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Article

Genome-Wide Analysis of the SAUR Gene Family and Its Expression Profiles in Response to Salt Stress in Santalum album

by
Qing Zhu
1,†,
Haoyue Zheng
1,†,
Xu Hu
1,†,
Yi Liu
1,
Xinyi Zheng
1,
Libei Li
2,* and
Minqiang Tang
1,*
1
Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Collaborative Innovation Center of Ecological Civilization, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
2
College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou 311300, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Plants 2024, 13(10), 1286; https://doi.org/10.3390/plants13101286
Submission received: 10 April 2024 / Revised: 1 May 2024 / Accepted: 5 May 2024 / Published: 7 May 2024
(This article belongs to the Special Issue Crop Functional Genomics and Biological Breeding)
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Abstract

:
The SAUR (small auxin-up RNA) family constitutes a category of genes that promptly respond to the hormone auxin and play a pivotal role in diverse biological processes encompassing plant growth and the response to abiotic stress. Santalum album L., a semi-parasitic evergreen tree, is renowned for its economically valuable essential oils, positioning it among the most prized tree species. In this study, a meticulous identification and comprehensive analysis of 43 SAUR genes was conducted within S. album. Based on phylogenetic relationships, the SaSAUR genes were systematically categorized into five groups. A collinearity analysis revealed intriguing insights, disclosing 14 segmental duplications and 9 tandem duplications within the SaSAUR genes, emphasizing the pivotal role of duplication in the expansion of this gene family. Noteworthy variations in the expression levels of SaSAUR genes were observed by delving into the SaSAUR transcriptome data from various tissues, including leaves, roots, and heartwood, as well as under salt-stress conditions. Notably, SaSAUR08 and SaSAUR13 were significantly upregulated in heartwood compared with roots and leaves, while SaSAUR18 was markedly more expressed in roots compared with heartwood and leaves. Furthermore, SaSAUR27 and SaSAUR28 were found to respond closely to salt stress, hinting at their potential involvement in the salt-stress response mechanism. This research offers a comprehensive investigation of SAUR genes in S. album and establishes a foundation for future exploration of the SAUR gene family, particularly its relation to growth and salt-stress responses.

1. Introduction

Santalum album L. is an evergreen semi-parasitic tree belonging to the Santalum genus in the Santalaceae family and is mainly distributed in Southeast Asia and the Pacific region [1]. As S. album is one of the tree species with remarkable economic worth, all its parts can be utilized as raw materials. The heartwood oil is renowned for its unique aroma [2] and has vital roles as an anti-cancer [3], anti-inflammatory [4], and antioxidative substance [5]. Therefore, it has widespread application in various industries, including in perfumery, pharmaceuticals, cosmetics, etc. Heartwood oil is often referred to as “liquid gold” [6]. S. album’s heartwood possesses a remarkable hardness and a beautiful texture, making it one of the important raw materials for wood carving and the production of expensive furniture [7]. Therefore, S. album currently stands as one of the most widely commercially developed and utilized tropical tree species. In recent years, the demand for its heartwood and sandalwood essential oils has been increasing in both domestic and foreign markets; however, the growth rate and heartwood formation of S. album is relatively slow. Consequently, the prices of S. album have risen dramatically, leading to the overexploitation of this resource [8]. Therefore, proper cultivation and protection management measures of the sandalwood tree is of the utmost need at this time [9].
SAUR (small auxin-up RNA) belongs to one of the three major early auxin-response genes [10]. Early auxin-response genes can be rapidly activated and transcribed upon auxin induction without the need for new protein synthesis. Moreover, the molecular weights of the proteins encoded by SAUR genes are generally small, ranging from 9–30 kDa [11]. Auxin, as the earliest discovered plant hormone, can promote rooting, regulate shoot development, and control cell division and differentiation [12]. It plays a crucial role in plant growth and stress resistance [13]. The SAUR genes were first discovered in soybean hypocotyls that were stimulated to elongate by auxin [14]. Subsequently, SAURs have been found in a variety of plants, including Arabidopsis (Arabidopsis thaliana) [15], rice (Oryza sativa) [16], sorghum (Sorghum bicolor) [17], and pineapple (Ananas comosus) [18]. Among the early auxin-responsive genes, the SAUR gene family has the largest number of genes and a high degree of structural similarity [19]. Most SAURs contain only one exon and no introns. They are found in clusters on the chromosome, indicating that high frequencies of tandem and segmental duplications have occurred during evolution [20]. Auxin regulates gene expression by the binding of auxin response factor (ARF) to auxin response elements (AuxREs) in the promoter region of auxin-responsive genes [21]. The number and diversity of AuxREs in different SAURs vary significantly. Nine AuxREs have been identified in rice [16] and seven in tomato [22]. The mRNA encoded by the SAURs is highly unstable due to the presence of a conserved downstream element (DST) in its 3′ untranslated region (3′ UTR) [23]. This instability reduces the association between auxin and their regulated SAUR genes.
The SAUR gene family is involved in multiple processes in plants, i.e., plant growth and development. It plays an important role in responding to changes in auxins [24], affecting their synthesis and transport, as well as cell elongation and senescence resistance [25]. In Arabidopsis thaliana, overexpression of the AtSAUR36 [26] and AtSAUR41 [27] genes results in the significant elongation of hypocotyl epidermal cells, while the AtSAUR36 gene responds to leaf senescence [28]. The SAUR gene family is involved in abiotic stress tolerance [29], and many SAUR genes are down-regulated under abiotic stress as an adaptation to adverse environments [30]. In the model species Arabidopsis thaliana, seedlings from AtSAUR41 overexpression lines showed higher sensitivity to salt stress, while the AtSAUR41 subfamily of genes was found to be associated with salt tolerance [31]. In the perennial plant Medicago sativa, several SAUR genes have been associated with abiotic-stress tolerance. Specifically, MsSAUR14, MsSAUR94, MsSAUR297, MsSAUR306, and MsSAUR254 respond to both drought and salinity stress [32]. In Glycine max, it was discovered that GmSAUR299 may be related to drought tolerance [33]. In poplar, the PagWOX11/12a proteins directly bind to the promoter of the SAUR36 gene, while enhanced binding is observed under salt stress, thereby improving the salt tolerance [34]. Expression of the poplar genes PtSAUR12, PtSAUR34, PtSAUR54, PtSAUR67, PtSAUR91, and PtSAUR97 was up-regulated at low temperatures [35]. These findings reflect the significant role of the SAUR gene family in different plants and trees; however, a comprehensive genome-wide identification of the SAUR gene family in S. album has yet to be documented.
In this study, bioinformatics methods were employed to identify the members of the SAUR gene family in S. album, while also delving into their molecular characteristics, chromosomal distribution patterns, gene structures, conserved motifs, and their evolutionary and functional intricacies. Leveraging transcriptome data, we further investigated the expression profiles of SAUR genes across various tissues, including heartwood, root, and leaf, as well as their response to salt stress. In conclusion, this study provides valuable resource information for understanding the regulatory roles of SAUR gene family members in S. album’s growth and stress tolerance.

2. Materials and Methods

2.1. Identification of SAUR Genes and Chromosomal Distribution

A hidden Markov model profile of the SAUR DNA-binding domain (PF00642) was downloaded from the Pfam database (http://pfam.xfam.org/) [36]. The whole genome sequence and annotation files of S. album employed in this study were downloaded from the National Genomics Data Center of China under accession number GWHCBHT00000000, which is publicly accessible at https://ngdc.cncb.ac.cn/gwh/Assembly/37800/show (accessed on 9 December 2023). The initial members of the SAUR gene family were identified in the genome sequence of S. album through an HMM search (E < 1 × 10−5) [37]. Subsequently, we utilized the SMART (http://smart.embl.de/smart/batch.pl/, accessed on 11 December 2023) [38] and CDD online websites (https://www.ncbi.nlm.nih.gov/cdd/, accessed on 11 December 2023) [39] to meticulously screen the initial family members for any potential redundancy. The distribution of SAUR proteins on chromosomes was mapped using the MapChart version 5.4.6 software based on the data from the S. album genome annotation files [40]. The SAUR genes of S. album were renamed based on their chromosomal location, following the nomenclature of the Arabidopsis thaliana SAUR gene family members [41].

