium with 200 mM NaCl or 200 mM mannitol for stress treatment. Leaves were collected from at least three independent plants at 12 h, 24 h, and 48 h after treatment, and the controls were not subjected to any stress treatments. Three replicates were performed for each treatment. The collected samples were immediately stored in liquid nitrogen before total RNA extraction. The expression profiles of PeSBPs were detected using qRT-PCR.

4.10. Gene Ontology (GO) Enrichment Analysis

GO enrichment analysis was carried out using AgriGO (http://bioinfo.cau.edu.cn/agriGO/ (accessed on 1 November 2022)), and the result was visualized using R software (https://cran.r-project.org/web/packages/pheatmap/index.html (accessed on 1 November 2022)).

5. Conclusions

In the present study, a total of 14 SBP genes were identified in passion fruit. Based on the phylogenetic, gene structure, and conserved motifs analysis, all PeSBPs were classified into eight groups. The major gene expansion of the PeSBP gene family was segmental duplication and under negative selection. Cis-element analyses showed that PeSBPs responded to different stresses and plant hormones. In addition, the study of expression patterns under various stress types suggested that PeSBPs function across multiple stress responses. Taken together, our comprehensive analyses are helpful in selecting candidate SBP genes to further understand the classification and function of the SBP gene family in passion fruit.

Supplementary Materials

The supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/ijms232214153/s1.

Author Contributions

Y.L. performed the phylogenetic analysis and designed the figures; J.Y. annotated the genes on the chromosomes and conducted the evolution analysis; D.Z. and K.D. performed the qRT-PCR analysis; Y.H., G.C., and S.M. helped with the data analysis; Y.L. designed the research and performed the draft writing; and Y.Q. and L.W. revised the manuscript. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded and supported by the Natural Science Foundation of Guangxi (2022GXNSFBA035523), the China Postdoctoral Science Foundation (2022MD713731), the Guangxi Distinguished Experts Fellowship, the Science and Technology Innovation Project of Pingtan Science and Technology Research Institute (PT2021007, PT2021003) to YQ, the General Project of Guangxi Natural Science Foundation of Guangxi (2022GXNSFAA035535), the Science and Technology Development Fund of Guangxi Academy of Agricultural Sciences (Gui Nong Ke 2021JM10), Guangxi Academy of Agricultural Sciences Basic Research Project (Gui Nong Ke 2021YT046), and the National Modern Agricultural Industrial Technology System Guangxi Characteristic Fruit Innovation Team Passion Fruit Nanning Integrated test station (NYCYTXGXCXTD-17-02).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Not applicable.

