Identification of conserved gene structures and carboxy-terminal motifs in the Myb gene family of Arabidopsis and Oryza sativa L. ssp. indica

Genome-wide identification and investigation of monosaccharide transporter gene family based on their evolution and expression analysis under abiotic stress and hormone treatments in maize (Zea mays L.)

BACKGROUND

Monosaccharide transporter (MST) family, as a carrier for monosaccharide transport, plays an important role in carbon partitioning and widely involves in plant growth and development, stress response, and signaling transduction. However, little information on the MST family genes is reported in maize (Zea mays), especially in response to abiotic stresses. In this study, the genome-wide identification of MST family genes was performed in maize.

RESULT

A total of sixty-six putative members of MST gene family were identified and divided into seven subfamilies (including SPT, PMT, VGT, INT, pGlcT, TMT, and ERD) using bioinformatics approaches, and gene information, phylogenetic tree, chromosomal location, gene structure, motif composition, and cis-acting elements were investigated. Eight tandem and twelve segmental duplication events were identified, which played an important role in the expansion of the ZmMST family. Synteny analysis revealed the evolutionary features of MST genes in three gramineous crop species. The expression analysis indicated that most of the PMT, VGT, and ERD subfamilies members responded to osmotic and cadmium stresses, and some of them were regulated by ABA signaling, while only a few members of other subfamilies responded to stresses. In addition, only five genes were induced by NaCl stress in MST family.

CONCLUSION

These results serve to understand the evolutionary relationships of the ZmMST family genes and supply some insight into the processes of monosaccharide transport and carbon partitioning on the balance between plant growth and development and stress response in maize.

Genome-Wide Identification and Expression Analysis of the MYB Transcription Factor Family in Salvia nemorosa

The MYB transcription factor gene family is among the most extensive superfamilies of transcription factors in plants and is involved in various essential functions, such as plant growth, defense, and pigment formation. Salvia nemorosa is a perennial herb belonging to the Lamiaceae family, and S. nemorosa has various colors and high ornamental value. However, there is little known about its genome-wide MYB gene family and response to flower color formation. In this study, 142 SnMYB genes (MYB genes of S. nemorosa) were totally identified, and phylogenetic relationships, conserved motifs, gene structures, and expression profiles during flower development stages were analyzed. A phylogenetic analysis indicated that MYB proteins in S. nemorosa could be categorized into 24 subgroups, as supported by the conserved motif compositions and gene structures. Furthermore, according to their similarity with AtMYB genes associated with the control of anthocyanin production, ten SnMYB genes related to anthocyanin biosynthesis were speculated and chosen for further qRT-PCR analyses. The results indicated that five SnMYB genes (SnMYB75, SnMYB90, SnMYB6, SnMYB82, and SnMYB12) were expressed significantly differently in flower development stages. In conclusion, our study establishes the groundwork for understanding the anthocyanin biosynthesis of the SnMYB gene family and has the potential to enhance the breeding of S. nemorosa.

Integrated microRNA and whole-transcriptome sequencing reveals the involvement of small and long non-coding RNAs in the fiber growth of ramie plant

BACKGROUND

MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are the two main types of non-coding RNAs that play crucial roles in plant growth and development. However, their specific roles in the fiber growth of ramie plant (Boehmeria nivea L. Gaud) remain largely unknown.

METHODS

In this study, we performed miRNA and whole-transcriptome sequencing of two stem bark sections exhibiting different fiber growth stages to determine the expression profiles of miRNAs, lncRNAs, and protein-encoding genes.

RESULTS

Among the identified 378 miRNAs and 6,839 lncRNAs, 88 miRNAs and 1,288 lncRNAs exhibited differential expression. Bioinformatics analysis revealed that 29 and 228 differentially expressed protein-encoding genes were targeted by differentially expressed miRNAs and lncRNAs, respectively, constituting eight putative competing endogenous RNA networks. lncR00022274 exhibited downregulated expression in barks with growing fibers. It also had an antisense overlap with the MYB gene, BntWG10016451, whose overexpression drastically increased the xylem fiber number and secondary wall thickness of fibers in the stems of transgenic Arabidopsis, suggesting the potential association of lncR00022274-BntWG10016451 expression with fiber growth.

CONCLUSIONS

These findings provide insights into the roles of ncRNAs in the regulation of fiber growth in ramie, which can be used for the biotechnological improvement of its fiber yield and quality in the future.

Genome-wide analysis of the R2R3-MYB gene family in Spatholobus suberectus and identification of its function in flavonoid biosynthesis

Spatholobus suberectus Dunn (S. suberectus), a plant species within the Leguminosae family, has a long history of use in traditional medicines. The dried stem of S. suberectus exhibits various pharmacological activities because it contains various flavonoids. Diverse functions in plants are associated with the R2R3-MYB gene family, including the biosynthesis of flavonoids. Nonetheless, its role remains unelucidated in S. suberectus. Therefore, the newly sequenced S. suberectus genome was utilized to conduct a systematic genome-wide analysis of the R2R3-MYB gene family. The resulting data identified 181 R2R3-SsMYB genes in total, which were then categorized by phylogenetic analysis into 35 subgroups. Among the R2R3-SsMYB genes, 174 were mapped to 9 different chromosomes, and 7 genes were not located on any chromosome. Moreover, similarity in terms of exon-intron structures and motifs was exhibited by most genes in the same subgroup. The expansion of the gene family was primarily driven by segmental duplication events, as demonstrated by collinearity analysis. Notably, most of the duplicated genes underwent purifying selection, which was depicted through the Ka/Ks analysis. In this study, 22 R2R3-SsMYB genes were shown to strongly influence the level of flavonoids. The elevated expression level of these genes was depicted in the tissues with flavonoid accumulation in contrast with other tissues through qRT-PCR data. The resulting data elucidate the structural and functional elements of R2R3-SsMYB genes and present genes that could potentially be utilized for enhancing flavonoid biosynthesis in S. suberectus.

Systematic investigation of the R2R3-MYB gene family in Aquilaria sinensis reveals a transcriptional repressor AsMYB054 involved in 2-(2-phenylethyl)chromone biosynthesis

Trees in the genus Aquilaria produce agarwood, a valuable resin used in medicine, perfumes, and incense. 2-(2-Phenethyl)chromones (PECs) are characteristic components of agarwood; however, molecular mechanisms underlying PEC biosynthesis and regulation remain largely unknown. The R2R3-MYB transcription factors play important regulatory roles in the biosynthesis of various secondary metabolites. In this study, 101 R2R3-MYB genes in Aquilaria sinensis were systematically identified and analyzed at the genome-wide level. Transcriptomic analysis revealed that 19 R2R3-MYB genes were significantly regulated by an agarwood inducer, and showed significant correlations with PEC accumulation. Expression and evolutionary analyses revealed that AsMYB054, a subgroup 4 R2R3-MYB, was negatively correlated with PEC accumulation. AsMYB054 was located in the nucleus and functioned as a transcriptional repressor. Moreover, AsMYB054 could bind to the promoters of the PEC biosynthesis related genes AsPKS02 and AsPKS09, and inhibit their transcriptional activity. These findings suggested that AsMYB054 functions as a negative regulator of PEC biosynthesis via the inhibition of AsPKS02 and AsPKS09 in A. sinensis. Our results provide a comprehensive understanding of the R2R3-MYB subfamily in A. sinensis and lay a foundation for further functional analyses of R2R3-MYB genes in PEC biosynthesis.