2.2. Phylogenetic Analysis and Classification of SAUR Genes

Firstly, the protein sequences of the SAUR gene family members of Arabidopsis thaliana were downloaded from the TAIR database website (http://www.arabidopsis.org/, accessed on 1 December 2023). Subsequently, multiple sequence alignment was performed on SAUR proteins from A. thaliana and S. album using the MAFFT version 7 software [42]. The resulting alignment was then used to construct a phylogenetic tree using the IQ-TREE version 2 software and the maximum likelihood (ML) method [43]. The phylogenetic tree was bootstrapped 1000 times with default parameters, resulting in the final phylogenetic tree file. The phylogenetic tree was uploaded to the iTOL website (https://itol.embl.de) for visualization and information annotation [44]. The SAUR gene family members of S. album were classified based on the branch clustering of the phylogenetic tree.

2.3. Gene Duplication and Analysis of Protein Properties

The Multiple Collinearity Scan toolkit X version 1 (MCScanX) [45] with default parameters was used to identify gene duplications, which were then visualized by using the One Step MCScanX tool in TBtools [46]. Non-synonymous substitutions (Ka) and synonymous substitutions (Ks) were determined for each duplicated SAUR gene pair using the KaKs_Calculator 2.0 [47]. The length of amino acids, theoretical isoelectric point (pI), and molecular weight of the SAUR proteins were analyzed using the online tool ExPASy (https://web.expasy.org/protparam/, accessed on 13 December 2023) [48]. The subcellular localization of the SAUR proteins was predicted using the Plant-mPLoc predictor (http://www.csbio.sjtu.edu.cn/bioinf/plant-multi/, accessed on 13 December 2023) [49]. Conserved motifs in the S. album SAUR proteins were identified using the online software Multiple Em for Motif Elicitation (MEME) suite 5.5.5 (https://meme-suite.org/meme/tools/streme, accessed on 13 December 2023), with a maximum of 10 motifs [50]. Additionally, we extracted exon and intron positions from the S. album genome annotation file. We used the TBtools Gene Structural View (Advanced) [46] to visualize the identified conserved motifs and gene structures.

2.4. Transcriptome Data and Expression of SAUR Genes

To analyze the gene functions in growth and development, we downloaded the transcriptome data for various S. album tissues (PRJNA243306, PRJNA360335, PRJNA192417) from the NCBI (National Center for Biotechnology Information, http://www.ncbi.nlm.nih.gov/, accessed on 1 December 2023). To investigate the mechanism of the salt-stress response in S. album mediated by the SAUR genes, approximately 50 cm tall sandalwood seedlings were treated with 50 mmol/L and 100 mmol/L NaCl solutions, while the blank control group was treated with an aqueous solution. The third or fourth fully stretched leaf samples were taken at 0, 12, 24, and 48 h intervals. All seedlings were placed under controlled growth conditions in an artificial climate chamber set at a constant temperature of 26 °C and 50% relative humidity, with 16 h of light exposure (200 μmol photons m−2 s−1, 26 °C) and 8 h in the dark. The experiment was repeated three times, resulting in a total of 36 samples. All the samples were collected, directly frozen in liquid nitrogen, and stored at −80 °C for RNA extraction. Total RNA was extracted from the leaves of each treatment using the TRIzol reagent. The RNA quality and quantity were checked using an Agilent 2100 Bioanalyzer, and then cDNA libraries were constructed. These libraries were sequenced using the Illumina platform at the Novogene Bioinformatics Technology Co., Ltd. (Beijing, China). To ensure data quality, all RNA sequence data were filtered using Fastp with default parameters [51]. Subsequently, the reads were aligned with the cultivated sandalwood reference genome using the HISAT2 version 2.1.0 software with default parameters [52]. To assess the expression levels of individual genes, the fragments per kilobase per million mapped reads (FPKM) of each gene was quantified by FeatureCounts [53]. Subsequently, differentially expressed genes (DEGs) were identified using the DESeq2 package in R, with a stringent false discovery rate (FDR) threshold of ≤0.05 and a |log2 FC| ≥ 1 criterion to establish statistically significant differences in gene expression [54].

2.5. Real-Time Quantitative PCR Analysis

Total RNA was extracted using the TRIzol reagent, with subsequent removal of trace amounts of genomic DNA using the RNase-free DNase I method (RNase-free; TakaRa). According to the manufacturer’s protocol, the first-strand cDNA was synthesized using a PrimerScript RT MasterMix (Takara, Kusatsu, Japan). The Primer3 web (version 4.1.1) software was used to design RT-qPCR gene-specific primers (Supplementary Table S4), and the primer sequences were synthesized by Shanghai Biosune Platinum Bio-Technology Co. (Shanghai, China) Primers SaSAUR27-1 and SaSAUR28-4 were used in the final data analysis. The data of relative gene expression were analyzed using the 2−ΔΔCT method, with the actin gene (GI:156972025) of S. album as the internal reference to account for differences. There were three biological and three technical replicates performed for each sample. We used the GraphPad Prism version 8 software for statistical analysis and data visualization.

3. Results

3.1. Identification and Analysis of Physicochemical Properties of the SAUR Genes

The conserved domains in the SAUR proteins of S. album were validated using the SMART and CDD databases, resulting in the identification of 43 SAUR genes (Supplementary File S1). The physical locations of the SAUR genes on the chromosomes were determined by querying the genome annotation files and were named SaSAUR01 to SaSAUR43 sequentially (Table 1). The physicochemical characteristics of the 43 identified SAUR proteins were examined using the ExPASy program. The study revealed that the length of these proteins ranged from 75 (SaSAUR15) to 434 (SaSAUR01) amino acids, and their molecular weight ranged from 8.32 to 48.35 kDa. The average isoelectric point (pI) of all the SAUR proteins was calculated to be 8.37, and ranged from 4.45 (SaSAUR28) to 11.16 (SaSAUR08) (Table 1). Notably, one-quarter of the SAUR proteins were classified as acidic because their isoelectric point (pI) values were below 7, while the remaining three-quarters were alkaline (Table 1). The subcellular localization analysis of SAUR genes using Plant-mPLoc revealed that most SAUR genes were predicted to be located in chloroplasts. The remaining SAUR genes were predicted to be distributed in the nucleus, while only the SaSAUR36 gene was predicted to be located in the cytoplasm (Table 1). A thorough examination of the physicochemical characteristics and subcellular localization of the identified SAUR proteins was conducted in detail to gain deeper insight into their functions in S. album.