Acknowledgments

We would like to thank the reviewers for their helpful comments on the original manuscript.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Amoutzias, G.D.; Veron, A.S.; Weiner, J.; Robinson-Rechavi, M.; Bornberg-Bauer, E.; Oliver, S.G.; Robertson, D.L. One billion years of bZIP transcription factor evolution: Conservation and change in dimerization and DNA-binding site specificity. Mol. Biol. Evol. 2007, 24, 827–835. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  2. Du, H.; Yang, S.S.; Liang, Z.; Feng, B.R.; Liu, L.; Huang, Y.B.; Tang, Y.X. Genome-wide analysis of the MYB transcription factor superfamily in soybean. BMC Plant Biol. 2012, 12, 106. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  3. Xiong, Y.Q.; Liu, T.Y.; Tian, C.G.; Sun, S.H.; Li, J.Y.; Chen, M.S. Transcription factors in rice: A genome-wide comparative analysis between monocots and eudicots. Plant Mol. Biol. 2005, 59, 191–203. [Google Scholar] [CrossRef] [PubMed]
  4. Guo, A.Y.; He, K.; Liu, D.; Bai, S.N.; Gu, X.C.; Wei, L.P.; Luo, J.C. DATF: A database of Arabidopsis transcription factors. Bioinformatics 2005, 21, 2568–2569. [Google Scholar] [CrossRef]
  5. Guo, A.Y.; Chen, X.; Gao, G.; Zhang, H.; Zhu, Q.H.; Liu, X.C.; Zhong, Y.F.; Gu, X.C.; He, K.; Luo, J.C. PlantTFDB: A comprehensive plant transcription factor database. Nucleic Acids Res. 2008, 36, D966–D969. [Google Scholar] [CrossRef] [Green Version]
  6. Yang, Z.F.; Wang, X.F.; Gu, S.L.; Hu, Z.Q.; Xu, H.; Xu, C.W. Comparative study of SBP-box gene family in Arabidopsis and rice. Gene 2008, 407, 1–11. [Google Scholar] [CrossRef]
  7. Yamasaki, K.; Kigawa, T.; Inoue, M.; Tateno, M.; Yamasaki, T.; Yabuki, T.; Aoki, M.; Seki, E.; Matsuda, T.; Nunokawa, E.; et al. A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors. J. Mol. Biol. 2004, 337, 49–63. [Google Scholar] [CrossRef]
  8. Hou, H.M.; Li, J.; Gao, M.; Singer, S.D.; Wang, H.; Mao, L.Y.; Fei, Z.J.; Wang, X.P. Genomic Organization, Phylogenetic Comparison and Differential Expression of the SBP-Box Family Genes in Grape. PLoS ONE 2013, 8, e59358. [Google Scholar] [CrossRef]
  9. Klein, J.; Saedler, H.; Huijser, P.J.M.-M.; Genetics, G.; Klein, J.; Saedler, H.; Huijser, P. A new family of DNA binding proteins includes putative transcriptional regulators of the Antirrhinum majus floral meristem identity gene SQUAMOSA. Mol. Gen. Genet. 1995, 250, 7–16. [Google Scholar]
  10. Cardon, G.H.; Hohmann, S.; Nettesheim, K.; Saedler, H.; Huijser, P. Functional analysis of the Arabidopsis thaliana SBP-box gene SPL3: A novel gene involved in the floral transition. Plant J. 1997, 12, 367–377. [Google Scholar] [CrossRef]
  11. Tripathi, R.K.; Goel, R.; Kumari, S.; Dahuja, A. Genomic organization, phylogenetic comparison, and expression profiles of the SPL family genes and their regulation in soybean. Dev. Genes Evol. 2017, 227, 101–119. [Google Scholar] [CrossRef] [PubMed]
  12. Chang, J.Z.; Yan, F.X.; Qiao, L.Y.; Zheng, J.; Zhang, F.Y.; Liu, Q.S. Genome-wide identification and expression analysis of SBP-box gene family in Sorghum bicolor L. Yi Chuan 2016, 38, 569–580. [Google Scholar] [CrossRef] [PubMed]