Genome-wide analysis of R2R3-MYB genes in cultivated peanut (Arachis hypogaea L.): Gene duplications, functional conservation, and diversification

The cultivated Peanut (Arachis hypogaea L.), an important oilseed and edible legume, are widely grown worldwide. The R2R3-MYB transcription factor, one of the largest gene families in plants, is involved in various plant developmental processes and responds to multiple stresses. In this study we identified 196 typical R2R3-MYB genes in the genome of cultivated peanut. Comparative phylogenetic analysis with Arabidopsis divided them into 48 subgroups. The motif composition and gene structure independently supported the subgroup delineation. Collinearity analysis indicated polyploidization, tandem, and segmental duplication were the main driver of the R2R3-MYB gene amplification in peanut. Homologous gene pairs between the two subgroups showed tissue specific biased expression. In addition, a total of 90 R2R3-MYB genes showed significant differential expression levels in response to waterlogging stress. Furthermore, we identified an SNP located in the third exon region of AdMYB03-18 (AhMYB033) by association analysis, and the three haplotypes of the SNP were significantly correlated with total branch number (TBN), pod length (PL) and root-shoot ratio (RS ratio), respectively, revealing the potential function of AdMYB03-18 (AhMYB033) in improving peanut yield. Together, these studies provide evidence for functional diversity in the R2R3-MYB genes and will contribute to understanding the function of R2R3-MYB genes in peanut.

New Short RNA Motifs Potentially Relevant in the SARS-CoV-2 Genome

Background

The coronavirus disease has led to an exhaustive exploration of the SARS-CoV-2 genome. Despite the amount of information accumulated, the prediction of short RNA motifs encoding peptides mediating protein-protein or protein-drug interactions has received limited attention.

Objective

The study aims to predict short RNA motifs that are interspersed in the SARS-CoV-2 genome.

Methods

A method in which 14 trinucleotide families, each characterized by being composed of triplets with identical nucleotides in all possible configurations, was used to find short peptides with biological relevance. The novelty of the approach lies in using these families to search how they are distributed across genomes of different CoV genera and then to compare the distributions of these families with each other.

Results

We identified distributions of trinucleotide families in different CoV genera and also how they are related, using a selection criterion that identified short RNA motifs. The motifs were reported to be conserved in SARS-CoVs; in the remaining CoV genomes analysed, motifs contained, exclusively, different configurations of the trinucleotides A, T, G and A, C, G. Eighty-eight short RNA motifs, ranging in length from 12 to 49 nucleotides, were found: 50 motifs in the 1a polyprotein-encoding orf, 27 in the 1b polyprotein-encoding orf, 5 in the spike-encoding orf, and 6 in the nucleocapsid-encoding orf. Although some motifs (~27%) were found to be intercalated or attached to functional peptides, most of them have not yet been associated with any known functions.

Conclusion

Some of the trinucleotide family distributions in different CoV genera are not random; they are present in short peptides that, in many cases, are intercalated or attached to functional sites of the proteome.

Genome-wide analysis of R2R3-MYB transcription factors in Boehmeria nivea (L.) gaudich revealed potential cadmium tolerance and anthocyanin biosynthesis genes

Gene family, especially MYB as one of the largest transcription factor family in plants, the study of its subfunctional characteristics is a key step in the study of plant gene function. The sequencing of ramie genome provides a good opportunity to study the organization and evolutionary characters of the ramie MYB gene at the whole genome level. In this study, a total of 105 BnGR2R3-MYB genes were identified from ramie genome and subsequently grouped into 35 subfamilies according to phylogeny divergence and sequences similarity. Chromosomal localization, gene structure, synteny analysis, gene duplication, promoter analysis, molecular characteristics and subcellular localization were accomplished using several bioinformatics tools. Collinearity analysis showed that the segmental and tandem duplication events is the dominant form of the gene family expansion, and duplications prominent in distal telomeric regions. Highest syntenic relationship was obtained between BnGR2R3-MYB genes and that of Apocynum venetum (88). Furthermore, transcriptomic data and phylogenetic analysis revealed that BnGMYB60, BnGMYB79/80 and BnGMYB70 might inhibit the biosynthesis of anthocyanins, and UPLC-QTOF-MS data further supported the results. qPCR and phylogenetic analysis revealed that the six genes (BnGMYB9, BnGMYB10, BnGMYB12, BnGMYB28, BnGMYB41, and BnGMYB78) were cadmium stress responsive genes. Especially, the expression of BnGMYB10/12/41 in roots, stems and leaves all increased more than 10-fold after cadmium stress, and in addition they may interact with key genes regulating flavonoid biosynthesis. Thus, a potential link between cadmium stress response and flavonoid synthesis was identified through protein interaction network analysis. The study thus provided significant information into MYB regulatory genes in ramie and may serve as a foundation for genetic enhancement and increased productivity.

PrMYB5 activates anthocyanin biosynthetic PrDFR to promote the distinct pigmentation pattern in the petal of Paeonia rockii

Paeonia rockii is well-known for its distinctive large dark-purple spot at the white petal base and has been considered to be the main genetic source of spotted tree peony cultivars. In this study, the petal base and petal background of Paeonia ostii (pure white petals without any spot), P. rockii, and other three tree peony cultivars were sampled at four blooming stages from the small bell-like bud stage to the initial blooming stage. There is a distinct difference between the pigmentation processes of spots and petal backgrounds; the spot pigmentation was about 10 days earlier than the petal background. Moreover, the cyanin and peonidin type anthocyanin accumulation at the petal base mainly contributed to the petal spot formation. Then, we identified a C1 subgroup R2R3-MYB transcription factor, PrMYB5, predominantly transcribing at the petal base. This is extremely consistent with PrDFR and PrANS expression, the contents of anthocyanins, and spot formation. Furthermore, PrMYB5 could bind to and activate the promoter of PrDFR in yeast one-hybrid and dual-luciferase assays, which was further verified in overexpression of PrMYB5 in tobacco and PrMYB5-silenced petals of P. rockii by comparing the color change, anthocyanin contents, and gene expression. In summary, these results shed light on the mechanism of petal spot formation in P. rockii and speed up the molecular breeding process of tree peony cultivars with novel spot pigmentation patterns.

Genome-wide identification and expression analysis of the R2R3-MYB gene family in tobacco (Nicotiana tabacum L.)

BACKGROUND

The R2R3-MYB transcription factor is one of the largest gene families in plants and involved in the regulation of plant development, hormone signal transduction, biotic and abiotic stresses. Tobacco is one of the most important model plants. Therefore, it will be of great significance to investigate the R2R3-MYB gene family and their expression patterns under abiotic stress and senescence in tobacco.

RESULTS

A total of 174 R2R3-MYB genes were identified from tobacco (Nicotiana tabacum L.) genome and were divided into 24 subgroups based on phylogenetic analysis. Gene structure (exon/intron) and protein motifs were especially conserved among the NtR2R3-MYB genes, especially members within the same subgroup. The NtR2R3-MYB genes were distributed on 24 tobacco chromosomes. Analysis of gene duplication events obtained 3 pairs of tandem duplication genes and 62 pairs of segmental duplication genes, suggesting that segmental duplications is the major pattern for R2R3-MYB gene family expansion in tobacco. Cis-regulatory elements of the NtR2R3-MYB promoters were involved in cellular development, phytohormones, environmental stress and photoresponsive. Expression profile analysis showed that NtR2R3-MYB genes were widely expressed in different maturity tobacco leaves, and however, the expression patterns of different members appeared to be diverse. The qRT-PCR analysis of 15 NtR2R3-MYBs confirmed their differential expression under different abiotic stresses (cold, salt and drought), and notably, NtMYB46 was significantly up-regulated under three treatments.

CONCLUSIONS

In summary, a genome-wide identification, evolutionary and expression analysis of R2R3-MYB gene family in tobacco were conducted. Our results provided a solid foundation for further biological functional study of NtR2R3-MYB genes in tobacco.