3.2. Gene Structure and Phylogenetic Analysis of SaSAUR Genes

A phylogenetic tree was constructed for the SAUR proteins from Santalum album and Arabidopsis thaliana using MAFFT version 7 and IQ-TREE version 2 software. The results of the phylogenetic tree revealed that sandalwood SAUR genes could be classified into five groups. The study found that there was a total of 43 SAUR proteins, with one in Group I, four in Group II, five in Group III, ten in Group IV, and twenty-one in Group V. Additionally, there were two SAUR genes that could not be classified into any of the groups (Figure 1). Group V had the highest number of family members, while Group I had the lowest. In all groups, the number of SAUR genes in A. thaliana exceeded that in S. album. However, it is worth noting that the number of SAUR genes in Group V approximates that in A. thaliana, with 28 in A. thaliana and 20 in S. album. The conserved motifs, conserved domains, and exon–intron structure were analyzed to explore the structural diversity of SaSAURs (Figure 2). The online MEME tool identified 10 conserved motifs (motif 1 to motif 10) in SAUR proteins (Figure 2B). Motifs 1, 2, and 3 were widely distributed among the SAUR gene family in the order of 2–1–3, indicating strong conservation of the conserved domains of the SAUR gene family in S. album. Only SaSAUR15, SaSAUR21, SaSAUR24, and SaSAUR28 do not contain motif 2. SaSAUR15 and SaSAUR24 do not have motif 1, while SaSAUR09, SaSAUR10, and SaSAUR19 do not have motif 3. However, some motifs are unique to specific SAUR genes. For instance, motif 5 and motif 7 were exclusively found in SaSAUR26 and SaSAUR27; motif 9 was identified in SaSAUR19 and SaSAUR22; motif 6 was observed in SaSAUR10, SaSAUR12, and SaSAUR37; and motif 8 was specifically present in SaSAUR03, SaSAUR07, and SaSAUR08. Members of the same group, such as SaSAUR32 and SaSAUR34, SaSAUR04 and SaSAUR06, and SaSAUR26 and SaSAUR27, exhibited similar motif patterns (Figure 2B). This indicates that they likely share similar functions. All SaSAUR genes contain conserved auxin domains, as shown in Figure 2C. In Figure 2D, the exon–intron structure of the SaSAURs clearly verify the diversity of the gene structures. The 43 SaSAUR genes exhibited different numbers of exons, ranging from 1 to 12. SaSAUR09 has 12 exon structures, while SaSAUR01 and SaSAUR36 have 8 exons. Most of the SaSAUR genes did not contain introns. Nine (20.93%) of the SaSAUR genes contained one or more introns, while the remaining 34 (79.07%) SaSAUR genes were intron-free (Figure 2D). The similar conserved motifs and gene structures of SAUR genes within the same group strongly supported the accuracy of the group classification.

3.3. SAUR Gene Duplication and Chromosomal Location

The locations of the SAUR genes were extracted from the genome-annotated generic-feature format (GFF) file of Santalum album, and the physical locations of these SAUR genes on the chromosomes were visualized using the MapChart version 5.4.6 software. Figure 3 illustrates the irregular distribution of the 43 SAUR genes across 10 chromosomes. Specifically, one gene was located on chr01 (2.32% of the total), eleven genes on chr02 (25.58%), two genes on chr03 (4.65%), seven genes on chr04 (16.28%), one gene on chr05 (2.32%), three genes on chr06 (6.98%), twelve genes on chr07 (27.91%), three genes on chr08 (6.98%), two genes on chr09 (4.65%), and one gene on chr10 (2.32%). Some of the SaSAUR genes can be observed in Figure 3 as gene clusters.
Gene duplication events typically include tandem and segmental duplications, and they are important for studying the expansion of gene families. The results revealed the presence of 14 pairs of segmentally duplicated (SD) genes and 9 pairs of tandemly duplicated (TD) genes within the SaSAUR genes (Table 2). SaSAUR genes involved in tandem duplications typically belong to the same group. The presence of multiple duplication events in SaSAUR genes suggests that certain genes have arisen through both tandem and segmental duplication, potentially serving as drivers of gene evolution. The majority of segmental duplications in the SAUR gene family of Santalum album were located on chr02, chr04, and chr07, as shown in Figure 4. Ka/Ks ratios can predict the selection pressure on genes encoding proteins. Our analysis revealed that the Ka/Ks ratios of all the duplicated gene pairs were below 1, with the exception of three gene pairs where the Ka/Ks value was incalculable (Table 2). A Ka/Ks value below 1 indicates a purifying (negative) selection, while a Ka/Ks value of 1 indicates neutral evolution, and Ka/Ks values above 1 indicate adaptive (positive) selection. Our findings suggest that negative selection may have played a role in the development of these duplicated genes in the SAUR gene family in Santalum album.

3.4. Expression Analysis of SaSAUR Genes

The current research work investigated the expression patterns of all 43 SaSAUR genes using transcriptome data from various tissues of Santalum album to understand their potential functions (Supplementary Table S2). As shown in Figure 5A, SaSAUR genes exhibited distinct tissue-specific expression patterns. Notably, all the SaSAUR genes were expressed in leaves, displaying no significant differences in their expression levels in leaves, which was consistent with the results of the subcellular localization indicating that the majority of SaSAUR genes are localized in chloroplasts. While approximately half of the SaSAUR genes did not show expression in roots, it is worth noting that SaSAUR18 exhibited high expression levels in roots, hinting a pivotal role in the function of root development. Only a limited number of SaSAUR genes (SaSAUR33, SaSAUR07, SaSAUR08, SaSAUR09, SaSAUR11, SaSAUR13, SaSAUR18, SaSAUR19, and SaSAUR34) were expressed in the heartwood, with SaSAUR08 and SaSAUR13 showing significantly higher expression levels. SaSAUR08, SaSAUR11, SaSAUR13, and SaSAUR18 were expressed in all three tissues, indicating their significant roles in plant growth and development.
The SAUR gene family plays a crucial role in various abiotic stresses. To comprehend the function of the SAUR gene family in salt stress, we exposed seedling leaves of Santalum album to different salt concentrations (W: CK; L: 50 mmol/L NaCl; H: 100 mmol/L NaCl) for 0, 12, 24, and 48 h, with three biological replicates. Quality control was conducted on the data obtained from sequencing the libraries on the platform, revealing that all samples adhered to the established standards. The sequencing produced a total of 413.17 Gb of raw data, which was subsequently filtered to produce 402.13 Gb of high-quality data. The specific sequencing quality for each sample is comprehensively presented in Supplementary Table S1. An analysis of the transcriptomic data for SaSAURs under salt stress using a bioinformatics approach revealed that most SaSAUR genes were expressed both before and after salt stress (Figure 5B and Supplementary Table S3). It is worth noting that SaSAUR04, SaSAUR07, SaSAUR08, SaSAUR09, and SaSAUR18 exhibited significantly higher expression levels. SaSAUR27 and SaSAUR28 are salt-stress-associated differential genes (log2FC > 1), with almost no expression before salt stress and significantly up-regulated expression after salt stress, indicating that these genes may play a role in the response to salt stress. The two predicted differential genes (SaSAUR27 and SaSAUR28) were selected to detect their expression characteristics under salt treatment using real-time quantitative polymerase chain reaction (RT-qPCR). Figure 6 shows that SaSAUR27 exhibited significant differences from the control at all treatment time periods after treatment with the salt solution. SaSAUR28 did not exhibited any significant differences at the 12 h treatment time but exhibited significant differences at the 24 h and 48 h treatment times. The RT-qPCR results were consistent with the transcriptome results.

