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Article

Genome-Wide Characterization, Evolutionary Analysis of ARF Gene Family, and the Role of SaARF4 in Cd Accumulation of Sedum alfredii Hance

by
Dong Xu
1,2,3,†,
Chunyu Yang
1,†,
Huijin Fan
2,3,
Wenmin Qiu
2,3,
Biyun Huang
2,3,
Renying Zhuo
2,3,
Zhengquan He
1,*,
Haiying Li
4,* and
Xiaojiao Han
2,3,*
1
Key Laboratory of Three Gorges Regional Plant Genetic & Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang 443000, China
2
State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
3
Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
4
Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Plants 2022, 11(9), 1273; https://doi.org/10.3390/plants11091273
Submission received: 23 March 2022 / Revised: 28 April 2022 / Accepted: 5 May 2022 / Published: 9 May 2022
(This article belongs to the Topic Plant-Soil Interactions)
Browse Figures
Versions Notes

Abstract

:
Auxin response factors (ARFs) play important roles in plant development and environmental adaption. However, the function of ARFs in cadmium (Cd) accumulation are still unknown. Here, 23 SaARFs were detected in the genome of hyperaccumulating ecotype of Sedum alfredii Hance (HE), and they were not evenly distributed on the chromosomes. Their protein domains remained highly conservative. SaARFs in the phylogenetic tree can be divided into three groups. Genes in the group Ⅰ contained three introns at most. However, over ten introns were found in other two groups. Collinearity relationships were exhibited among ten SaARFs. The reasons for generating SaARFs may be segmental duplication and rearrangements. Collinearity analysis among different species revealed that more collinear genes of SaARFs can be found in the species with close relationships of HE. A total of eight elements in SaARFs promoters were related with abiotic stress. The qRT-PCR results indicated that four SaARFs can respond to Cd stress. Moreover, that there may be functional redundancy among six SaARFs. The adaptive selection and functional divergence analysis indicated that SaARF4 may undergo positive selection pressure and an adaptive-evolution process. Overexpressing SaARF4 effectively declined Cd accumulation. Eleven single nucleotide polymorphism (SNP) sites relevant to Cd accumulation can be detected in SaARF4. Among them, only one SNP site can alter the sequence of the SaARF4 protein, but the SaARF4 mutant of this site did not cause a significant difference in cadmium content, compared with wild-type plants. SaARFs may be involved in Cd-stress responses, and SaARF4 may be applied for decreasing Cd accumulation of plants.

1. Introduction

Cadmium (Cd) is released into the environment mainly by industrial activities [1]. This released Cd can enter the human body via the food chain cycle [2], and excess Cd will lead to serious health problems [3]. For crop production, we should decline the Cd content in edible parts of plants to minimize Cd intake for people [2]. However, plants applied in phytoremediation should have the ability to accumulate higher Cd on their aerial parts, as this ability can enhance the effect of phytoremediation for removing Cd from the environment [4]. Whereas plants cannot accumulate excess Cd, as Cd is also toxic to plants [5]. Meanwhile, plants do not effectively separate Cd and essential elements, and Cd is thus inevitably accumulated in edible parts of plants. For example, OsHMA2 can transport zinc and Cd simultaneously [6]. Therefore, it is a requirement for people to flexibly modulate the current status of Cd accumulation in plants according to their different purposes. The transgenic technology is an important strategy to alter Cd accumulation in plants. Furthermore, exploring ideal genes is a precondition for this technology. For example, overexpression of HMA3 from low Cd-accumulating cultivars of rice can block the Cd translocation process from the roots to above-ground tissues [7]. SaMT2 from Sedum alfredii Hance can significantly increase Cd accumulation of the transgenic tobacco [8]. Therefore, genes related with Cd accumulation in plants may all have the practical application value. Exploring the related novel genes is significant for ensuring food security and controlling Cd pollution.
Up to date, many genes were identified to be relevant with Cd accumulation [9,10]. The functions of these genes can mainly be divided into three groups: The first group is responsible for the intracellular transport of Cd between different organelles. For example, SpHMA1 protected the photochemical reactions by exporting Cd from chloroplasts to cytoplasm [11]. The second group plays roles in the transmembrane transport of Cd. For example, expressing OsABCG36 of rice in yeast exhibited efflux activities for Cd [12]. Genes in the third group act on Cd long-distance transportation. For example, AtHMA4 plays roles in Cd loading in the xylem, and this process was responsible for transporting Cd from the roots to the shoot [13]. These genes associated with Cd accumulation are mainly from ZIP, CDF, NRAMPs, HMAs, and ABC gene families [14,15,16,17,18]. However, most of them are metal transporters; whether transcription factors could change Cd accumulation remains further confirmed.
Auxin is the initial signal for triggering the expression of downstream genes in the auxin pathway [19]. Moreover, previous studies indicated that auxin can change Cd accumulation [20]. Therefore, genes in auxin pathway may play roles in modifying Cd metabolism in plants. Auxin response factors (ARFs) are important transcription factors for the transduction of auxin signals in the auxin pathway [21]. They are involved in almost all the auxin-related processes [22]. For example, overexpression of ARF4 affected the salt resistance of poplars by inhibiting the lateral root development [23]. Decreasing the expression of SlMIR160a and SlARF10A in tomato can restore the abnormal phenotypes of leaves and flowers of tomato CR-slmir160a mutants [24]. However, it is unclear that ARFs are responsible for the Cd accumulation process.
The hyperaccumulating ecotype of S. Alfredii (HE) is one of the most famous Cd hyperaccumulators [25,26]. Recently, it has been applied for harnessing Cd-contaminated soils [27]. Although HE has an excellent ability of accumulating Cd in aerial parts of plants, another ecotype of S. alfredii (NHE) is unable to accumulate excessive Cd [28]. Therefore, the two ecotypes have been become the ideal materials for studying the Cd accumulation mechanisms [29,30]. For example, HMA3 from HE was transformed into NHE to identify its roles in the Cd accumulation process [16]. However, the lack of genomic information of HE blocked the identification of candidate genes. We finished the whole-genome sequencing of HE and NHE (unpublished), which can be helpful for the genome-wide detection and analysis of candidate genes in the past few years.
In this study, we detected 23 ARF genes from the HE genome. The candidate genes with their possible roles in Cd accumulation were screened from the ARF gene family, mainly based on the evolutionary analysis. Then, the transgenic method was used for verifying the roles of the candidate genes in Cd accumulation, and this function was further demonstrated by generating the key single nucleotide polymorphism (SNP) mutant of the candidate gene.