  13. Li, C.; Lu, S. Molecular characterization of the SPL gene family in Populus trichocarpa. BMC Plant Biol. 2014, 14, 131. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  14. Zhang, H.X.; Jin, J.H.; He, Y.M.; Lu, B.Y.; Li, D.W.; Chai, W.G.; Khan, A.; Gong, Z.H. Genome-Wide Identification and Analysis of the SBP-Box Family Genes under Phytophthora capsici Stress in Pepper (Capsicum annuum L.). Front. Plant Sci. 2016, 7, 504. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  15. Hultquist, J.F.; Dorweiler, J.E. Feminized tassels of maize mop1 and ts1 mutants exhibit altered levels of miR156 and specific SBP-box genes. Planta 2008, 229, 99–113. [Google Scholar] [CrossRef]
  16. Salinas, M.; Xing, S.; Hohmann, S.; Berndtgen, R.; Huijser, P. Genomic organization, phylogenetic comparison and differential expression of the SBP-box family of transcription factors in tomato. Planta 2012, 235, 1171–1184. [Google Scholar] [CrossRef]
  17. Lannenpaa, M.; Janonen, I.; Holtta-Vuori, M.; Gardemeister, M.; Porali, I.; Sopanen, T. A new SBP-box gene BpSPL1 in silver birch (Betula pendula). Physiol. Plant. 2004, 120, 491–500. [Google Scholar] [CrossRef]
  18. Unte, U.S.; Sorensen, A.-M.; Pesaresi, P.; Gandikota, M.; Leister, D.; Saedler, H.; Huijser, P. SPL8, an SBP-Box Gene That Affects Pollen Sac Development in Arabidopsis. Plant Cell 2003, 15, 1009–1019. [Google Scholar] [CrossRef] [Green Version]
  19. Zhang, B.; Xu, W.N.; Liu, X.; Mao, X.G.; Li, A.; Wang, J.Y.; Chang, X.P.; Zhang, X.Y.; Jing, R.L. Functional Conservation and Divergence among Homoeologs of TaSPL20 and TaSPL21, Two SBP-Box Genes Governing Yield-Related Traits in Hexaploid Wheat. Plant Physiol. 2017, 174, 1177–1191. [Google Scholar] [CrossRef] [Green Version]
  20. Cui, L.; Zheng, F.Y.; Wang, J.F.; Zhang, C.L.; Xiao, F.M.; Ye, J.; Li, C.X.; Ye, Z.B.; Zhang, J.H. miR156a-targeted SBP-Box transcription factor SlSPL13 regulates inflorescence morphogenesis by directly activating SFT in tomato. Plant Biotechnol. J. 2020, 18, 1670–1682. [Google Scholar] [CrossRef] [Green Version]
  21. Luo, L.; Li, W.Q.; Miura, K.; Ashikari, M.; Kyozuka, J. Control of Tiller Growth of Rice by OsSPL14 and Strigolactones, Which Work in Two Independent Pathways. Plant Cell Physiol. 2012, 53, 1793–1801. [Google Scholar] [CrossRef] [PubMed]
  22. Wang, S.K.; Wu, K.; Yuan, Q.B.; Liu, X.Y.; Liu, Z.B.; Lin, X.Y.; Zeng, R.Z.; Zhu, H.T.; Dong, G.J.; Qian, Q.; et al. Control of grain size, shape and quality by OsSPL16 in rice. Nat. Genet. 2012, 44, 950–954. [Google Scholar] [CrossRef] [PubMed]
  23. Ning, K.; Chen, S.; Huang, H.J.; Jiang, J.; Yuan, H.M.; Li, H.Y. Molecular characterization and expression analysis of the SPL gene family with BpSPL9 transgenic lines found to confer tolerance to abiotic stress in Betula platyphylla Suk. Plant Cell Tissue Organ Cult. 2017, 130, 469–481. [Google Scholar] [CrossRef]
  24. Ortiz, D.C.; Bohorquez, A.; Duque, M.C.; Tohme, J.; Cuellar, D.; Vasquez, T.M. Evaluating purple passion fruit (Passiflora edulis Sims f. edulis) genetic variability in individuals from commercial plantations in Colombia. Genet. Resour. Crop. Evol. 2012, 59, 1089–1099. [Google Scholar] [CrossRef]
  25. Araya, S.; Martins, A.M.; Junqueira, N.T.V.; Costa, A.M.; Faleiroa, F.G.; Ferreira, M.E. Microsatellite marker development by partial sequencing of the sour passion fruit genome (Passiflora edulis Sims). BMC Genom. 2017, 18, 549. [Google Scholar] [CrossRef] [Green Version]
  26. Williams, N. Passion flowers. Curr. Biol. 2003, 13, R750–R751. [Google Scholar] [CrossRef] [Green Version]