4. Discussion

The SAUR gene family has been identified in a variety of plants and shown to play a critical role in plant growth and stress tolerance [24]. Spartz found that overexpression of AtSAUR19 in Arabidopsis thaliana resulted in increased expression in the leaf area, which positively regulated leaf growth by promoting leaf cell enlargement [55]. Overexpressing both AtSAUR41 [27] and AtSAUR63 [26] resulted in enlarged petals and elongated filaments, highlighting their significance in plant growth. In Belladonna, AbSAUR1 promotes the growth and development of the plant, resulting in increased plant height and root meristem, which significantly enhances yield and alkaloid content [56]. The auxin-induced SAUR protein can regulate PM H+-ATPase activity by modulating PP2C-D phosphatase, causing an increase in plasma membrane potential, providing expansion pressure for cell growth [24]. Consequently, it promotes cell expansion, plant growth and development. The results of several studies have shown that TaSAUR75 plays a positive regulatory role in plants’ responses to drought and salt stress [57]. In cucumber, CsaSAUR1, CsaSAUR13, CsaSAUR15, CsaSAUR49, and CsaSAUR50 were up-regulated by high-temperature-induced expression, suggesting that they may be involved in high-temperature tolerance response processes [58]. The OsSAUR51 gene in rice could inhibit the spread of pathogenic bacteria by reducing the accumulation of auxin, which made the plant resistant to bacterial leaf blight (BLB) and played a positive role in biotic-stress tolerance in rice [59]. Guo found that overexpression of the TaSAUR78 gene could enhance the tolerance of wheat to salt and drought stresses [60]. Analysis of the S. album transcriptome data revealed that the majority of SaSAUR genes showed no significant changes in their expression level before and after salt stress. Expression patterns were categorized into two distinct cases: one where genes remained unexpressed both before and after salt stress, and another where genes exhibited consistent expression levels before and after salt stress. The SaSAUR27 and SaSAUR28 (4.65% of total) genes in S. album exhibited significant responses to salt stress. These two genes were classified within Group V alongside AtSAUR36 and AtSAUR41, suggesting their potential functional similarities. These results are confirmed by comparative analysis with other species. Pineapple possesses 52 SAUR genes, with 3 genes (5.77%) exhibiting responsiveness to salt stress [18]. In contrast, alfalfa possesses 433 SAUR genes, of which 11 genes (2.54%) respond to salt stress [28].
Based on the genomic data of S. album, a total of 43 SaSAUR genes were identified in this study. The number of SAUR gene family members was significantly lower than that of peanut (162) [61], poplar (105) [35], and maize (79) [22], but higher than that of oil palm (40) [62]. The limited number of members might be associated with the extended growth cycle characteristic of S. album. SaSAUR genes were classified into five groups depending on their phylogenetic relationships, and SAUR genes of melons [63] have also been classified into five groups. In rice [16], tomato [22], and watermelon [64], five, three, and two clusters of SAUR gene family members have been identified, respectively. Chromosomal localization revealed that the SaSAUR genes were unevenly distributed among chr01 to chr10, with SaSAUR26 to SaSAUR36 clustered in the short arm of chr07. In addition, there was a high degree of sequence similarity among the members of these gene clusters. Four genes (SaSAUR32, SaSAUR33, SaSAUR34, SaSAUR35) on chr07 were classified in group II, and these genes were clustered together on the same branch of the phylogenetic tree, exhibiting a high level of similarity in motif arrangement and gene structure. In terms of gene structure, the SAUR genes contain almost no introns, but AUX and GH3, which also belong to the three large early auxin-responsive families, have a high number of introns. The number and location of introns can often influence the level of gene expression. The incidence of alternative splicing in intron-less genes tends to be low, so the SAUR genes may be relatively functionally conserved. The identified members of SAUR gene family with intronic structures accounted for 20.9% of the total, which is higher than maize (7.5%) and poplar (10.5%), and similar to that in millet (18.1%). Segmental and tandem duplications are the primary drivers of gene family expansion and evolution [65]. We identified nine tandem duplications and 14 segmental duplication events in 43 SaSAUR genes (Table 2). This suggests that segmental duplication plays a critical role in amplifying and evolving the SAUR gene family of S. album. Motif 1, Motif 2, and Motif 3 were widely distributed among the SaSAUR genes and were arranged in the order of 2–1–3, which is consistent with the study of the cabbage SAUR gene family by Zhao [66]. The exon–intron structures and motif arrangements were highly conserved, and the genes of close relatives exhibited similar genetic structures. The similarity and variation in gene structure, motifs, and conserved domains of SaSAUR genes are certainly related to the evolutionary and gene duplication of S. album. Previous studies documented the subcellular location of SAUR genes within the nucleus [67] and cytoplasm [68]. Contrary to these findings, our study indicated that a predominant fraction, exceeding 70%, of the SaSAUR proteins was predicted to be localized within the chloroplasts, a pattern similarly observed in maize [69]. Plant chloroplasts are important intracellular organelles that produce ATP (Adenosine triphosphate) through photosynthetic phosphorylation, suggesting that auxins may play a role in the energy transfer process that takes place at the chloroplast membrane [70].
To explore the principal functions of SaSAUR genes and the role of salt stress on them, we embarked on an expression analysis across distinct tissues—roots, leaves, heartwood—and at incremental salt exposure durations (0, 12, 24, and 48 h), leveraging transcriptome datasets. A meticulous tissue-specific expression scrutiny unveiled that disparate SAUR genes assume unique roles in the ambit of plant growth and morphogenesis. Notably, the expression profile of SAUR genes in the leaves of S. album was significantly higher than in other parts of the plant, a pattern similar to that observed in watermelon [64]. This suggests a conserved role of SAUR genes in foliar development across species. Specifically, SaSAUR27 and SaSAUR28, both localized on chr07 and categorized under group IV, emerged as salt-stress-responsive genes (log2FC > 1), suggesting their potential involvement in the salt-stress response mechanism. Subsequent RT-qPCR analysis results were consistent with those of the transcriptome. SaSAUR27 differed from the blank control group at every time interval, and SaSAUR28 also showed differential performance at all time intervals, except at 12 h. This pattern intimates a robust involvement of these genes in salt-stress adaptation. This study has revealed the expression response of SaSAUR genes in different tissues and under various salt treatments. With the advent of comprehensive plant genomic sequencing, it is anticipated that an expanded repertoire of SAUR genes will be identified across diverse taxa. These findings will contribute to a more in-depth study of the functional characterization and the evolutionary genesis and diversification of the SAUR gene family.

5. Conclusions

The SAUR gene family in Santalum album was comprehensively analyzed for the first time in this study. A total of 43 SaSAUR genes were identified, which were unevenly distributed across 10 chromosomes. The phylogenetic tree and gene structure analyses revealed that SaSAUR genes can be classified into five groups, each exhibiting similar gene structures. Additionally, most SaSAURs were found to lack introns. The duplication events of SaSAUR genes suggests that segmental duplication served as the primary means of evolutionary expansion for SAUR gene family. Analysis of SaSAUR gene expression levels in various tissues and under salt-stress conditions uncovered that all SaSAUR genes are expressed in leaves. SaSAUR08 and SaSAUR13 exhibit significantly higher expression levels in heartwood compared with roots and leaves. Conversely, SaSAUR18 shows significantly higher expression in roots than in heartwood and leaves. Additionally, SaSAUR27 and SaSAUR28 have emerged as potential differential genes in response to salt stress. Overall, our study will contribute to a better understanding of the complexity of the S. album SAUR gene family and will serve as a valuable guide for future functional analysis studies.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/plants13101286/s1.

Author Contributions

M.T. and L.L. designed this study and revised the manuscript. Q.Z. carried out the study and wrote the manuscript. H.Z. and X.H. revised the manuscript and provided constructive suggestions. Y.L. and X.Z. revised the manuscript. All authors have read and agreed to the published version of the manuscript.

Funding

This project was supported by the National Natural Science Foundation of China (32201624), the Hainan Provincial Natural Science Foundation of China (321RC469), the Hainan Province Science and Technology Special Fund (ZDYF2023XDNY078), the Collaborative Innovation Center Project of Nanfan and High-Efficiency Tropical Agriculture at Hainan University (XTCX2022NYB08), the Collaborative Innovation Center Project of Ecological Civilization in Hainan University (XTCX2022STC10), and the Priming Scientific Research Foundation at Hainan University (KYQD(ZR)-21039).

Data Availability Statement

The original contributions presented in this study are included in the article and Supplementary Material. The whole genome sequence and annotation files of S. album can be downloaded from the National Genomics Data Center of China at https://ngdc.cncb.ac.cn/gwh/Assembly/37800/show (accessed on 3 April 2024). The RNA-seq data under salt stress of S. album can be downloaded from the National Genomics Data Center of China at https://bigd.big.ac.cn/gsa/browse/CRA015677 (accessed on 3 April 2024).

Acknowledgments

We are sincerely thankful to the contributors of the RNA sequence data uploaded to the NCBI (accession numbers: PRJNA243306, PRJNA360335, PRJNA192417). We would like to thank the editors and reviewers for their efforts and constructive comments.