2. Results

2.1. Phylogenetic Analysis, Protein Domains, Promoter Motifs, Exons, and Introns of SaARFs

A total of 23 SaARFs were detected in the HE genome (Supplementary Material S5). The basic information of SaARF proteins is listed in Table S2, including their genomic location, molecular weight, protein isoelectric point, extinction coefficient, length, and hydrophilicity. The phylogenetic tree of the SaARF gene family was constructed, and three clades were thus divided (Figure 1A). The protein domains, the DNA binding domain (DBD), and the auxin_responsive domain (Auxin_resp), can be detected in all SaARFs. The first clade contained nine members, and these members all lacked the Phox and Bem1 (PB1) domain (Figure 1B). Conversely, the PB1 domain can be found in other members (except SaARF3 and SaARF8). Then, we analyzed the composition of the introns and exons of these SaARFs. The results showed that many introns (at least 10 introns) can be observed in members of the second and third two clades (Figure 1C, the red lines). Furthermore, the longest exon (full or at least part of its sequences) in each gene was located in the PB1 domain (Figure 1C, the red dotted boxes). In sharp contrast, very few introns (at most three introns) were contained in members of the first clade. For example, SaARF18 in the first clade only contained three introns in its full-length sequences. After that, the promoter–element analysis of SaARFs revealed that the elements related with abiotic stress responses, developmental processes, and plant hormones can be detected in their promoters (Figure 1D).

2.2. Genomic Location and Collinearity Analysis of SaARFs

Analyzing the distribution of ARFs in chromosomes may contribute to clarify the evolutionary history of the gene family [31]. We found that SaARFs were uneven throughout chromosomes. In detail (Figure 2A), only one member was each situated on chromosomes 1, 4, 7, 8, 10, 11, 21, 25, 28; two SaARFs positioned each in chromosomes 2, 6, 9, 19; while chromosome 15 and 33 each contained three SaARFs. Whereas no SaARFs were located in other chromosomes.
The segmental and tandem gene duplication are considered as the two important reasons for generating gene family members [32]. The collinearity relationships across the whole HE genome were detected to identify the reasons for SaARFs formation. The results showed that there were collinearity relationships between five pairs of SaARF members (Figure 2A,B). Meanwhile, most of them were distributed in the first clade of the phylogenetic tree (Figure 1A, red lines). We also found that these genes were all located in the corresponding collinear blocks of the genome (Figure 2A, indicated by black dotted lines). Combined with the possible reasons for the formation of these blocks (Figure 2B, the grey arrows), we considered that the segmental duplication and rearrangements may be two important reasons for the generation of these SaARFs (Figure 2B).

2.3. Comparative Genome Analysis of ARFs among Different Species

Collinearity relationships usually exist between genes originated from common ancestors in angiosperms [33]. As HE is a dicotyledonous plant, we analyzed the collinearity relationships of HE genes with those in two dicotyledonous plants (Arabidopsis thaliana and Populus trichocarpa) and two Crassulaceae plants (Kalanchoe fedtschenkoi and NHE) to clarify the phylogenetic mechanisms of ARF family. Our results indicated that 7.08% of A. thaliana genes have collinearity relationships with genes in HE, while this percentage was 10.14% in P. trichocarpa. In contrast, it is much higher in the corresponding percentages in K. fedtschenkoi and NHE (34.90% and 76.29%, respectively) than those in A. thaliana and P. trichocarpa (Figure 3). In other words, the higher percentage can be observed in the species that are more closely related to HE. Meanwhile, we found that one gene in Arabidopsis and three genes in P. trichocarpa have collinearity relationships with SaARF6.1, SaARF8.1 and SaARF9.2, SaARF18.2, and SaARF19.2, respectively. However, a large amount of collinearity genes of SaARFs can be found in NHE and K. fedtschenkoi genome (21 collinearity genes and 11 collinearity genes, respectively). The corresponding collinearity genes of all 23 SaARFs in HE can be detected in NHE genome. Moreover, one collinearity gene in NHE usually corresponded to two or three SaARFs in HE (Figure 3, the blue arrows). These results indicated that more collinearity genes of SaARFs can be found in the species that have a close relationship with HE.