  27. Santos, E.A.; Souza, M.M.; Abreu, P.P.; da Conceicao, L.D.H.C.S.; Araujo, I.S.; Viana, A.P.; de Almeida, A.A.F.; Freitas, J.C.D. Confirmation and characterization of interspecific hybrids of Passiflora L. (Passifloraceae) for ornamental use. Euphytica 2012, 184, 389–399. [Google Scholar] [CrossRef]
  28. Ma, D.N.; Dong, S.S.; Zhang, S.C.; Wei, X.Q.; Xie, Q.J.; Ding, Q.S.; Xia, R.; Zhang, X.T. Chromosome-level reference genome assembly provides insights into aroma biosynthesis in passion fruit (Passiflora edulis). Mol. Ecol. Resour. 2021, 21, 955–968. [Google Scholar] [CrossRef]
  29. Xia, Z.Q.; Huang, D.M.; Zhang, S.K.; Wang, W.Q.; Ma, F.N.; Wu, B.; Xu, Y.; Xu, B.Q.; Chen, D.; Zou, M.L.; et al. Chromosome-scale genome assembly provides insights into the evolution and flavor synthesis of passion fruit (Passiflora edulis Sims). Hortic Res. 2021, 8, 14. [Google Scholar] [CrossRef]
  30. Liu, Y.H.; Aslam, M.; Yao, L.A.; Zhang, M.; Wang, L.L.; Chen, H.H.; Huang, Y.M.; Qin, Y.; Niu, X.P. Genomic analysis of SBP gene family in Saccharum spontaneum reveals their association with vegetative and reproductive development. BMC Genom. 2021, 22, 767. [Google Scholar] [CrossRef]
  31. Li, L.; Shi, F.; Wang, Y.; Yu, X.; He, G.J.P.S. TaSPL13 regulates inflorescence architecture and development in transgenic wheat (Triticum aestivum L.). Plant Sci. 2020, 296, 110516. [Google Scholar] [CrossRef] [PubMed]
  32. Fujita, Y.; Fujita, M.; Satoh, R.; Maruyama, K.; Parvez, M.M.; Seki, M.; Hiratsu, K.; Ohme-Takagi, M.; Shinozaki, K.; Yamaguchi-Shinozaki, K. AREB1 is a transcription activator of novel ABRE-dependent ABA signaling that enhances drought stress tolerance in Arabidopsis. Plant Cell 2005, 17, 3470–3488. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  33. Yamaguchi-Shinozaki, K.; Shinozaki, K. Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annu. Rev. Plant Biol. 2006, 57, 781–803. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  34. Xu, M.L.; Hu, T.Q.; Zhao, J.F.; Park, M.Y.; Earley, K.W.; Wu, G.; Yang, L.; Poethig, R.S. Developmental Functions of miR156-Regulated SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) Genes in Arabidopsis thaliana. PLoS Genet. 2016, 12, e1006263. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  35. Cerqueira-Silva, C.B.M.; Jesus, O.N.; Santos, E.S.L.; Correa, R.X.; Souza, A.P. Genetic Breeding and Diversity of the Genus Passiflora: Progress and Perspectives in Molecular and Genetic Studies. Int. J. Mol. Sci. 2014, 15, 14122–14152. [Google Scholar] [CrossRef] [Green Version]
  36. Liu, M.Y.; Sun, W.J.; Ma, Z.T.; Huang, L.; Wu, Q.; Tang, Z.Z.; Bu, T.L.; Li, C.L.; Chen, H. Genome-wide identification of the SPL gene family in Tartary Buckwheat (Fagopyrum tataricum) and expression analysis during fruit development stages. BMC Plant Biol. 2019, 19, 299. [Google Scholar] [CrossRef] [Green Version]
  37. Corrêa, L.; Riaño-Pachón, D.; Schrago, C.G.; Santos, R.; Mueller-Roeber, B.; Vincentz, M.J.P.O. The Role of bZIP Transcription Factors in Green Plant Evolution: Adaptive Features Emerging from Four Founder Genes. PLoS ONE 2008, 3, e2944. [Google Scholar] [CrossRef]
  38. Xie, K.; Wu, C.; Xiong, L. Genomic Organization, Differential Expression, and Interaction of SQUAMOSA Promoter-Binding-Like Transcription Factors and microRNA156 in Rice. Plant Physiol. 2006, 142, 280–293. [Google Scholar] [CrossRef] [Green Version]
  39. Liu, Y.; Chai, M.; Zhang, M.; He, Q.; Qin, Y.J.I.J.o.G. Genome-Wide Analysis, Characterization, and Expression Profile of the Basic Leucine Zipper Transcription Factor Family in Pineapple. J. Genom. 2020, 2020, 3165958. [Google Scholar] [CrossRef]