Conflicts of Interest

The authors declare that they have no conflicts of interest.

References

  1. Solanki, N.S.; Chauhan, C.S.; Vyas, B.; Marothia, D. Santalum album Linn: A review. Int. J. PharmTech Res. 2015, 7, 629–640. [Google Scholar]
  2. Baldovini, N.; Delasalle, C.; Joulain, D. Phytochemistry of the Heartwood from Fragrant Santalum Species: A Review. Flavour. Fragr. J. 2011, 26, 7–26. [Google Scholar] [CrossRef]
  3. Santha, S.; Dwivedi, C. Anticancer Effects of Sandalwood (Santalum Album). Anticancer. Res. 2015, 35, 3137–3145. [Google Scholar] [PubMed]
  4. Saneja, A.; Kaushik, P.; Kaushik, D.; Kumar, S.; Kumar, D. Antioxidant, Analgesic and Anti-Inflammatory Activities of Santalum album Linn. Planta Med. 2009, 75, 102. [Google Scholar] [CrossRef]
  5. Mohankumar, A.; Kalaiselvi, D.; Levenson, C.; Shanmugam, G.; Thiruppathi, G.; Nivitha, S.; Sundararaj, P. Antioxidant and stress modulatory efficacy of essential oil extracted from plantation-grown Santalum album L. Ind. Crops Prod. 2019, 140, 111623. [Google Scholar] [CrossRef]
  6. Ouyang, Y.; Zhang, X.; Chen, Y.; Teixeira da Silva, J.A.; Ma, G. Growth, Photosynthesis and Haustorial Development of Semiparasitic Santalum album L. Penetrating into Roots of Three Hosts: A Comparative Study. Trees 2016, 30, 317–328. [Google Scholar] [CrossRef]
  7. Tah, J. White Sandal (Santalum album L.), A Precious Mediclnal and Tiber yielding Plant: A Short Review. World J. Pharm. Pharm. Sci. 2017, 18, 616–634. [Google Scholar] [CrossRef]
  8. Nageswara-Rao, M.; Soneji, J.R. While Exploitation Threatens Indian Sandalwood, a Plea for Conservation and Regeneration Resounds. Flavour. Fragr. J. 2008, 33, 38–43. [Google Scholar]
  9. Dhanya, B.; Viswanath, S.; Purushothaman, S. Sandal (Santalum album L.) Conservation in Southern India: A Review of Policies and Their Impacts. J. Trop. Agric. 2010, 48, 1–10. [Google Scholar]
  10. Hagen, G.; Guilfoyle, T. Auxin-Responsive Gene Expression: Genes, Promoters and Regulatory Factors. Plant Mol. Biol. 2002, 49, 373–385. [Google Scholar] [CrossRef]
  11. Gil, P.; Liu, Y.; Orbović, V.; Verkamp, E.; Poff, K.L.; Green, P.J. Characterization of the Auxin-Inducible SAUR-AC1 Gene for Use as a Molecular Genetic Tool in Arabidopsis. Plant Physiol. 1994, 104, 777–784. [Google Scholar] [CrossRef]
  12. Woodward, A.W.; Bartel, B. Auxin: Regulation, Action, and Interaction. Ann. Bot. 2005, 95, 707–735. [Google Scholar] [CrossRef]
  13. Vanneste, S.; Friml, J. Auxin: A Trigger for Change in Plant Development. Cell 2009, 136, 1005–1016. [Google Scholar] [CrossRef] [PubMed]
  14. McClure, B.A.; Guilfoyle, T. Characterization of a Class of Small Auxin-Inducible Soybean Polyadenylated RNAs. Plant Mol. Biol. 1987, 9, 611–623. [Google Scholar] [CrossRef] [PubMed]
  15. Goda, H.; Sawa, S.; Asami, T.; Fujioka, S.; Shimada, Y.; Yoshida, S. Comprehensive Comparison of Auxin-Regulated and Brassinosteroid-Regulated Genes in Arabidopsis. Plant Physiol. 2004, 134, 1555–1573. [Google Scholar] [CrossRef]
  16. Jain, M.; Tyagi, A.K.; Khurana, J.P. Genome-Wide Analysis, Evolutionary Expansion, and Expression of Early Auxin-Responsive SAUR Gene Family in Rice (Oryza sativa). Genomics 2006, 88, 360–371. [Google Scholar] [CrossRef]
  17. Wang, S.; Bai, Y.; Shen, C.; Wu, Y.; Zhang, S.; Jiang, D.; Guilfoyle, T.J.; Chen, M.; Qi, Y. Auxin-Related Gene Families in Abiotic Stress Response in Sorghum Bicolor. Funct. Integr. Genom. 2010, 10, 533–546. [Google Scholar] [CrossRef]
  18. Zhang, Y.; Ye, T.; She, Z.; Huang, S.; Wang, L.; Aslam, M.; Qin, R.; Wang, X.; Qin, Y.; Niu, X. Small Auxin Up RNA (SAUR) Gene Family Identification and Functional Genes Exploration during the Floral Organ and Fruit Developmental Stages in Pineapple (Ananas comosus L.) and Its Response to Salinity and Drought Stresses. Int. J. Biol. Macromol. 2023, 237, 124061. [Google Scholar] [CrossRef] [PubMed]
  19. Stortenbeker, N.; Bemer, M. The SAUR Gene Family: The Plant’s Toolbox for Adaptation of Growth and Development. J. Exp. Bot. 2019, 70, 17–27. [Google Scholar] [CrossRef]
  20. Zhang, H.; Yu, Z.; Yao, X.; Chen, J.; Chen, X.; Zhou, H.; Lou, Y.; Ming, F.; Jin, Y. Genome-Wide Identification and Characterization of Small Auxin-up RNA (SAUR) Gene Family in Plants: Evolution and Expression Profiles during Normal Growth and Stress Response. BMC Plant Biol. 2021, 21, 4. [Google Scholar] [CrossRef]
  21. Ghanashyam, C.; Jain, M. Role of Auxin-Responsive Genes in Biotic Stress Responses. Plant Signal. Behav. 2009, 4, 846–848. [Google Scholar] [CrossRef] [PubMed]
  22. Wu, J.; Liu, S.; He, Y.; Guan, X.; Zhu, X.; Cheng, L.; Wang, J.; Lu, G. Genome-Wide Analysis of SAUR Gene Family in Solanaceae Species. Gene 2012, 509, 38–50. [Google Scholar] [CrossRef] [PubMed]
  23. Newman, T.C.; Ohme-Takagi, M.; Taylor, C.B.; Green, P.J. DST Sequences, Highly Conserved among Plant SAUR Genes, Target Reporter Transcripts for Rapid Decay in Tobacco. Plant Cell 1993, 5, 701–714. [Google Scholar] [PubMed]
  24. Ren, H.; Gray, W.M. SAUR Proteins as Effectors of Hormonal and Environmental Signals in Plant Growth. Mol. Plant 2015, 8, 1153–1164. [Google Scholar] [CrossRef]
  25. Mueller-Roeber, B.; Balazadeh, S. Auxin and Its Role in Plant Senescence. J. Plant Growth Regul. 2014, 33, 21–33. [Google Scholar] [CrossRef]
  26. Chae, K.; Isaacs, C.G.; Reeves, P.H.; Maloney, G.S.; Muday, G.K.; Nagpal, P.; Reed, J.W. Arabidopsis Small Auxin up RNA63 Promotes Hypocotyl and Stamen Filament Elongation. Plant J. For. Cell Mol. Biol. 2012, 71, 684–697. [Google Scholar] [CrossRef] [PubMed]
  27. Kong, Y.; Zhu, Y.; Gao, C.; She, W.; Lin, W.; Chen, Y.; Han, N.; Bian, H.; Zhu, M.; Wang, J. Tissue-Specific Expression of Small Auxin up RNA41 Differentially Regulates Cell Expansion and Root Meristem Patterning in Arabidopsis. Plant Cell Physiol. 2013, 54, 609–621. [Google Scholar] [CrossRef]