2.4. Expression Patterns of SaARFs under Cd Stress

Then we needed to identify whether the expression of SaARFs are affected by Cd stress. We detected SaARFs expression in different organs during 0–12 h under Cd stress. The qRT-PCR results indicated that the expression of SaARFs can respond to Cd stress. In general, the highest expression level of 14 SaARFs in roots were observed during 1–4 h under Cd stress (Figure 4A, the black dotted box); in stems, the peak values of 18 SaARFs expressions were distributed between 2 h and 8 h (Figure 4B, the black dotted box); however, the peak values of 18 SaARFs expressions in leaves were mainly found after 4 h under Cd stress (Figure 4C, the black dotted box). In other words, the responses of SaARFs in roots seemed to be faster than those in the two other organs, and their responses in leaves were slower than those of other organs. This trend was consistent with the order in the Cd signal delivered in plants. We considered that the response rate of SaARFs under Cd stress should be in accordance with this order. Therefore, SaARF4, SaARF6.2, SaARF8.1, and SaARF18.2 in 23 SaARFs may be the ideal candidate genes (Figure 4). For example, the peak value of SaARF18.2 expression was observed in the roots at 1 h after Cd treatment (Figure 4A, SaARF18.2, the red arrow). However, the expression level of SaARF18.2 in the stems was highest at the 2 h (Figure 4B, SaARF18.2, the red arrow), while the highest expression of SaARF18.2 was detected in leaves at the 12 h (Figure 4C, SaARF18.2, the red arrow).

2.5. Coexpression Network Analysis

As the typical transcription factors, SaARFs should be controlled by upstream genes, and they can regulate the expression of downstream genes. Therefore, there should be strong expression relationships between SaARFs and the related genes. The transcriptome data obtained under Cd stress were used for generating a coexpression network [34], and the related information about SaARFs was extracted from the coexpression network. We found that six SaARFs (SaARF2, SaARF4, SaARF8.2, SaARF9, SaARF18.2, and SaARF19) in 23 SaARFs were identified as hub genes in the coexpression network. The expression of 3002 genes was related with the six SaARFs (Figure 5A,B). Moreover, further analysis of these related genes indicated that the six SaARFs can be divided into two groups, and there were lots of common genes in each group (Figure 5A,B). Our attention was mainly focused on the transcription factors, transporters, and the genes involved in the pathway of plant hormone. The results indicated that the transcription factors in the coexpression network were mainly distributed in WRKY, bZIP, and bHLH gene families; many ABC transporters were contained in the transporters group; meanwhile, the genes related with the ethylene and auxin pathway were also found in the coexpression network (Figure 5C,D). After that, we extracted the promoter sequences of the hub genes and analyzed the similar segments in these sequences. The results indicated that many similar segments of promoters can be found in each group (Figure 5E), indicating that they may be regulated by the same or similar factors.

2.6. Functional Divergence and Positive Selection Analysis

Genes that contain positive selection loci are subjected to selection pressure of adaptive evolution [35]. The paml4.8 was used to identify which SaARFs contained the positive selection sites. Two other Crassulaceae plants (K. fedtschenkoi and K. laxiflora) and HE were together chosen for further analysis (Supplementary Material S5). Among them, only HE was the Cd hyperaccumulator plant. A total of 81 ARFs were detected, and these ARFs can be divided into four clades (Figure 6). We adapted the branch site model for analyzing positive selection sites. The results indicated that 10 positive selection sites (1 M, 9 T, 18 T, 22 I, 30 Q, 36 A, 38 T, 40 E, 42 C, and 43 H) were distributed in the first clade (Table 1). Only two sites were detected in the second clade (6M and 23S), and few sites were in other clades. Furthermore, the functional divergence analysis showed that the first clade has significant functional differentiation compared with other clades (p < 0.01, Table 2). Only SaARF3 and SaARF4 were distributed into the first clade. In other words, SaARF3 and SaARF4 may undergo the positive selection pressure. According to the above analysis, SaARF4 was chosen for identifying its function in Cd accumulation.

2.7. Overexpressing SaARF4 Decreases Cd Accumulation

In order to identify whether the candidate gene, SaARF4, could affect Cd accumulation, we transformed 35S::SaARF4 into NHE, and then we measured the Cd accumulation of the overexpression transgenic lines. Furthermore, we performed the whole-genome resequencing to identify the possible SNP sites related with Cd accumulation using more than 100 natural individuals (Supplementary Material S6). We found that 10 SNP sites with p < 0.01 were distributed in SaARF4 sequences (three in upstream sequences and seven in coding-region sequences, Figure S3). Only one SNP can change the protein sequences of SaARF4. Thus, we used overlapping-PCR technology to restructure SaARF4 sequences (SaARF4-SNPm). After that, 35S::SaARF4-SNPm was also transformed into NHE to identify whether this site could influence Cd accumulation.
As shown in Figure 7, the structure of SaARF4-SNPm was seriously changed (Figure 7A-1) compared with SaARF4 (Figure 7A). The interaction proteins surrounding the mutant amino acid (aa) were changed from five aa (TYR-523, SER-524, LEU-535, THR-538, and PHE-516) of SaARF4 (Figure 7B, the orange one) to three aa (GLN-540, HIS-562, and HIS-566) of SaARF4-SNPm (Figure 7B-1, the orange one). Furthermore, the charge distribution of the two proteins indicated that the surrounding charges of the mutant AA (Figure 7C, the white arrow) were altered from the positive charges (Figure 7C, the blue areas) to the neutral charge (Figure 7C-1, the white areas). We also found that overexpressing SaARF4 can effectively decline the Cd content compared with WT plants of NHE (p < 0.01). However, the overexpression of SaARF4-SNPm did not significantly decrease Cd accumulation (Figure 7D), indicating that this SNP may play important roles in Cd accumulation.

