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Article

Genome-Wide Identification of Superoxide Dismutase and Expression in Response to Fruit Development and Biological Stress in Akebia trifoliata: A Bioinformatics Study

by
Huai Yang
1,
Qiuyi Zhang
1,
Shengfu Zhong
1,
Hao Yang
1,
Tianheng Ren
1,
Chen Chen
1,
Feiquan Tan
1,
Guoxing Cao
2,
Jun Liu
2 and
Peigao Luo
1,*
1
Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
2
College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
*
Author to whom correspondence should be addressed.
Antioxidants 2023, 12(3), 726; https://0-doi-org.brum.beds.ac.uk/10.3390/antiox12030726
Submission received: 22 February 2023 / Revised: 7 March 2023 / Accepted: 14 March 2023 / Published: 15 March 2023
(This article belongs to the Special Issue Reactive Oxygen and Nitrogen Species in Plants)
Browse Figures
Versions Notes

Abstract

:
Akebia trifoliata is a newly domesticated perennial fruit tree, and the lack of molecular research on stress resistance seriously affects its genetic improvement and commercial value development. Superoxide dismutase (SOD) can effectively eliminate the accumulation of reactive oxygen species (ROS) during the rapid growth of plant organs under biotic and abiotic stresses, maintaining a steady state of physiological metabolism. In this study, 13 SODs consisting of two FeSODs (FSDs), four MnSODs (MSDs) and seven Cu/ZnSODs (CSDs) were identified in the A. trifoliata genome. Structurally, the phylogeny, intron–exon pattern and motif sequences within these three subfamilies show high conservation. Evolutionarily, segmental/wide genome duplication (WGD) and dispersed duplication form the current SOD profile of A. trifoliata. Weighted gene coexpression network analysis (WGCNA) revealed the metabolic pathways of nine (69.2%) SODs involved in fruit development, among which AktMSD4 regulates fruit development and AktCSD4 participates in the stress response. In addition, under the stress of multiple pathogens, six (46.6%) SODs were continuously upregulated in the rinds of resistant lines; of these, three SODs (AktMSD1, AktMSD2 and AktMSD3) were weakly or not expressed in susceptible lines. The results pave the way for theoretical research on SODs and afford the opportunity for genetic improvement of A. trifoliata.

1. Introduction

Reactive oxygen species (ROS), including superoxide radicals (O2·−), hydroxyl radicals (·OH) and hydrogen peroxide (H2O2), are inevitable byproducts of biological oxidation reactions in plant cells [1], and the production of ROS is further intensified when plants are subjected to biotic and abiotic stresses [2,3,4]. On the one hand, accumulated ROS can act as signaling molecules to regulate the expression of downstream genes to cope with adversity [5]. On the other hand, excessively accumulated ROS can damage plant cell membranes, destroy biological macromolecules, and even cause cell death [1]. In response to the toxic mechanism of ROS, plants have evolved a set of sophisticated antioxidant enzyme systems to maintain ROS homeostasis in cells [6], among which superoxide dismutase (SOD) is the first line of defense [7]. Therefore, to explore the molecular mechanism of plant stress tolerance, many scholars have carried out much research on the structure, function and phylogeny of plant SOD genes [8,9].
The SOD gene family is a class of metal-binding enzymes. Plant SOD genes are divided into three groups according to metal cofactors: iron SOD (FeSOD), manganese SOD (MnSODs) and copper/zinc SOD (Cu/ZnSOD) [10]. Another type of SOD, nickel SOD (NiSOD), exists mainly in bacteria, and has not been detected in plants [11]. In terms of the three subfamilies in plants, the subcellular localization of SOD proteins is usually related to the production site of O2·−. The compartmentalization of SOD proteins in the cell organelles is extremely important for plant response to oxidation stress induced by abiotic factors and cell signal transformation [12]. Evolutionarily, FeSODs and MnSODs have ancient origins and are present in bacteria, protozoa, and primitive algae [13]. It is generally believed that FeSODs and MnSODs have a common ancestor due to their striking similarities [14]. The separate evolution of FeSODs and MnSODs may be related to changes in oxygen levels on early Earth [13]. For example, the specific Mn/FeSODs in a few archaea, such as Aeropyrum pernix and Pyrobaculum calidifontis, are active with Fe but prefer to bind Mn, especially under aerobic conditions [15,16]. In addition, Cu/ZnSODs in plants are considered to have evolved separately from other SODs because to date, Cu/ZnSOD has not been detected in primitive plants such as Chlamydomonas or mosses [13,17].
A large number of reports have confirmed that the inducible expression of SOD helps plants respond to abiotic and biotic stresses. For example, the SOD activity of salt-tolerant varieties of Brassica napus is higher than that of salt-sensitive varieties under salt stress [18]. Under cold stress, the ROS content of cold-tolerant tea tree varieties is higher than that of cold-sensitive varieties, resulting in less damage to the leaves of the former [19]. Furthermore, the plant immune system relies on SODs to precisely regulate ROS content, to mediate the immune response to invading pathogenic bacteria. For example, after transferring the tomato SOD gene into sugarbeet, the transgenic lines showed strong resistance to oxidative agents as well as the fungus Cercospora beticola [20]. In addition to responding to biotic and abiotic stresses, changes in expression and enzyme activity of SOD genes during apple fruit ripening suggest that SOD plays an important role in fruit development [21,22].
Akebia trifoliata (Thunb.) Koidz., is a newly domesticated perennial woody vine with a high commercial development value. The root, stem and unripe fruit of A. trifoliata have been used as Chinese medicinal materials for thousands of years [23]. In recent years, A. trifoliata has been planted in a large area in Southwest China because of its delicious fruit pulp and high-quality seed oil [24,25]. However, genetic improvement of A. trifoliata is still in its infancy due to the short time of development and utilization, especially in terms of resistance to biotic and abiotic stresses. Therefore, improving tolerance of A. trifoliata to biotic and abiotic stresses is an urgent task for breeders.
SOD and nucleotide binding sites (NBS) genes are two major means by which plants resist abiotic and biotic stresses [1,26]. To date, the NBS gene family in A. trifoliata has been systematically identified and analyzed [27], but SOD genes have not yet been reported. To speed up theoretical research on adversity stress of A. trifoliata to promote progress in commercial exploitation, we systematically identified and analyzed the SOD genes of A. trifoliata (AktSOD), including gene structure, conserved motifs, homology and phylogenetic developmental relationships, based on its published high-quality reference genome. Based on the reported transcriptome data, the expression characteristics of SOD genes were also revealed during the fruit development of A. trifoliata and critical stage of resisting pathogen invasion, which will help us to initially explore the role of AktSOD genes in fruit development and resistance to biotic stress.