  28. Hou, K.; Wu, W.; Gan, S.-S. SAUR36, a Small Auxin up RNA Gene, Is Involved in the Promotion of Leaf Senescence in Arabidopsis. Plant Physiol. 2013, 161, 1002–1009. [Google Scholar] [CrossRef]
  29. Du, M.; Spalding, E.P.; Gray, W.M. Rapid Auxin-Mediated Cell Expansion. Annu. Rev. Plant Biol. 2020, 71, 379–402. [Google Scholar] [CrossRef]
  30. Kodaira, K.-S.; Qin, F.; Tran, L.-S.P.; Maruyama, K.; Kidokoro, S.; Fujita, Y.; Shinozaki, K.; Yamaguchi-Shinozaki, K. Arabidopsis Cys2/His2 Zinc-Finger Proteins AZF1 and AZF2 Negatively Regulate Abscisic Acid-Repressive and Auxin-Inducible Genes under Abiotic Stress Conditions1. Plant Physiol. 2011, 157, 742–756. [Google Scholar] [CrossRef]
  31. Qiu, T.; Qi, M.; Ding, X.; Zheng, Y.; Zhou, T.; Chen, Y.; Han, N.; Zhu, M.; Bian, H.; Wang, J. The SAUR41 Subfamily of Small Auxin up RNA Genes Is Abscisic Acid Inducible to Modulate Cell Expansion and Salt Tolerance in Arabidopsis Thaliana Seedlings. Ann. Bot. 2020, 125, 805–819. [Google Scholar] [CrossRef]
  32. Liu, H.; Li, X.; He, F.; Wang, X.; Li, M.; Long, R.; Kang, J.; Yang, Q.; Chen, L. Identification of the alfalfa SAUR gene family and its expression pattern under abiotic stress. Acta Prataculturae Sin. 2024, 4, 135–153. [Google Scholar] [CrossRef]
  33. Li, G.; Wang, Q.; Lu, L.; Wang, S.; Chen, X.; Khan, M.H.U.; Zhang, Y.; Yang, S. Identification of the Soybean Small Auxin Upregulated RNA (SAUR) Gene Family and Specific Haplotype for Drought Tolerance. Biologia 2022, 77, 1197–1217. [Google Scholar] [CrossRef]
  34. Liu, R.; Wen, S.S.; Sun, T.-T.; Wang, R.; Zuo, W.-T.; Yang, T.; Wang, C.; Hu, J.J.; Lu, M.Z.; Wang, L.Q. PagWOX11/12a Positively Regulates the PagSAUR36 Gene That Enhances Adventitious Root Development in Poplar. J. Exp. Bot. 2022, 73, 7298–7311. [Google Scholar] [CrossRef] [PubMed]
  35. Hu, W.; Yan, H.; Luo, S.; Pan, F.; Wang, Y.; Xiang, Y. Genome-Wide Analysis of Poplar SAUR Gene Family and Expression Profiles under Cold, Polyethylene Glycol and Indole-3-Acetic Acid Treatments. Plant Physiol. Biochem. 2018, 128, 50–65. [Google Scholar] [CrossRef]
  36. Finn, R.D.; Bateman, A.; Clements, J.; Coggill, P.; Eberhardt, R.Y.; Eddy, S.R.; Heger, A.; Hetherington, K.; Holm, L.; Mistry, J.; et al. Pfam: The Protein Families Database. Nucleic Acids Res. 2014, 42, 222–230. [Google Scholar] [CrossRef]
  37. Finn, R.D.; Clements, J.; Eddy, S.R. HMMER Web Server: Interactive Sequence Similarity Searching. Nucleic Acids Res. 2011, 39, 29–37. [Google Scholar] [CrossRef] [PubMed]
  38. Schultz, J.; Milpetz, F.; Bork, P.; Ponting, C.P. SMART, a Simple Modular Architecture Research Tool: Identification of Signaling Domains. Proc. Natl. Acad. Sci. USA 1998, 95, 5857–5864. [Google Scholar] [CrossRef]
  39. Marchler-Bauer, A.; Anderson, J.B.; Chitsaz, F.; Derbyshire, M.K.; DeWeese-Scott, C.; Fong, J.H.; Geer, L.Y.; Geer, R.C.; Gonzales, N.R.; Gwadz, M.; et al. CDD: Specific Functional Annotation with the Conserved Domain Database. Nucleic Acids Res. 2009, 37, 205–210. [Google Scholar] [CrossRef]
  40. Voorrips, R.E. MapChart: Software for the Graphical Presentation of Linkage Maps and QTLs. J. Hered. 2002, 93, 77–78. [Google Scholar] [CrossRef]
  41. Markakis, M.N.; Boron, A.K.; Loock, B.V.; Saini, K.; Cirera, S.; Verbelen, J.-P.; Vissenberg, K. Characterization of a Small Auxin-Up RNA (SAUR)-Like Gene Involved in Arabidopsis Thaliana Development. PLoS ONE 2013, 8, e82596. [Google Scholar] [CrossRef] [PubMed]
  42. Katoh, K.; Standley, D.M. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Mol. Biol. Evol. 2013, 30, 772–780. [Google Scholar] [CrossRef] [PubMed]
  43. Nguyen, L.T.; Schmidt, H.A.; von Haeseler, A.; Minh, B.Q. IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies. Mol. Biol. Evol. 2015, 32, 268–274. [Google Scholar] [CrossRef] [PubMed]
  44. Letunic, I.; Bork, P. Interactive Tree of Life (iTOL) v5: An Online Tool for Phylogenetic Tree Display and Annotation. Nucleic Acids Res. 2021, 49, 293–296. [Google Scholar] [CrossRef] [PubMed]
  45. Wang, Y.; Tang, H.; Debarry, J.D.; Tan, X.; Li, J.; Wang, X.; Lee, T.; Jin, H.; Marler, B.; Guo, H.; et al. MCScanX: A Toolkit for Detection and Evolutionary Analysis of Gene Synteny and Collinearity. Nucleic Acids Res. 2012, 40, e49. [Google Scholar] [CrossRef] [PubMed]
  46. 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]
  47. Wang, D.; Zhang, Y.; Zhang, Z.; Zhu, J.; Yu, J. KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies. Genom. Proteom. Bioinform. 2010, 8, 77–80. [Google Scholar] [CrossRef] [PubMed]
  48. Gasteiger, E.; Gattiker, A.; Hoogland, C.; Ivanyi, I.; Appel, R.D.; Bairoch, A. ExPASy: The Proteomics Server for in-Depth Protein Knowledge and Analysis. Nucleic Acids Res. 2003, 31, 3784–3788. [Google Scholar] [CrossRef] [PubMed]
  49. Chou, K.C.; Shen, H.B. Plant-mPLoc: A Top-down Strategy to Augment the Power for Predicting Plant Protein Subcellular Localization. PLoS ONE 2010, 5, e11335. [Google Scholar] [CrossRef]
  50. Bailey, T.L.; Johnson, J.; Grant, C.E.; Noble, W.S. The MEME Suite. Nucleic Acids Res. 2015, 43, 39–49. [Google Scholar] [CrossRef]
  51. Chen, S.; Zhou, Y.; Chen, Y.; Gu, J. Fastp: An Ultra-Fast All-in-One FASTQ Preprocessor. Bioinformatics 2018, 34, 884–890. [Google Scholar] [CrossRef]
  52. Kim, D.; Paggi, J.M.; Park, C.; Bennett, C.; Salzberg, S.L. Graph-Based Genome Alignment and Genotyping with HISAT2 and HISAT-Genotype. Nat. Biotechnol. 2019, 37, 907–915. [Google Scholar] [CrossRef]
  53. Liao, Y.; Smyth, G.K.; Shi, W. featureCounts: An Efficient General Purpose Program for Assigning Sequence Reads to Genomic Features. Bioinformatics 2014, 30, 923–930. [Google Scholar] [CrossRef]
  54. Love, M.I.; Huber, W.; Anders, S. Moderated Estimation of Fold Change and Dispersion for RNA-Seq Data with DESeq2. Genome Biol. 2014, 15, 550. [Google Scholar] [CrossRef]