Genome-wide Identification and Expression Analysis of RcMYB Genes in Rhodiola crenulata

Modern research has proved that the main medicinal component of Rhodiola crenulata, which has a wide range of medicinal value, is its secondary metabolite salidroside. The MYB transcription factor family is widely involved in biosynthesis of second metabolism and other roles in the stress response in plants, so a genome-wide identification and analysis for this family in R. crenulata is worth conducting. In this research, genome-wide analysis identified 139 MYB genes based on conserved domains in the R. crenulata genome, and 137 genes were used to construct a phylogenetic tree and modified with expression files to reveal evolutionary characteristics. Physical and chemical characteristics, gene structure, and conserved motif analysis were also used to further analyze RcMYBs. Additionally, cis-acting elements related to transcription, hormone, and MYB binding were found in the promoter region of the selected RcMYBs. Four RcMYBs were cloned, sequenced, and their gene expression pattern was analyzed for further analysis of their functions. The research results lay the foundation for further research on the function of RcMYB and R. crenulata.

Evolution and functional diversification of R2R3-MYB transcription factors in plants

R2R3-MYB genes (R2R3-MYBs) form one of the largest transcription factor gene families in the plant kingdom, with substantial structural and functional diversity. However, the evolutionary processes leading to this amazing functional diversity have not yet been clearly established. Recently developed genomic and classical molecular technologies have provided detailed insights into the evolutionary relationships and functions of plant R2R3-MYBs. Here, we review recent genome-level and functional analyses of plant R2R3-MYBs, with an emphasis on their evolution and functional diversification. In land plants, this gene family underwent a large expansion by whole genome duplications and small-scale duplications. Along with this population explosion, a series of functionally conserved or lineage-specific subfamilies/groups arose with roles in three major plant-specific biological processes: development and cell differentiation, specialized metabolism, and biotic and abiotic stresses. The rapid expansion and functional diversification of plant R2R3-MYBs are highly consistent with the increasing complexity of angiosperms. In particular, recently derived R2R3-MYBs with three highly homologous intron patterns (a, b, and c) are disproportionately related to specialized metabolism and have become the predominant subfamilies in land plant genomes. The evolution of plant R2R3-MYBs is an active area of research, and further studies are expected to improve our understanding of the evolution and functional diversification of this gene family.

Evaluation of reference genes and characterization of the MYBs in xylem radial change of Chinese fir stem

The radial change (RC) of tree stem is the process of heartwood formation involved in complex molecular mechanism. Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.), an evergreen species, is an important fast-growing timber tree in southern China. In this study, the top four stable genes (IDH, UBC2, RCA and H2B) were selected in RC tissues of 15 years old Chinese fir stem (RC15) and the genes (H2B, 18S, TIP41 and GAPDH) were selected in RC tissues of 30 years old Chinese fir stem (RC30). The stability of the reference genes is higher in RC30 than in RC15. Sixty-one MYB transcripts were obtained on the PacBio Sequel platform from woody tissues of one 30 years old Chinese fir stem. Based on the number of MYB DNA-binding domain and phylogenetic relationships, the ClMYB transcripts contained 21 transcripts of MYB-related proteins (1R-MYB), 39 transcripts of R2R3-MYB proteins (2R-MYB), one transcript of R1R2R3-MYB protein (3R-MYB) belonged to 18 function-annotated clades and two function-unknown clades. In RC woody tissues of 30 years old Chinese fir stem, ClMYB22 was the transcript with the greatest fold change detected by both RNA-seq and qRT-PCR. Reference genes selected in this study will be helpful for further verification of transcript abundance patterns during the heartwood formation of Chinese fir.

Identification of a Strong Anthocyanin Activator, VbMYBA, From Berries of Vaccinium bracteatum Thunb

Wufanshu (Vaccinium bracteatum Thunb.), which is a wild member of the genus Vaccinium, accumulates high concentration of anthocyanin in its berries. In this study, the accumulated anthocyanins and their derivatives in Wufanshu berries were identified through UHPLC-MS/MS analysis. Candidate anthocyanin biosynthetic genes were identified from the transcriptome of Wufanshu berries. qRT-PCR analyses showed that the expression of anthocyanin structural genes correlated with anthocyanin accumulation in berries. The R2R3-MYB, VbMYBA, which is a homolog of anthocyanin promoting R2R3-MYBs from other Vaccinium species, was also identified. Transient expression of VbMYBA in Nicotiana tabacum leaves confirmed its role as an anthocyanin regulator, and produced a higher anthocyanin concentration when compared with blueberry VcMYBA expression. Dual-luciferase assays further showed that VbMYBA can activate the DFR and UFGT promoters from other Vaccinium species. VbMYBA has an additional 23 aa at the N terminus compared with blueberry VcMYBA, but this was shown not to affect the ability to regulate anthocyanins. Taken together, our results provide important information on the molecular mechanisms responsible for the high anthocyanin content in Wufanshu berries.

Genome-wide analysis and expression profiles of PdeMYB transcription factors in colored-leaf poplar (Populus deltoids)

BACKGROUND

MYB transcription factors, comprising one of the largest transcription factor families in plants, play many roles in secondary metabolism, especially in anthocyanin biosynthesis. However, the functions of the PdeMYB transcription factor in colored-leaf poplar remain elusive.

RESULTS

In the present study, genome-wide characterization of the PdeMYB genes in colored-leaf poplar (Populus deltoids) was conducted. A total of 302 PdeMYB transcription factors were identified, including 183 R2R3-MYB, five R1R2R3-MYB, one 4R-MYB, and 113 1R-MYB transcription factor genes. Genomic localization and paralogs of PdeMYB genes mapped 289 genes on 19 chromosomes, with collinearity relationships among genes. The conserved domain, gene structure, and evolutionary relationships of the PdeMYB genes were also established and analyzed. The expression levels of PdeMYB genes were obtained from previous data in green leaf poplar (L2025) and colored leaf poplar (QHP) as well as our own qRT-PCR analysis data in green leaf poplar (L2025) and colored leaf poplar (CHP), which provide valuable clues for further functional characterization of PdeMYB genes.

CONCLUSIONS

The above results provide not only comprehensive insights into the structure and functions of PdeMYB genes but also provide candidate genes for the future improvement of leaf colorization in Populus deltoids.

Recent Advanced Metabolic and Genetic Engineering of Phenylpropanoid Biosynthetic Pathways

The MYB transcription factors (TFs) are evolving as critical role in the regulation of the phenylpropanoid and tanshinones biosynthetic pathway. MYB TFs relate to a very important gene family, which are involved in the regulation of primary and secondary metabolisms, terpenoids, bioactive compounds, plant defense against various stresses and cell morphology. R2R3 MYB TFs contained a conserved N-terminal domain, but the domain at C-terminal sorts them different regarding their structures and functions. MYB TFs suppressors generally possess particular repressive motifs, such as pdLNLD/ELxiG/S and TLLLFR, which contribute to their suppression role through a diversity of complex regulatory mechanisms. A novel flower specific "NF/YWSV/MEDF/LW" conserved motif has a great potential to understand the mechanisms of flower development. In the current review, we summarize recent advanced progress of MYB TFs on transcription regulation, posttranscriptional, microRNA, conserved motif and propose directions to future prospective research. We further suggest there should be more focus on the investigation for the role of MYB TFs in microalgae, which has great potential for heterologous protein expression system for future perspectives.

Genome-wide analysis of MYB transcription factors of Vaccinium corymbosum and their positive responses to drought stress

Background

Blueberry (Vaccinium corymbosum L.) is an important species with a high content of flavonoids in fruits. As a perennial shrub, blueberry is characterized by shallow-rooted property and susceptible to drought stress. MYB transcription factor was reported to be widely involved in plant response to abiotic stresses, however, the role of MYB family in blueberry responding to drought stress remains elusive.