  40. Du, H.; Feng, B.R.; Yang, S.S.; Huang, Y.B.; Tang, Y.X. The R2R3-MYB Transcription Factor Gene Family in Maize. PLoS ONE 2012, 7, e37463. [Google Scholar] [CrossRef] [Green Version]
  41. Koonin, E.V. Orthologs, paralogs, and evolutionary genomics. Annu. Rev. Genet. 2005, 39, 309–338. [Google Scholar] [CrossRef] [PubMed]
  42. Gandikota, M.; Birkenbihl, R.P.; Hohmann, S.; Cardon, G.H.; Saedler, H.; Huijser, P. The miRNA156/157 recognition element in the 3′ UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings. Plant J. 2007, 49, 683–693. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  43. Zhang, Y.; Schwarz, S.; Saedler, H.; Huijser, P. SPL8, a local regulator in a subset of gibberellin-mediated developmental processes in Arabidopsis. Plant Mol. Biol. 2007, 63, 429. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  44. Jung, J.H.; Seo, P.J.; Kang, S.K.; Park, C.M. miR172 signals are incorporated into the miR156 signaling pathway at the SPL3/4/5 genes in Arabidopsis developmental transitions. Plant Mol. Biol. 2011, 76, 35–45. [Google Scholar] [CrossRef] [PubMed]
  45. Yu, S.; Lian, H.; Wang, J.W. Plant developmental transitions: The role of microRNAs and sugars. Curr. Opin. Plant Biol. 2015, 27, 1–7. [Google Scholar] [CrossRef] [PubMed]
  46. Padmanabhan, M.S.; Ma, S.; Burch-Smith, T.M.; Czymmek, K.; Huijser, P.; Dinesh-Kumar, S.P. Novel positive regulatory role for the SPL6 transcription factor in the N TIR-NB-LRR receptor-mediated plant innate immunity. PLoS Pathog. 2013, 9, e1003235. [Google Scholar] [CrossRef] [Green Version]
  47. Wu, G.; Poethig, R.S. Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3. Development 2006, 133, 3539–3547. [Google Scholar] [CrossRef] [Green Version]
  48. Shikata, M.; Koyama, T.; Mitsuda, N.; Ohme-Takagi, M. Arabidopsis SBP-box genes SPL10, SPL11 and SPL2 control morphological change in association with shoot maturation in the reproductive phase. Plant Cell Physiol. 2009, 50, 2133–2145. [Google Scholar] [CrossRef] [Green Version]
  49. Chao, L.M.; Liu, Y.Q.; Chen, D.Y.; Xue, X.Y.; Mao, Y.B.; Chen, X.Y. Arabidopsis Transcription Factors SPL1 and SPL12 Confer Plant Thermotolerance at Reproductive Stage. Mol. Plant 2017, 10, 735–748. [Google Scholar] [CrossRef]
  50. El-Gebali, S.; Mistry, J.; Bateman, A.; Eddy, S.R.; Luciani, A.; Potter, S.C.; Qureshi, M.; Richardson, L.J.; Salazar, G.A.; Smart, A.; et al. The Pfam protein families database in 2019. Nucleic Acids Res. 2019, 47, D427–D432. [Google Scholar] [CrossRef]
  51. Artimo, P.; Jonnalagedda, M.; Arnold, K.; Baratin, D.; Csardi, G.; de Castro, E.; Duvaud, S.; Flegel, V.; Fortier, A.; Gasteiger, E.; et al. ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res. 2012, 40, W597–W603. [Google Scholar] [CrossRef] [PubMed]
  52. Pierleoni, A.; Martelli, P.L.; Fariselli, P.; Casadio, R. BaCelLo: A balanced subcellular localization predictor. Bioinformatics 2006, 22, e408–e416. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  53. Letunic, I.; Bork, P. Interactive Tree Of Life (iTOL) v4: Recent updates and new developments. Nucleic Acids Res. 2019, 47, W256–W259. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  54. Hu, B.; Jin, J.; Guo, A.Y.; Zhang, H.; Luo, J.; Gao, G. GSDS 2.0: An upgraded gene feature visualization server. Bioinformatics 2015, 31, 1296–1297. [Google Scholar] [CrossRef] [Green Version]