3. Discussion

In this study, a total of 23 SaARFs were identified across the whole genome, and then their phylogenetic analysis (Figure 1A), structure analysis (Figure 1B,C), chromosomal location (Figure 2A), and coexpression network analysis (Figure 5) were made. Furthermore, the combination with other species, the collinearity analysis (Figure 3), the positive selection analysis (Figure 6 and Table 1), and the functional divergence analysis (Table 2) were conducted. Meanwhile, qRT-PCR analysis indicated that their expression patterns were altered with different Cd-treatment times (Figure 4). Based on these results, we finally chose SaARF4 as the candidate gene for further analysis. The result of the transgenic experiment showed that overexpressing SaARF4 can effectively decrease Cd content (Figure 7D). In order to further determine the effect of SaARF4 on Cd accumulation, the SNP sites related with Cd accumulation were detected in SaARF4 sequences. Among these SNP sites, only one SNP can change SaARF4 protein sequences. We artificially altered SaARF4 sequences based on the SNP site. The results indicated that overexpression of the mutant sequences did not significantly decrease the Cd content (Figure 7D).
Eukaryotic genes are divided into intron-less (no introns), intron-poor (at most three introns), and intron-rich [36]. A recent study indicated that intron-poor genes were evolved from a subfamily of genes that are intron-rich [37]. We found that 23 SaARFs can be divided into three groups, and genes in the first group contained at most three introns (Figure 1A,C). Moreover, the branch length of the first group was longer than those of other groups (Figure 1A). New members of a gene family are produced by gene duplication, and the evolutionary process makes their sequences divergent to produce different proteins. Interestingly, in this study, the collinearity genes in the ARF family (Figure 1A, the red lines) were mainly also distributed in the first group, indicating that these genes may be undergoing the evolutionary process. This evidence indicates that the evolution of these genes may be later than other SaARFs. Furthermore, the PB1 domain in ARFs is responsible for the response to auxin level in plants [21]. In detail, AUX/IAA proteins can bind to the PB1 domain to repress ARFs functions under low auxin concentrations. However, the AUX/IAA proteins will be degraded under a high auxin level, and the ARFs are thus released to play their roles on the relevant downstream genes [21]. Therefore, after removing the PB1 domain from ARFs, the transformed plants exhibited ‘high auxin’ phenotypes (even though, under low auxin concentration) when overexpressing these ARFs mutants [38]. This domain was absent from the genes in the first group (Figure 1B), indicating that the regulatory effect of auxin concentration on their expression may be weaker than other ARFs. Furthermore, in the second and third groups, the sequences of the longest exon were all or partly located in the PB1 domain (Figure 1C, the red dotted boxes), indicating that the translation product of this domain may be more stable than other domains with a low effect of differential splicing. This may be required for the fine regulation of ARFs by auxin.
Collinearity genes are considered to evolute from the same ancestor [39]. The construction of collinearity relationships throughout the whole genome will be conductive to clarify the evolutionary history of a gene family [40]. In general, the segmental and tandem gene duplication are two important ways for generating new members of a gene family [39]. In this study, we found that there were collinearity relationships between five pairs of SaARFs (Figure 2). Meanwhile, they were located in the collinearity blocks of the HE genome (Figure 2A), indicating that the segmental duplication may be a reason for the generation of these SaARFs. When comparing the collinearity relationships among different species, the results indicated that the number of collinearity genes of SaARFs in Crassulaceae plants was more than those in two other species (Figure 3). Moreover, there were positive relationships between the number of collinearity genes of SaARFs in different species and the amount of all collinearity genes in different species (Figure 3). In other words, more collinearity genes of SaARFs can be detected in the genome of the species that is closely related with HE. In combination with previous studies, we found that ARFs seemed to play roles in the nodes of plant differentiation. For example, roots are important for plants to adapt to the terrestrial environment. Correspondingly, ARF2, ARF3, and ARF4 are relevant for the development of lateral roots [41]. The developmental differences of flower organs are significant between gymnosperms and angiosperms. SlARF10A is critical for flower development [42]. Meanwhile, herbaceous and woody plants are distinguished by the differences in xylem development. In poplars, PtoARF5 has been demonstrated to be related with the secondary xylem development [43]. Therefore, our results and previous studies together verified that the ARF gene family may play important roles in species differentiation.
There was functional redundancy among SaARFs, based on the results of the coexpression network (Figure 5). For example, a total of 289 genes have close expression relationships with SaARF4 (Figure 5B). Among them, the expression of 213 genes was also relevant with SaARF8.2. Furthermore, similar sequences can also be found in their promoters (Figure 5E), indicating that they may be regulated by similar or same factors. This phenomenon can also be found in the ARF family of Arabidopsis. Okushima reported that ARF7 and ARF19 in Arabidopsis together act in the lateral root formation, and overlapping functions were between them [44]. According to previous studies, ARFs mainly acted in developmental events of plants [45,46]. Therefore, overlapping functions among ARFs may be an important strategy for plants to ensure the normal development, because if one gene was impaired, another can rescue this deficit. In this study, our attention was the influence of the candidate gene on Cd accumulation. The Cd accumulation of transgenic plants was the phenotype that we focused on. The protein structure and surface charge distribution of a transcription factor are important factors to affect its binding with the downstream gene promoter [47,48,49]. We found that the surface charge distribution and protein structure of SaARF4 were all altered (Figure 7A,A-1,C,C-1), after changing its protein sequences using the method of site-directed mutagenesis. Therefore, the downstream genes regulated by SaARF4 may be different from those genes controlled by SaARF4-SNPm. Interestingly, the Cd accumulation of 35S::SaARF4 was significantly decreased, compared with those of NHE WT plants. However, the significant difference in Cd accumulation was not observed between the 35S::SaARF4-SNPm and WT plants (Figure 7D). This evidence indicated that SaARF4 and its downstream genes may play important roles in Cd accumulation. We will explain the detailed mechanism about how SaARF4 regulates its downstream genes to decrease Cd accumulation in a further study.