Results

In this study, we conducted a comprehensive analysis of VcMYBs in blueberry based on the genome data under drought stress, including phylogenetic relationship, identification of differentially expressed genes (DEGs), expression profiling, conserved motifs, expression correlation and protein-protein interaction prediction, etc. The results showed that 229 non-redundant MYB sequences were identified in the blueberry genome, and divided into 23 subgroups. A total of 102 MYB DEGs with a significant response to drought stress were identified, of which 72 in leaves and 69 in roots, and 8 differential expression genes with a > 20-fold change in the level of expression. 17 DEGs had a higher expression correlation with other MYB members. The interaction partners of the key VcMYB proteins were predicted by STRING analysis and in combination with physiological and morphological observation. 10 key VcMYB genes such as VcMYB8, VcMYB102 and VcMYB228 were predicted to be probably involved in reactive oxygen species (ROS) pathway, and 7 key VcMYB genes (VcMYB41, VcMYB88 and VcMYB100, etc..) probably participated in leaf regulation under drought treatment.

Conclusions

Our studies provide a new understanding of the regulation mechanism of VcMYB family in blueberry response to drought stress, and lay fundamental support for future studies on blueberry grown in regions with limited water supply for this crop.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07850-5.

The R2R3-type MYB transcription factor MdMYB90-like is responsible for the enhanced skin color of an apple bud sport mutant

The anthocyanin content in apple skin determines its red coloration, as seen in a Fuji apple mutant. Comparative RNA-seq analysis was performed to determine differentially expressed genes at different fruit development stages between the wild-type and the skin color mutant. A novel R2R3-MYB transcription factor, MdMYB90-like, was uncovered as the key regulatory gene for enhanced coloration in the mutant. The expression of MdMYB90-like was 21.3 times higher in the mutant. MdMYB90-like regulates anthocyanin biosynthesis directly through the activation of anthocyanin biosynthesis genes and indirectly through the activation of other transcription factors that activate anthocyanin biosynthesis. MdMYB90-like bound to the promoters of both structural genes (MdCHS and MdUFGT) and other transcription factor genes (MdMYB1 and MdbHLH3) in the yeast one-hybrid system, electrophoretic mobility shift assay, and dual-luciferase assay. Transgenic analysis showed that MdMYB90-like was localized in the nucleus, and its overexpression induced the expression of other anthocyanin-related genes, including MdCHS, MdCHI, MdANS, MdUFGT, MdbHLH3, and MdMYB1. The mutant had reduced levels of DNA methylation in two regions (-1183 to -988 and -2018 to -1778) of the MdMYB90-like gene promoter, which might explain the enhanced expression of the gene and the increased anthocyanin content in the mutant apple skin.

Systematic analysis of differentially expressed ZmMYB genes related to drought stress in maize

MYB transcription factors play pivotal roles in hormone conduction signaling and abiotic stress response. In this study, 54 differentially expressed ZmMYB genes were identified and comprehensive analyses were conducted including gene's structure, chromosomal localization, phylogenetic tree, motif prediction, cis-elements and expression patterns. The results showed that 54 genes were unevenly distributed on 10 chromosomes and classified into eleven main subgroups by phylogenetic analysis, supported by motif and exon/intron analyses. The mainly stress-related cis-elements were ABRE, ARE, MBS and DRE-core. In addition, 8 core ZmMYB genes were identified by co-expression network. qRT-PCR results showed that the 8 ZmMYB genes exhibited different expression levels under different abiotic stresses, indicating that they were responsive to various abiotic stress. These results will provide insight for further functional investigation of ZmMYB genes.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01013-2.

The role of VvMYBA2r and VvMYBA2w alleles of the MYBA2 locus in the regulation of anthocyanin biosynthesis for molecular breeding of grape (Vitis spp.) skin coloration

In grape, MYBA1 and MYBA2 at the colour locus are the major genetic determinants of grape skin colour, and the mutation of two functional genes (VvMYBA1 and VvMYBA2) from these loci leads to white skin colour. This study aimed to elucidate the regulation of grape berry coloration by isolating and characterizing VvMYBA2w and VvMYBA2r alleles. The overexpression of VvMYBA2r up-regulated the expression of anthocyanin biosynthetic genes and resulted in higher anthocyanin accumulation in transgenic tobacco than wild-type (WT) plants, especially in flowers. However, the ectopic expression of VvMYBA2w inactivated the expression of anthocyanin biosynthetic genes and could not cause obvious phenotypic modulation in transgenic tobacco. Unlike in VvMYBA2r, CA dinucleotide deletion shortened the C-terminal transactivation region and disrupted the transcriptional activation activity of VvMYBA2w. The results indicated that VvMYBA2r positively regulated anthocyanin biosynthesis by forming the VvMYBA2r-VvMYCA1-VvWDR1 complex, and VvWDR1 enhanced anthocyanin accumulation by interacting with the VvMYBA2r-VvMYCA1 complex; however, R⁴⁴ L substitution abolished the interaction of VvMYBA2w with VvMYCA1. Meanwhile, both R⁴⁴ L substitution and CA dinucleotide deletion seriously affected the efficacy of VvMYBA2w to regulate anthocyanin biosynthesis, and the two non-synonymous mutations were additive in their effects. Investigation of the colour density and MYB haplotypes of 213 grape germplasms revealed that dark-skinned varieties tended to contain HapC-N and HapE2, whereas red-skinned varieties contained high frequencies of HapB and HapC-Rs. Regarding ploidy, the higher the number of functional alleles present in a variety, the darker was the skin colour. In summary, this study provides insight into the roles of VvMYBA2r and VvMYBA2w alleles and lays the foundation for the molecular breeding of grape varieties with different skin colour.

MYB_SH[AL]QKY[RF] transcription factors MdLUX and MdPCL-like promote anthocyanin accumulation through DNA hypomethylation and MdF3H activation in apple

Heritable DNA methylation is a highly conserved epigenetic mark that is important for many biological processes. In a previous transcriptomic study on the fruit skin pigmentation of apple (Malus domestica Borkh.) cv. 'Red Delicious' (G0) and its four continuous-generation bud sport mutants including 'Starking Red' (G1), 'Starkrimson' (G2), 'Campbell Redchief' (G3) and 'Vallee spur' (G4), we identified MYB transcription factors (TFs) MdLUX and MdPCL-like involved in regulating anthocyanin synthesis. However, how these TFs ultimately determine the fruit skin color traits remains elusive. Here, bioinformatics analysis revealed that MdLUX and MdPCL-like contained a well-conserved motif SH[AL]QKY[RF] in their C-terminal region and were located in the nucleus of onion epidermal cells. Overexpression of MdLUX and MdPCL-like in 'Golden Delicious' fruits, 'Gala' calli and Arabidopsis thaliana promoted the accumulation of anthocyanin, whereas MdLUX and MdPCL-like suppression inhibited anthocyanin accumulation in 'Red Fuji' apple fruit skin. Yeast one-hybrid assays revealed that MdLUX and MdPCL-like may bind to the promoter region of the anthocyanin biosynthesis gene MdF3H. Dual-luciferase assays indicated that MdLUX and MdPCL-like activated MdF3H. The whole-genome DNA methylation study revealed that the methylation levels of the mCG context at the upstream (i.e., promoter region) of MdLUX and MdPCL-like were inversely correlated with their mRNA levels and anthocyanin accumulation. Hence, the data suggest that MYB_SH[AL]QKY[RF] TFs MdLUX and MdPCL-like promote anthocyanin biosynthesis in apple fruit skins through the DNA hypomethylation of their promoter regions and the activation of the structural flavonoid gene MdF3H.