2. Materials and Methods

2.1. Identification and Analysis of AktSOD Genes in A. trifoliata

Genome sequence, protein sequence and annotation files of A. trifoliata downloaded from the National Genomics Data Center database under BioProject PRJCA003847 were employed to identify and analyze SOD genes. To identify SOD-encoding proteins, hidden Markov model (HMM) Cu/ZnSOD (PF00080) and Fe-MnSOD (PF02777 and PF00081) files downloaded from the Pfam database (http://smart.embl.de/smart/batch.pl, accessed on 28 December 2022) were used to filter protein sequences of A. trifoliata with the 1 × 10−5 e-value parameter [28]. The domains of candidate AktSOD proteins were further verified using Conserved Domain Database (CDD) at the National Center for Biotechnology Information (NCBI) (https://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/cdd/, accessed on 3 January 2023). The molecular weight (MW) and theoretical isoelectric point (pI) of proteins were computed via Expasy (https://www.expasy.org/, accessed on 3 January 2023). Subcellular localization was predicted by the online website Plant-mPLoc (http://www.csbio.sjtu.edu.cn/bioinf/plant-multi/, accessed on 3 January 2023). Conserved AktSOD protein sequence motifs were analyzed by MEME Suite (https://meme-suite.org/meme/tools/meme, accessed on 5 January 2023). To constberruct the phylogenetic relationship of AktSOD protein sequences, after multiple alignments of the SOD protein sequences using ClustalW (Kyoto University Bioinformatics Center, Japan) [29], a phylogenetic tree was constructed and drawn by the maximum likelihood method using MEGA 11 software with 1000 bootstrap replicates [29]. Finally, integrated mapping of the AktSOD protein structure, conserved motifs and intron–exon pattern was performed using TBtools software (version 1.0876, CJ chen, Guangzhou, China) [30].

2.2. Phylogenetic Tree Construction of Plants at Different Evolutionary Nodes

SOD protein sequences of Amborella trichopoda (basal angiosperm), Aquilegia coerulea (basal dicot), Arabidopsis thaliana (core dicot), and Oryza sativa (monocotyledon) were identified in the same way as those of A. trifoliata. The protein sequences of A. trichopoda and A. coerulea were downloaded from NCBI; those of A. thaliana and O. sativa were downloaded from Ensembl Plants (http://plants.ensembl.org/index.html, accessed on 6 January 2023). The evolutionary relationship was constructed using IQtree with 1000 bootstrap replicates [31], and the online tool iTOL (https://itol.embl.de/, accessed on 15 January 2023) was used for subsequent visualization [32].

2.3. Synteny, Replication and Chromosomal Distribution Analysis of AktSOD Genes

Synteny and replication analysis of AktSOD genes was performed using the MCScanX module of TBtools software [30]. Information regarding the physical location of AktSOD genes was obtained from the annotation file of the A. trifoliata genome. Then, chromosomal distribution and collinearity mapping of AktSOD genes were called using the Circos Gene View module of TBtools [30].

2.4. Cis-Acting Elements of the AktSOD Gene Family

To predict putative cis-acting elements in AktSOD gene promoters, the 2000 bp upstream sequence of AktSOD gene coding regions was analyzed using PlantCARE (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/, accessed on 10 January 2023) [33]. A heatmap of the quantity statistics results was prepared using the HeatMap module of TBtools [30].

2.5. Expression Analysis of AktSOD Genes in Fruit Development and Rinds at Different Disease Resistance Levels

Transcriptome data for A. trifoliata fruit tissues (flesh, rind and seeds) at four developmental stages (young, enlargement, coloring and maturity) were downloaded from the NCBI database (accession IDs: SAMN16551931-33, young stage; SAMN16551934-36, enlargement stage; SAMN16551937-39, coloring stage; SAMN16551940-42, mature stage). Transcriptome data for both the mixed pool of 24 lines exhibiting resistance and another mixed pool of 50 lines exhibiting susceptibility to fungal disease at three different developmental stages were also downloaded from the National Genomics Data Center database under BioProject PRJCA014987. First, transcriptome reads were aligned to the A. trifoliata reference genome using HISAT2 software with default parameters [34]. Second, fragments per kilobase of transcript per million fragments mapped (FPKM) values calculated by ESeq2 were used to estimate gene expression levels [35]. Finally, the expression level of AktSOD genes was converted to a heatmap by TBtools [30].

2.6. WGCNA of the Fruit Development Transcriptome

To investigate the metabolic network in which AktSOD genes may participate, 12 transcriptome sets consisting of three fruit tissues at four developmental stages were subjected to weighted gene coexpression network analysis (WGCNA) using the WGCNA shiny plugin of TBtools [30]. A total of 12,016 genes were included in the analysis after filtering out genes with FPKM < 1. Other analysis-related parameters were as follows: R2 cutoff = 0.85, module size = 30, and module cutree height = 0.25.

2.7. GO Annotation Analysis

Genes in the transcriptome during fruit development were divided into 18 modules by WGCNA. We determined the set of genes expressed in association with the AktSOD genes from the module where the genes are located. These gene sets were further subjected to Gene Ontology (GO) annotation analysis via the eggNOG website (http://eggnog-mapper.embl.de/, accessed on 20 January 2023) [36]. The GO Enrichment module of TBtools was used to perform GO enrichment analysis [30].

3. Results

3.1. Genome-Wide Identification of the SOD Gene Family in A. trifoliata

In this study, a total of 13 SOD genes were identified in the A. trifoliata genome through HMM analysis and domain validation (Table 1). These 13 SOD genes were renamed AktFSD1, AktFSD2, AktMSD1–AktMSD4, and AktCSD1–AktCSD7 according to metal factor type and chromosomal position. The length of the open reading frame of AktSOD genes varies greatly, from 2569 bp to 25,161 bp. The results showed that the sequence lengths of the 13 AktSOD proteins range from 120 (AktCSD7) to 329 (AktCSD5) aa, the molecular weights from 12.730 (AktCSD7) to 35.181 (AktCSD5) kDa, and the isoelectric points from 4.95 (AktFSD2) to 9.02 (AktMSD2) kDa. According to the prediction of subcellular localization, the products of the two FeSOD genes localize to mitochondria (AktFSD1) and chloroplasts (AktFSD2), those of the 4 MnSOD genes to mitochondria, those of the 7 Cu/ZnSOD to chloroplasts, and those of AktCSD2 and AktCSD7 to the cytoplasm.

3.2. Phylogenetic Classification of AktSODs in Plants at Different Evolutionary Nodes

To clarify the evolutionary relationship and the classification of AktSOD gene subfamilies, 38 reference SOD protein sequences from plants at different evolutionary nodes (Table S1), including 7 SODs of A. trichopoda (basal angiosperm), 11 SODs of A. coerulea (basal dicot), 9 SODs of A. thaliana (core dicot), 11 SODs of O. sativa (monocotyledon) and 13 SODs of A. trifoliata, were used to construct a phylogenetic tree. In the phylogenetic tree (Figure 1), all 30 Cu/ZnSOD genes in the 5 species grouped into one group, all 6 MnSOD genes and 12 FeSOD genes grouped into another group. Interestingly, the SODs of A. trifoliata frequently clustered with the SODs of A. coerulea.

3.3. Phylogeny and Conserved Motifs of AktSOD Genes

The 13 AktSODs were divided into two groups in the phylogenetic tree (Figure 2a): 7 Cu/ZnSODs were classified into one group; the other 6, consisting of 2 FeSODs and 4 MnSODs, were classified into another group. Identification of conserved domains indicated that the 2 Akt-FSODs and 4 Akt-MnSODs have similar domain compositions, with both containing an Sod_Fe_C and Sod_Fe_N domain. In contrast, Akt-Cu/ZnSODs have only 1 Sod_Cu domain (Figure 2b). Motif analysis further revealed similarities and differences in the protein sequences of the three subfamilies of AktSODs. A total of 10 conserved motifs were identified in the 13 AktSODs (Figure 2c, Table S2): motifs 1, 2, 6, and 9 are only present in Akt-Cu/ZnSODs; motifs 4, 5, 7, and 10 are common to Akt-FeSODs and Akt-MnSODs; motif 8 exists only in Akt-FeSODs; and motif 3 is unique to Akt-MnSODs. Structurally, the coding sequences of the 13 AktSODs are separated by multiple introns, with the number of introns ranging from 4 to 8 (Figure 2d; Table 1).

3.4. Chromosomal Distributions and Duplication Types of AktSODs

The chromosomal physical locations of the 13 AktSODs are depicted in Figure 3. Among the 16 chromosomes of A. trifoliata, 9 chromosomes harbor 13 AktSOD genes. Chromosomes 5, 6, 9, 10, 13 and 16 each carry an SOD gene, chromosomes 3 and 8 both carry 2 SOD genes, and chromosome 15 carries the remaining 3 SOD genes. Gene duplication analysis of the AktSOD family revealed dispersed duplication in 8 SOD genes; the other 5 SOD genes experienced segmental/wide genome duplication (WGD) (Table 1; Figure 3).

3.5. Detection of Cis-Acting Elements in the Promoter Sequence of AktSODs

Statistical results for putative cis-acting elements showed a large number of environmental and hormone-responsive elements to be distributed throughout the promoter region of AktSODs (Figure 4; Table S3). All AktSODs contain at least one light-responsive, stress-responsive and drought-inducible element. The number of light-responsive elements is greatest; AktFSD1 has the lowest number, at 5; AktMSD4 has the highest number, at 20. In addition, 5 plant hormone-responsive elements, including for abscisic acid (ABA), methyl jasmonate (MeJA), gibberellin (GA), salicylic acid (SA) and auxin, were detected in the promoter region of AktSODs, with the distribution varying. For example, AkCSD5 has only one hormone-responsive element, namely, the TCA element, which is annotated as responsive to salicylic acid (Table S3). AkCSD4, AkCSD7, AkFSD1, and AkMSD2 contain four types of hormone-responsive elements.

3.6. Expression Analysis of AktSODs in Different Tissues of A. trifoliata Fruit

Based on the expression analysis of AktSODs using flesh, seed and rind tissues, the expression of 12 AktSODs was detected, with the levels of most being similar in the flesh, seed and rind tissues at four developmental stages (young, enlargement, coloring, and mature stage) (Figure 5a; Table S4). Only the expression of AktCSD7 could not be detected in any of the samples. In contrast, the expression level of Cu/ZnSODs was higher than that of the other two subfamilies of SODs; AktCSD3 showed the highest expression level. Two FeSODs (AktFSD1 and AktFSD2) showed persistent low expression levels during the development of flesh, seed and rind tissues. Among the 4 MnSODs, AktMSD4 was continuously expressed at a high level, but AktMSD2 and AktMSD3 were only detected in trace amounts in some fruit tissues (Table S4). By comparing the total expression of AktSODs in flesh, seed and rind tissues, higher expression levels of AktCSD2, AktCSD3, AktMSD1 and AktMSD4 in flesh were observed; AktCSD1, AktCSD4 and AktCSD5 showed slightly higher expression levels in seeds, and only AktCSD6 displayed higher expression in rinds (Figure 5b). Overall, expression levels of AktFSD1 and AktFSD2 were extremely similar in the three fruit tissues (Figure 5b).

3.7. Metabolic Regulatory Network Involved in AktSODs in Fruit Development

We performed WGCNA on 12 transcriptome datasets during fruit development of A. trifoliata, and found that AktSODs participate in the metabolic regulatory network. The genes expressed in the transcriptomes after filtering low-expression genes were divided into 18 modules (Figure S1); 9 AktSODs were assigned to 6 modules, and the remaining 4 AktSODs were excluded due to low expression or no expression in fruit tissues. AktFSD1, AktFSD2 and AktCSD6 were assigned to the same module. AktCSD1 and AktCSD2 were assigned to another module, and the remaining 4 AktSODs were assigned to four different modules.
We further focused on the set of genes expressed in association with the 9 AktSODs from the module in which the AktSODs are located (Table S5). GO enrichment analysis was performed on the 9 AktSOD-associated gene sets, and the results are illustrated in Figure 6. The AktSOD genes assigned to the same module collectively participate in a large number of identical metabolic networks, but there are also differences. For example, the gene sets associated with the expression levels of AktCSD1 and AktCSD2 were enriched in the negative regulation of gene expression and chromatin organization. Conversely, AktCSD1-related genes were more assigned to the negative regulation of macromolecule metabolic processes, unlike AktCSD2. The gene sets associated with the expression levels of AktFSD1, AktFSD2 and AktCSD6 were all enriched in the obsolete cytoplasmic part and ribosomal subunit, and the metabolic network involving AktFSD1 and AktFSD2 was more similar than that of AktCSD6. In addition, it is worth noting that the gene set associated with the expression level of AktCSD4 is associated with the response to stress, and that the gene set associated with the expression level of AktMSD4 is related to fruit development.

3.8. Differential Expression of AktSODs in Resistant and Susceptible Rinds

Transcriptome data for rind tissues with different disease resistance levels were used to explore the expression of AktSODs in response to various pathogenic bacteria. By comparing the expression levels of AktSODs in resistant rinds (a mixed pool of 24 lines) and susceptible rinds (a mixed pool of 50 lines), it was found that almost all AktSODs were significantly expressed in resistant or susceptible rinds, except for AktCSD7 (Figure 7; Table S6). Among the 12 AktSODs, AktCSD2, AktFSD1, and AktFSD2 showed more drastic upregulation in resistant rinds during the period of rapid fruit expansion than in susceptible lines. In addition, the three MnSODs (AktMSD1, AktMSD2 and AktMSD3) were rapidly upregulated in resistant rinds, with extremely weak or even no expression in susceptible rinds.

4. Discussion

A. trifoliata is a newly domesticated fruit tree, horticultural crop and potential oil crop [37]. Abiotic and biotic stresses are the main factors that cause serious declines in the fruit yield and quality of artificially cultivated A. trifoliata. SOD genes have been reported to play a crucial role in biotic stress, abiotic stress and fruit growth and development. In our current research, the reference genome and transcriptome data available for A. trifoliata provided an opportunity to explore the function of AktSODs and their expression in response to fruit development and biotic stress.

4.1. The AktSOD Family Is Highly Conserved during Evolutionary Adaptation

In the current study, we identified 13 SOD genes in the A. trifoliata genome, including 2 FeSODs, 4 MnSODs and 7 Cu/ZnSODs. Similar to most angiosperms, the number of AktSOD family members is highly conserved in evolution, with almost no large-scale expansion, such as the 7 SOD genes in barley [38] and A. thaliana [39], the 9 SOD genes in tomato [40], the 10 SOD genes in grapevine [41], the 13 SOD genes in maize [42], and the 26 SOD genes in wheat [43]. The three AktSOD subfamilies are also highly conserved with regard to gene structure. Akt-FeSODs, Akt-MnSODs and Akt-Cu/ZnSODs include different motifs in their protein sequences, with a bias observed (Figure 2c). Gain and loss of introns/exons is a driving force of gene evolution [44]. Unlike the SOD genes of the tea plant [45] and rapeseed [46], the number of introns/exons of AktSOD genes has changed only slightly, especially in the same subfamily (Table 1). The intron–exon pattern of AktSODs also indicates their conservation in the evolutionary process.
Evolutionarily, different types of gene duplication may occur along different evolutionary trajectories, and may be preserved in a biased manner in different types of gene families [47]. In A. trifoliata, 5 (38.5%) AktSODs derived from genome-wide duplication events, among which 4 pairs of homologous Cu/ZnSODs show collinearity (Figure 3); the remaining 8 (61.5%) AktSODs derived from dispersed duplications (Table 1). It is worth noting that two WGD events occurred in the A. trifoliata genome for adaptation to drastic changes in the environment [48]. In A. trifoliata, the strong WGD only expanded Cu/ZnSOD genes by a few copies, whereas FeSODs and MnSODs appear to have been unaffected by WGD. This evolutionary evidence further demonstrates that AktSODs are highly conserved.

4.2. AktSODs Are Largely Functionally Diverse and Widely Involved in A. trifoliata Fruit Development

Overall, the physical properties of proteins play an important role in determining the biochemical function of the molecule [49]. Physical characterization of SOD proteins showed extensive differences in protein sequence length, isoelectric point and molecular weight in the 13 AktSOD proteins (Table 1). Further focusing on cis-elements in their promoter regions revealed a large number of light-responsive and hormone-responsive elements distributed in the 13 AktSODs (Figure 4). The abundant environmental and plant hormone-responsive elements in AktSOD promoters may be related to different roles or regulatory mechanisms in response to biotic and abiotic stresses. In addition, great variation in number and type exists, and some elements responding to metabolism and gene expression are specific to some SOD genes. For example, 6 (46.15%) AktSODs have meristem expression responsive cis-elements, but 5 (38.16%) AktSODs lack transcriptional activator responsive cis-elements (Figure 4). In general, differences in the structure of AktSODs may cause changes in protein function.
Differences in expression levels and tissue specificity of a gene family are often associated with functional differentiation [50]. Gene expression analysis showed 12 (92.31%) of the AktSODs to be involved in fruit growth and development. AktCSD3 and AktMSD4 were persistently expressed at high levels in flesh, seed and rind tissues, whereas AktMSD2 and AktMSD3 showed spatiotemporally specific expression during fruit development. Such specific expression of AktSODs indicates that they are involved in different physiological activities.
In previous studies, it has been reported that the main function of SOD genes is to respond extensively to various abiotic stresses [45], and increasing SOD activity is an effective way to improve stress resistance in plants [51,52]. However, in the process of fruit development, ROS is continuously released during vigorous metabolic activities [53], and the surface of the fruit is also attacked by various pathogenic bacteria, so the SOD genes also play an important role in the process of fruit development. In the current study, WGCNA of transcriptome data further revealed that these AktSODs participate in distinct metabolic networks during fruit development. First, the 9 (69.23%) AktSODs included in the analysis were assigned to 6 modules, and expression levels of 5 (39.46%) AktSODs were associated with other SOD genes, suggesting a cooperative division of labor between AktSOD genes. Second, the gene sets associated with AktSODs were enriched in different molecular function, biological process and cellular component networks, also confirming that the metabolic network pathways regulated by AktSODs are different. Through enrichment analysis, we also inferred that AktCSD4 is extremely likely to be involved in the stress response, and that AktMSD4 may be involved in the regulation of fruit development because the associated expression gene set was enriched in the corresponding pathway.

4.3. Three MnSODs May Play an Important Role in Resisting Invasion of Pathogenic Bacteria

The relationship between SODs and plant disease resistance has been extensively studied due to its focus on the regulation of endogenous ROS [54]. A large number of reports indicate that some SOD genes can enhance the resistance of plants to specific pathogens. For example, tobacco has been transformed with a Cu/ZnSOD gene from Spinacia oleracea, not only improving its tolerance to water stress but also its resistance to Pseudomonas syringae pv. tabaci [55]. Another study reported that after a MnSOD gene derived from oil radish was transferred to broccoli, the transgenic lines showed a higher resistance to downy mildew [56]. Comparing expression levels of SOD genes in the rinds of various resistant and susceptible lines, we found that some SOD genes may be induced by pathogenic bacteria under natural conditions. For instance, 3 Akt-MnSOD genes, AktMSD1, AktMSD2 and AktMSD3, were expressed at very low levels or even not expressed during the development of fruit tissues and in susceptible rinds, but they were stably upregulated in resistant rinds (Figure 7). Such inducible expression of these 3 MnSOD genes in resistant rinds suggests that they might play an important role in the defense against pathogenic bacteria.

5. Conclusions

In this bioinformatics study, a total of 13 SODs classified into three categories were identified in the reference genome of A. trifoliata. The phylogeny, motif composition, intron–exon pattern and replication type of the AktSODs all indicate that these SODs of A. trifoliata are extremely conserved in the evolutionary process, and that only a few copies have undergone expansion by segmental duplication/WGD and dispersed duplication. WGCNA of the transcriptome of A. trifoliata fruit revealed the metabolic network in which AktSOD genes may be involved during fruit development, with AktMSD4 being involved in responding to stress and AktCSD4 possibly regulating fruit development. Comparing the expression of AktSOD genes in resistant and susceptible rinds, it was found that AktMSD1, AktMSD2 and AktMSD3 are induced by pathogens and may be involved in defense against these organisms. Overall, this study lays the foundation for improving biotic and abiotic stress responses of A. trifoliata and provides information on the regulation of AktSOD gene expression, especially during fruit development.

Supplementary Materials

The following supporting information can be downloaded at https://0-www-mdpi-com.brum.beds.ac.uk/article/10.3390/antiox12030726/s1, Figure S1: WGCNA of the fruit developmental transcriptome; Table S1: SOD sequences in four different evolutionary node species; Table S2: The information of identified 10 motifs in AktSOD proteins; Table S3: Detailed information of cis-acting elements in the 2000 bp region of SOD gene coding regions; Table S4: The expression level of 13 SOD genes in the fruit transcriptome of A. trifoliata; Table S5: List of genes expressed in association with AktSOD genes in the same module; Table S6: The expression level of SOD genes in resistant and susceptible rinds of A. trifoliata.

Author Contributions

Conceptualization, H.Y. (Huai Yang), G.C. and P.L.; methodology, H.Y. (Huai Yang), Q.Z. and S.Z.; software, Q.Z., H.Y. (Huai Yang) and H.Y. (Hao Yang); validation, C.C., F.T. and T.R.; formal analysis, H.Y. (Huai Yang); resources, P.L.; data curation, H.Y. (Huai Yang) and S.Z.; writing—original draft preparation, H.Y. (Huai Yang); writing—review and editing, H.Y. (Huai Yang) and P.L.; visualization, H.Y. (Huai Yang); supervision, J.L., T.R. and F.T.; project administration, P.L.; funding acquisition, P.L. All authors have read and agreed to the published version of the manuscript.

Funding

This research was supported by the Science and Technology Department of Sichuan Province, grant numbers 2020YFN0057 and 2022ZHXC0002, and the Bureau of Science and Technology of Chengdu, grant numbers 2021-YF05-01863-SN and 2021-YF05-01328-SN.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

All data analyzed during this study are included in the manuscript and Supplementary Information files. Genome sequence files of A. trifoliata were downloaded from the National Genomics Data Center database under BioProject PRJCA003847. Transcriptome data for A. trifoliata were downloaded from the NCBI database under accession numbers PRJNA671772, SAMN16551931–33, SAMN16551934–36, SAMN16551937–39, SAMN16551940–42 and the National Genomics Data Center database under BioProject PRJCA014987.

Acknowledgments

We are grateful to the Science and Technology Department of Sichuan Province and the Bureau of Science and Technology of Chengdu for supporting this study.

Conflicts of Interest

The authors declare no conflict of interest.

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Figure 1. Phylogenetic tree of SOD genes from 4 plants: A. trichopoda, A. coerulea, A. thaliana and O. sativa (the numbers at nodes indicates bootstrap numbers per 1000 replicates determined by maximum likelihood methods).
Figure 1. Phylogenetic tree of SOD genes from 4 plants: A. trichopoda, A. coerulea, A. thaliana and O. sativa (the numbers at nodes indicates bootstrap numbers per 1000 replicates determined by maximum likelihood methods).
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Figure 2. Gene and protein structure analyses of AktSOD families. (a) Phylogenetic tree of AktSOD genes. (b) Conserved domains of AktSOD proteins. (c) Motifs of AktSOD proteins. (d) Exon–intron structures of AktSOD genes.
Figure 2. Gene and protein structure analyses of AktSOD families. (a) Phylogenetic tree of AktSOD genes. (b) Conserved domains of AktSOD proteins. (c) Motifs of AktSOD proteins. (d) Exon–intron structures of AktSOD genes.
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Figure 3. Chromosomal localization and interchromosomal synteny of AktSODs. Red lines in the inner circle represent syntenic gene pairs from WGD/fragment duplications.
Figure 3. Chromosomal localization and interchromosomal synteny of AktSODs. Red lines in the inner circle represent syntenic gene pairs from WGD/fragment duplications.
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Figure 4. Analysis of cis-regulatory elements in the 2 kb region upstream of the transcription start site of AktSODs.
Figure 4. Analysis of cis-regulatory elements in the 2 kb region upstream of the transcription start site of AktSODs.
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Figure 5. Expression levels of 13 AktSODs in different tissues and developmental stages (FT: flesh, ST: seed, RT: rind, 1: young stage, 2: enlargement stage, 3: coloring stage, 4: mature stage). (a) Heatmap of expression of 13 AktSODs in three fruit tissues at four stages. (b) Total expression of AktSODs in three fruit tissues contains the total FPKM of each fruit tissue in its four development stages. The error bars of the column represent the standard deviation of FPKM in the four development stages. The different colors of the column represent three subfamilies of AktSODs.
Figure 5. Expression levels of 13 AktSODs in different tissues and developmental stages (FT: flesh, ST: seed, RT: rind, 1: young stage, 2: enlargement stage, 3: coloring stage, 4: mature stage). (a) Heatmap of expression of 13 AktSODs in three fruit tissues at four stages. (b) Total expression of AktSODs in three fruit tissues contains the total FPKM of each fruit tissue in its four development stages. The error bars of the column represent the standard deviation of FPKM in the four development stages. The different colors of the column represent three subfamilies of AktSODs.
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Figure 6. GO enrichment analysis of gene sets associated with AktSOD expression.
Figure 6. GO enrichment analysis of gene sets associated with AktSOD expression.
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Figure 7. Expression-level analysis of 13 AktSODs in resistant and susceptible rinds.
Figure 7. Expression-level analysis of 13 AktSODs in resistant and susceptible rinds.
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Table
Table 1. Characteristics of the SOD gene families identified in the A. trifoliata genome.
Table 1. Characteristics of the SOD gene families identified in the A. trifoliata genome.
NameGene IDSOD TypeAApIMW (kDa)Number of ExonNumber of IntronDuplication TypeSubcellular
Localization
AktCSD1EVM0009170Cu/ZnSOD1525.6615.36287WGD/SegmentalChloroplas.
AktCSD2EVM0011294Cu/ZnSOD1606.7923.23876DispersedChloroplast, Cytoplasm
AktCSD3EVM0015107Cu/ZnSOD1695.2717.11887WGD/SegmentalChloroplast
AktCSD4EVM0004711Cu/ZnSOD2146.3921.89587WGD/SegmentalChloroplast
AktCSD5EVM0014685Cu/ZnSOD3295.3635.18176DispersedChloroplast
AktCSD6EVM0003060Cu/ZnSOD2236.7923.23887WGD/SegmentalChloroplast
AktCSD7EVM0005862Cu/ZnSOD1206.212.73065WGD/SegmentalChloroplast, Cytoplasm
AktFSD1EVM0017725FeSOD2057.1124.06587DispersedMitochondrion
AktFSD2EVM0016720FeSOD3014.9534.73498DispersedChloroplast
AktMSD1EVM0002565MnSOD1717.8918.53876DispersedMitochondrio
AktMSD2EVM0008804MnSOD1479.0216.15454DispersedMitochondrion
AktMSD3EVM0020914MnSOD1587.7817.43354DispersedMitochondrion
AktMSD4EVM0011812MnSOD2438.3827.29365DispersedMitochondrion
Abbreviations: AA, the number of amino acids; pI, isoelectric point; MW, theoretical subunit size of the proteins.
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Yang, H.; Zhang, Q.; Zhong, S.; Yang, H.; Ren, T.; Chen, C.; Tan, F.; Cao, G.; Liu, J.; Luo, P. Genome-Wide Identification of Superoxide Dismutase and Expression in Response to Fruit Development and Biological Stress in Akebia trifoliata: A Bioinformatics Study. Antioxidants 2023, 12, 726. https://0-doi-org.brum.beds.ac.uk/10.3390/antiox12030726

AMA Style

Yang H, Zhang Q, Zhong S, Yang H, Ren T, Chen C, Tan F, Cao G, Liu J, Luo P. Genome-Wide Identification of Superoxide Dismutase and Expression in Response to Fruit Development and Biological Stress in Akebia trifoliata: A Bioinformatics Study. Antioxidants. 2023; 12(3):726. https://0-doi-org.brum.beds.ac.uk/10.3390/antiox12030726

Chicago/Turabian Style

Yang, Huai, Qiuyi Zhang, Shengfu Zhong, Hao Yang, Tianheng Ren, Chen Chen, Feiquan Tan, Guoxing Cao, Jun Liu, and Peigao Luo. 2023. "Genome-Wide Identification of Superoxide Dismutase and Expression in Response to Fruit Development and Biological Stress in Akebia trifoliata: A Bioinformatics Study" Antioxidants 12, no. 3: 726. https://0-doi-org.brum.beds.ac.uk/10.3390/antiox12030726

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