1. Introduction
Transcription factors (TFs) are important regulators of the expression of functional genes under different biological processes, including development, reproduction, and various environmental conditions [
1]. Within the landscape of TFs that are present in the genome, the
MYB family constitutes one of the largest and functionally diverse [
2]. The MYB proteins are characterized by the MYB domain at the N-terminus which encodes 52 amino acid residues and contains one to four imperfect tandems repeats (R) [
2]. According to the numbers of MYB repeat,
MYB genes are classified into four different subfamilies, namely MYB –related proteins or 1R–MYB proteins (with 1R), R2R3–MYB proteins (with 2R), R1R2R3-MYB proteins (with 3R), and 4R-MYB proteins (with 4R) [
3]. The R1R2R3-MYB proteins are found in animals, but the R2R3-MYB proteins are more frequent in plants [
4]. The
MYB TFs have been studied in diverse species and particularly in plants. Various numbers of
MYBs have been detected suggesting that they have expanded to differing degrees: 177
MYB genes were found in
Citrus sinensis [
5], 231 in
Pyrus bretschneideri [
1], 475 in
Brassica rapa ssp. pekinensis [
6], 524 in
Gossypium hirsutum [
7], and 104 and 166 in
Lotus japonicas and
Medicago truncatula, respectively [
8].
In plants, MYB proteins are key factors in physiological processes, shoot growth, root formation, organ development, metabolism, hormone signal transduction, and responses to biotic and abiotic stress tolerance [
9,
10,
11,
12,
13]. For example, expression profiles analysis in
Arachis hypogaea identified 30
MYB genes responsive to abiotic stress treatments [
14]. Over-expression of
SpMYB gene from
Solanum pimpinellifolium improved abiotic and biotic stress resistance in tobacco [
15]. A total of 44.67% and 47.21%
MYB genes were found up- and down-regulated in
Arabidopsis under cold stress, respectively [
16]. Later on, Zhang et al. [
17] reported the gene
TaLHY, a 1R-
MYB type as a positive regulator of resistance against stripe rust fungus and ear heading in
Triticum aestivum. More recently, Xu et al. [
18] demonstrated that the R2R3-type
MYB gene
DcMYB6, is involved in regulating anthocyanin biosynthesis in purple
Daucus carota taproots. In the case of drought stress, many
MYB genes have been isolated and demonstrated to be involved in drought responses in plants [
19]. The transcriptional activation of cuticular wax biosynthesis by
MYB96 contributed to drought resistance in
Arabidopsis thaliana [
20]. A recent study revealed that
PbrMYB21 plays a positive role in drought tolerance by modulating polyamine synthesis through the regulation of the
ADC expression in
Pyrus betulaefolia [
21]. Furthermore, Yin et al. [
22] showed that
OsMYBR1 that was isolated from
Oryza sativa improves drought tolerance of transgenic plants through the up-regulation of stress-related genes and the accumulation of osmoprotectants. Similarly, Butt et al. [
23] demonstrated that
GaMYB85 confers good drought tolerance in
Gossypium arboreum, most probably via an ABA-induced pathway. Altogether, these evidences demonstrated the versatility and importance of this gene family in plants.
Sesame (
Sesamum indicum L.) is one of the oldest oilseed crops, which is widely grown in tropical and subtropical areas [
24]. It has one of the highest oil contents (~55%) among major oilseed crops [
25]. Drought and waterlogging represent the most important abiotic stresses that affect sesame plant growth and yield [
26]. Sesame is a very sensitive crop to waterlogging [
27]. The majority of sesame resources are susceptible to waterlogging damage at the different developmental stages [
28], and so far, few studies have been conducted to unravel the genetic basis of waterlogging response in sesame [
27,
29,
30]. In contrast, sesame is moderately tolerant to drought stress [
31]. However, severe drought adversely impairs the plant normal growth and development [
32], the reproduction and yield [
26], and both the quality and quantity of the sesame oil as well [
33,
34,
35]. Therefore, breeding sesame varieties with higher tolerance to these abiotic stresses is drawing great attention from breeders [
36].