Characterization of the Liriodendron Chinense MYB Gene Family and Its Role in Abiotic Stress Response

Liriodendron chinense (Lchi) is a Magnoliaceae plant, which is a basic angiosperm left behind by the Pleistocene and mainly distributed in the south of the Yangtze River. Liriodendron hybrids has good wood properties and is widely used in furniture and in other fields. It is not clear if they can adapt to different environmental conditions, such as drought and high and low temperatures, and the molecular mechanisms for this adaptation are unknown. Among plant transcription factors (TFs), the MYB gene family is one of the largest and is often involved in stress or adversity response signaling, growth, and development. Therefore, studying the role of MYBTFs in regulating abiotic stress signaling, growth, and development in Lchi is helpful to promote afforestation in different environments. In our research, a genome-wide analysis of the LchiMYB gene family was performed, including the phylogenetic relationship tree, gene exon-intron structure, collinearity, and chromosomal position. According to the evolutionary tree, 190 LchiMYBs were divided into three main branches. LchiMYBs were evenly distributed across 19 chromosomes, with their collinearity, suggesting that segment duplication events may have contributed to LchiMYB gene expansion. Transcriptomes from eight tissues, 11 stages of somatic embryogenesis, and leaves after cold, heat, and drought stress were used to analyze the function of the MYB gene family. The results of tissue expression analysis showed that most LchiMYB genes regulated bark, leaf, bud, sepal, stigma, and stamen development, as well as the four important stages (ES3, ES4, ES9, and PL) of somatic embryogenesis. More than 60 LchiMYBs responded to heat, cold, and drought stress; some of which underwent gene duplication during evolution. LchiMYB3 was highly expressed under all three forms of stress, while LchiMYB121 was strongly induced by both cold and heat stress. Eight genes with different expression patterns were selected and verified by quantitative real-time PCR (qRT-PCR) experiments. The results suggested that these LchiMYBs may regulate Lchi growth development and resistance to abiotic stress. This study shows the cross-regulatory function of LchiMYBs in the growth and development, asexual reproduction, and abiotic resistance of Lchi. This information will prove pivotal to directing further studies on the biological function of Lchi MYBTFs in genetic improvement and abiotic stress response.

Systematic Analysis of the R2R3-MYB Family in Camellia sinensis: Evidence for Galloylated Catechins Biosynthesis Regulation

The R2R3-MYB transcription factor (TF) family regulates metabolism of phenylpropanoids in various plant lineages. Species-expanded or specific MYB TFs may regulate species-specific metabolite biosynthesis including phenylpropanoid-derived bioactive products. Camellia sinensis produces an abundance of specialized metabolites, which makes it an excellent model for digging into the genetic regulation of plant-specific metabolite biosynthesis. The most abundant health-promoting metabolites in tea are galloylated catechins, and the most bioactive of the galloylated catechins, epigallocatechin gallate (EGCG), is specifically relative abundant in C. sinensis. However, the transcriptional regulation of galloylated catechin biosynthesis remains elusive. This study mined the R2R3-MYB TFs associated with galloylated catechin biosynthesis in C. sinensis. A total of 118 R2R3-MYB proteins, classified into 38 subgroups, were identified. R2R3-MYB subgroups specific to or expanded in C. sinensis were hypothesized to be essential to evolutionary diversification of tea-specialized metabolites. Notably, nine of these R2R3-MYB genes were expressed preferentially in apical buds (ABs) and young leaves, exactly where galloylated catechins accumulate. Three putative R2R3-MYB genes displayed strong correlation with key galloylated catechin biosynthesis genes, suggesting a role in regulating biosynthesis of epicatechin gallate (ECG) and EGCG. Overall, this study paves the way to reveal the transcriptional regulation of galloylated catechins in C. sinensis.

Genome-wide identification and expression analysis of the MYB transcription factor in Japanese plum (Prunus salicina)

MYB proteins constitute one of the largest transcription factor families in plants, members of which are involved in various plant physiological and biochemical processes. Japanese plum (Prunus salicina) is one of the important stone fruit crops worldwide. To date, no comprehensive study of the MYB family in Japanese plum has been reported. In this study, we performed genome-wide analysis of MYB genes in Japanese plum including the phylogeny, gene structures, protein motifs, chromosomal locations, collinearity and expression patterns analysis. A total of 96 Japanese plum R2R3-MYB (PsMYB) genes were characterized and distributed on 8 chromosomes at various densities. Collinearity analysis indicated that the segmental duplication events played a crucial role in the expansion of PsMYB genes, and the interspecies synteny analysis revealed the orthologous gene pairs between Japanese plum and other four selected Rosaceae species. The 96 PsMYB genes could be classified into 27 subgroups based on phylogenetic topology, as supported by the conserved gene structures and motif compositions. Further comparative phylogenetic analysis revealed the functional divergence of MYB gene family during evolution, and three subgroups which included only Rasaceae MYB genes were identified. Expression analysis revealed the distinct expression profiles of the PsMYB genes, and further functional predictions found some of them might be associated with the plum fruit quality traits. Our researches provide a global insight into the organization, phylogeny, evolution and expression patterns of the PsMYB genes, and contribute to the greater understanding of their functional roles in Japanese plum.

Xylem systems genetics analysis reveals a key regulator of lignin biosynthesis in Populus deltoides

Despite the growing resources and tools for high-throughput characterization and analysis of genomic information, the discovery of the genetic elements that regulate complex traits remains a challenge. Systems genetics is an emerging field that aims to understand the flow of biological information that underlies complex traits from genotype to phenotype. In this study, we used a systems genetics approach to identify and evaluate regulators of the lignin biosynthesis pathway in Populus deltoides by combining genome, transcriptome, and phenotype data from a population of 268 unrelated individuals of P. deltoides The discovery of lignin regulators began with the quantitative genetic analysis of the xylem transcriptome and resulted in the detection of 6706 and 4628 significant local- and distant-eQTL associations, respectively. Among the locally regulated genes, we identified the R2R3-MYB transcription factor MYB125 (Potri.003G114100) as a putative trans-regulator of the majority of genes in the lignin biosynthesis pathway. The expression of MYB125 in a diverse population positively correlated with lignin content. Furthermore, overexpression of MYB125 in transgenic poplar resulted in increased lignin content, as well as altered expression of genes in the lignin biosynthesis pathway. Altogether, our findings indicate that MYB125 is involved in the control of a transcriptional coexpression network of lignin biosynthesis genes during secondary cell wall formation in P. deltoides.

Insights into the Diversification and Evolution of R2R3-MYB Transcription Factors in Plants

As one of the largest families of transcription factors (TFs) in plants, R2R3-MYB proteins play crucial roles in regulating a series of plant-specific biological processes. Although the diversity of plant R2R3-MYB TFs has been studied previously, the processes and mechanisms underlying the expansion of these proteins remain unclear. Here, we performed evolutionary analyses of plant R2R3-MYB TFs with dense coverage of streptophyte algae and embryophytes. Our analyses revealed that ancestral land plants exhibited 10 subfamilies of R2R3-MYB proteins, among which orthologs of seven subfamilies were present in chlorophytes and charophycean algae. We found that asymmetric gene duplication events in different subfamilies account for the expansion of R2R3-MYB proteins in embryophytes. We further discovered that the largest subfamily of R2R3-MYBs in land plants, subfamily VIII, emerged in the common ancestor of Zygnematophyceae and embryophytes. During plant terrestrialization, six duplication events gave rise to seven clades of subfamily VIII. Subsequently, this TF subfamily showed a tendency for expansion in bryophytes, lycophytes, and ferns and extensively diversified in ancestral gymnosperms and angiosperms in clades VIII-A-1, VIII-D, and VIII-E. In contrast to subfamily VIII, other subfamilies of R2R3-MYB TFs have remained less expanded across embryophytes. The findings regarding phylogenetic analyses, auxiliary motifs, and DNA-binding specificities provide insight into the evolutionary history of plant R2R3-MYB TFs and shed light on the mechanisms underlying the extensive expansion and subsequent sub- and neofunctionalization of these proteins.