4. Methods and Materials

4.1. Plant Materials

HE and NHE were originally obtained from Quzhou [50] and Fuyang [16] countries, respectively, Zhejiang Province, China. The branches from these materials were used for cuttage propagation under the condition of 25 °C, 16 h light/8 h dark cycle.

4.2. Genome-Wide Identification of ARFs in Different Species

Genome sequencing of HE and NHE were performed, and then chromatin assembly of HE was also finished. The protein sequence file of HE was used for screening ARF genes. Except for HE and NHE, the genomic files of other species were all downloaded from Phytozome (https://phytozome.jgi.doe.gov/pz/portal.html (accessed on 18 March 2022)) [51]. The Hidden Markov Model (HMM) profile of the Auxin_resp domain (PF06507.12) was downloaded from pfam website (http://pfam.sanger.ac.uk/ (accessed on 18 March 2022)). Then, these protein sequence files and the pfam profile were used for identification of ARFs on the platform of SPDE [52]. Genes with default E-value (<0.1) were considered as ARFs. The intactness of conserved protein domains was tested by using NCBI-BLASTP (https://blast.ncbi.nlm.nih.gov/Blast.cgi (accessed on 18 March 2022)), and the incorrect genes were removed. After obtaining the gene identifications (IDs), SPDE was used for extracting the relevant sequences in batch. After that, these obtained sequences were blasted to the database using the website of TAIR (https://www.arabidopsis.org/ (accessed on 18 March 2022)) and named according to their homologous genes in Arabidopsis. If two or more genes have a same homologous gene of Arabidopsis, they were named as 1.1, 1.2, etc.

4.3. Phylogenetic Analysis, Protein Structures, Promoter Elements, Exons, and Introns

The phylogenetic trees were constructed using MEGA-X (https://www.megasoftware.net/ (accessed on 18 March 2022)) with Minimal Evolution, Neighbor-Joining, and maximum likelihood (ML) methods (bootstrap, 1000). Only ML tree was displayed, as the three trees were consistent. The NCBI-BLASTP (https://blast.ncbi.nlm.nih.gov/Blast.cgi (accessed on 18 March 2022)) was used to identify the protein-domain locations of SaARFs. The promoter analysis of SaARFs was conducted using PlantCARE (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/ (accessed on 18 March 2022)). Then, GSDS2.0 (http://gsds.gao-lab.org/ (accessed on 18 March 2022)) and TBtools [53] were used for displaying the protein structures, promoter elements, exons, and introns.

4.4. Chromosomal Locations and Collinearity Analysis

The required files were generated by SPDE using genomic data. Then, these files were used to display the genomic information by the software of Circos (http://circos.ca/ (accessed on 18 March 2022)). The collinearity analysis was made by MCScanX software with E-value < 1 × 10−5 (http://chibba.pgml.uga.edu/mcscan2/ (accessed on 18 March 2022)). Other operations were conducted as stated in the manual.

4.5. Comparative Genomics Analysis

The related genomic files were downloaded from Phytozome. Then, these files were used for comparing the genomic information between different species with TBtools.

4.6. Coexpression Network Construction

The data reported in our previous studies [34] were used for extracting the relevant information to construct the coexpression network. After identification of hub genes in SaARFs, the 2000 bp promoter sequences of the hub genes were extracted from genome sequences using SPDE. Then, the conserved segments of these sequences were detected using the website of MEME (http://meme-suite.org/tools/meme (accessed on 18 March 2022)). The venn diagrams were drawn by Bioinfrmatics & Evolutionary Genomics (http://bioinformatics.psb.ugent.be/webtools/Venn/ (accessed on 18 March 2022)). The cytoscape software was used for constructing the coexpression network [54]. After that, the images were further processed by Abode Illustrator.

4.7. Functional Divergence and Positive Selection Analysis

The functional divergence of SaARFs was analyzed using DIVERGE v3.0 program [55]. The positive selection analysis was conducted by using the PAML package, and the parameters were set as previously described [56].

