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Article

Conservation and Divergence of the Trihelix Genes in Brassica and Expression Profiles of BnaTH Genes in Brassica napus under Abiotic Stresses

by
Cuiping Zhang
,
Lijing Lu
,
Ruolin Gong
,
Xing Su
,
Fengbo Liu
,
Ru Zhang
* and
Jihong Hu
*
State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2022, 23(24), 15766; https://doi.org/10.3390/ijms232415766
Submission received: 31 October 2022 / Revised: 6 December 2022 / Accepted: 9 December 2022 / Published: 12 December 2022
(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 2.0)
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Abstract

:
Trihelix (TH) proteins are a family of plant-specific transcription factors that play a role in light response and are extensively involved in plant growth and development, as well as in various stress responses. However, the function of TH genes in Brassica napus (B. napus) remains unclear, as does the evolution and differentiation pattern of TH genes in Brassica plants. Here, we identified a total of 455 TH genes in seven species, including six Brassica species and Arabidopsis, which were grouped into five clades, GT-1, GT-2, GTγ, SH4, and SIP1, each with 69, 142, 44, 55, and 145 members, respectively. The types and distributions of motifs of the TH proteins and the structures of the TH genes are conserved in the same subgroup, and some variations in certain amino acid residues occur in B. napus when inheriting motifs from Brassica rapa (B. rapa) and Brassica oleracea (B. oleracea). Collinearity analysis revealed that the massive expansion of TH genes in tetraploid species was attributed to the hetero-tetraploidization of diploid ancestors and gene duplication events within the tetraploid species. Comparative analysis of the membership numbers of five subgroups in different species revealed that the GT-2 and SIP1 genes underwent significant expansion during evolution, possibly to support the better adaptation of plants to their environments. The differential expression of the BnaTH genes under five stresses indicates that the BnaTH genes are involved in plant responses to stresses such as drought, cold, and heat. The presence of different stress-responsive cis-elements in the upstream promoter region of the genes indicated that BnaTH genes have the potential to cope with variable environments. Meanwhile, qRT-PCR analyses also confirmed that five TH genes respond to different abiotic stresses. Our results provide information and candidates for further studies on the role of TH genes in stress resistance of B. napus.

1. Introduction

Trihelix (TH) transcription factors, as a key regulatory factor, were originally called GT elements due to their specific binding to GT elements, which is required for light-responsive transcription [1,2]. TH factors contain a conserved trihelix DNA-binding domain characterized by a typical trihelix (helix–loop–helix–loop–helix) structure, which binds specifically to GT elements in the promoters of target genes [3,4] and plays a pivotal role in a variety of developmental processes and environmental stress responses. Based on its conserved domains and evolutionary relationships, the TH gene family is divided into five clades, namely GT-1, GT-2, SH4, SIP1, and GTγ. Studies have revealed that GT factors, which have a trihelix structure that resembles the Myb/SANT-LIKE DNA-binding domain, likely originated from an MYB-like gene carrying only one repeat [3]. However, the recognition sequences of the GT transcription factor and the MYB protein are different, which may be caused by the insertion of gaps between the two helices [3].
In recent years, with the completion of the genome assembly of various species, the genome-wide identification of the TH gene family has been reported in many species. In total, 30 and 31 TH genes were identified in Arabidopsis and rice, respectively [2,5]. In addition, 31, 35, 94, 52, 56, 52, 20, and 36 TH genes were identified in Fagopyrum esculentum, Moso bamboo, Triticum aestivum, Gossypium arboreum, Populus trichocarpa, B. rapa, Chrysanthemum, and Solanum lycopersicum, respectively [6,7,8,9,10,11,12,13]. Recent studies have revealed that TH factors not only respond to light stress and regulate the expression of light-responsive genes but are also involved in abiotic stress responses [2,14]. For instance, the TH family gene ShCIGT mediates cold tolerance and drought tolerance by interacting with SnRK1 in tomato [15]. Overexpression or knockout of the AST1 in Arabidopsis could positively influence tolerance to salt, osmotic, and drought stress [16]. BnSIP1-1 of B. napus has been proved to be capable of coping with various abiotic stresses, and the overexpression of BnSIP1-1 can improve the germination rate of B. napus under osmotic and salt stresses [17]. Arabidopsis, AtGT2L, as a Ca2+-dependent CaM-binding protein, is strongly induced to express under cold and salt stresses [18]. However, the function of TH family genes in Brassica species and their roles in abiotic stresses have not been systematically reported. Thus, it is essential to systematically characterize the TH family genes in Brassica species, to explore their evolutionary relationships among species, and to further investigate their roles under abiotic stresses.
B. napus (AnAnCnCn, 2n = 38), a member of the Brassica species, is an allopolyploid that was formed by hybridization between B. rapa (AnAn, n = 10) and B. oleracea (CnCn, n = 9) about 7500 years ago [19,20]. In addition, the Brassica genus also includes Brassica nigra (B. nigra; BnBn, n = 8), along with two allotetraploids, Brassica juncea (B. juncea; AnAnBnBn, 2n = 36) and Brassica carinata (B. carinata; BnBnCnCn, 2n = 34) [21,22]. The evolutionary relationships of these six Brassica species are known as the classic U’s triangle model [23]. Studies have confirmed that the Brassica species B. nigra, B. rapa, B. oleracea, B. juncea, B. carinata, and B. napus have undergone a whole-genome triplication (WGT) since their divergence from the Arabidopsis species [24,25]. The genome underwent chromosomal rearrangement, gene loss, and the divergence of retained paralogues after WGT, with substantial gene loss occurring in an asymmetric and reciprocal manner [26]. A large number of over-retained genes after WGT belongs to the gene families that underlie adaptation to environmental factors such as salt, cold, osmotic stress, light, wounding, pathogen defense, and so on [24]. To date, whole genome sequencing of six species in the U’s model has been completed. Plant growth and development are accompanied by adaptation to the environment, which is always complex and changeable. Therefore, exploring genes such as TH genes, and identifying their roles in abiotic stresses, will provide insights into improving crop yields and environmental adaptation.
B. napus is an important oilseed crop, and the production of rapeseed is second only to that of soybeans in terms of the worldwide production of oilseed crops. However, with continuous changes in the global climate, environmental factors such as drought and low temperatures have become the main limiting factors for rapeseed production, resulting in a decline in rapeseed yields and quality. Although many breeding works have used heterosis to screen and breed varieties with high yields and oil content, the research into abiotic stress in rapeseed is still relatively underdeveloped. Therefore, it is urgent to cultivate stress-resistant B. napus varieties capable of adapting to the changing environment in order to ensure yield and quality.
In our study, we identified and characterized the TH transcription factors in six Brassica species and expression patterns in B. napus under different abiotic stresses. The evolution of the TH gene family was investigated in Brassica genus. To establish the role of the TH genes in rapeseed, we evaluated their expression patterns in different tissues and under different abiotic stresses, including drought, cold, and heat. Our research provides new insights into enhancing stress resistance in B. napus with the goal of improving yield and quality.

2. Results

2.1. Identification of TH Genes in Seven Species

A total of 455 TH genes was identified in seven species, with 29, 51, 49, 54, 92, 86, and 94 in Arabidopsis, B. nigra, B. rapa, B. oleracea, B. juncea, B. carinate, and B. napus, respectively. All TH genes were subsequently renamed according to their species and chromosomal locations (Table S1), yielding AtTH-1 to -29, BniTH-1 to -51, BraTH-1 to -49, BolTH-1 to -54, BjuTH-1 to -92, BolTH-1 to -86, and BraTH-1 to -94. Next, the physicochemical properties of the TH proteins, including protein length, molecular weight (MW), theoretical isoelectric point (pI), instability index (II), aliphatic index (AI), and the grand average of hydropathicity (GRAVY), were calculated to provide further information (Table S2). The length of TH proteins varied from 109 (BolTH-35) to 1149 (BnaTH-19) amino acids (aa), with an MW range of 12,940.84 (BolTH-35) –27,364.53 (BolTH-18) kDa. The pI values were between 4.65 (AtTH-18) and 10.83 (BniTH-44), and the II ranged from 28.75 (BraTH-4) to 86.3 (BcaTH-32). The AI can vary from 38.53 (BolTH-35) to 87 (BcaTH-51). All the TH proteins presented GRAVY values of <0, ranging from −0.357 (BcaTH-42) to −1.358 (BcaTH-51), implying their hydrophilic characterization. Subcellular localization revealed that nearly all the TH proteins (389, 85.5%) were located in the nucleus. This result is consistent with their roles as transcription factors. In addition, small proportions of the proteins are located in other regions, such as the chloroplast (22, 4.8%), cytoplasm (34, 7.5%), peroxisome (8, 1.8%), endoplasmic reticulum (1, 0.2%), and vacuole (1, 0.2%).