A R2R3-MYB gene-based marker for the non-darkening seed coat trait in pinto and cranberry beans (Phaseolus vulgaris L.) derived from 'Wit-rood boontje'

KEY MESSAGE

The gene Phvul.010G130600 which codes for a MYB was shown to be tightly associated with seed coat darkening in Phaseolus vulgaris and a single nucleotide deletion in the allele in Wit-rood disrupts a transcription activation region that likely prevents its functioning in this non-darkening genotype. The beige and white background colors of the seed coats of conventional pinto and cranberry beans turn brown through a process known as postharvest darkening (PHD). Seed coat PHD is attributed to proanthocyanidin accumulation and its subsequent oxidation in the seed coat. The J gene is an uncharacterized classical genetic locus known to be responsible for PHD in common bean (P. vulgaris) and individuals that are homozygous for its recessive allele have a non-darkening (ND) seed coat phenotype. A previous study identified a major colorimetrically determined QTL for seed coat color on chromosome 10 that was associated with the ND trait. The objectives of this study were to identify a gene associated with seed coat postharvest darkening in common bean and understand its function in promoting seed coat darkening. Amplicon sequencing of 21 candidate genes underlying the QTL associated with the ND trait revealed a single nucleotide deletion (c.703delG) in the candidate gene Phvul.010G130600 in non-darkening recombinant inbred lines derived from crosses between ND 'Wit-rood boontje' and a regular darkening pinto genotype. In silico analysis indicated that Phvul.010G130600 encodes a protein with strong amino acid sequence identity (70%) with a R2R3-MYB-type transcription factor MtPAR, which has been shown to regulate proanthocyanidin biosynthesis in Medicago truncatula seed coat tissue. The deletion in the 'Wit-rood boontje' allele of Phvul.010G130600 likely causes a translational frame shift that disrupts the function of a transcriptional activation domain contained in the C-terminus of the R2R3-MYB. A gene-based dominant marker was developed for the dominant allele of Phvul.010G130600 which can be used for marker-assisted selection of ND beans.

MYB81, a microspore-specific GAMYB transcription factor, promotes pollen mitosis I and cell lineage formation in Arabidopsis

Sexual reproduction in flowering plants relies on the production of haploid gametophytes that consist of germline and supporting cells. During male gametophyte development, the asymmetric mitotic division of an undetermined unicellular microspore segregates these two cell lineages. To explore genetic regulation underlying this process, we screened for pollen cell patterning mutants and isolated the heterozygous myb81-1 mutant that sheds ~50% abnormal pollen. Typically, myb81-1 microspores fail to undergo pollen mitosis I (PMI) and arrest at polarized stage with a single central vacuole. Although most myb81-1 microspores degenerate without division, a small fraction divides at later stages and fails to acquire correct cell fates. The myb81-1 allele is transmitted normally through the female, but rarely through pollen. We show that myb81-1 phenotypes result from impaired function of the GAMYB transcription factor MYB81. The MYB81 promoter shows microspore-specific activity and a MYB81-RFP fusion protein is only expressed in a narrow window prior to PMI. Ectopic expression of MYB81 driven by various promoters can severely impair vegetative or reproductive development, reflecting the strict microspore-specific control of MYB81. Our data demonstrate that MYB81 has a key role in the developmental progression of microspores, enabling formation of the two male cell lineages that are essential for sexual reproduction in Arabidopsis.

Dissecting the Genome-Wide Evolution and Function of R2R3-MYB Transcription Factor Family in Rosa chinensis

Rosa chinensis, an important ancestor species of Rosa hybrida, the most popular ornamental plant species worldwide, produces flowers with diverse colors and fragrances. The R2R3-MYB transcription factor family controls a wide variety of plant-specific metabolic processes, especially phenylpropanoid metabolism. Despite their importance for the ornamental value of flowers, the evolution of R2R3-MYB genes in plants has not been comprehensively characterized. In this study, 121 predicted R2R3-MYB gene sequences were identified in the rose genome. Additionally, a phylogenomic synteny network (synnet) was applied for the R2R3-MYB gene families in 35 complete plant genomes. We also analyzed the R2R3-MYB genes regarding their genomic locations, Ka/Ks ratio, encoded conserved motifs, and spatiotemporal expression. Our results indicated that R2R3-MYBs have multiple synteny clusters. The RcMYB114a gene was included in the Rosaceae-specific Cluster 54, with independent evolutionary patterns. On the basis of these results and an analysis of RcMYB114a-overexpressing tobacco leaf samples, we predicted that RcMYB114a functions in the phenylpropanoid pathway. We clarified the relationship between R2R3-MYB gene evolution and function from a new perspective. Our study data may be relevant for elucidating the regulation of floral metabolism in roses at the transcript level.

R2R3 MYB Transcription Factors - Functions outside the DNA-Binding Domain

Several transcription factor (TF) families, including the MYB family, regulate a wide array of biological processes. TFs contain DNA-binding domains (DBDs) and regulatory regions; although information on protein structure is scarce for plant MYB TFs, various in silico methods suggest that the non-MYB regions contain extensive intrinsically disordered regions (IDRs). Although IDRs do not fold into stable globular structures, they comprise functional regions including interaction motifs, and recent research has shown that IDRs perform crucial biological roles. We map here domain organization, disorder predictions, and functional regions across the entire Arabidopsis thaliana R2R3 MYB TF family, and highlight where an increased research focus will be necessary to shape a new understanding of structure-function relationships in plant TFs.

Conserved DNA-derived polymorphism, new markers for genetic diversity analysis of Tunisian Pistacia vera L

Pistachio trees (Pistacia vera L.) have been cultivated in Tunisia for decades and the plantation was extended mostly in the center of the country contributing to the economic growth of marginalized areas. Herein we used conserved DNA derived polymorphism (CDDP) technique, which target specifically conserved sequences of plant functional genes, to assess the genetic diversity and construct genetic relationships among 65 Tunisian pistachio trees. A set of nine primers were used and 157 CDDP markers were revealed with an average of 17.44 showing a high degree of polymorphism (99.37%). The average of polymorphism information content of CDDP markers was of 0.86, which indicates the efficiency of CDDP primers in the estimation of genetic diversity between pistachios. UPGMA dendrogram and the principal component analysis showed four clusters of analyzed pistachios trees. Our results showed that the genetic structure depends on: (1) the gene exchanges between groups, (2) the geographical origin and (3) the sex of the tree. The same result was revealed by the Bayesian analysis implemented in STRUCTURE at K = 4, in which the pistachio genotypes of El Guettar, Kasserine and Sfax were assigned with more than 80% of probability. Our results prove polymorphism and efficiency of CDDP markers in the characterization and genetic diversity analysis of P. vera L. genotypes to define conservation strategy.