4.8. Quantitative Reverse Transcription-PCR (qRT-PCR)

Wild-type (WT) plants of HE were water-cultured under the condition (25 °C, 16 h light/8 h dark cycle) for about 3 weeks. Then, these materials were treated under 400 μM CdCl2. The roots, stems and leaves were collected at 0 h, 0.5 h, 1 h, 2 h, 4 h, 8 h and 12 h, respectively. Each sample with three biological replicates was immediately put into liquid nitrogen for RNA extraction. Total RNA was extracted from leaves using an RNA extraction kit (RNAprep Pure Plant Kit, TIANGEN, Beijing, China) followed by DNase I to remove genomic DNA. Next, first-strand cDNA was produced using the cDNA synthesis kit (PrimeScript™ RT Master Mix, TAKARA, Beijing, China). qRT-PCR was performed as Shuang-Shuang et al. described [50]. The primers were designed by SPDE in batch and listed in the Table S1.

4.9. SNP Sites Detection and Three-Dimensional Structure Visualization

After sequencing HE genome, we collected 106 individuals (including 52 HE and 54 NHE) from eleven natural populations. Then, the whole-genome resequencing approach was performed to SNP sites. Meanwhile, we determined the Cd content of the 106 individuals. Association analysis between SNP sites and Cd content was made using Tassel 5 [57], and SNP sites with p-value < 0.01 were remained. The SNP site that can change the protein sequence of SaARF4 was utilized for further functional verification. The three-dimensional structures of proteins were constructed using I-TASSER website (https://zhanglab.ccmb.med.umich.edu/I-TASSER/ (accessed on 18 March 2022)), and then the software of Chimera was used for displaying their three-dimensional structures [58].

4.10. Plasmid Construction and Transgenic Experiment

Total RNA was extracted from the HE leaves, according to the above method (stated in Section 4.8). Then, the total RNA (2 µg) was used for synthesizing the first-strand cDNA by Superscript RT III first-strand cDNA synthesis kit (Invitrogen, Carlsbad, NM, USA) followed by RNase H treatment. The primers for SaARF4 clone were listed in Table S1. The coding sequence of SaARF4 was cloned from HE cDNA. Furthermore, the sequence mutant of SaARF4 (SaARF4-SNPm) was produced using overlapping PCR, according to the results of SNP analysis. The vectors, pDONR222 and pK2GW7.0, were used for constructing 35S::SaARF4 and 35S::SaARF4-SNPm, respectively. Next, the recombinant vectors were transformed into the Agrobacterium tumefeciens strain EHA105. The NHE leaves were used for A. tumefeciens infection. The transgenic experiment was performed as previously described [16]. Minor modifications: differentiation medium: MS + 2 mg·L−1 6-benzylaminopurine + 0.3 mg·L−1 1-naphthaleneacetic acid; rooting medium: 1/2 MS + 2 mg·L−1 3-indolebutyric acid. The concentration of kanamycin was 30 mg·L−1.

4.11. Cd Content Determination

The RNA extraction and qRT-PCR were conducted as stated above for choosing the three different transgenic lines with similar expression levels (Figures S1 and S2). The WT, 35S::SaARF4 (Figure S1, the red arrows), and 35S::SaARF4-SNPm (Figure S2, the red arrows) plants were cultured in the same condition (25 °C, 16 h light/8 h dark cycle) for three months. Then, different lines with three biological repeats were cultured under 50 μM CdCl2 for 14 d. The Cd content was measured as described before [16]. In detail, the aerial parts of these plants were collected and weighted. Each sample was dried at 60 °C, and treated with concentrated nitric acid at 200 °C. The Cd content was determined by ICP-OES (inductively coupled plasma optical emission spectrometer).

4.12. Statistical Analysis

One-way ANOVA was utilized for significance analysis. All data were showed as means ± SD. The least significant difference (LSD) test was applied to analyze differences at a 0.05 or 0.01 level (*, p < 0.05; **, p < 0.01).

5. Conclusions

In this study, bioinformatic analysis was used to screen the candidate gene from the ARF family of HE, and then a transgenic method was utilized to identify whether the candidate gene could influence the Cd accumulation of plants. We found that SaARF4 underwent the positive selection pressure, and there may be a functional divergence between SaARF4 and other SaARFs. Furthermore, SaARF4 was a hub gene in the coexpression network, and it may affect over 280 genes under Cd stress. The results of qRT-PCR indicated that the expression of SaARF4 can be induced by Cd stress; therefore, it was chosen as the candidate gene to determine its roles in Cd accumulation. Overexpressing SaARF4 effectively decreased Cd accumulation of NHE. According to the previous study, the protein structure and surface charge distribution may influence the binding of a transcription factor and the promoter of its downstream genes. We detected an SNP site that can alter the protein structure and charge distribution of SaARF4. The technology of site-directed mutagenesis was used to change SaARF4 sequences based on this SNP site. Overexpressing the mutant of SaARF4 did not significantly decline the Cd accumulation of NHE. Therefore, we considered that SaARF4 and its downstream genes may play important roles in Cd accumulation.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/plants11091273/s1, Figure S1: Relative expression level of SaARF4; Figure S2: Relative expression level of SaARF4-SNPm; Figure S3: SNP sites; Table S1: Primers; Table S2: Basic information; Table S3: Positive selection sites in each clade; Table S4: Function divergences of ARF gene family; Supplementary Material S5: ARFs in Crassulaceae plants; Supplementary Material S6: Cd content.