Given the potential roles of MYB proteins in the regulation of gene expression in response to environmental stresses, it is of the utmost interest to perform a genome-wide survey of this gene family in sesame. In this study, we identified at the genome-wide level 287 MYB genes and revealed that the MYB proteins are highly active in growth and adaptation to the major abiotic stresses namely drought and waterlogging in sesame. We also presented here a comprehensive analysis of the protein characteristics, gene classification and structure, chromosomal distribution, gene duplication, and phylogenetic relationships of sesame MYBs.
4. Discussion
The function of
MYB genes has been extensively investigated in numerous plants species, but, to date, no comprehensive analysis of the
MYB gene family members has been reported in sesame and their functions are still largely unknown. In this study, we comprehensively studied this important gene family based on bioinformatic tools and expression profiling. We identified 287
SIMYB genes, which is quite higher than the 198
MYB genes reported in
Arabidopsis, 183 in rice [
16], 247 in soybean [
54], 177 in sweet orange [
5], 125 in
Jatropha curcas [
55], 231 in
Pyrus bretschneideri [
1], and 104 and 166 in
Lotus japonicus and
Medicago truncatula, respectively [
8]. To date, only two species, namely, cotton and Chinese cabbage had much higher
MYB genes than sesame, which could be attributed to their bigger genome sizes [
6,
7]. Hence, according to the previous reports related to the expansion of gene families in sesame [
44,
53,
56,
57], we speculated that sesame has retained and expanded during the evolutionary process, the
MYB family members that may play essential roles in various biological processes. Similarly as reported in cotton [
7], soybean [
54], rice, and
Arabidopsis [
16], tandem duplication events have contributed to the expansion of the
MYB gene family in sesame. More importantly, we deduced that tandem duplication events have also contributed to the functional divergence of
SIMYBs since some tandem duplicated
SIMYB genes were predicted distinct functions.
One surprising feature of the
SIMYB gene family is the over-representation of the 1R-MYB subfamily. The 2R-MYB subfamily has been reported to be the largest subfamily of MYB family, followed by the 1R-MYB in many plant species [
7,
16,
58,
59]. Contrarily to the 2R-MYB, the 1R-MYB subfamily is less-studied and their functions were assigned for circadian and light regulation, cell differentiation, and telomeric DNA binding [
9]. In sesame, we have found its members to be highly active in abiotic stress response, suggesting a novel role of this subfamily. Nonetheless, the abundance of 1R-MYB subfamily members in the sesame genome is intriguing and may deserve in-depth functional investigations.
To date, only three
MYB genes (
SIMYB186 (
SIN_1010473),
SIMYB261 (
SIN_1025617), and
SIMYB257 (
SIN_1004921)) have been functionally characterized as being involved in the corolla and petiole pigmentation in sesame [
52]. Wherefore, revealing the functions of the members of this important gene family should be the focus of future studies in sesame. The R2R3-
MYB genes are known to be involved in plant specific processes, such as control of secondary metabolism or cellular morphogenesis, defense, pigmentation, and root formation [
60]. Structurally similar MYB proteins within species were found to be functionally orthologous. For example, the genes
ZmMYBC1,
ZmMYBPL from maize and
PhMYBAN2 from
Petunia are structurally related and play the same function: control of anthocyanin synthesis [
7]. Hence, we performed an evolutionary relationship analysis of the R2R3-MYB subfamily in sesame when compared with the well-studied species
Arabidopsis. Out of 30 sesame clades, 23 clades were consistent with those in
Arabidopsis [
1,
2], providing an excellent reference to explore the functions of sesame R2R3-
MYB genes [
61]. For example,
SIMYB50,
SIMYB74,
SIMYB242, and
SMYB261 were assembled together with
Arabidopsis AtMYB044 and
AtMYB077 into the clade 21, referring to abiotic stress response and anthocyanin biosynthesis [
62]. The genes
SIMYB24 and
SIMYB80 were grouped into the clade 22 with two
Arabidopsis genes
AtMYB90 and
AtMYB113, representing the functional clade of anthocyanin biosynthesis [
63]. The genes
SIMYB72 and
SIMYB200 were found in the groups C3 and C10, respectively, related to root development. Accordingly, based on tissue RNA-seq analysis, we uncovered that these genes were exclusively expressed in sesame roots. Seven R2R3-
SIMYB subgroups of sesame have no representative in
Arabidopsis, suggesting that these proteins might have specialized roles that were either lost in
Arabidopsis or gained after divergence from the last common ancestor [
2]. Furthermore, the close relationship between sesame and
Arabidopsis helped to identify some homolog
MYB genes and allowed for us to predict the functions of
SIMYB genes [
53].