  55. Spartz, A.K.; Lee, S.H.; Wenger, J.P.; Gonzalez, N.; Itoh, H.; Inzé, D.; Peer, W.A.; Murphy, A.S.; Overvoorde, P.J.; Gray, W.M. The SAUR19 Subfamily of Small Auxin up RNA Genes Promote Cell Expansion. Plant J. For. Cell Mol. Biol. 2012, 70, 978–990. [Google Scholar] [CrossRef] [PubMed]
  56. Bai, F.; Li, S.; Yang, C.; Zhao, T.; Zhang, T.; Lan, X.; Liao, Z. Overexpression of the AbSAUR1 gene enhanced biomass production and alkaloid yield in Atropa belladonna. Ind. Crops Prod. 2019, 140, 111705. [Google Scholar] [CrossRef]
  57. Guo, Y.; Jiang, Q.; Hu, Z.; Sun, X.; Fan, S.; Zhang, H. Function of the Auxin-Responsive Gene TaSAUR75 under Salt and Drought Stress. Crop J. 2018, 6, 181–190. [Google Scholar] [CrossRef]
  58. Wang, H.; Shang, Q. Genome-wide Identification and Expression Analysis of the SAUR Gene Family in Cucumis sativus. Acta Hortic. Sin. 2019, 46, 1093–1111. [Google Scholar] [CrossRef]
  59. Aoki, H.; Onishi, A.; Miyashita, M.; Miyagawa, H.; Yatou, O.; Saito, K. Involvement of the Rice OsSAUR51 Gene in the Auxin-Related Field Resistance Mechanism against Bacterial Blight Disease. Jpn. Agric. Res. Q. JARQ 2016, 50, 219–227. [Google Scholar] [CrossRef]
  60. Guo, Y.; Xu, C.; Sun, X.; Hu, Z.; Fan, S.; Jiang, Q.; Zhang, H. TaSAUR78 Enhances Multiple Abiotic Stress Tolerance by Regulating the Interacting Gene TaVDAC1. J. Integr. Agric. 2019, 18, 2682–2690. [Google Scholar] [CrossRef]
  61. Liu, Y.; Xiao, L.; Chi, J.; Li, R.; Han, Y.; Cui, F.; Peng, Z.; Wan, S.; Li, G. Genome-Wide Identification and Expression of SAUR Gene Family in Peanut (Arachis hypogaea L.) and Functional Identification of AhSAUR3 in Drought Tolerance. BMC Plant Biol. 2022, 22, 178. [Google Scholar] [CrossRef] [PubMed]
  62. Zhou, L.X.; Yang, M.D.; Cao, H.X.; Yang, Y.D. Genome-Wide Identification and Bioinformatics Analysis of the Oil Palm SAUR Gene Family. J. South. Agric. 2022, 23, 13271. [Google Scholar] [CrossRef]
  63. Jiao, L.; Si, X.; Guo, Z.; Li, P.; Liu, D. Identification and bioinformatics analysis of the SAUR gene family in melon. China Veg. 2023, 5, 42–55. [Google Scholar] [CrossRef]
  64. Zhang, N.; Huang, X.; Bao, Y.; Wang, B.; Zeng, H.; Cheng, W.; Tang, M.; Li, Y.; Ren, J.; Sun, Y. Genome-Wide Identification of SAUR Genes in Watermelon (Citrullus lanatus). Physiol. Mol. Biol. Plants 2017, 23, 619–628. [Google Scholar] [CrossRef]
  65. Cannon, S.B.; Mitra, A.; Baumgarten, A.; Young, N.D.; May, G. The Roles of Segmental and Tandem Gene Duplication in the Evolution of Large Gene Families in Arabidopsis Thaliana. BMC Plant Biol. 2004, 4, 10. [Google Scholar] [CrossRef] [PubMed]
  66. Zhao, J.; Zhang, T. Bioinformatics analysis of SAUR gene family in Brassica rapa. Chin. Agric. Sci. Bull. 2012, 22, 130–137. [Google Scholar]
  67. Knauss, S.; Rohrmeier, T.; Lehle, L. The Auxin-Induced Maize Gene ZmSAUR2 Encodes a Short-Lived Nuclear Protein Expressed in Elongating Tissues. J. Biol. Chem. 2003, 278, 23936–23943. [Google Scholar] [CrossRef]
  68. Kant, S.; Bi, Y.-M.; Zhu, T.; Rothstein, S.J. SAUR39, a Small Auxin-up RNA Gene, Acts as a Negative Regulator of Auxin Synthesis and Transport in Rice. Plant Physiol. 2009, 151, 691–701. [Google Scholar] [CrossRef] [PubMed]
  69. Chen, Y.; Hao, X.; Cao, J. Small Auxin Upregulated RNA (SAUR) Gene Family in Maize: Identification, Evolution, and Its Phylogenetic Comparison with Arabidopsis, Rice, and Sorghum. J. Integr. Plant Biol. 2014, 56, 133–150. [Google Scholar] [CrossRef]
  70. Chen, D.; Deng, Y.; Zhao, J. Distribution and Change Patterns of Free IAA, ABP 1 and PM H+-ATPase during Ovary and Ovule Development of Nicotiana tabacum L. J. Plant Physiol. 2012, 169, 127–136. [Google Scholar] [CrossRef]
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Figure 1. Phylogenetic tree of SAUR proteins sequences in Santalum album and Arabidopsis thaliana (different-colored shaded areas are used to differentiate distinct groups, and bold text indicates SAUR proteins of Santalum album).
Figure 1. Phylogenetic tree of SAUR proteins sequences in Santalum album and Arabidopsis thaliana (different-colored shaded areas are used to differentiate distinct groups, and bold text indicates SAUR proteins of Santalum album).
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Figure 2. Conserved motifs, conserved domains, and gene structures of the SaSAUR genes. (A) Phylogenetic tree of the SaSAUR proteins. (B) Conserved motifs in the SaSAUR genes. (C) Conserved domains in the SaSAUR genes. (D) Exon–intron structure of the SaSAUR genes.
Figure 2. Conserved motifs, conserved domains, and gene structures of the SaSAUR genes. (A) Phylogenetic tree of the SaSAUR proteins. (B) Conserved motifs in the SaSAUR genes. (C) Conserved domains in the SaSAUR genes. (D) Exon–intron structure of the SaSAUR genes.
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Figure 3. Chromosomal locations of the 43 SAUR genes in S. album. The ruler on the left indicates the physical position of the reference genome. The pair of tandemly duplicated genes is shown in red font.
Figure 3. Chromosomal locations of the 43 SAUR genes in S. album. The ruler on the left indicates the physical position of the reference genome. The pair of tandemly duplicated genes is shown in red font.
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Figure 4. The intrachromosomal segmental duplication map in S. album. Gray lines are collinear blocks in S. album. Red lines are the syntenic gene pairs of SaSAUR genes.
Figure 4. The intrachromosomal segmental duplication map in S. album. Gray lines are collinear blocks in S. album. Red lines are the syntenic gene pairs of SaSAUR genes.
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Figure 5. Expression profiles of the SaSAUR genes. (A) Expression of SaSAUR genes in various tissues (heartwood, root, leaf). (B) Expression of SaSAUR genes under salt stress. Differential genes are labeled in red boxes. The initials of the horizontal coordinates represent the salt solutions (W: CK; L: 50 mmol/L; H: 100 mmol/L), followed by treatment times 0 (0 h), 12 (12 h), 24 (24 h), and 48 (48 h), with the numbers after the underscore indicating the biological replicate. Expression profiles were normalized to log10(FPKM).