2.2. Phylogenetic Analysis and Classification of TH Genes

To uncover the phylogenetic relationships of the TH genes, we constructed an unrooted phylogenetic tree based on the multiple sequence alignment of 455 TH proteins among the seven species, namely Arabidopsis, B. nigra, B. juncea, B. carinate, B. rapa, B. napus, and B. oleracea (Figure 1). These TH genes were classified into five clades, namely GT- 1, GT-2, GTγ, SH4, and SIP1 [11], containing 69, 142, 44, 55, and 145 TH genes, respectively. The SIP1 clades contained the most TH members (145, 31.9%), while the GTγ clades had the fewest TH genes (44, 9.7%). These results indicated that the number of TH genes is uneven across the five subgroups.

2.3. Gene Structure and Protein Conservative Domain Analysis

Through MEME domain analysis, we identified 10 distinct motifs for the structural diversification of 455 TH genes, which we refer to as motifs 1 to 10 (Figure S1 and Table S3). Overall, similar motif compositions and distributions were found in the same subgroups, whereas they differed significantly among the subgroups. All subgroup members contain about three motifs, except the GT-2 subgroup, which has about 10 motifs. All TH proteins contain motif 1, whereas motif 3 is almost unique to GT-2. Furthermore, the GT-2 clade with the most abundant motif types, contains all of the motifs except for motif 4 and motif 9, and most members contain two of motif 1, two of motif 2, and two of motif 3. In addition, motif 4 which has the longest sequence, is mostly present in GT-1 and only appears a few times in SIP1. These results suggested that subgroup-specific motifs might play pivotal roles in specific functions. Gene structure analysis showed that the exon lengths of genes in the same subgroup were diverse, but the number was almost always conserved (Figure S1). For example, most GTγ and SIP1 members contain one exon, and GT-1 and SH4 members contain 2–5 exons. In contrast, the GT-2 subfamily has a more complex exon number and length than the others.
In order to explore the gene structural changes in B. napus during evolution, we performed structural analysis for B. napus with its diploid progenitors B. rapa and B. oleracea. We separately predicted ten motifs in these three species and compared their amino acid residues (Figure 2, Table S4). We found that most motifs in B. napus were similar to those in B. rapa and B. oleracea. In particular, the amino acid residues of motif 1 and motif 6 were almost identical to their corresponding sequences in the progenitors, indicating that these two motifs were highly conserved during rapeseed evolution. In addition, we found that some motifs in B. napus were more likely to be derived from B. rapa. For example, motif 5 in B. napus is more similar to motif 4 in B. rapa than motif 5 in B. oleracea, and motif 4 in B. napus is more likely to have originated from motif 6 in B. rapa. Furthermore, the orthologous among the three species have similar gene structures and motif features (Figure 2 and Table S5). For instance, BnaTH-57 has similar exons with its homologs BraTH-28 and BolTH-18; additionally, the composition and distribution of motifs in protein sequences and the amino acid residues in the motifs are identical. Moreover, there is a unique motif 9 in B. napus, which may have been newly formed during B. napus evolution.
Moreover, we found that some BraTH motifs originated from only one species, such as BnaTH-11, which has the orthologs BraTH-14 and BolTH-13, whose motifs appear to be derived from BolTH-13 only, as the corresponding motif cannot be found in BraTH-14. However, most BnaTH motifs have more complex origins, and they may be derived from both B. rapa and B. oleracea, such as, BnaTH-51 and BnaTH-8. Our analysis of members of the SIP1 subgroup in B. napus and its diploid ancestors revealed that some BnaTHs inherited motifs from ancestors with motif insertions and deletions (Figure S2). For example, there are six motifs in BnaTH-28, while its homologs BolTH-20 and BraTH-25 have seven and five, respectively, and there are six motifs in BnaTH-46 compared to four in the homolog BolTH-2. These results implied that the evolution of TH genes in B. napus is intricate and diverse, and that they have inherited genetic material from ancestral species while undergoing a number of mutations in order to meet autogenous growth and development.

2.4. Cis-Acting Elements in the Promoter Region of TH Genes

In order to better understand the potential regulatory roles of TH genes, the cis-acting elements in the 1500 bp upstream region of TH gene promoters were predicted using PlantCARE software. Twenty-seven distinct cis-acting elements were identified and grouped into three main categories (Tables S6 and S7). The first one was engaged in light responsiveness, such as Box 4 elements, I-boxes, TCT motif, ATC motif, GATA motif, MRE, G-box, SP1, AE-box, ATCT-motif, MRE, TCCC-motif, chs-CMA1a, and GT1-motif; the second was associated with stress responses, including drought stress (MBS), anaerobic induction (ARE), and low-temperature stress (LTR); the third was involved in plant growth and development, including circadian (circadian control), meristem expression (CAT-box), and phytohormone responses, such as abscisic acid (ABRE), methyl jasmonate (CGTCA-motif and TGACG-motif), auxin (TGA element), salicylic acid (TCA element), and so on (Tables S6 and S7). A total of 99.3% (442/445) of genes contained light-responsive elements, with BcaTH-15 containing the most light-responsive elements (24) and BnaTH-66 having the least (1). Among the 168 genes featuring drought-responsive elements, BcaTH-74 contains the most numbers of MBS (4). In addition, the most abundant of these 168 genes are members of the SIP1 subgroup (53, 31.5%), followed by the GT-1 subgroup (39, 23.2%); meanwhile, the SH4 subgroup (17, 10.1%) had the fewest members (Table S7). There are 220 genes involved in low temperature response elements; of these, members of the SIP1 subgroup account for the largest proportion (75, 34.1%), followed by GT-2 (55, 25.0%). BolTH-43 contains 9 low-temperature-response elements, which is the most among the 220 genes. In addition, there are a large number of other elements in the TH genes, such as methyl-jasmonate (MeJA)-responsive elements, abscisic-acid (ABA)-responsive elements, salicylic-acid (SA)-responsive elements, auxin-responsive elements, gibberellin-responsive elements, and ethylene (Eth)-responsive elements, indicating that they may be involved in phytohormone signaling pathways (Table S7). These results suggested that TH genes play an important role in plant growth and response to stress resistance. Moreover, compared with other subgroups, GT-2 and SIP1 have more of these elements, implying that the gene expansions of the subgroups GT-2 and SIP1 may be associated with environmental adaptation.

2.5. Chromosomal Distribution and Gene Duplication Events of the TH Family

Location information of TH genes from seven species was obtained according to the genome annotations (Table S1). Some genes were not accurately mapped to chromosomes because of the incomplete assembly of certain genomes. Overall, TH genes are unevenly distributed on the chromosomes of the respective species (Figure 3). We found that the numbers and distributions of TH genes located in the C subgenome of B. napus and B. oleracea were remarkably consistent. Additionally, the TH genes located on the A subgenome of the B. napus and B. rapa genome also have high consistency, but the similarity is relatively low. In addition, the number of TH genes in B. napus is slightly lower than that on the corresponding chromosomes of B. rape and B. oleracea. This may be due to the loss of some functionally redundant TH genes during the evolution of B. napus, or the incomplete assembly of chromosomes.
The intra-species synteny relationships of TH genes were analyzed using the genomic information of the seven species (Figure 4, Table S8). A total of 393 paralogous pairs was identified, including 6, 90, 131, 85, 25, 29, and 27 pairs in Arabidopsis, B. carinate, B. juncea, B. napus, B. nigra, B. oleracea, and B. rapa, respectively. These paralogous gene pairs contained 358 TH genes, and most of them belong to subgroup GT-2 (110, 30.7%), followed by subgroup SIP1 (106, 29.6%). Overall, compared with the diploid species, the tetraploid species experienced more segmental duplication events. In addition, we detected nine pairs of tandem duplicated genes with 17 TH genes, which mainly belonged to subgroup GT-2 (Table S9).
The nonsynonymous rate (Ka), synonymous rate (Ks), and evolutionary constraint (Ka/Ks) ratio of duplicated gene pairs of TH genes were calculated (Table S8). The Ka/Ks ratios of all paralogous gene pairs were less than 1; 383 (98.5%) pairs were less than 0.5, and 162 (41.2%) pairs were less than 0.2, which might have encountered extremely strong purification selection after triplication, resulting in the severe inhibition of the functional differentiation of TH genes.