  55. Bailey, T.L.; Boden, M.; Buske, F.A.; Frith, M.; Grant, C.E.; Clementi, L.; Ren, J.; Li, W.W.; Noble, W.S. MEME SUITE: Tools for motif discovery and searching. Nucleic Acids Res. 2009, 37, W202–W208. [Google Scholar] [CrossRef]
  56. Chen, C.; Chen, H.; Zhang, Y.; Thomas, H.R.; Frank, M.H.; He, Y.; Xia, R. TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data. Mol. Plant 2020, 13, 1194–1202. [Google Scholar] [CrossRef]
  57. Lescot, M.; Dehais, P.; Thijs, G.; Marchal, K.; Moreau, Y.; Van de Peer, Y.; Rouze, P.; Rombauts, S. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 2002, 30, 325–327. [Google Scholar] [CrossRef]
Ijms 23 14153 g001 550
Figure 1. Multiple sequence alignment of SBP domains of PeSBP proteins. The darkblue, purple, and lightblue backgrounds indicate entire conservative residues, 75% conservative residues, and 50% conservative residues respectively.
Figure 1. Multiple sequence alignment of SBP domains of PeSBP proteins. The darkblue, purple, and lightblue backgrounds indicate entire conservative residues, 75% conservative residues, and 50% conservative residues respectively.
Ijms 23 14153 g001
Ijms 23 14153 g002 550
Figure 2. The evolutionary relationship of the SBP gene family of 18 species among seven lineages. Different green plant families are distinguished by different backgrounds.
Figure 2. The evolutionary relationship of the SBP gene family of 18 species among seven lineages. Different green plant families are distinguished by different backgrounds.
Ijms 23 14153 g002
Ijms 23 14153 g003 550
Figure 3. Phylogenetic tree of SBP family proteins among passion fruit, rice, Arabidopsis, grape, and sorghum. Pe, Passiflora edulis Sims; Os, Oryza sativa; AT, Arabidopsis thaliana; Vv, Vitis vinifera; and Sb, Sorghum bicolor.
Figure 3. Phylogenetic tree of SBP family proteins among passion fruit, rice, Arabidopsis, grape, and sorghum. Pe, Passiflora edulis Sims; Os, Oryza sativa; AT, Arabidopsis thaliana; Vv, Vitis vinifera; and Sb, Sorghum bicolor.
Ijms 23 14153 g003
Ijms 23 14153 g004 550
Figure 4. The exon–intron structure of SBP genes in passion fruit. The yellow round-corner rectangle represents CDS, the black shrunk line represents introns, and the green round-corner rectangle represents UTR.
Figure 4. The exon–intron structure of SBP genes in passion fruit. The yellow round-corner rectangle represents CDS, the black shrunk line represents introns, and the green round-corner rectangle represents UTR.
Ijms 23 14153 g004
Ijms 23 14153 g005 550
Figure 5. Distribution of the conserved motifs in passion fruit SBP proteins. Ten identified conserved motifs are marked in different colored boxes.
Figure 5. Distribution of the conserved motifs in passion fruit SBP proteins. Ten identified conserved motifs are marked in different colored boxes.
Ijms 23 14153 g005
Ijms 23 14153 g006 550
Figure 6. Synteny analysis of the SBP genes from passion fruit and Arabidopsis. The red lines indicate SBP gene pairs within passion fruit, and the blue lines indicate SBP gene pairs between passion fruit and Arabidopsis. Chr indicates the chromosome of Arabidopsis, and LG and contig indicate the chromosome of passion fruit.
Figure 6. Synteny analysis of the SBP genes from passion fruit and Arabidopsis. The red lines indicate SBP gene pairs within passion fruit, and the blue lines indicate SBP gene pairs between passion fruit and Arabidopsis. Chr indicates the chromosome of Arabidopsis, and LG and contig indicate the chromosome of passion fruit.