Author Contributions

D.X., Z.H., X.H. designed the research. D.X., C.Y. conducted the experiments. H.F., B.H., W.Q., R.Z. and H.L. contributed to this paper. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by National Nonprofit Institute Research Grant of CAF (CAFYBB2020SY016), the Chinese Academy of Forestry foundation (CAFYBB2019QB002), the National Natural Science Foundation of China (No. 31872168).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Not applicable.

Conflicts of Interest

The authors declare no conflict of interest.

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Figure 1. Phylogenetic analysis and sequence analysis of SaARFs. (A) Phylogenetic tree and amino acid number for each gene. Members signed by red were collinearity genes. aa, amino acid. (B) Protein domains, different colors indicated different domains. The blue, orange, and green areas indicated the DBD, Auxin_resp and PB1 domain, respectively. (C) Exons (blue areas) and introns (red lines). (D) Promoter motifs. The motifs were displayed, which were related with plant hormones, abiotic stress, and plant development. Different colors indicated different motifs.
Figure 1. Phylogenetic analysis and sequence analysis of SaARFs. (A) Phylogenetic tree and amino acid number for each gene. Members signed by red were collinearity genes. aa, amino acid. (B) Protein domains, different colors indicated different domains. The blue, orange, and green areas indicated the DBD, Auxin_resp and PB1 domain, respectively. (C) Exons (blue areas) and introns (red lines). (D) Promoter motifs. The motifs were displayed, which were related with plant hormones, abiotic stress, and plant development. Different colors indicated different motifs.
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Figure 2. Genomic localization and hypothetical evolutionary histories of SaARFs. (A) The distribution of SaARFs in chromosomes and the collinearity relationships throughout the whole genome. The cyan lines indicated the collinearity relationships of genes (except SaARFs). Other colored lines indicated the collinearity relationships among SaARFs. The genes marked by purple IDs were located in the positive strand of DNA, while others signed by orange IDs were in negative strand. The black dotted lines indicated the collinearity area. (B) The grey lines indicated the predicted modes of chromosomal segment duplication.
Figure 2. Genomic localization and hypothetical evolutionary histories of SaARFs. (A) The distribution of SaARFs in chromosomes and the collinearity relationships throughout the whole genome. The cyan lines indicated the collinearity relationships of genes (except SaARFs). Other colored lines indicated the collinearity relationships among SaARFs. The genes marked by purple IDs were located in the positive strand of DNA, while others signed by orange IDs were in negative strand. The black dotted lines indicated the collinearity area. (B) The grey lines indicated the predicted modes of chromosomal segment duplication.
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Figure 3. Collinearity relationships between HE and other species. The grey lines indicated collinearity relationships of other genes (except SaARFs). The red lines indicated the collinearity relationships of SaARFs. The blue arrows indicated that one ARF gene of NHE corresponded to two or three ARF genes of HE.
Figure 3. Collinearity relationships between HE and other species. The grey lines indicated collinearity relationships of other genes (except SaARFs). The red lines indicated the collinearity relationships of SaARFs. The blue arrows indicated that one ARF gene of NHE corresponded to two or three ARF genes of HE.
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Figure 4. Expression patterns of SaARFs in different organs under Cd stress. (A)The expression level of 14 SaARFs in roots under Cd stress. The black dotted box indicated the highest expression level of 14 SaARFs in roots were observed during 1–4 h. The red arrows indicated the highest level of corresponding SaARFs during Cd stress. (B) The expression level of 18 SaARFs in stems under Cd stress. The black dotted box indicated the peak values of 18 SaARFs expressions were distributed between 2–8 h. (C) The expression level of 18 SaARFs in leaves under Cd stress. The black dotted box indicated the peak values of 18 SaARFs expressions in leaves were mainly found after 4 h.
Figure 4. Expression patterns of SaARFs in different organs under Cd stress. (A)The expression level of 14 SaARFs in roots under Cd stress. The black dotted box indicated the highest expression level of 14 SaARFs in roots were observed during 1–4 h. The red arrows indicated the highest level of corresponding SaARFs during Cd stress. (B) The expression level of 18 SaARFs in stems under Cd stress. The black dotted box indicated the peak values of 18 SaARFs expressions were distributed between 2–8 h. (C) The expression level of 18 SaARFs in leaves under Cd stress. The black dotted box indicated the peak values of 18 SaARFs expressions in leaves were mainly found after 4 h.