2.6. Evolutionary and Collinearity Analysis of TH Genes in Brassica

In order to trace the evolution of the TH gene family of Brassica, we analyzed the orthologous relationship between Arabidopsis and six Brassica species, and between the tetraploid Brassica species and their diploid ancestors (Figure 5, Table S5). A total of 655 pairs of TH genes showed collinearity, among which 245 pairs of orthologous genes were composed of 27 Arabidopsis TH genes and corresponding Brassica TH genes (Figure 6). The orthologous gene pairs between Arabidopsis and B. rapa, B. oleracea, and B. napus are 30, 31, and 45, respectively, indicating that some redundant genes were lost during the allo-tetraploidization of B. napus. In contrast, TH genes lost the most during the formation of the tetraploid B. carinate, while B. juncea lost the least (Figure 6). In addition, compared with the numbers of TH genes in tetraploid species and the numbers of orthologous genes between tetraploid species and their diploid ancestors, we observed that the TH genes in B. napus had the most variation in tetraploid species, which might differentiate into more functional genes. The number of orthologous gene pairs between B. napus and B. rapa and between B. napus and B. oleracea was 53 and 64, respectively, which may suggest that TH genes from B. oleracea are more inclined to be retained in B. napus.
To evaluate the expansion of different clades, we investigated the relationships between TH genes and clades in each species (Figure 7). Overall, the GT-2 and SIP1 clades hold the largest number of TH genes, especially in tetraploid. However, the proportion of genes in different subgroups does not seem to change much in each species. As shown in Figure 6, the orthologous genes between B. rapa and B. napus are 37 and 52, respectively, and the orthologous genes of B. oleracea and B. napus are 42 and 59, respectively, but there are 94 TH genes in B. napus. In addition, by calculating the difference between the total TH genes in diploid species and the inherited TH genes, we found that many of the missing genes in B. napus belonged to the GT-2 subgroup, and most of the missing genes in B. carinate belonged to SIP1, but almost no genes were discarded in B. juncea. Compared with other subgroups, the genes in the GT-2 and SIP1 subgroups might produce more genes with new functions through duplication events after allotetraploidy. These genes with new functions may promote the growth and development of plants or improve the adaptability to their environment.

2.7. Interaction Analysis of BnaTH Genes

There are 21 BnaTH genes with interaction relationships, most of which belong to the GT-2 subgroup (14, 66.7%) (Figure S3). In the protein interaction network, we identified two hub genes, namely BnaTH-94 and BnaTH-41, which can interact with eleven and eight BnaTH genes, respectively. In total, 28 miRNAs were found to target 35 BnaTH genes, and 73 pairs of interaction relationships were generated, among which the GT-2 (19, 54.3%) and SIP1 (12, 34.3%) subgroups accounted for the vast majority. Most miRNAs can target 1–3 BnaTH genes, but the miR396a can regulate 16 BnaTH genes (Figure S3). In addition, BnaTH-19 can be regulated by nine miRNAs, which indicates that the function of this gene may be diverse.

2.8. Expression Patterns of BnaTH Genes in Different Tissues and under Abiotic Stresses

In order to investigate the putative functions of TH genes in plant growth and development, we analyzed the expression patterns of BnaTH genes in nine different tissues (cotyledon, leaf stem, root, petal, sepal, pollen, ovule, silique, and seed) of B. napus and at different developmental stages of buds, seeds, and siliques (Figure 8). The results revealed that the expression profiles of the TH genes were diverse, but that, to a certain extent, the genes of the same subgroup displayed similar expression patterns. Overall, almost every tissue has gene expressions from five different subfamilies, but, in the same subfamily, the expression profiles are not exactly the same, indicating the different functions of the genes in the same subfamily. Seven genes (BnaTH-76, BnaTH-27, BnaTH-33, BnaTH-25, BnaTH-73, BnaTH-29, and BnaTH-72) belonging to the GT-2 subgroup are highly expressed in the cotyledons and leaves, which may mean that they play a role in the light responses of plants and in photosynthesis. With the growth of siliques, the expression of three genes (BnaTH-89, BnaTH-19, and BnaTH-57) in siliques also increased gradually, which may indicate involvement in the silique. We found that BnaTH-49 was highly expressed in ovules and seeds, but weakly expressed in other tissues. Moreover, it was observed that the expression of BnaTH-49 decreased with the maturation of seeds, which suggested that this gene might have negative regulation with seed maturation. In addition, a large number of BnaTH genes is abundantly expressed in stems, roots, buds, and most other tissues, which indicates that TH genes are generally involved in plant growth and development.
To determine the response of BnaTH genes to abiotic stresses, the expression levels of BnaTH genes in B. napus under drought stress, cold stress, heat stress, salt stress, and ABA treatment were analyzed (Figure 9). Expression profile analysis revealed that many BnaTH genes could be induced under different stresses. Most TH genes were significantly up- or down-regulated under heat treatment, implying that TH genes are generally responsive to heat stress and that they have different regulatory networks. Some genes showed similar expression patterns under different stress treatments. For example, the expression levels of BnaTH-85, BnaTH-26, BnaTH-78, BnaTH-92, and BnaTH-4 were significantly increased after drought treatment and salt stress, indicating that these genes may be associated with multiple stress response processes. In addition, we found that some homologous genes showed similar expression patterns, such as BnaTH-2 and BnaTH-56, while others had opposite expression profiles, such as BnaTH-5 and BnaTH-27. Overall, most of the genes that can respond to abiotic stresses belong to GT-2 and SIP1 clades, which suggests that the GT-2 and SIP1 clade genes may be significantly expanded to adapt to the environment.
To validate the expression patterns of TH genes under drought, cold, and heat stresses, qRT-PCRs were used to detect the expression levels of five randomly selected TH genes (Figure 10). The differential expression profiles of these selected genes under different stresses imply that they have different functions. For example, under cold treatment, the expression of BnaTH-26 decreased significantly at 1 h, and remained at low levels at 6 and 12 h, while the BnaTH-83 continued to increase. The expression of BnaTH-74 decreased gradually with the prolonged drought treatment, while BnaTH-83 showed the opposite expression pattern. All five of the selected genes responded to heat stress. Moreover, interestingly, except for BnaTH-85, the expression levels of the genes decreased first and then increased after heat treatment. Thus, all five genes were induced by various abiotic stresses with differential expression levels.

3. Discussion

As sessile organisms, plants must endure various abiotic stresses, including drought, cold, high temperatures, salt, and other environmental factors. Transcription factor TH has been found to be involved in regulating plant growth and development, as well as responses to biotic and abiotic stresses. With the release of the genome sequences of many plants, genome-wide identification of TH genes has been carried out in many species. However, other than for around 10 reported TH genes (Table S10), the identification and the function of Brasscia TH genes, especially in B. napus, have not been well reported [5,16,17,18,27,28,29,30,31,32,33]. In this study, a total of 455 TH genes was identified in six Brassica species and Arabidopsis, and the phylogenetic relationship, structure, cis-acting elements, chromosome distribution, gene duplication events, and collinearity were investigated. Furthermore, the expression patterns of these TH genes in B. napus were analyzed using RNA-seq with the highly sensitive method of qRT-PCRs [34,35]. Through comparative genomics, we explored the evolution of the TH gene family in Brassica, and present comprehensive information about this gene family, which provides clues for the functional study of TH genes in B. napus.