Ijms 23 14153 g006
Ijms 23 14153 g007 550
Figure 7. The expression pattern and qRT-PCR results of SBP genes in passion fruit. (A) Expression patterns of SBP genes in different tissues and different development stages based on the transcriptome data. br, bract; se, sepal; pe, petal; ca, corona filament; st, stamen; sg, stigma; and ov, ovule. The number represents different stages: 1 and 2 represent early stage, while 7 and 8 represent late stage. (B) Expression patterns of SBP genes in different tissues in the seed, root, leaf, and flower. The red color bar indicates high expression patterns, and the blue color bar indicates low expression. (C) Validation of 5 randomly selected PeSBP genes by qRT-PCR. The yellow line indicates the expression trend in four tissues.
Figure 7. The expression pattern and qRT-PCR results of SBP genes in passion fruit. (A) Expression patterns of SBP genes in different tissues and different development stages based on the transcriptome data. br, bract; se, sepal; pe, petal; ca, corona filament; st, stamen; sg, stigma; and ov, ovule. The number represents different stages: 1 and 2 represent early stage, while 7 and 8 represent late stage. (B) Expression patterns of SBP genes in different tissues in the seed, root, leaf, and flower. The red color bar indicates high expression patterns, and the blue color bar indicates low expression. (C) Validation of 5 randomly selected PeSBP genes by qRT-PCR. The yellow line indicates the expression trend in four tissues.
Ijms 23 14153 g007
Ijms 23 14153 g008 550
Figure 8. The distribution of cis-acting elements identified in the 2000-bp upstream promoter region of PeSBP genes.
Figure 8. The distribution of cis-acting elements identified in the 2000-bp upstream promoter region of PeSBP genes.
Ijms 23 14153 g008
Ijms 23 14153 g009 550
Figure 9. The relative expression levels of seven SBP genes in response to different stress treatments in passion fruit. Significant differences between samples labeled a, b, c, and d were determined by one-way ANOVA, p < 0.05.
Figure 9. The relative expression levels of seven SBP genes in response to different stress treatments in passion fruit. Significant differences between samples labeled a, b, c, and d were determined by one-way ANOVA, p < 0.05.
Ijms 23 14153 g009
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Share and Cite

MDPI and ACS Style

Liu, Y.; Yuan, J.; Zhang, D.; Deng, K.; Chai, G.; Huang, Y.; Ma, S.; Qin, Y.; Wang, L. Genome-Wide Identification and Characterization of the SBP Gene Family in Passion Fruit (Passiflora edulis Sims). Int. J. Mol. Sci. 2022, 23, 14153. https://doi.org/10.3390/ijms232214153

AMA Style

Liu Y, Yuan J, Zhang D, Deng K, Chai G, Huang Y, Ma S, Qin Y, Wang L. Genome-Wide Identification and Characterization of the SBP Gene Family in Passion Fruit (Passiflora edulis Sims). International Journal of Molecular Sciences. 2022; 23(22):14153. https://doi.org/10.3390/ijms232214153

Chicago/Turabian Style

Liu, Yanhui, Jieyu Yuan, Dan Zhang, Kao Deng, Gaifeng Chai, Youmei Huang, Suzhuo Ma, Yuan Qin, and Lulu Wang. 2022. "Genome-Wide Identification and Characterization of the SBP Gene Family in Passion Fruit (Passiflora edulis Sims)" International Journal of Molecular Sciences 23, no. 22: 14153. https://doi.org/10.3390/ijms232214153

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop