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Article

Genome-Wide Identification and Expression Analysis of the Mediator Complex Subunit Gene Family in Cassava

by
Lingling Zhou
1,†,
Shuhui Sun
1,†,
Linlong Zhu
1,
Xian Chen
1,
Ran Xu
1,
Lian Wu
1,2,* and
Shuang Gu
1,2,*
1
School of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China
2
School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Int. J. Mol. Sci. 2025, 26(4), 1666; https://doi.org/10.3390/ijms26041666
Submission received: 19 January 2025 / Revised: 9 February 2025 / Accepted: 13 February 2025 / Published: 15 February 2025
(This article belongs to the Special Issue Research on Plant Genomics and Breeding: 2nd Edition)
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Abstract

The Mediator complex (MED) functions as a co-activator in plants, transmitting transcriptional signals to regulate gene expression, including responses to environmental stresses. While the MED gene family has been identified in several species, it has not yet been reported in cassava. In this study, we identified 32 members of the MeMED gene family in cassava (Manihot esculenta Crantz) distributed across 13 chromosomes. These genes were categorized into distinct Mediator subunits based on their similarity to Arabidopsis modules. Promoter analysis revealed the presence of various cis-regulatory elements, which likely play key roles in regulating plant growth, development, and stress responses. RNA-seq data showed tissue-specific expression patterns for the MeMED genes, with significant expression observed in leaves, roots, petioles, stems, friable embryogenic callus, and shoot apical meristems. Further RT-qPCR analysis under various abiotic stress conditions—including drought, exogenous hydrogen peroxide, cold, heat, and salt—demonstrated that 10 selected MeMED genes exhibited significant differential expression, indicating their potential functional involvement in stress adaptation. These findings offer insights into the biological roles of the MeMED gene family in cassava, with implications for improving stress tolerance in future breeding programs.

1. Introduction

The Mediator complex is an evolutionarily conserved multi-protein complex found across eukaryotes, playing a crucial role in regulating plant growth, development, defense, and hormone signaling [1,2]. It facilitates transcription by recruiting RNA polymerase II (Pol II) to specific gene promoters, linking transcription factors (TFs) bound at activators and repressors to the pre-initiation complex (PIC). Upon receiving regulatory signals, the Mediator complex undergoes conformational changes, creating a flexible surface that helps assemble the PIC. Acting as a molecular bridge, Mediator interacts with both the PIC and TFs to promote transcriptional activation [3,4].
Structurally, the core Mediator complex is divided into three main modules, namely the head, middle, and tail modules [5]. Each module comprises distinct subunits, contributing to the unique functional roles in transcription regulation [6]. While the number of subunits varies across species, plants typically have around 34 Mediator subunits [7]. The head module mainly interacts with Pol II to facilitate transcription, while the tail module is integral for binding gene-specific TFs. The middle module is responsible for transferring transcriptional signals between the tail and head modules and may also interact with Pol II directly [8]. Additionally, the kinase module, known as the CDK8 module, consists of CDK8, C-type cyclin (CycC), MED12, and MED13.
In recent years, multiple studies have highlighted the essential role of the Mediator complex in activating gene transcription in plants, particularly under environmental stresses such as salt, drought, cold, and heat [9,10,11]. Among its subunits, MED25 plays a positive role in salt stress responses by activating salt stress-responsive genes through interactions with key regulatory proteins, including DREB2A, ZINC FINGER HOMEODOMAIN 1 (ZFHD1), and MYB-like. The function of MED25 in salt tolerance appears to be conserved across land plants. For instance, knocking out PpMED25A in Physcomitrella patens (a moss) increases the plant’s sensitivity to salt stress [12]. Similarly, the med18 mutant in Arabidopsis exhibits salt sensitivity, and MED18 interacts with NUCLEOPORIN85 (NUP85) to regulate stress-responsive genes [13]. A recent study identified four Mediator subunits—MED9, MED16, MED18, and CDK8—each representing a distinct module, as essential regulators of transcriptional responses to salt and heat stress in Arabidopsis, as revealed by RNA-seq analysis [14]. The med19a mutant exhibits reduced drought resistance, characterized by faster water loss from its leaves and a lower survival rate under drought conditions [15]. Additionally, MED16, MED14, and MED2 are crucial for activating the ABRE motif in response to ABA signaling. Mutants of these subunits are insensitive to ABA-induced growth inhibition and lose water more rapidly than wild-type plants, highlighting their specific role in drought adaptation [16]. Recent studies have also linked CDK8 to drought stress regulation. Mutations in CDK8 lead to increased stomatal density, impaired stomatal aperture control, and reduced drought tolerance. Conversely, the overexpression of CDK8 enhances drought resistance [17].
Among the Mediator subunits, MED16 is one of the earliest identified components involved in abiotic stress responses. It plays a critical role in cold stress tolerance by initiating physiological and metabolic adjustments that sustain cellular homeostasis. Before being classified as part of the Mediator complex, MED16 was referred to as SENSITIVE TO FREEZING6 (SFR6) and was recognized for its contribution to cold acclimation and enhanced freezing tolerance [18]. Additionally, VuMED16 genes in asparagus bean have been found to influence cell wall modifications under cold stress, suggesting that the function of MED16 in cold stress responses may be evolutionarily conserved across different plant species [19]. Further investigations into the rao1 mutant of Arabidopsis, which carries a mutation in CDK8, have revealed that CDK8 is also involved in mitochondrial retrograde signaling under H2O2-induced oxidative stress and cold stress conditions [20].
More recently, the Mediator complex has been implicated in heat stress responses. In Arabidopsis, MED14 and MED17 mutants exhibit lower survival rates after heat treatment, reduced heat tolerance, and impaired acquired thermotolerance. Notably, approximately 25% of heat stress-induced genes are significantly downregulated in these mutants, further emphasizing the role of the Mediator complex in heat stress adaptation [21].
Overall, these studies collectively highlight the crucial role of the Mediator complex and its associated subunits in plant responses to abiotic stresses, including salt, drought, cold, and heat. Further research is needed to elucidate the precise molecular mechanisms through which these Mediator subunits coordinate stress adaptation in plants.
Cassava (Manihot esculenta Crantz), a member of the Euphorbiaceae family, is the sixth-largest food crop globally [22] and the third-largest source of caloric energy [23]. It provides essential dietary energy to nearly one billion people in tropical regions, including Africa and Latin America, playing a vital role in smallholder economies and food security. Known for its tolerance to drought and poor soils, cassava has become increasingly important as a climate-resilient crop in response to growing population pressures. However, improving cassava yield and quality remains challenging due to both biotic and abiotic stresses, as well as limited breeding technologies.
Members of the MED gene family have been relatively well characterized in species such as Arabidopsis, rice, and asparagus bean through genomic analysis [7,19]. However, the MeMED gene family in cassava has not been thoroughly studied. In this study, we conducted a comprehensive analysis of the MeMED gene family in cassava using assembled genome data. We examined the phylogenetic relationships, gene structures, chromosomal locations, synteny, and cis-elements to better understand their evolutionary patterns and potential functions. Additionally, we explored the expression profiles of MeMED genes across various cassava tissues using publicly available transcriptome data. We also assessed the responses of MeMED genes to different abiotic stresses through quantitative real-time RT-PCR (qRT-PCR). Our findings provide valuable insights that will guide the future functional characterization of MeMED genes in cassava.

2. Results

2.1. Identification of the MeMED Gene Family in Cassava

Through BlastP sequence alignment and querying the Conserved Domains Database (CDD), we identified a total of 32 members of the MeMED gene family in the cassava genome (Table 1). These 32 MeMED genes are distributed across 13 chromosomes (LG1, LG3, LG4, LG5, LG6, LG8, LG9, LG11, LG13, LG14, LG15, LG16, and LG17), and were named MeMED33_3 to MeCdk8_1 based on their Arabidopsis homologs (Table 1). The physicochemical characteristics of the 32 MeMED genes are summarized in Table 1.
The CDS lengths of these genes ranged from 318 bp (MeMED28_2) to 6798 bp (MeMED12_1), with an average CDS length of 2004 bp. Corresponding amino acid lengths varied from 106 (MeMED28_2) to 2266 (MeMED12_1), with an average length of 668.22 amino acids. The molecular weights of the proteins ranged from 12.41 kD (MeMED28_2) to 250.6 kD (MeMED12_1), with an average weight of 73.33 kD. The theoretical isoelectric points (pI) ranged from 4.4 (MeMED21_1) to 9.28 (MeMED31_1), with 24 proteins (75%) having a pI lower than seven, indicating they are weakly acidic, and eight proteins (25%) having a pI greater than seven, indicating they are alkaline. The hydrophilicity of the proteins encoded by the MeMED genes ranged from −0.948 to 0.227.
The Mediator subunits in cassava were categorized according to the Arabidopsis Mediator modules. Among them, nine subunits were assigned to the head module, nine to the middle module, nine to the tail module, four to the kinase module, and one subunit could not be classified (Table 1). Chromosomes 8 and 9 each contained a relatively large number of genes, with five genes on each chromosome. Chromosomes 4, 11, 15, and 16 each harbored one MeMED gene. Additionally, chromosomes 1, 5, and 9 each contained a gene cluster, with the following gene pairs: MeMED33_3 and MeMED28_2, MeMED28_1 and MeMED33_4, and MeMED21_2 and MeMED26_2 (Figure 1).

2.2. Phylogenetic Analysis of Cassava MeMED Proteins

We constructed a phylogenetic tree for 125 MeMED proteins (42 from Arabidopsis, 32 from Manihot esculenta Crantz, and 51 from Oryza sativa) to study the evolutionary relationships of MeMED proteins across these species (Figure 2). Based on their evolutionary divergence, the MeMED proteins in cassava can be classified into three subclades. The first subclade includes nine proteins, namely MeMED11_1, MeMED7_1, MeMED6_1, MeMED6_2, MeMED16_1, MeMED25_1, MeMED21_2, MeMED21_1, and MeMED4_1. Among them, three pairs of orthologous MED members are shared between cassava and rice as follows: MeMED11_1 and OsMED11_1, MeMED25_1 and OsMED25_1, and MeMED4_1 and OsMED4_1. The second subclade includes 10 proteins, namely MeMED22_1, MeMED27_1, MeMED32_1, MeMED12_2, MeMED10_1, MeMED13_1, MeMED14_2, MeMED20_1, MeMED31_1, and MeCdk8_1. Among these, one pair of orthologous MED members is shared between cassava and rice, which is MeMED13_1 and OsMED13_1. The third subclade includes 13 proteins, with two pairs of orthologous MED members shared between cassava and rice as follows: MeMED23_1 and OsMED23_1, and MeMED17_1 and OsMED17_1. Based on the Ka/Ks ratio, the selective pressure on genes can generally be inferred: a Ka/Ks ratio greater than one suggests positive selection, a ratio less than one indicates purifying selection, and a ratio of one is associated with neutral selection. The Ka/Ks ratios for the MeMED gene pairs range from 0.08 to 0.59, reflecting that all the MeMED gene pairs are under negative or purifying selection (Ka/Ks < 1) (Table S1). These results indicate that purifying selection has played a role in preserving the conservation of the MeMED gene structure during domestication or evolutionary processes.
Gene synteny analysis across species revealed that 12 MeMED members in cassava exhibit synteny with AtMED members in Arabidopsis. These cassava genes are distributed on chromosomes 1, 4, 5, 8, 9, 11, 13, 14, 15, and 17, while the corresponding Arabidopsis genes are located on five chromosomes (Figure 3). Additionally, five MeMED members in cassava show synteny with OsMED members in Oryza sativa. These cassava genes are located on chromosomes 6, 8, 13, and 17, while the corresponding rice genes are distributed on chromosomes 2, 5, 9, and 10 (Figure 3).

2.3. Analysis of Gene Structure and Cis-Acting Elements of the Cassava MeMED Genes

Based on gene sequence similarity, we classified the 32 MeMED genes into three distinct groups. The largest group contains 19 MeMED genes, while the other two groups consist of nine and four MeMED genes, respectively (Figure 4). The number of exons in MeMED genes ranges from 1 to 23. For example, MeMED4_1, MeCdk8_1, and MeMED32_1 each contain a single exon, while MeMED13_1 contains 23 exons (Figure 4). These results indicate significant functional divergence among the MeMED genes during their evolutionary process.
Cis-regulatory elements play a crucial role in regulating gene expression. To identify the types of regulatory elements, we analyzed the 2 kb promoter sequences of all MeMED genes using the PlantCARE database. The promoter regions of MeMED genes primarily contain four categories of cis-regulatory elements, including light-responsive, hormone-responsive, stress-inducible, and core elements/binding sites (Figure 5). Most MeMED genes are associated with light-responsive elements, such as G-Box, GA-motif, GT1-motif, GATA-motif, TCT-motif, ACE, I-box, Gap-box, TCCC-motif, AE-box, 3-AF1 binding site, chs-CMA1a, Sp1, LAMP-element, and ATCT-motif. Hormone-responsive elements include abscisic acid-responsive elements (ABRE), methyl jasmonate-responsive elements (TGACG-motif, CGTCA-motif), salicylic acid-responsive elements (TCA-element), auxin-responsive elements (AuxRE, TGA-element), and gibberellin-responsive elements (GARE-motif, P-box, TATC-box). Stress-inducible elements include low-temperature-responsive elements (LTR) and defense/stress-related elements (TC-rich repeats, WUN-motif). Core elements and binding sites include O2-site, CCAAT-box, and MBS (Table S2). These findings suggest that MeMED genes may play significant roles in plant growth, development, and stress resistance.

2.4. Expression Profiles of MeMED Genes in Different Tissues of Cassava Based on RNA-Seq

To explore the potential function of the MeMED gene in cassava, we analyzed RNA-seq data from the GEO database to examine the expression patterns of MeMED gene family members across seven different tissues. Transcriptome analysis revealed that 32 MeMED genes exhibited detectable transcriptional abundance across seven different organs, with significant expression differences observed among genes in various tissues (Figure 6). Specifically, MeMED22_1, MeMED10_1, MeMED7_1, and MeMED11_1 were highly expressed in leaves; MeMED22_1, MeMED10_1, and MeMED11_1 showed high expression levels in roots; MeMED22_1, MeMED10_1, MeMED32_1, MeCycC_1, MeMED7_1, and MeMED11_1 were highly expressed in petioles; MeMED22_1, MeMED10_1, and MeMED21_1 were highly expressed in stems; and MeMED23_1, MeMED22_1, and MeMED10_1 were highly expressed in friable embryogenic callus. Notably, MeMED22_1 and MeMED10_1 were highly expressed in shoot apical meristems. Additionally, MeMED28_2 and MeMED37_1, except in friable embryogenic callus, showed relatively low expression across the seven organs, indicating that they may be non-functional (Figure 6). These findings suggest that members of the MeMED gene family may exhibit functional differentiation in cassava.

2.5. Expression Analysis of MeMED Genes in Response to Abiotic Stresses

Based on the RNA-seq expression profile, we selected 10 MeMED genes that are highly expressed across various tissues to analyze their expression in response to abiotic stresses. To investigate the expression of these genes under abiotic stresses (drought, exogenous hydrogen peroxide, cold, heat, and salt), tissues were analyzed at 4 h, 8 h, 12 h, and 24 h after treatment using RT-qPCR. The results indicated that the 10 MeMED genes were relatively sensitive to drought, exogenous hydrogen peroxide, cold, heat, and salt treatments (Figure 7). For example, the expression of MeCdk8_1 significantly increased from 4 h to 24 h hours under drought and heat treatments, whereas it significantly decreased under exogenous hydrogen peroxide treatment. The expression of MeMED7_1 was significantly upregulated after 4 h of salt treatment, reaching its highest level at 8 h. The expression of MeMED16_1 was significantly upregulated at 4 h post-cold treatment and then decreased to its lowest level at 24 h. MeMED11_1 showed a significant upregulation at 12 h after heat treatment. Interestingly, MeMED20_1, MeMED22_1, MeMED23_1, and MeMED31_1 exhibited similar expression patterns after drought treatment, with significant upregulation, while their expression levels decreased under exogenous hydrogen peroxide, cold, heat, and salt treatments. Furthermore, the expression of MeMED21_1 displayed a unique pattern, significantly increasing after 8 h of drought and cold treatments. These findings suggest that the MeMED genes may exhibit functional differentiation in response to various stress conditions.

3. Discussion

Given the crucial role of MeMED genes in various physiological processes, including responses to biotic and abiotic stresses [16], it is important to investigate their potential functions in cassava. Currently, MeMED genes have been identified and phylogenetically analyzed in only a few plants [7,19]. However, MeMED genes have not yet been identified in cassava. In this study, we identified 32 MeMED genes in the cassava genome (Table 1 and Figure 1). This number is lower than that found in Arabidopsis, rice, and asparagus bean. The variation in the number of MeMED genes across species not only reflects differences in their evolutionary history but may also be linked to factors such as genome characteristics, ecological adaptation, and stress response mechanisms.

3.1. Phylogenetic Relationships and Evolution of the MeMED Gene Family

Analyzing the phylogenetic relationships and evolutionary patterns of gene families across different species provides valuable insights into gene conservation, functional diversification, and the evolutionary history of these genes. In our phylogenetic analysis of the 32 MeMED genes in cassava, we compared them with homologous genes from Arabidopsis and rice. The results revealed that the cassava MeMED gene family is closely related to the MED gene families of other plant species, suggesting a conserved evolutionary history. For example, three pairs of orthologous MED genes were identified between cassava and rice, namely MeMED11_1 and OsMED11_1, MeMED25_1 and OsMED25_1, and MeMED4_1 and OsMED4_1 (Figure 2).
Furthermore, the presence of orthologous gene pairs between cassava and rice strengthens the hypothesis of a shared ancestral origin for these genes. Despite the divergence of cassava (Euphorbiaceae) and rice (Poaceae) into separate plant families, the observed synteny between the two species suggests that the MeMED gene family in both plants likely originated from a common ancestor. This highlights the conserved nature of the MeMED family and provides insights into its evolutionary conservation across distantly related species.

3.2. Regulation of MeMED Genes by Cis-Acting Elements

Analyzing the cis-regulatory elements in the promoter regions of plant genes is essential for understanding the mechanisms that regulate gene expression [24]. The analysis of cis-regulatory elements in the promoter regions of MeMED genes revealed that many of these genes are associated with light-responsive, hormone-responsive, and stress-inducible elements (Figure 5). These findings suggest that MeMED genes play crucial roles in regulating plant growth, development, and responses to various environmental stresses. The observation that most MeMED genes contain light-responsive elements further supports the possibility that they are involved in regulating processes that respond to changing environmental light conditions, such as photomorphogenesis or circadian rhythm regulation.
The presence of stress-related elements, such as low-temperature-responsive (LTR) motifs and defense-/stress-related sequences, underscores the potential importance of these genes in cassava’s adaptation to abiotic stresses, particularly low temperature. This is especially relevant considering the increasing frequency and intensity of climate-induced stresses affecting crop production globally. In other plants, some MeMED genes associated with low temperature have been well studied. For example, AtMED16 in Arabidopsis is involved in the CBF (C-repeat binding factor) pathway, which is a central mechanism in cold stress response [25]. Furthermore, AtMED16, along with AtMED14 and AtMED2, is required for the expression of certain cold-responsive genes that are induced by low temperatures. However, it is important to note that not all cold-responsive genes are regulated by these factors, indicating a complex and specific regulation of gene expression under cold stress [16]. This emphasizes the multifaceted role of MeMED genes, which may function similarly in cassava, regulating a subset of cold-responsive genes while leaving others unaffected.

3.3. Expression Characteristics of MeMED Genes in Response to Stress

The Mediator complex plays a pivotal role as a co-activator in transcriptional regulation in plants, participating in nearly all gene transcription processes. Numerous studies have emphasized its involvement in abiotic stress responses, highlighting the complex’s role in modulating stress-related genes [7,26]. In this study, we investigated the expression changes in ten cassava MeMED genes under various stress treatments (Figure 7). Most of these genes exhibited significant alterations in expression throughout the stress treatments, underscoring the crucial role of MeMED genes in cassava’s response to environmental stresses. Previous studies have confirmed the crucial role of CDK8 in responses to drought, salt, and cold stresses [14,17,20]. Our study yielded similar results, demonstrating that MeCdk8_1 exhibited a significant increase in expression under both drought and heat stress, suggesting its potential involvement in regulating the cell cycle and stress responses. Notably, its expression was markedly lower under hydrogen peroxide treatment, indicating a possible role in oxidative stress regulation. These findings highlight the versatility of MeCdk8_1 in responding to various stress signals and suggest that it may play a similarly critical role in multiple stress responses in cassava. Further research is needed to elucidate its precise function and underlying mechanisms in stress tolerance.
Interestingly, MeMED16_1 was significantly upregulated at 4 h post-cold treatment before its expression declined to its lowest level at 24 h, suggesting its involvement in early cold stress signaling. These findings align with previous studies, which demonstrated that At-MED16 detects nuclear signals, participates in cold response pathways, and enhances nuclear replication and cell growth in Arabidopsis [25,27]. Moreover, our results are consistent with those of VuMED16 in asparagus bean, which has been shown to modulate cell wall responses to cold stress [19].
Multiple studies in Arabidopsis have also reported the role of AtMED genes in salt stress, including AtMED25 [12], AtMED18 [13], and Atcdk8 genes [14]. In Arabidopsis, AtMED16, AtMED14, and AtMED2, as essential Mediator subunits, participate in the activation of ABRE motif-mediated regulation. Mutant plants lacking these genes are insensitive to ABA-induced growth inhibition but exhibit a significantly higher water loss rate in detached leaves compared to the wild-type, underscoring the specific role of these genes in drought response [16]. In contrast, MeMED11_1 showed a marked upregulation after heat stress, further suggesting that it may be implicated in the heat stress response. The consistent upregulation of MeMED20_1, MeMED22_1, MeMED23_1, and MeMED31_1 under drought conditions, followed by a decline in expression under other stresses, indicates that these genes may play more specific roles in drought tolerance and possibly share common regulatory pathways related to water deficit.
Of particular interest is MeMED21_1, which exhibited a unique expression pattern: it significantly increased after 8 h of drought and cold treatments, suggesting that it may play a dual role in mediating responses to both drought and cold stresses. This dual regulation could enhance cassava’s adaptability to multiple environmental stresses, potentially contributing to its stress tolerance. These findings are consistent with previous research on Arabidopsis, where AtMED25 has been shown to regulate responses to both drought and salt stresses [12]. Further research on MeMED21_1 could elucidate its precise molecular mechanisms and provide valuable insights for improving stress resilience in cassava cultivation.

4. Material and Methods

4.1. Mining of MED Family in Manihot esculenta

In our study, we searched the TAIR database to obtain the MED protein sequences for Arabidopsis (https://www.arabidopsis.org/, accessed on 2 July 2024) [28]. These sequences were used as query sequences and were blasted against the cassava genome (Manihot esculenta v8.1) available online at phytozome (https://phytozome-next.jgi.doe.gov/info/Mesculenta_v8_1, accessed on 1 July 2024) using the BlastP tool (https://phytozome-next.jgi.doe.gov/blast-search, accessed on 2 July 2024). After removing duplicates, the non-redundant protein sequences were analyzed using SMART (http://smart.embl-heidelberg.de/, accessed on 2 July 2024) and NCBI conserved domain searches (https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi, accessed on 4 July 2024) [29]. The final MED proteins were renamed according to their physical positions in the cassava genome (Manihot esculenta v8.1). The MED modules (head, tail, middle, unknown, and kinase) were named according to the A. thaliana MED genes module [7]. Additionally, the physicochemical properties of the 32 MeMED proteins, including protein length (aa), theoretical isoelectric point (pI), molecular weight (kDa), and grand average of hydropathicity (GRAVY), were computed using ProtParam (https://web.expasy.org/protparam/, accessed on 8 July 2024) [30].

4.2. Phylogeny of Cassava MED Proteins

To construct the phylogenetic tree of MeMED proteins, the protein sequences of cassava, A. thaliana, and Oryza sativa were first aligned using MEGA software (Version 7) [31]. The maximum likelihood tree was then generated using IQ-TREE software, version 2.0 (http://www.iqtree.org, accessed on 11 July 2024) [32] with bootstrap values set to 1000 replicates. The resulting phylogeny was further refined using ITOL (https://itol.embl.de/, accessed on 14 July 2024) [33].

4.3. Gene Structural Analysis of Cassava MED Proteins

The intron and exon organization of the MeMED genes was predicted using TBtools (version V2.056) [34]. To identify the cis-acting elements within the promoters of the MeMED genes, a 2 kb sequence upstream of the start codon was submitted to the PlantCARE website [35]. The graphical representation of the cis-regulatory elements in MeMED genes was generated using TBtools.

4.4. Evolutionary Analysis of MeMED Genes

The synteny relationships among Cassava, Oryza sativa, and Arabidopsis were assessed using MCScanX, MCScanX software, version 1.0 and visualization was performed with TBtools (v2.012) [36]. Additionally, the nonsynonymous (Ka) and synonymous (Ks) substitution rates between gene pairs were calculated. The divergence time (T, in millions of years ago; MYA) was estimated using the following formula: T = Ks/2R, where R = 15 × 10−8 represents the rate of synonymous substitutions per site per year [37].

4.5. Expression Analyses of MeMED Genes in Different Tissues

The Bart Lab Cassava Atlas database (https://shiny.danforthcenter.org/cassava_atlas/, accessed on 28 July 2024) was searched to obtain the expression data for the MeMED genes. Temporal and spatial expression patterns of the MeMED proteins were evaluated using RNA-seq data from various cassava tissues, including the root, stem, leaf, and petiole, at different developmental stages. The heatmap was generated using TBtools. The FPKM values were calculated as described in previous studies [38].

4.6. RNA Extraction, cDNA Synthesis, and RT-qPCR Analysis

Total RNA was extracted using the RNAprep Pure Plant Kit (Lot no. Q5510, Tiangen, Beijing, China), following the manufacturer’s instructions. The first complementary DNA strand (cDNA) was synthesized using the HiScript 1st Strand cDNA Synthesis Kit V221 (Vazyme Biotech Co., Ltd., Sanya, China). RT-qPCR was performed using ChamQ™ SYBR RT-qPCR Master Mix (Vazyme Biotech Co., Ltd., Sanya, China). Each reaction had a total volume of 20 μL, comprising 0.4 μL forward primer, 0.4 μL reverse primer, 2 μL cDNA, 10 μL SYBR mix, and 7.2 μL ddH2O. The cycling program included an initial denaturation step at 95 °C for 30 s, followed by 40 cycles of denaturation at 95 °C for 10 s and annealing/extension at 60 °C for 30 s. Me-actin was used as an internal control. The data were analyzed using the 2−ΔΔCt method [39]. The primers for the selected MeMED genes are listed in Table S3. The heatmap was generated using GraphPad Prism 8 software.

4.7. Plant Material and Stress Treatment Conditions

In this study, the typical cultivated cassava variety SC9 (South China 9) was used for stress treatments. The SC9 seeds were obtained from the National Cassava Germplasm Repository (NCGR) at the Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, HaikouHainan Province, China. Vigorous seeds were selected and sterilized with a 10% hypochlorous acid solution for 5 min. The seeds were then grown on a water-saturated filter paper in a growth chamber (25 °C day/night with a 16 h/8 h light/dark cycle), after which the plants were transferred to pots containing soil. For stress treatments, the plants were subjected to 300 mM NaCl for salt stress, 20% PEG6000 for drought stress, 4 °C for cold stress, 42 °C for heat stress, and 10% hydrogen peroxide (H2O2) for oxidative stress. Samples were collected at 0 (control), 4, 8, 12, and 24 h post-treatment. Three biological replicates were performed for each treatment. All samples were rapidly frozen in liquid nitrogen and stored at −80 °C for subsequent expression analysis.

5. Conclusions

This study provides the first genome-wide analysis of the MeMED gene family in cassava. We identified 32 MeMED genes and examined their basic features, gene structure, evolutionary relationships, and expression patterns. RT-qPCR analysis showed significant changes in the expression of the selected 10 MED genes, including MeMED7-1, MeCdk8-1, MeMED10-1, MeMED11-1, MeMED16-1, MeMED20-1, MeMED21-1, MeMED22-1, MeMED23-1, and MeMED31-1 (under various abiotic stresses, suggesting their potential role in enhancing cassava’s stress tolerance). The MeMED21_1, which exhibited a unique expression pattern towards abiotic stress, could offer new strategies to improve cassava resilience. These findings have a significant implication for climate change and sustainable agriculture. The identified genes in our study may contribute to new cassava varieties that may show more tolerance towards the harsh environmental conditions, which are becoming more prevalent due to climate change. This study can help to ensure food production and contribute to the sustainable production of cassava. Overall, our research provides valuable insights into the MeMED gene family and lays the groundwork for future studies on important crops like cassava.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/ijms26041666/s1.

Author Contributions

S.G., R.X. and L.W. conceived and designed the experiments. L.Z. (Lingling Zhou) performed all the bioinformatics analyses. S.S., L.Z. (Linlong Zhu) and X.C. conducted the experiments. S.G. and L.W. wrote the manuscript. R.X. supervised the project and provided funding. All authors have read and agreed to the published version of the manuscript.

Funding

This study was supported by the Project of Sanya Yazhou Bay Science and Technology City (SCKJ-JYRC-2024-28), the Natural Science Foundation of Hainan Province (322RC592), and the National Natural Science Foundation of China (32360083 and 31960159).

Data Availability Statement

The authors confirm that the data supporting the findings of this study are available within the article and its Supplementary Materials.

Acknowledgments

The authors thank Stephen Cong and Li Rui for their continuous support and manuscript invitations, as well as all the editors and reviewers for their valuable and insightful comments on this manuscript.

Conflicts of Interest

The authors declare no conflicts of interest.