3.1. The Retention and Loss of TH Genes in Brassica during Evolution

Previous studies have proposed that the genome of Brassica originated from a genome with a similar structure to Arabidopsis through three rearrangement variants and inherited from a common hexaploid ancestor [25,36]. After whole-genome duplication or triplication (WGD/WGT), plants generally tend to restore the number of genes to the diploid level through gene loss [37]. However, in Brassica, this is more suitable for collinear genes in conserved syntenic regions. It is estimated that 60% of the genome is lost after triplication, and the number of genes before triplication is almost recovered [26]. Massive gene loss and the frequent recombination of triplicated genomic blocks occurred in the Brassica genome after WGT, resulting in complex mosaics of triplicated ancestral genomic blocks in the A and C genomes [26]. B. napus, as a relatively young amphidiploid, has not undergone significant chromosome rearrangement since the genome fusion of the progenitors A and C. However, homologous recombination events between the two corresponding genomes are universal in newly shaped B. napus lines, and low levels of homologous recombination have been recognized in established canola cultivars [38,39,40]. Through comparative mapping of B. napus and Arabidopsis, three collinear fragments were usually identified in each diploid genome for every region of Arabidopsis studied [41,42].
In this study, 49 and 54 TH genes were identified in B. rapa and B. oleracea, respectively, while 94 TH genes were identified in B. napus. This situation also been observed in two other allotetraploids, B. carinate and B. juncea, indicating that some redundant TH genes were lost in the process of evolution. In order to explore the reasons for the loss of TH genes in tetraploid species, we took the number of TH genes in Arabidopsis as a reference, and first compared and analyzed the TH genes in diploid plants. Furthermore, we found that 20 TH genes in Arabidopsis have only one homologous gene in B. rapa, and five TH genes have two homologous genes in B. rapa. In B. oleracea, 19 TH genes correspond to a homologous gene with Arabidopsis, and 12 TH genes correspond evenly to six Arabidopsis TH genes. However, we found a large number of AtTH genes with more than one homologous gene in B. nigra; among these, 12 AtTH genes only found one homologous gene in B. nigra, but 11 AtTH genes found two homologous genes in B. nigra, and even AtTH-24 corresponded to three homologous genes (BniTH-9, -27, -46) in B. nigra. This indicated that the genome of Brassica ancestors lost a large number of TH genes after WGT, and the number may tend to recover to its pre-tripling level. In addition, B. nigra retained more TH genes during the evolution of Brassica diploid species from hexaploid ancestors. In the collinearity analysis of Arabidopsis and Brassica tetraploid species, we found that most TH genes in Arabidopsis only found one or two homologous genes in each species. However, in every species of Brassica, a high proportion of TH segmental duplication genes was recognized, especially in tetraploid species, and most of these genes were from subgroups GT-2 and SIP1. To sum up, segmental duplication events may drive the expansion of TH genes in the evolution of Brassica species, and these duplicated genes may support plants to better adapt to various environments.

3.2. A Conserved Pattern of Motifs and TH Gene Structures

We confirmed that the conserved motifs and gene structures of 455 TH family members were consistent with the classifications of subfamilies. These subfamily members with similar gene structures and motif distributions may have arisen from gene duplication events and, therefore, they may have similar functions. Alternatively, these genes may have undergone pseudogenization, neofunctionalization, or subfunctionalization during evolution. We found that some motifs are present in all subgroups, while some motifs are almost unique to subfamilies, and these subgroup-specific motifs may perform a distinct function. In addition, our comparative analysis of the 10 conserved motifs of the TH proteins in B. rapa, B. oleracea, and B. napus revealed that almost all motifs in B. napus could find their counterparts in B. rapa or B. oleracea, but a small number of amino acid residues in these sequences were mutated, suggesting that B. napus inherited motifs from ancestral diploids in a relatively conserved state during hetero-tetraploidization.

3.3. Expression and Function Characteristics of TH Genes in B. napus

In the present study, we revealed the broad expression patterns of TH genes in B. napus; their transcripts expressed in almost all tissues and universally participated in the growth and development of B. napus, based on the RNA-seq data. Changes in TH gene expression patterns under abiotic stresses such as drought and osmotic stresses have been reported [16]. In our study, we determined the expression patterns of TH genes in B. napus seedlings exposed to five stresses to elucidate the roles of TH genes in response to adverse environmental conditions. The results showed that TH genes could be induced by various stresses, and the expression levels of some genes were significantly up-regulated after stresses; in contrast, TH genes could only be weakly induced by ABA. The genes BnaTH-8, BnaTH-59, and BnaTH-28 were all abundantly expressed under heat stress, whereas the genes BnaTH-4, BnaTH-80, and BnaTH-67 were differentially expressed under drought, cold, and salt stresses, respectively, indicating that these genes are involved in many biological processes in B. napus and respond to different stresses. The interaction relationships of BnaTH proteins and miRNA targeted BnaTH genes also revealed that BnaTHs regulated plant development and stress responses. In addition, the involvement of cis-acting elements in the expression of genes at different stages of plant growth and development and under different stresses has been widely reported. In our study, we identified a large number of stress-related cis-acting elements, such as MBS (drought), LTR (low temperature stress), and phytohormone response elements such as abscisic acid (ABRE), methyl jasmonate (CGTCA-motif and TGACG-motif), auxin (TGA element), salicylic acid (TCA element). Some phytohormones are important for plant stress resistance, such as ABA, which mediates the physiological response to stress induced by dehydration and salt stresses, suggesting that some hormone response elements not only affect plant growth and development but also have the potential to respond to stresses. Further qRT-PCR analysis verified that some genes were up-regulated under drought, cold, and heat stress, but most of them showed weak changes at the initial stage and significant differences at 12 h after the stress treatment (Figure 10).

4. Materials and Methods

4.1. Plant Materials

Seeds of B. napus Zhongshuang 9 (ZS9) were cultured in an illuminated incubator with a 16 h/8 h light dark cycle and a temperature of 22 °C. The seedlings were subjected to various stresses (drought, cold, and heat treatments) at the three-leaf stage. For the drought stress treatments, the seedlings were watered with a Hoagland nutrient solution containing 18% polyethylene glycol (PEG)-6000 (w/v). In the cold stress treatment, plants were kept in an illuminated incubator at 4 °C with the other conditions unchanged. Seedlings were also grown in an oven at 40 °C for heat stress treatment. We collected leaves from the plants treated with drought, cold, and heat stresses at 0 h, 1 h, 6 h, and 12 h after the beginning of treatment. After collection, all samples were frozen immediately in liquid nitrogen and stored at −80 °C for RNA extraction.

4.2. Identification and Characterization of the Trihelix (TH) Genes

We downloaded the entire genome sequence information of six Brassica species from the Brassica database (BRAD version 3.0; http://brassicadb.cn/, accessed on 18 July 2022) [43]. Additionally, the Arabidopsis genome information was acquired from Ensembl (http://plants.ensembl.org/, accessed on 18 July 2022) [44]. The Hidden Markov Model (HMM) profile (PF13837) downloaded from the Pfam database (http://pfam.xfam.org/, accessed on 18 July 2022) was utilized to search the trihelix domain (E-value < 1 × 10−3) by means of HMMER v3.0 software (http://hmmer.janelia.org/, accessed on 18 July 2022) [45,46]. We constructed seven species-specific HMM profiles, using the extracted protein domain sequences with E-value < 1 × 10−28 in the first search result. Then, we performed a second scan of the protein sequence (E-value < 1 × 10−3) to identify the TH genes based on the newly created species-specific HMM profiles. The output putative TH protein sequences were further authenticated via the online websites Pfam (http://pfam.xfam.org/, accessed on 19 July 2022) and SMART (https://smart.embl.de/, accessed on 19 July 2022) [47,48]. The basic physical and chemical characteristics of the candidate TH proteins, including molecular weight (MW), theoretical isoelectric point (pI), the aliphatic index (AI), the instability index (II), and the grand average of hydropathicity (GRAVY), were calculated using the ProtParam program (https://web.expasy.org/protparam/, accessed on 20 July 2022) [49]. In addition, the subcellular localization of TH proteins was predicted using WOLF PSORT (https://wolfpsort.hgc.jp/, accessed on 20 July 2022) [50].

4.3. Phylogenetic Analysis and Classification

Multiple sequence alignment of the AtTH, BcaTH, BjuTH, BnaTH, BniTH, BolTH, and BraTH protein sequences was performed using the ClustalX v2.1 program. Then, an unrooted phylogenetic tree was constructed via the neighbor-joining (NJ) method using MEGA 7.0 software with 1000 bootstrap repetitions [51]. The phylogenetic tree was visualized using Evolview software (https://evolgenius.info//evolview-v2/#login, accessed on 20 July 2022) [52].

4.4. Gene Structure and Conserved Motif Analysis

The exon-intron structure information was attained from the annotation file (gff3) of the sequenced genome. The online software MEME (https://meme-suite.org/, accessed on 21 July 2022) [53] was used to investigate the conserved motifs of TH proteins; the parameters were set with the maximum number of motifs as 10 and the motif width as 5–200 amino acids. TBtools was utilized to visualize the map of the exon–intron structures and motifs [54].

4.5. Analysis of Cis-Acting Elements in the Promoter Region

The PlantCARE (https://bioinformatics.psb.ugent.be/webtools/plantcare/html/, accessed on 22 July 2022) database was utilized to calculate the cis-acting elements within the 1500 bp sequence upstream of the transcription start site of the TH genes [55]. GSDS online software (http://gsds.gao-lab.org/, accessed on 22 July 2022) was employed to visualize the distribution map of cis-acting elements [56].