Few
MYB genes have been reported to be involved in plant developmental processes [
6]. In sesame, 65% of
SIMYB genes were expressed in all of the tissues, indicating that these genes might contribute in various aspects of growth and developmental processes. In contrast, we detected few tissue-specific
SIMYBs that may play major role in their respective tissues [
2]. To cite an instance, the gene
SIMYB200, which is exclusively expressed in the sesame root, is the homolog of the gene
AtMYB93 which regulates lateral root development in
Arabidopsis [
64]. Until now, the sesame root system architecture has not been yet examined at the molecular level [
36]. Therefore,
SIMYB200 could be a potential gene to be targeted for functional characterization in the sesame root. In addition, the homolog of the sesame seed-specific genes
SIMYB74,
SIMYB242, and
SIMYB249 in
Arabidopsis (
AtMYB113) was found to be involved in anthocyanin biosynthesis [
65]. We suspected that these genes may be involved in seed coat coloration in sesame.
Waterlogging is a common adverse environmental condition that limits sesame plant growth and reproduction [
30]. Similarly, drought stress constitutes the second major abiotic stress in sesame production [
26]. Unfortunately, advances in developing abiotic stress tolerant sesame varieties have been hampered by the lack of functional gene resources [
36]. Increasing evidences have shown that
MYB TFs are implicated in drought response in various plant species, including
Arabidopsis thaliana,
Zea mays,
Gossypium herbaceum,
Vitis vinifera,
Oryza sativa,
Solanum tuberosum,
Triticum aestivum, and
Glycine max [
66,
67,
68,
69,
70,
71,
72]. In sesame, 16% of the total
SIMYB genes were significantly active in drought stress responses, and most of their homologs in
Arabidopsis are described as abiotic stress responsive genes. By way of illustration, the homologs of the sesame drought responsive genes
SIMYB204 (
AtMYB015),
SIMYB77,
SIMYB245,
SIMYB78 (
AtMYB073), and
SIMYB8 (
AtMYB2) were proved to be implicated in drought responses in
Arabidopsis. This suggests a conservation of gene function across the two species, implying that these identified genes could be regarded as candidate gene resources for drought tolerance improvement in sesame [
1,
2].
On the other hand, little is known concerning the role of MYB genes in the waterlogging response in plants. It was shown that
AtMYB2 is induced by hypoxia, with mRNA levels peaking after 2–4 h under hypoxic conditions [
73]. The gene
TaMyb1 (ortholog of
AtMYB2) exhibited a dramatic increase in transcripts under waterlogging stress, indicating its positive involvement in alleviating the damages in common wheat root [
74]. The gene
SIMYB8, which is the homolog of
AtMYB2, was also highly induced after 9 h waterlogging stress in sesame, indicating a functional conservation. Recently, based on a transcriptome profiling under waterlogging stress in kiwifruit plants, Zhang et al. [
75] found that the
MYB TFs were abundant in the differentially expressed genes. In the present study, 40% of
SIMYBs was significantly associated with waterlogging stress responses, representing potential genes for enhancing sesame endurance under this important abiotic stress. The higher number of
SIMYBs regulated under waterlogging as compared to drought confirms sesame’s greater susceptibility to waterlogging stress [
30].
SIMYBs commonly involved in drought and waterlogging responses are of a great interest as they could be targeted for improvement towards tolerance to both stresses simultaneously. Our results are in agreements with previous reports which showed that some
MYB gene members are key regulators of several abiotic stresses, including cold, osmotic stress, salt, etc. [
76,
77,
78]. However, it appears that
SIMYBs may function differentially under drought and waterlogging stresses as shown by their contrasting expression patterns under these stresses. Therefore, in-depth analysis of these particular genes is needed to get insight into the mechanisms of co-regulation of drought and waterlogging stresses in sesame.