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Figure 1. Chromosomal localization and distribution of MeMED Gene in Cassava. The yellow color was used solely to enhance the visibility of the chromosomes, providing a clear contrast. It does not convey any additional specific meaning or indication.
Figure 1. Chromosomal localization and distribution of MeMED Gene in Cassava. The yellow color was used solely to enhance the visibility of the chromosomes, providing a clear contrast. It does not convey any additional specific meaning or indication.
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Figure 2. Phylogenetic analysis of MeMED proteins from three plant species, namely Manihot esculenta, Arabidopsis thaliana, and Oryza sativa. The phylogenetic tree was constructed by using mega 7 with the maximum likelihood method and a bootstrap value of 1000 replicates. The different colors in the tree represent different MED modules. The red-colored star represents the MED genes in Manihot esculenta.
Figure 2. Phylogenetic analysis of MeMED proteins from three plant species, namely Manihot esculenta, Arabidopsis thaliana, and Oryza sativa. The phylogenetic tree was constructed by using mega 7 with the maximum likelihood method and a bootstrap value of 1000 replicates. The different colors in the tree represent different MED modules. The red-colored star represents the MED genes in Manihot esculenta.
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Figure 3. Collinear analysis between the cassava MeMED genes and the genomes of Arabidopsis and Oryza sativa.
Figure 3. Collinear analysis between the cassava MeMED genes and the genomes of Arabidopsis and Oryza sativa.
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Figure 4. Gene structure analysis of the cassava MeMED gene family.
Figure 4. Gene structure analysis of the cassava MeMED gene family.
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Figure 5. Evaluation of cis-regulatory elements in the MeMED gene promoters’ regions. The colored boxes denote different cis-regulatory elements, each linked to specific biological responses or functions.
Figure 5. Evaluation of cis-regulatory elements in the MeMED gene promoters’ regions. The colored boxes denote different cis-regulatory elements, each linked to specific biological responses or functions.
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Figure 6. Tissue-specific expression analysis of the MeMED gene family in cassava. The red color represents higher expression, the yellow color indicated low expression, whereases the blue color indicated no expression in the RNA-seq expression data.
Figure 6. Tissue-specific expression analysis of the MeMED gene family in cassava. The red color represents higher expression, the yellow color indicated low expression, whereases the blue color indicated no expression in the RNA-seq expression data.
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Figure 7. Expression patterns of selected MeMED genes under different abiotic stresses. Data are presented as means ± standard errors. Statistically significant differences are indicated by asterisks (p ≤ 0.05). CK, control; D, drought; HP, exogenous hydrogen peroxide; C, cold; H, heat; S, salt. Time intervals of 4, 8, 12, and 24 h are denoted by the numbers 4, 8, 12, and 24, respectively. Samples collected at 0 h served as the control (CK). Statistical significance was determined using a one-way ANOVA followed by Tukey’s HSD post hoc test. Different letters indicate significant differences (p < 0.05) within each group.
Figure 7. Expression patterns of selected MeMED genes under different abiotic stresses. Data are presented as means ± standard errors. Statistically significant differences are indicated by asterisks (p ≤ 0.05). CK, control; D, drought; HP, exogenous hydrogen peroxide; C, cold; H, heat; S, salt. Time intervals of 4, 8, 12, and 24 h are denoted by the numbers 4, 8, 12, and 24, respectively. Samples collected at 0 h served as the control (CK). Statistical significance was determined using a one-way ANOVA followed by Tukey’s HSD post hoc test. Different letters indicate significant differences (p < 0.05) within each group.
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Table 1. Information on the MeMED genes in cassava.
Table 1. Information on the MeMED genes in cassava.
Gene NameChrCDS (bp)Protein Length (A.A)Protein Molecular Weight (KDa)pIGravyMediator Module
Manes.01G210100.1MeMED33_3139871329144.55 6.710.169Tail
Manes.01G220201.1MeMED28_2131810612.41 6.13−0.185Head
Manes.03G077300.1MeMED22_1347715917.00 6.12−0.226Head
Manes.03G185600.9MeMED33_1339691323144.45 6.680.227Tail
Manes.03G199800.1MeMED20_1366622225.36 6.08−0.266Head
Manes.03G210700.11MeMED21_1340513514.69 4.4−0.37Middle
Manes.04G136400.1MeMED6_1474124727.51 5.18−0.378Head
Manes.05G034300.10MeMED12_1567982266250.60 8.92−0.27Kinase
Manes.05G061600.1MeMED28_1543814617.12 5.78−0.886Head
Manes.05G073300.1MeMED33_4539931331143.11 7.220.185Tail
Manes.06G049700.1MeMED17_16199866674.30 5.65−0.3Head
Manes.06G129600.1MeMED31_1662120723.70 9.28−0.637Middle
Manes.08G002200.1MeMED4_18123941344.99 4.97−0.542Middle
Manes.08G033200.3MeMED27_18126342146.41 8.76−0.292Tail
Manes.08G039900.1MeMED7_1850716919.64 9.16−0.675Middle
Manes.08G061400.1MeMED26_18143147753.66 5.56−0.948Middle
Manes.08G118700.1MeMED37_18198366173.14 5.28−0.463Unknow
Manes.09G000400.6MeMED21_2940513514.74 4.42−0.407Middle
Manes.09G002800.2MeMED26_29144348154.11 5.94−0.844Middle
Manes.09G101000.3MeMED10_1956418820.41 5.23−0.384Middle
Manes.09G152800.6MeMED14_1954781826197.87 7.96−0.202Middle
Manes.11G030300.3MeMED6_21174424827.74 5.2−0.468Head
Manes.13G095300.2MeMED18_11369023024.59 6.710.137Head
Manes.14G098600.1MeMED25_114251183789.26 8.79−0.343Tail
Manes.14G121800.7MeMED13_11459251975213.55 5.64−0.208Kinase
Manes.15G022100.1MeMED33_21539721324143.98 6.290.185Tail
Manes.16G001300.1MeMED11_11635111713.26 5.78−0.521Head
Manes.17G043400.1MeMED16_11737561252135.29 6.1−0.232Tail
Manes.17G082000.1MeMED23_11748391613180.90 6.64−0.08Tail
Manes.17G099700.2MeMED32_11744114715.40 4.69−0.098Tail
Manes.13G050900.1MeCycC_11376225429.76 6.54−0.098Kinase
Manes.09G052700.5MeCdk8_19143447853.00 9.24−0.491Kinase
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Zhou, L.; Sun, S.; Zhu, L.; Chen, X.; Xu, R.; Wu, L.; Gu, S. Genome-Wide Identification and Expression Analysis of the Mediator Complex Subunit Gene Family in Cassava. Int. J. Mol. Sci. 2025, 26, 1666. https://doi.org/10.3390/ijms26041666

AMA Style

Zhou L, Sun S, Zhu L, Chen X, Xu R, Wu L, Gu S. Genome-Wide Identification and Expression Analysis of the Mediator Complex Subunit Gene Family in Cassava. International Journal of Molecular Sciences. 2025; 26(4):1666. https://doi.org/10.3390/ijms26041666

Chicago/Turabian Style

Zhou, Lingling, Shuhui Sun, Linlong Zhu, Xian Chen, Ran Xu, Lian Wu, and Shuang Gu. 2025. "Genome-Wide Identification and Expression Analysis of the Mediator Complex Subunit Gene Family in Cassava" International Journal of Molecular Sciences 26, no. 4: 1666. https://doi.org/10.3390/ijms26041666

APA Style

Zhou, L., Sun, S., Zhu, L., Chen, X., Xu, R., Wu, L., & Gu, S. (2025). Genome-Wide Identification and Expression Analysis of the Mediator Complex Subunit Gene Family in Cassava. International Journal of Molecular Sciences, 26(4), 1666. https://doi.org/10.3390/ijms26041666

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