4.6. Chromosomal Distribution, Gene Duplication (Collinear), and Evolution of TH Genes

The chromosome location data for the TH genes were obtained from the genomic annotation file GFF3 of the seven species, then MapChart software [57] was used to locate the distribution of the TH genes on the chromosome, respectively. The analysis of the intra-species collinearity of TH genes in seven species was performed using collinear scanning toolkits (McScanX) [58], and the collinearity of gene pairs was presented using Circos v0.55 [59]. Moreover, McScanX software was used to analyze and plot collinearity between species.

4.7. Ka, Ks, and Ka/Ks Analysis

The synonymous (Ks) and nonsynonymous (Ka) substitution rates, and the selection pressure Ka/Ks ratio of homologous gene pairs and tandem array genes (adjacent TH genes on individual chromosomes), were calculated using TBtools [54].

4.8. Interaction Analysis of BnaTHs

The interaction of BraTH proteins was predicted using the STRING website (https://cn.string-db.org/, accessed on 15 September 2022). The potential miRNA-regulating sites of BnaTH genes were analyzed using psRNATarget [60]. The interaction relationships of BnaTH was visually edited using Cytoscape 3.8.2 [61].

4.9. RNA Isolation and qRT-PCR Analysis

Total RNA was extracted from leaves treated with different abiotic stresses using an RNA Prep Pure Plant Kit (Tiangen Biochemical Technology (Beijing, China) Co., Ltd.: DP201101X). The concentration and purity of the RNA were determined using a Nanodrop micro spectrophotometer (Thermo Scientific, Waltham, MA, USA) and agarose gel electrophoresis. The first strand of cDNA derived from mRNA was synthesized using HiScript®Q RT SuperMix (Vazyme, Nanjing, China). Quantitative real-time PCR (qRT-PCR) was carried out by SYBR-green fluorescence with a QuantStudioTM Real-Time PCR System (Thermo Fisher Scientific). Five TH genes were randomly selected to validate the expression patterns under drought, cold, and heat stresses (Table S11). The data were normalized by the internal control gene BnACTIN (BnaA03g55890D) and the 2−ΔΔCT analysis method was utilized to calculate relative expression levels [62].

4.10. Expression Profile Analysis

To explore the spatiotemporal expression patterns of rapeseed under different tissues and stresses, the relative FPKM value (fragments per kilobase of transcript per million fragments mapped) of RNA-seq data, PRJNA389508 (seedlings treated with five stress conditions) and PRJNA311067 (seeds harvested at different times after pollination), were retrieved in the BrassicaEDB website (https://brassica.biodb.org/downloads, accessed on 20 August 2022), and the expression levels of different tissues (cotyledon, leaf, stem, root, petal, sepal, etc.) were acquired from the Brassica napus information resource (http://yanglab.hzau.edu.cn/BnIR/expression_zs11, accessed on 20 August 2022) [63,64,65,66]. The FPKM values were log2 transformed and the heat map of hierarchical clustering was visualized using TBtools software [54].

5. Conclusions

In summary, a total of 455 TH genes was identified in six Brassica species and Arabidopsis. The evolutionary history of the TH genes was explored by integrating phylogenetic analysis, conserved motif identification, gene duplication event analysis, collinearity analysis between six Brassica species and Arabidopsis, and comparative genomic analysis. Many of the missing genes in B. napus belonged to the GT-2 subgroup, and most of the missing genes in B. carinate belonged to SIP1, but almost no genes were discarded in B. juncea. In addition, some mutations occurred in the motifs of TH proteins following hetero-tetraploidization in B. napus, with changes in the sequences of their amino acid residues. Expression pattern analysis revealed that BnaTH genes have different expression patterns, which can be induced by various stresses. Further transgenic validation or CRISPR/Cas9 knock out of these BnaTH genes could reveal their roles in stresses. In this study, a systematic analysis of TH genes in Brassica species, including their origin and evolution, and the function of BnaTH genes, was carried out to provide insights for further studies on the function of TH genes in B. napus.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/ijms232415766/s1.

Author Contributions

J.H., C.Z. and R.Z. conceived and designed this study. C.Z. and R.Z. performed the data analysis. C.Z., L.L., R.G., X.S. and F.L. prepared the samples and performed experiments. C.Z. drafted the manuscript. J.H. and R.Z. revised and edited the manuscript. All authors have read and agreed to the published version of the manuscript.

Funding

This study was supported by the Start-Up Funds of Northwest A&F University (Z1090222020).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The transcriptome data are available from the online website BrassicaEDB (https://brassica.biodb.org/downloads accessed on 20 August 2022, PRJNA389508 and PRJNA311067) and Brassica napus information resource (http://yanglab.hzau.edu.cn/BnIR/expression_zs11, accessed on 20 August 2022).

Conflicts of Interest

The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

References

  1. Green, P.J.; Kay, S.A.; Chua, N.H. Sequence-specific interactions of a pea nuclear factor with light-responsive elements upstream of the rbcS-3A gene. EMBO J. 1987, 6, 2543–2549. [Google Scholar] [CrossRef] [PubMed]
  2. Kaplan-Levy, R.N.; Brewer, P.B.; Quon, T.; Smyth, D.R. The trihelix family of transcription factors—Light, stress and development. Trends Plant Sci. 2012, 17, 163–171. [Google Scholar] [CrossRef] [PubMed]
  3. Nagano, Y. Several features of the GT-factor trihelix domain resemble those of the Myb DNA-binding domain. Plant Physiol. 2000, 124, 491–494. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  4. Nagano, Y.; Inaba, T.; Furuhashi, H.; Sasaki, Y. Trihelix DNA-binding protein with specificities for two distinct cis-elements: Both important for light down-regulated and dark-inducible gene expression in higher plants. J. Biol. Chem. 2001, 276, 22238–22243. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  5. Gao, M.J.; Lydiate, D.J.; Li, X.; Lui, H.; Gjetvaj, B.; Hegedus, D.D.; Rozwadowski, K. Repression of seed maturation genes by a trihelix transcriptional repressor in Arabidopsis seedlings. Plant Cell 2009, 21, 54–71. [Google Scholar] [CrossRef] [Green Version]
  6. Ma, Z.; Liu, M.; Sun, W.; Huang, L.; Wu, Q.; Bu, T.; Li, C.; Chen, H. Genome-wide identification and expression analysis of the trihelix transcription factor family in tartary buckwheat (Fagopyrum tataricum). BMC Plant Biol. 2019, 19, 344. [Google Scholar] [CrossRef] [Green Version]
  7. Cheng, X.; Xiong, R.; Yan, H.; Gao, Y.; Liu, H.; Wu, M.; Xiang, Y. The Trihelix family of transcription factors: Functional and evolutionary analysis in Moso bamboo (Phyllostachys edulis). BMC Plant Biol. 2019, 19, 154. [Google Scholar] [CrossRef] [Green Version]
  8. Xiao, J.; Hu, R.; Gu, T.; Han, J.; Qiu, D.; Su, P.; Feng, J.; Chang, J.; Yang, G.; He, G. Genome-wide identification and expression profiling of trihelix gene family under abiotic stresses in wheat. BMC Genom. 2019, 20, 287. [Google Scholar] [CrossRef]
  9. Mo, H.; Wang, L.; Ma, S.; Yu, D.; Lu, L.; Yang, Z.; Yang, Z.; Li, F. Transcriptome profiling of Gossypium arboreum during fiber initiation and the genome-wide identification of trihelix transcription factors. Gene 2019, 709, 36–47. [Google Scholar] [CrossRef]
  10. Wang, Z.; Liu, Q.; Wang, H.; Zhang, H.; Xu, X.; Li, C.; Yang, C. Comprehensive analysis of trihelix genes and their expression under biotic and abiotic stresses in Populus trichocarpa. Sci Rep. 2016, 6, 36274. [Google Scholar] [CrossRef]
  11. Wang, W.; Wu, P.; Liu, T.; Ren, H.; Li, Y.; Hou, X. Genome-wide analysis and expression divergence of the Trihelix family in Brassica rapa: Insight into the evolutionary patterns in plants. Sci. Rep. 2017, 7, 6463. [Google Scholar] [CrossRef] [Green Version]
  12. Song, A.; Wu, D.; Fan, Q.; Tian, C.; Chen, S.; Guan, Z.; Xin, J.; Zhao, K.; Chen, F. Transcriptome-wide identification and expression profiling analysis of chrysanthemum Trihelix transcription factors. Int. J. Mol. Sci. 2016, 17, 198. [Google Scholar] [CrossRef] [Green Version]
  13. Yu, C.; Cai, X.; Ye, Z.; Li, H. Genome-wide identification and expression profiling analysis of trihelix gene family in tomato. Biochem. Biophys. Res. Commun. 2015, 468, 653–659. [Google Scholar] [CrossRef]
  14. Qin, Y.; Ma, X.; Yu, G.; Wang, Q.; Wang, L.; Kong, L.; Kim, W.; Wang, H.W. Evolutionary history of trihelix family and their functional diversification. DNA Res. 2014, 21, 499–510. [Google Scholar] [CrossRef] [Green Version]
  15. Yu, C.; Song, L.; Song, J.; Ouyang, B.; Guo, L.; Shang, L.; Wang, T.; Li, H.; Zhang, J.; Ye, Z. ShCIGT, a Trihelix family gene, mediates cold and drought tolerance by interacting with SnRK1 in tomato. Plant Sci. 2018, 270, 140–149. [Google Scholar] [CrossRef]
  16. Xu, H.; Shi, X.; He, L.; Guo, Y.; Zang, D.; Li, H.; Zhang, W.; Wang, Y. Arabidopsis thaliana Trihelix transcription factor AST1 mediates salt and osmotic stress tolerance by binding to a novel AGAG-Box and some GT motifs. Plant Cell Physiol. 2018, 59, 946–965. [Google Scholar] [CrossRef] [Green Version]
  17. Luo, J.; Tang, S.; Mei, F.; Peng, X.; Li, J.; Li, X.; Yan, X.; Zeng, X.; Liu, F.; Wu, Y.; et al. BnSIP1-1, a Trihelix family gene, mediates abiotic stress tolerance and ABA signaling in Brassica napus. Front. Plant Sci. 2017, 8, 44. [Google Scholar] [CrossRef] [Green Version]
  18. Xi, J.; Qiu, Y.; Du, L.; Poovaiah, B.W. Plant-specific trihelix transcription factor AtGT2L interacts with calcium/calmodulin and responds to cold and salt stresses. Plant Sci. 2012, 185–186, 274–280. [Google Scholar] [CrossRef]
  19. Chalhoub, B.; Denoeud, F.; Liu, S.; Parkin, I.A.P.; Tang, H.; Wang, X.; Chiquet, J.; Belcram, H.; Tong, C.; Samans, B.; et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 2014, 345, 950–953. [Google Scholar] [CrossRef] [Green Version]
  20. Hu, J.; Chen, B.; Zhao, J.; Zhang, F.; Xie, T.; Xu, K.; Gao, G.; Yan, G.; Li, H.; Li, L.; et al. Genomic selection and genetic architecture of agronomic traits during modern rapeseed breeding. Nat. Genet. 2022, 54, 694–704. [Google Scholar] [CrossRef]
  21. Kang, L.; Qian, L.; Zheng, M.; Chen, L.; Chen, H.; Yang, L.; You, L.; Yang, B.; Yan, M.; Gu, Y.; et al. Genomic insights into the origin, domestication and diversification of Brassica juncea. Nat. Genet. 2021, 53, 1392–1402. [Google Scholar] [CrossRef] [PubMed]
  22. Song, X.; Wei, Y.; Xiao, D.; Gong, K.; Sun, P.; Ren, Y.; Yuan, J.; Wu, T.; Yang, Q.; Li, X.; et al. Brassica carinata genome characterization clarifies U’s triangle model of evolution and polyploidy in Brassica. Plant Physiol. 2021, 186, 388–406. [Google Scholar] [CrossRef] [PubMed]
  23. Nagaharu, U. Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Jpn. J. Bot. 1935, 7, 389–452. [Google Scholar]
  24. Wang, X.; Wang, H.; Wang, J.; Sun, R.; Wu, J.; Liu, S.; Bai, Y.; Mun, J.-H.; Bancroft, I.; Cheng, F.; et al. The genome of the mesopolyploid crop species Brassica rapa. Nat. Genet. 2011, 43, 1035–1039. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  25. Lysak, M.A.; Koch, M.A.; Pecinka, A.; Schubert, I. Chromosome triplication found across the tribe Brassiceae. Genome Res. 2005, 15, 516–525. [Google Scholar] [CrossRef] [Green Version]
  26. Liu, S.; Liu, Y.; Yang, X.; Tong, C.; Edwards, D.; Parkin, I.A.P.; Zhao, M.; Ma, J.; Yu, J.; Huang, S.; et al. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nat. Commun. 2014, 5, 3930. [Google Scholar] [CrossRef] [Green Version]
  27. Luo, J.; Jiang, W.; Tang, S.; Mei, F.; Yan, X.; Zeng, X.; Wu, G. BnSIP1-1 involves in light response and regulation of endogenous hormones and flowering time of Brassica Napus. J. Plant Growth Regul. 2021, 40, 2049–2057. [Google Scholar] [CrossRef]
  28. Breuer, C.; Kawamura, A.; Ichikawa, T.; Tominaga-Wada, R.; Wada, T.; Kondou, Y.; Muto, S.; Matsui, M.; Sugimoto, K. The trihelix transcription factor GTL1 regulates ploidy-dependent cell growth in the Arabidopsis trichome. Plant Cell. 2009, 21, 2307–2322. [Google Scholar] [CrossRef] [Green Version]
  29. Yoo, C.Y.; Pence, H.E.; Jin, J.B.; Miura, K.; Gosney, M.J.; Hasegawa, P.M.; Mickelbart, M.V. The Arabidopsis GTL1 transcription factor regulates water use efficiency and drought tolerance by modulating stomatal density via transrepression of SDD1. Plant Cell. 2010, 22, 4128–4141. [Google Scholar] [CrossRef] [Green Version]
  30. Völz, R.; Kim, S.K.; Mi, J.; Mariappan, K.G.; Guo, X.; Bigeard, J.; Alejandro, S.; Pflieger, D.; Rayapuram, N.; Al-Babili, S.; et al. The Trihelix transcription factor GT2-like 1 (GTL1) promotes salicylic acid metabolism, and regulates bacterial-triggered immunity. PLoS Genet. 2018, 14, e1007708. [Google Scholar] [CrossRef] [Green Version]
  31. Wang, X.H.; Li, Q.T.; Chen, H.W.; Zhang, W.K.; Ma, B.; Chen, S.Y.; Zhang, J.S. Trihelix transcription factor GT-4 mediates salt tolerance via interaction with TEM2 in Arabidopsis. BMC Plant Biol. 2014, 14, 339. [Google Scholar] [CrossRef]
  32. Li, X.; Qin, G.; Chen, Z.; Gu, H.; Qu, L.J. A gain-of-function mutation of transcriptional factor PTL results in curly leaves, dwarfism and male sterility by affecting auxin homeostasis. Plant Mol. Biol. 2008, 66, 315–327. [Google Scholar] [CrossRef]
  33. Kaplan-Levy, R.N.; Quon, T.; O’Brien, M.; Sappl, P.G.; Smyth, D.R. Functional domains of the PETAL LOSS protein, a trihelix transcription factor that represses regional growth in Arabidopsis thaliana. Plant J. 2014, 79, 477–491. [Google Scholar] [CrossRef]
  34. Marguerat, S.; Bähler, J. RNA-seq: From technology to biology. Cell Mol. Life Sci. 2010, 67, 569–579. [Google Scholar] [CrossRef] [Green Version]
  35. Auer, P.L.; Doerge, R.W. Statistical design and analysis of RNA sequencing data. Genetics 2010, 185, 405–416. [Google Scholar] [CrossRef] [Green Version]
  36. Town, C.D.; Cheung, F.; Maiti, R.; Crabtree, J.; Haas, B.J.; Wortman, J.R.; Hine, E.E.; Althoff, R.; Arbogast, T.S.; Tallon, L.J.; et al. comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell 2006, 18, 1348–1359. [Google Scholar] [CrossRef] [Green Version]
  37. Sankoff, D.; Zheng, C.; Zhu, Q. The collapse of gene complement following whole genome duplication. BMC Genom. 2010, 11, 313. [Google Scholar] [CrossRef] [Green Version]
  38. Udall, J.A.; Quijada, P.A.; Osborn, T.C. Detection of chromosomal rearrangements derived from homologous recombination in four mapping populations of Brassica napus L. Genetics 2005, 169, 967–979. [Google Scholar] [CrossRef] [Green Version]
  39. Sharpe, A.G.; Parkin, I.A.; Keith, D.J.; Lydiate, D.J. Frequent nonreciprocal translocations in the amphidiploid genome of oilseed rape (Brassica napus). Genome 1995, 38, 1112–1121. [Google Scholar] [CrossRef]
  40. Parkin, I.A.; Sharpe, A.G.; Keith, D.J.; Lydiate, D.J. Identification of the A and C genomes of amphidiploid Brassica napus (oilseed rape). Genome 1995, 38, 1122–1131. [Google Scholar] [CrossRef]
  41. Parkin, I.A.; Lydiate, D.J.; Trick, M. Assessing the level of collinearity between Arabidopsis thaliana and Brassica napus for A. thaliana chromosome 5. Genome 2002, 45, 356–366. [Google Scholar] [CrossRef] [PubMed]
  42. Cavell, A.C.; Lydiate, D.J.; Parkin, I.A.; Dean, C.; Trick, M. Collinearity between a 30-centimorgan segment of Arabidopsis thaliana chromosome 4 and duplicated regions within the Brassica napus genome. Genome 1998, 41, 62–69. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  43. Chen, H.; Wang, T.; He, X.; Cai, X.; Lin, R.; Liang, J.; Wu, J.; King, G.; Wang, X. BRAD V3.0: An upgraded Brassicaceae database. Nucleic Acids Res. 2021, 50, D1432–D1441. [Google Scholar] [CrossRef] [PubMed]
  44. Cunningham, F.; Allen, J.E.; Allen, J.; Alvarez-Jarreta, J.; Amode, M.R.; Armean, I.M.; Austine-Orimoloye, O.; Azov, A.G.; Barnes, I.; Bennett, R.; et al. Ensembl 2022. Nucleic Acids Res. 2022, 50, D988–D995. [Google Scholar] [CrossRef] [PubMed]
  45. El-Gebali, S.; Mistry, J.; Bateman, A.; Eddy, S.R.; Luciani, A.; Potter, S.C.; Qureshi, M.; Richardson, L.J.; Salazar, G.A.; Smart, A.; et al. The Pfam protein families database in 2019. Nucleic Acids Res. 2019, 47, D427–D432. [Google Scholar] [CrossRef]
  46. Eddy, S.R. Profile hidden Markov models. Bioinformatics 1998, 14, 755–763. [Google Scholar] [CrossRef] [Green Version]
  47. Mistry, J.; Chuguransky, S.; Williams, L.; Qureshi, M.; Salazar, G.A.; Sonnhammer, E.L.L.; Tosatto, S.C.E.; Paladin, L.; Raj, S.; Richardson, L.J.; et al. Pfam: The protein families database in 2021. Nucleic Acids Res. 2021, 49, D412–D419. [Google Scholar] [CrossRef]
  48. Letunic, I.; Khedkar, S.; Bork, P. SMART: Recent updates, new developments and status in 2020. Nucleic Acids Res. 2021, 49, D458–D460. [Google Scholar] [CrossRef]
  49. Artimo, P.; Jonnalagedda, M.; Arnold, K.; Baratin, D.; Csardi, G.; de Castro, E.; Duvaud, S.; Flegel, V.; Fortier, A.; Gasteiger, E.; et al. ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res. 2012, 40, W597–W603. [Google Scholar] [CrossRef]
  50. Horton, P.; Park, K.J.; Obayashi, T.; Fujita, N.; Harada, H.; Adams-Collier, C.J.; Nakai, K. WoLF PSORT: Protein localization predictor. Nucleic Acids Res. 2007, 35, W585–W587. [Google Scholar] [CrossRef] [Green Version]
  51. Kumar, S.; Stecher, G.; Tamura, K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 2016, 33, 1870–1874. [Google Scholar] [CrossRef]
  52. He, Z.; Zhang, H.; Gao, S.; Lercher, M.J.; Chen, W.H.; Hu, S. Evolview v2: An online visualization and management tool for customized and annotated phylogenetic trees. Nucleic Acids Res. 2016, 44, W236–W241. [Google Scholar] [CrossRef]
  53. Bailey, T.L.; Boden, M.; Buske, F.A.; Frith, M.; Grant, C.E.; Clementi, L.; Ren, J.; Li, W.W.; Noble, W.S. MEME SUITE: Tools for motif discovery and searching. Nucleic Acids Res. 2009, 37, W202–W208. [Google Scholar] [CrossRef]
  54. Chen, C.; Chen, H.; Zhang, Y.; Thomas, H.R.; Frank, M.H.; He, Y.; Xia, R. TBtools: An integrative toolkit developed for interactive analyses of big Biological Data. Mol. Plant 2020, 13, 1194–1202. [Google Scholar] [CrossRef]
  55. Lescot, M.; Déhais, P.; Thijs, G.; Marchal, K.; Moreau, Y.; Van de Peer, Y.; Rouzé, P.; Rombauts, S. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 2002, 30, 325–327. [Google Scholar] [CrossRef]
  56. Hu, B.; Jin, J.; Guo, A.Y.; Zhang, H.; Luo, J.; Gao, G. GSDS 2.0: An upgraded gene feature visualization server. Bioinformatics 2015, 31, 1296–1297. [Google Scholar] [CrossRef] [Green Version]
  57. Voorrips, R.E. MapChart: Software for the graphical presentation of linkage maps and QTLs. J. Hered. 2002, 93, 77–78. [Google Scholar] [CrossRef] [Green Version]
  58. Wang, Y.; Tang, H.; Debarry, J.D.; Tan, X.; Li, J.; Wang, X.; Lee, T.H.; Jin, H.; Marler, B.; Guo, H.; et al. MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012, 40, e49. [Google Scholar] [CrossRef] [Green Version]
  59. Krzywinski, M.; Schein, J.; Birol, I.; Connors, J.; Gascoyne, R.; Horsman, D.; Jones, S.J.; Marra, M.A. Circos: An information aesthetic for comparative genomics. Genome Res. 2009, 19, 1639–1645. [Google Scholar] [CrossRef] [Green Version]
  60. Dai, X.; Zhuang, Z.; Zhao, P.X. psRNATarget: A plant small RNA target analysis server (2017 release). Nucleic Acids Res. 2018, 46, W49–W54. [Google Scholar] [CrossRef] [Green Version]
  61. Shannon, P.; Markiel, A.; Ozier, O.; Baliga, N.S.; Wang, J.T.; Ramage, D.; Amin, N.; Schwikowski, B.; Ideker, T. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13, 2498–2504. [Google Scholar] [CrossRef] [PubMed]
  62. Livak, K.J.; Schmittgen, T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(T) (-Delta Delta C) method. Methods 2001, 25, 402–408. [Google Scholar] [CrossRef] [PubMed]
  63. Wang, P.; Yang, C.; Chen, H.; Luo, L.; Leng, Q.; Li, S.; Han, Z.; Li, X.; Song, C.; Zhang, X.; et al. Exploring transcription factors reveals crucial members and regulatory networks involved in different abiotic stresses in Brassica napus L. BMC Plant Biol. 2018, 18, 202. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  64. Wan, H.; Cui, Y.; Ding, Y.; Mei, J.; Dong, H.; Zhang, W.; Wu, S.; Liang, Y.; Zhang, C.; Li, J.; et al. Time-Series Analyses of Transcriptomes and proteomes reveal molecular networks underlying oil accumulation in canola. Front. Plant Sci. 2016, 7, 2007. [Google Scholar] [CrossRef] [Green Version]
  65. Liu, D.; Yu, L.; Wei, L.; Yu, P.; Wang, J.; Zhao, H.; Zhang, Y.; Zhang, S.; Yang, Z.; Chen, G.; et al. BnTIR: An online transcriptome platform for exploring RNA-seq libraries for oil crop Brassica napus. Plant Biotechnol. J. 2021, 19, 1895–1897. [Google Scholar] [CrossRef]
  66. Chao, H.; Li, T.; Luo, C.; Huang, H.; Ruan, Y.; Li, X.; Niu, Y.; Fan, Y.; Sun, W.; Zhang, K.; et al. BrassicaEDB: A Gene Expression Database for Brassica Crops. Int. J. Mol. Sci. 2020, 21, 5831. [Google Scholar] [CrossRef]
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Figure 1. Phylogenetic tree using 455 TH proteins from 7 species, including Arabidopsis, B. carinate, B. juncea, B. napus, B. oleracea, B. nigra, B. oleracea, and B. rapa, marked as yellow pentagram, purple triangle, pink triangle, red pentagram, purple pentagram, green triangle, and purple pentagram, respectively. The clades of group GT-1, GT-2, GTγ, SH4, and SIP1 are distinguished by different colors.
Figure 1. Phylogenetic tree using 455 TH proteins from 7 species, including Arabidopsis, B. carinate, B. juncea, B. napus, B. oleracea, B. nigra, B. oleracea, and B. rapa, marked as yellow pentagram, purple triangle, pink triangle, red pentagram, purple pentagram, green triangle, and purple pentagram, respectively. The clades of group GT-1, GT-2, GTγ, SH4, and SIP1 are distinguished by different colors.
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Figure 2. Comparative analysis of conserved domains and gene structures of BraTH genes, BolTH genes, and BnaTH genes. The colored boxes with numbers indicate the different conserved motifs identified by MEME. The scale bar at the bottom estimates the lengths of the motifs, exons, and introns. (A) Phylogenetic relationships, conserved protein motifs, and gene structures of 49 BraTH genes. (B) Phylogenetic relationships, conserved protein motifs, and gene structures of 94 BnaTH genes. (C) Phylogenetic relationships, conserved protein motifs, and gene structures of 54 BolTH genes.