Figure 5. Expression profiles of the SaSAUR genes. (A) Expression of SaSAUR genes in various tissues (heartwood, root, leaf). (B) Expression of SaSAUR genes under salt stress. Differential genes are labeled in red boxes. The initials of the horizontal coordinates represent the salt solutions (W: CK; L: 50 mmol/L; H: 100 mmol/L), followed by treatment times 0 (0 h), 12 (12 h), 24 (24 h), and 48 (48 h), with the numbers after the underscore indicating the biological replicate. Expression profiles were normalized to log10(FPKM).
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Figure 6. Expression profiles of SaSAUR27 and SaSAUR28 in response to salt treatment as determined by RT-qPCR. The x-axis indicates the different concentrations of NaCl solution treatments (W: CK; L: 50 mmol/L; H: 100 mmol/L), and the y-axis indicates the relative expression levels. The values are the means ± SD of three independent experiments, and the asterisks indicate a significant difference (* p < 0.05; ** p < 0.01) compared with the corresponding controls.
Figure 6. Expression profiles of SaSAUR27 and SaSAUR28 in response to salt treatment as determined by RT-qPCR. The x-axis indicates the different concentrations of NaCl solution treatments (W: CK; L: 50 mmol/L; H: 100 mmol/L), and the y-axis indicates the relative expression levels. The values are the means ± SD of three independent experiments, and the asterisks indicate a significant difference (* p < 0.05; ** p < 0.01) compared with the corresponding controls.
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Table 1. Detailed information on the SAUR gene family in S. album.
Table 1. Detailed information on the SAUR gene family in S. album.
Gene NameGene IdLength AAMolecular Weight (kD)pIChrPredicted Localization
SaSAUR01SA01G0233943448.358.961Chloroplast
SaSAUR02SA02G0013215117.1310.662Chloroplast
SaSAUR03SA02G0020611212.596.332Nucleus
SaSAUR04SA02G0051610711.819.342Chloroplast, Nucleus
SaSAUR05SA02G0067713715.159.402Chloroplast
SaSAUR06SA02G0110610211.188.562Chloroplast
SaSAUR07SA02G0240613515.608.452Nucleus
SaSAUR08SA02G0262918420.3511.162Chloroplast, Mitochondrion
SaSAUR09SA02G0266741646.608.762Chloroplast
SaSAUR10SA02G03132919.909.672Chloroplast
SaSAUR11SA02G0313310912.414.992Nucleus
SaSAUR12SA02G0313412713.959.072Chloroplast
SaSAUR13SA03G0008816318.159.483Nucleus
SaSAUR14SA03G0086711513.3110.023Chloroplast
SaSAUR15SA04G00058758.3210.284Chloroplast, Nucleus
SaSAUR16SA04G007299711.439.584Chloroplast, Nucleus
SaSAUR17SA04G0079210912.099.754Chloroplast, Nucleus
SaSAUR18SA04G0135312014.156.344Nucleus
SaSAUR19SA04G0221915517.149.724Chloroplast, Nucleus
SaSAUR20SA04G0281613114.828.714Chloroplast
SaSAUR21SA04G0283915617.358.584Chloroplast, Cytoplasm, Nucleus
SaSAUR22SA05G0069615217.178.825Chloroplast, Nucleus
SaSAUR23SA06G0062615617.879.856Chloroplast
SaSAUR24SA06G0088714915.816.506Nucleus
SaSAUR25SA06G0088915817.415.386Nucleus
SaSAUR26SA07G0020814616.178.727Nucleus
SaSAUR27SA07G0020914616.268.337Chloroplast, Mitochondrion, Nucleus
SaSAUR28SA07G00210889.634.457Nucleus
SaSAUR29SA07G0027711512.738.017Chloroplast, Mitochondrion, Nucleus
SaSAUR30SA07G0027810912.586.297Chloroplast, Nucleus
SaSAUR31SA07G002799310.206.827Chloroplast
SaSAUR32SA07G002809410.768.967Chloroplast, Mitochondrion, Nucleus
SaSAUR33SA07G002819410.738.937Chloroplast
SaSAUR34SA07G002829410.596.577Chloroplast
SaSAUR35SA07G002839410.749.377Chloroplast, Nucleus
SaSAUR36SA07G0028442047.027.717Cytoplasm
SaSAUR37SA08G0180013714.989.108Chloroplast, Cytoplasm, Nucleus
SaSAUR38SA08G0191513014.926.338Chloroplast
SaSAUR39SA08G0192810111.618.318Nucleus
SaSAUR40SA09G0011912314.219.269Chloroplast
SaSAUR41SA09G0071911913.985.619Chloroplast
SaSAUR42SA09G0080312514.339.189Nucleus
SaSAUR43SA10G0034825628.879.6610Chloroplast, Nucleus
Table 2. Ka, Ks, and Ka/Ks of duplicated gene pairs of the SaSAURs.
Table 2. Ka, Ks, and Ka/Ks of duplicated gene pairs of the SaSAURs.
Duplicated Gene PairsNon-Synonymous (Ka)Synonymous (Ks)Ka/KsDuplicated Type
SaSAUR10&SaSAUR110.200.450.44tandem
SaSAUR11&SaSAUR120.220.480.46tandem
SaSAUR26&SaSAUR270.100.330.32tandem
SaSAUR29&SaSAUR300.42NaNNaNtandem
SaSAUR30&SaSAUR310.35NaNNaNtandem
SaSAUR31&SaSAUR320.301.460.21tandem
SaSAUR32&SaSAUR330.120.940.13tandem
SaSAUR33&SaSAUR340.100.330.30tandem
SaSAUR34&SaSAUR350.110.310.35tandem
SaSAUR01&SaSAUR040.221.880.12segmental
SaSAUR01&SaSAUR060.140.800.17segmental
SaSAUR01&SaSAUR170.302.110.14segmental
SaSAUR01&SaSAUR360.20NaNNaNsegmental
SaSAUR04&SaSAUR060.211.810.11segmental
SaSAUR02&SaSAUR080.250.510.48segmental
SaSAUR05&SaSAUR130.411.710.24segmental
SaSAUR07&SaSAUR180.321.540.21segmental
SaSAUR06&SaSAUR170.261.610.16segmental
SaSAUR06&SaSAUR190.621.590.39segmental
SaSAUR04&SaSAUR360.121.600.07segmental
SaSAUR06&SaSAUR360.181.430.12segmental
SaSAUR16&SaSAUR260.563.450.16segmental
SaSAUR38&SaSAUR400.231.000.23segmental
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MDPI and ACS Style

Zhu, Q.; Zheng, H.; Hu, X.; Liu, Y.; Zheng, X.; Li, L.; Tang, M. Genome-Wide Analysis of the SAUR Gene Family and Its Expression Profiles in Response to Salt Stress in Santalum album. Plants 2024, 13, 1286. https://doi.org/10.3390/plants13101286

AMA Style

Zhu Q, Zheng H, Hu X, Liu Y, Zheng X, Li L, Tang M. Genome-Wide Analysis of the SAUR Gene Family and Its Expression Profiles in Response to Salt Stress in Santalum album. Plants. 2024; 13(10):1286. https://doi.org/10.3390/plants13101286

Chicago/Turabian Style

Zhu, Qing, Haoyue Zheng, Xu Hu, Yi Liu, Xinyi Zheng, Libei Li, and Minqiang Tang. 2024. "Genome-Wide Analysis of the SAUR Gene Family and Its Expression Profiles in Response to Salt Stress in Santalum album" Plants 13, no. 10: 1286. https://doi.org/10.3390/plants13101286

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