Expression Patterns of MYB (V-myb Myeloblastosis Viral Oncogene Homolog) Gene Family in Resistant and Susceptible Tung Trees Responding to Fusarium Wilt Disease

Vernicia fordii (tung oil tree) is famous in the world for its production of tung oil. Unfortunately, it was infected by the soil-borne fungus Fusarium oxysporum f. sp. fordii 1 (Fof-1) and suffered serious wilt disease. Conversely, its sister species V. montana is highly resistant to Fof-1. The MYB (v-myb myeloblastosis viral oncogene homolog) transcription factors were activated during the pathogen Fof-1 infection according to our previous comparative transcriptomic results. Depending on whether the sequence has a complete MYB-DNA-binding domain, a total of 75 VfMYB and 77 VmMYB genes were identified in susceptible V. fordii and resistant V. montana, respectively. In addition, we detected 49 pairs of one-to-one orthologous Vf/VmMYB genes with the reciprocal-best BLAST-hits (RBH)method. In order to investigate the expression modes and the internal network of MYB transcription factors in the two species responding to Fusarium wilt disease, the expressions of Vf/VmMYBs were then investigated and we found that most orthologous Vf/VmMYB genes exhibited similar expression patterns during the Fof-1 infection. However, four pairs of Vf/VmMYB genes, annotated as unknown proteins and mediator of root architecture, demonstrated absolute opposite expression patterns in the two Vernicia species responding to Fof-1. The interaction network of VmMYB genes were further constructed using weighted gene co-expression network analysis (WGCNA) method and four hub genes showing extremely high interaction with the other 1157 genes were identified. RT-qPCR result verified the opposite expression pattern of the hub gene VmMYB011 and VmMYB041 in two Vernicia species. In summary, co-expression network of the Vf/VmMYBs and significantly opposite related pairs of genes in resistant and susceptible Vernicia species provided knowledge for understanding the molecular basis of Vernicia responding to Fusarium wilt disease.

Genome-wide identification and expression analysis of the MYB transcription factor in moso bamboo (Phyllostachys edulis)

The MYB family, one of the largest transcription factor (TF) families in the plant kingdom, plays vital roles in cell formation, morphogenesis and signal transduction, as well as responses to biotic and abiotic stresses. However, the underlying function of bamboo MYB TFs remains unclear. To gain insight into the status of these proteins, a total of 85 PeMYBs, which were further divided into 11 subgroups, were identified in moso bamboo (Phyllostachys edulis) by using a genome-wide search strategy. Gene structure analysis showed that PeMYBs were significantly different, with exon numbers varying from 4 to 13. Phylogenetic analysis indicated that PeMYBs clustered into 27 clades, of which the function of 18 clades has been predicted. In addition, almost all of the PeMYBs were differently expressed in leaves, panicles, rhizomes and shoots based on RNA-seq data. Furthermore, qRT-PCR analysis showed that 12 PeMYBs related to the biosynthesis and deposition of the secondary cell wall (SCW) were constitutively expressed, and their transcript abundance levels have changed significantly with increasing height of the bamboo shoots, for which the degree of lignification continuously increased. This result indicated that these PeMYBs might play fundamental roles in SCW thickening and bamboo shoot lignification. The present comprehensive and systematic study on the members of the MYB family provided a reference and solid foundation for further functional analysis of MYB TFs in moso bamboo.

Tomato MYB49 enhances resistance to Phytophthora infestans and tolerance to water deficit and salt stress

MYB49-overexpressing tomato plants showed significant resistance to Phytophthora infestans and tolerance to drought and salt stresses. This finding reveals the potential application of tomato MYB49 in future molecular breeding. Biotic and abiotic stresses severely reduce the productivity of tomato worldwide. Therefore, it is necessary to find key genes to simultaneously improve plant resistance to pathogens and tolerance to various abiotic stresses. In this study, based on homologous relationships with Arabidopsis R2R3-MYBs (AtMYBs) involved in responses to biotic and abiotic stresses, we identified a total of 24 R2R3-MYB transcription factors in the tomato genome. Among these tomato R2R3-MYBs, MYB49 (Solyc10g008700.1) was clustered into subgroup 11 by phylogenetic analysis, and its expression level was significantly induced after treatment with P. infestans, NaCl and PEG6000. Overexpression of MYB49 in tomato significantly enhanced the resistance of tomato to P. infestans, as evidenced by decreases in the number of necrotic cells, sizes of lesion, abundance of P. infestans, and disease index. Likewise, MYB49-overexpressing transgenic tomato plants also displayed increased tolerance to drought and salt stresses. Compared to WT plants, the accumulation of reactive oxygen species (ROS), malonaldehyde content, and relative electrolyte leakage was decreased, and peroxidase activity, superoxide dismutase activity, chlorophyll content, and photosynthetic rate were increased in MYB49-overexpressing tomato plants under P. infestans, salt or drought stress. These results suggested that tomato MYB49, as a positive regulator, could enhance the capacity to scavenge ROS, inhibit cell membrane damage and cell death, and protect chloroplasts, resulting in an improvement in resistance to P. infestans and tolerance to salt and drought stresses, and they provide a candidate gene for tomato breeding to enhance biotic stress resistance and abiotic stress tolerance.

Two amino acid changes in the R3 repeat cause functional divergence of two clustered MYB10 genes in peach

R2R3-MYB genes play a pivotal role in regulating anthocyanin accumulation. Here, we report two tandemly duplicated R2R3-MYB genes in peach, PpMYB10.1 and PpMYB10.2, with the latter showing lower ability to induce anthocyanin accumulation than the former. Site-directed mutation assay revealed two amino acid changes in the R3 repeat, Arg/Lys⁶⁶ and Gly/Arg⁹³, responsible for functional divergence between these two PpMYB10 genes. Anthocyanin-promoting activity of PpMYB10.2 was significantly increased by a single amino acid replacement of Arg⁹³ with Gly⁹³. However, either the Gly⁹³ → Arg⁹³ or Arg⁶⁶ → Lys⁶⁶ substitutions alone showed little impact on anthocyanin-promoting activity of PpMYB10.1, but simultaneous substitutions caused a significant decrease. Reciprocal substitution of Arg/Gly⁹³ could significantly alter binding affinity to PpbHLH3, while the Arg⁶⁶ → Lys⁶⁶ substitution is predicted to affect the folding of the MYB DNA-binding domain, instead of PpbHLH3-binding affinity. Overall, the change of anthocyanin-promoting activity was accompanied with that of bHLH-binding affinity, suggesting that DNA-binding affinity of R2R3-MYBs depends on their bHLH partners. Our study is helpful for understanding of functional evolution of R2R3-MYBs and their interaction with DNA targets.

Genome-wide analysis of basic/helix-loop-helix gene family in peanut and assessment of its roles in pod development

The basic/helix-loop-helix (bHLH) proteins constitute a superfamily of transcription factors that are known to play a range of regulatory roles in eukaryotes. Over the past few decades, many bHLH family genes have been well-characterized in model plants, such as Arabidopsis, rice and tomato. However, the bHLH protein family in peanuts has not yet been systematically identified and characterized. Here, 132 and 129 bHLH proteins were identified from two wild ancestral diploid subgenomes of cultivated tetraploid peanuts, Arachis duranensis (AA) and Arachis ipaensis (BB), respectively. Phylogenetic analysis indicated that these bHLHs could be classified into 19 subfamilies. Distribution mapping results showed that peanut bHLH genes were randomly and unevenly distributed within the 10 AA chromosomes and 10 BB chromosomes. In addition, 120 bHLH gene pairs between the AA-subgenome and BB-subgenome were found to be orthologous and 101 of these pairs were highly syntenic in AA and BB chromosomes. Furthermore, we confirmed that 184 bHLH genes expressed in different tissues, 22 of which exhibited tissue-specific expression. Meanwhile, we identified 61 bHLH genes that may be potentially involved in peanut-specific subterranean. Our comprehensive genomic analysis provides a foundation for future functional dissection and understanding of the regulatory mechanisms of bHLH transcription factors in peanuts.