Figure 2. Comparative analysis of conserved domains and gene structures of BraTH genes, BolTH genes, and BnaTH genes. The colored boxes with numbers indicate the different conserved motifs identified by MEME. The scale bar at the bottom estimates the lengths of the motifs, exons, and introns. (A) Phylogenetic relationships, conserved protein motifs, and gene structures of 49 BraTH genes. (B) Phylogenetic relationships, conserved protein motifs, and gene structures of 94 BnaTH genes. (C) Phylogenetic relationships, conserved protein motifs, and gene structures of 54 BolTH genes.
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Figure 3. Chromosomal distribution of BraTH genes, BolTH genes, and BnaTH genes. The colored bars represent chromosomes, and the chromosome numbers are shown at the top of the bars. TH genes are labeled at the right of the chromosomes. The scale on the left side indicates the chromosome length (Mb). (A) Chromosomal localization of BraTH genes in B. rapa. (B) Chromosomal localization of BnaTH genes in A subgenome of B. napus. (C) Chromosomal localization of BnaTH genes in C subgenome of B. napus. (D) Chromosomal localization of BolTH genes in B. oleracea. Genes in the red box are tandem duplication genes.
Figure 3. Chromosomal distribution of BraTH genes, BolTH genes, and BnaTH genes. The colored bars represent chromosomes, and the chromosome numbers are shown at the top of the bars. TH genes are labeled at the right of the chromosomes. The scale on the left side indicates the chromosome length (Mb). (A) Chromosomal localization of BraTH genes in B. rapa. (B) Chromosomal localization of BnaTH genes in A subgenome of B. napus. (C) Chromosomal localization of BnaTH genes in C subgenome of B. napus. (D) Chromosomal localization of BolTH genes in B. oleracea. Genes in the red box are tandem duplication genes.
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Figure 4. The collinearity of TH genes in B. rapa, B. nigra, B. oleracea, B. juncea, B. napus, and B. carinate. The green line indicates all synteny blocks between each chromosome and the red line indicates duplicated TH gene pairs. The chromosome number is shown at the top of each chromosome. The scale marked on the chromosome indicates the chromosome length (Mb).
Figure 4. The collinearity of TH genes in B. rapa, B. nigra, B. oleracea, B. juncea, B. napus, and B. carinate. The green line indicates all synteny blocks between each chromosome and the red line indicates duplicated TH gene pairs. The chromosome number is shown at the top of each chromosome. The scale marked on the chromosome indicates the chromosome length (Mb).
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Figure 5. The collinearity analysis of TH genes between Arabidopsis and six Brassica species and between tetraploid and their diploid ancestors. The grey lines in the background indicate the collinear blocks in the genomes of the two species connected by the grey lines, while the colored lines highlight the syntenic TH gene pairs. The colored bars represent the chromosomes of the different species. The chromosome number is labeled at the top of each chromosome.
Figure 5. The collinearity analysis of TH genes between Arabidopsis and six Brassica species and between tetraploid and their diploid ancestors. The grey lines in the background indicate the collinear blocks in the genomes of the two species connected by the grey lines, while the colored lines highlight the syntenic TH gene pairs. The colored bars represent the chromosomes of the different species. The chromosome number is labeled at the top of each chromosome.
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Figure 6. Numbers of orthologous gene pairs among different species and subfamily of orthologous genes. Orange represents the orthologous gene pair between Arabidopsis and Brassica species. Magenta represents the orthologous gene pair between Brassica species.
Figure 6. Numbers of orthologous gene pairs among different species and subfamily of orthologous genes. Orange represents the orthologous gene pair between Arabidopsis and Brassica species. Magenta represents the orthologous gene pair between Brassica species.
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Figure 7. Clade distribution of TH genes in Arabidopsis, B. rapa, B. nigra, B. oleracea, B. juncea, B. napus, and B. carinate. The species tree constructed on the basis of the evolutionary relationships between the seven species is shown on the left. The subgroup distribution of TH genes in each species is shown in the middle pie chart. The counts and percentages of TH gene subgroup members in each species are given in the table on the right.
Figure 7. Clade distribution of TH genes in Arabidopsis, B. rapa, B. nigra, B. oleracea, B. juncea, B. napus, and B. carinate. The species tree constructed on the basis of the evolutionary relationships between the seven species is shown on the left. The subgroup distribution of TH genes in each species is shown in the middle pie chart. The counts and percentages of TH gene subgroup members in each species are given in the table on the right.
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Figure 8. Expression pattern of BnaTH in different tissues and different developmental stages. The subgroup distribution and phylogenetic tree of BnaTH are shown on the left. FPKM values of BnaTH genes transformed by log2 were used in TBtools to construct heat maps. Expression levels are depicted by the different colors on the scale. Red and green represent high and low expression levels respectively.
Figure 8. Expression pattern of BnaTH in different tissues and different developmental stages. The subgroup distribution and phylogenetic tree of BnaTH are shown on the left. FPKM values of BnaTH genes transformed by log2 were used in TBtools to construct heat maps. Expression levels are depicted by the different colors on the scale. Red and green represent high and low expression levels respectively.
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Figure 9. Expression patterns of BnaTH under different stresses. FPKM values of BnaTH genes transformed by log2 were used in TBtools to construct heat maps. Expression levels are depicted by the different colors on the scale. Red and green represent high and low expression levels respectively.
Figure 9. Expression patterns of BnaTH under different stresses. FPKM values of BnaTH genes transformed by log2 were used in TBtools to construct heat maps. Expression levels are depicted by the different colors on the scale. Red and green represent high and low expression levels respectively.
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Figure 10. Expression profiles of five random selected TH genes in response to drought, cold, and heat treatments. Leaves were collected at 0 h, 1 h, 6 h, and 12 h after different treatments. Data were normalized to the BnACTIN gene. Vertical bars indicate standard deviations.
Figure 10. Expression profiles of five random selected TH genes in response to drought, cold, and heat treatments. Leaves were collected at 0 h, 1 h, 6 h, and 12 h after different treatments. Data were normalized to the BnACTIN gene. Vertical bars indicate standard deviations.
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Zhang, C.; Lu, L.; Gong, R.; Su, X.; Liu, F.; Zhang, R.; Hu, J. Conservation and Divergence of the Trihelix Genes in Brassica and Expression Profiles of BnaTH Genes in Brassica napus under Abiotic Stresses. Int. J. Mol. Sci. 2022, 23, 15766. https://doi.org/10.3390/ijms232415766

AMA Style

Zhang C, Lu L, Gong R, Su X, Liu F, Zhang R, Hu J. Conservation and Divergence of the Trihelix Genes in Brassica and Expression Profiles of BnaTH Genes in Brassica napus under Abiotic Stresses. International Journal of Molecular Sciences. 2022; 23(24):15766. https://doi.org/10.3390/ijms232415766

Chicago/Turabian Style

Zhang, Cuiping, Lijing Lu, Ruolin Gong, Xing Su, Fengbo Liu, Ru Zhang, and Jihong Hu. 2022. "Conservation and Divergence of the Trihelix Genes in Brassica and Expression Profiles of BnaTH Genes in Brassica napus under Abiotic Stresses" International Journal of Molecular Sciences 23, no. 24: 15766. https://doi.org/10.3390/ijms232415766

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