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Figure 5. Similar segments of the hub-gene promoters and coexpression network analysis. (A) All related genes in the group of SaARF2, 9, 18.2, and 19. (B) The related genes in the group of SaARF4 and 8.2. (C,D) showed the coexpression network containing the transcription factors, transporter proteins and genes related with plant hormone. (E) Similar segments in the promoters of hub genes. The same color in each group indicated a common similar segment.
Figure 5. Similar segments of the hub-gene promoters and coexpression network analysis. (A) All related genes in the group of SaARF2, 9, 18.2, and 19. (B) The related genes in the group of SaARF4 and 8.2. (C,D) showed the coexpression network containing the transcription factors, transporter proteins and genes related with plant hormone. (E) Similar segments in the promoters of hub genes. The same color in each group indicated a common similar segment.
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Figure 6. Phylogenetic analysis of ARFs among three Crassulaceae plants. I, II, III, IV indicated the first class to the fourth class in the figure. The circles with same color indicated the ARFs were in the same species. Green circle, K. fedtschenkoi; red circle, HE; blue circle, K. laxiflora.
Figure 6. Phylogenetic analysis of ARFs among three Crassulaceae plants. I, II, III, IV indicated the first class to the fourth class in the figure. The circles with same color indicated the ARFs were in the same species. Green circle, K. fedtschenkoi; red circle, HE; blue circle, K. laxiflora.
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Figure 7. Variations in protein structures of SaARF4-SNPm and Cd content of transgenic plants. The protein structures of SaARF4 and SaARF4-SNPm were displayed in (A) and (A-1), respectively. (B) (SaARF4) and (B-1) (SaARF4-SNPm) indicated the mutant aa (the orange one) and its surrounding interaction aa (the green ones). The charge distribution of SaARF4 and SaARF4-SNPm was showed in (C) and (C-1), respectively. The red color indicated the negative charge; the blue color indicated the positive charge; the white color indicated the neutral charge; the white arrows indicated the positions of the mutant sites. (D) The Cd accumulation of NHE WT plants (the blue color), 35S::SaARF4 (the green color) and 35S::SaARF4-SNPm (the orange color). DW, dry weight. Different capitals indicated different significance, p < 0.01.
Figure 7. Variations in protein structures of SaARF4-SNPm and Cd content of transgenic plants. The protein structures of SaARF4 and SaARF4-SNPm were displayed in (A) and (A-1), respectively. (B) (SaARF4) and (B-1) (SaARF4-SNPm) indicated the mutant aa (the orange one) and its surrounding interaction aa (the green ones). The charge distribution of SaARF4 and SaARF4-SNPm was showed in (C) and (C-1), respectively. The red color indicated the negative charge; the blue color indicated the positive charge; the white color indicated the neutral charge; the white arrows indicated the positions of the mutant sites. (D) The Cd accumulation of NHE WT plants (the blue color), 35S::SaARF4 (the green color) and 35S::SaARF4-SNPm (the orange color). DW, dry weight. Different capitals indicated different significance, p < 0.01.
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Table
Table 1. Positive selection sites in each clade.
Table 1. Positive selection sites in each clade.
CladeModelnpalnL2∆lnLPositive Selection Sites
IModel-null163−5552.702535 Not allowed
Model-alte164−5552.70253501 M 0.980 *, 9 T 0.984 *, 18 T 0.987 *, 22 I 1.000 **, 30 Q 1.000 **, 36 A 1.000 **, 38 T 1.000 **, 40 E 1.000 **, 42 C 1.000 **, 43 H 0.992 **
IIModel-null163−5565.273813 Not allowed
Model-alte164−5565.27381306 M 1.000 **, 23 S 0.971 *
IIIModel-null163−5570.062526 Not allowed
Model-alte164−5570.0625260None
IVModel-null163−5572.824836 Not allowed
Model-alte164−5572.8248360None
* means p < 0.05 and ** means p < 0.01. The reference sequence was SpARF19, according to the alignment results.
Table
Table 2. Function divergences of ARF gene family.
Table 2. Function divergences of ARF gene family.
Group 1Group 2Type I Type II
θI ± s.e.MFE z-scoreLRTθII ± s.e.
III0.398 ± 0.198−2.245.565 *−0.581 ± 0.618
IIII0.270 ± 0.179−1.658.117 **0.085 ± 0.328
IIV0.266 ± 0.167−1.7611.987 **0.194 ± 0.223
IIIII0.215 ± 0.114−2.205.477 *−0.172 ± 0.505
IIIII0.021 ± 0.074−0.302.7230.135 ± 0.338
IIIIV0.042 ± 0.070−0.6400.071 ± 0.258
* means p < 0.05 and ** means p < 0.01. The reference sequence was SpARF19, according to the alignment results.
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Xu, D.; Yang, C.; Fan, H.; Qiu, W.; Huang, B.; Zhuo, R.; He, Z.; Li, H.; Han, X. Genome-Wide Characterization, Evolutionary Analysis of ARF Gene Family, and the Role of SaARF4 in Cd Accumulation of Sedum alfredii Hance. Plants 2022, 11, 1273. https://doi.org/10.3390/plants11091273

AMA Style

Xu D, Yang C, Fan H, Qiu W, Huang B, Zhuo R, He Z, Li H, Han X. Genome-Wide Characterization, Evolutionary Analysis of ARF Gene Family, and the Role of SaARF4 in Cd Accumulation of Sedum alfredii Hance. Plants. 2022; 11(9):1273. https://doi.org/10.3390/plants11091273

Chicago/Turabian Style

Xu, Dong, Chunyu Yang, Huijin Fan, Wenmin Qiu, Biyun Huang, Renying Zhuo, Zhengquan He, Haiying Li, and Xiaojiao Han. 2022. "Genome-Wide Characterization, Evolutionary Analysis of ARF Gene Family, and the Role of SaARF4 in Cd Accumulation of Sedum alfredii Hance" Plants 11, no. 9: 1273. https://doi.org/10.3390/plants11091273

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