The transcription factor MYB115 contributes to the regulation of proanthocyanidin biosynthesis and enhances fungal resistance in poplar

Proanthocyanidins (PAs) are major defense phenolic compounds in the leaves of poplar (Populus spp.) in response to abiotic and biotic stresses. Transcriptional regulation of PA biosynthetic genes by the MYB-basic helix-loop-helix (bHLH)-WD40 complexes in poplar is not still fully understood. Here, an Arabidopsis TT2-like gene MYB115 was isolated from Populus tomentosa and characterized by various molecular, genetic and biochemical approaches. MYB115 restored PA productions in the seed coat of the Arabidopsis tt2 mutant. Overexpression of MYB115 in poplar activated expression of PA biosynthetic genes, resulting in a significant increase in PA concentrations. By contrast, the CRISPR/Cas9-generated myb115 mutant exhibited reduced PA content and decreased expression of PA biosynthetic genes. MYB115 directly activated the promoters of PA-specific structural genes. MYB115 interacted with poplar TT8. Coexpression of MYB115, TT8 and poplar TTG1 significantly enhanced the expression of ANR1 and LAR3. Additionally, transgenic plants overexpressing MYB115 had increased resistance to the fungal pathogen Dothiorella gregaria, whereas myb115 mutant exhibited greater sensitivity compared with wild-type plants. Our data provide insight into the regulatory mechanisms controlling PA biosynthesis by MYB115 in poplar, which could be effectively employed for metabolic engineering of PAs to improve resistance to fungal pathogens.

The Arabidopsis paralogs, PUB46 and PUB48, encoding U-box E3 ubiquitin ligases, are essential for plant response to drought stress

BACKGROUND

Plants respond to abiotic stress on physiological, biochemical and molecular levels. This includes a global change in their cellular proteome achieved by changes in the pattern of their protein synthesis and degradation. The ubiquitin-proteasome system (UPS) is a key player in protein degradation in eukaryotes. Proteins are marked for degradation by the proteasome by coupling short chains of ubiquitin polypeptides in a three-step pathway. The last and regulatory stage is catalyzed by a member of a large family of substrate-specific ubiquitin ligases.

RESULTS

We have identified AtPUB46 and AtPUB48-two paralogous genes that encode ubiquitin ligases (E3s)-to have a role in the plant environmental response. The AtPUB46, -47, and -48 appear as tandem gene copies on chromosome 5, and we present a phylogenetic analysis that traces their evolution from an ancestral PUB-ARM gene. Single homozygous T-DNA insertion mutants of AtPUB46 and AtPUB48 displayed hypersensitivity to water stress; this was not observed for similar mutants of AtPUB47. Although the three genes show a similar spatial expression pattern, the steady state levels of their transcripts are differentially affected by abiotic stresses and plant hormones.

CONCLUSIONS

AtPUB46 and AtPUB48 encode plant U-Box E3s and are involved in the response to water stress. Our data suggest that despite encoding highly homologous proteins, AtPUB46 and AtPUB48 biological activity does not fully overlap.

Genome-wide characterization and expression analysis of MYB transcription factors in Gossypium hirsutum

Background

MYB family proteins are one of the most abundant transcription factors in the cotton plant and play diverse roles in cotton growth and evolution. Previously, few studies have been conducted in upland cotton, Gossypium hirsutum. The recent release of the G. hirsutum genome sequence provides a great opportunity to identify and characterize the entire upland cotton MYB protein family.

Results

In this study, we undertook a comprehensive genome-wide characterization and expression analysis of the MYB transcription factor family during cotton fiber development. A total of 524 non-redundant cotton MYB genes, among 1986 MYB and MYB-related putative proteins, were identified and classified into four subfamilies including 1R-MYB, 2R-MYB, 3R-MYB, and 4R-MYB. Based on phylogenetic tree analysis, MYB transcription factors were divided into 16 subgroups. The results showed that the majority (69.1 %) of GhMYBs genes belong to the 2R-MYB subfamily in upland cotton.

Conclusion

Our comparative genomics analysis has provided novel insights into the roles of MYB transcription factors in cotton fiber development. These results provide the basis for a greater understanding of MYB regulatory networks and to develop new approaches to improve cotton fiber development.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-016-0436-8) contains supplementary material, which is available to authorized users.

Genome-Wide Identification and Analysis of the MYB Transcription Factor Superfamily in Solanum lycopersicum

MYB proteins constitute one of the largest transcription factor families in the plant kingdom, members of which perform a variety of functions in plant biological processes. However, there are only very limited reports on the characterization of MYB transcription factors in tomato (Solanum lycopersicum). In our study, a total of 127 MYB genes have been identified in the tomato genome. A complete overview of these MYB genes is presented, including the phylogeny, gene structures, protein motifs, chromosome locations and expression patterns. The 127 SlMYB proteins could be classified into 18 subgroups based on domain similarity and phylogenetic topology. Phylogenetic analysis of SlMYBs along with MYBs from Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) indicated 14 subfamilies. Conserved motifs outside the MYB domain may reflect their functional conservation. The identified tomato MYB genes were distributed on 12 chromosomes at various densities but mainly in chromosomes 6 and 10 (12.6% and 11.8%, respectively). Genome-wide segmental and tandem duplications were also found, which may contribute to the expansion of SlMYB genes. RNA-sequencing and microarray data revealed tissue-specific and stress-responsive expression patterns of SlMYB genes. The expression profiles of SlMYB genes in response to salicylic acid (SA) and jasmonic acid methyl ester (MeJA) were also investigated by real-time PCR. Moreover, ethylene-responsive element-binding factor-associated amphiphilic repression (EAR) motifs were found in 24 SlMYB proteins. Collectively, our comprehensive analysis of SlMYB genes will facilitate future functional studies of the tomato MYB gene family and probably other Solanaceae plants.

Identification, isolation and expression analysis of eight stress-related R2R3-MYB genes in tartary buckwheat (Fagopyrum tataricum)

Eight R2R3 - MYB genes in tartary buckwheat were identified, and their expression patterns were comprehensively analyzed, which reveals role in plant response to abiotic stresses. The proteins of the R2R3-MYB superfamily play key roles in the growth and development processes as well as defense responses in plants. However, their characteristics and functions have not been fully investigated in tartary buckwheat (Fagopyrum tataricum), a strongly abiotic resistant coarse cereal. In this article, eight tartary buckwheat R2R3-MYB genes were isolated with full-length cDNA and DNA sequences. Phylogenetic analysis of the members of the R2R3-MYB superfamily between Arabidopsis and tartary buckwheat revealed that the assumed functions of the eight tartary buckwheat R2R3-MYB proteins are divided into five Arabidopsis functional subgroups that are involved in abiotic stress. Expression analysis during abiotic stress and exogenous phytohormone treatments identified that the eight R2R3-MYB genes responded to one or more treatments. This study is the first comprehensive analysis of the R2R3-MYB gene family in tartary buckwheat under abiotic stress.

Genome-Wide Identification, Evolution and Functional Divergence of MYB Transcription Factors in Chinese White Pear (Pyrus bretschneideri)

The MYB superfamily is large and functionally diverse in plants. To date, MYB family genes have not yet been identified in Chinese white pear (Pyrus bretschneideri), and their functions remain unclear. In this study, we identified 231 genes as candidate MYB genes and divided them into four subfamilies. The R2R3-MYB (PbrMYB) family shared an R2R3 domain with 104 amino acid residues, including five conserved tryptophan residues. The Pbr MYB family was divided into 37 functional subgroups including 33 subgroups which contained both MYB genes of Rosaceae plants and AtMYB genes, and four subgroups which included only Rosaceae MYB genes or AtMYB genes. PbrMYB genes with similar functions clustered into the same subgroup, indicating functional conservation. We also found that whole-genome duplication (WGD) and dispersed duplications played critical roles in the expansion of the MYB family. The 87 Pbr MYB duplicated gene pairs dated back to the two WGD events. Purifying selection was the primary force driving Pbr MYB gene evolution. The 15 gene pairs presented 1-7 codon sites under positive selection. A total of 147 expressed genes were identified from RNA-sequencing data of fruit, and six Pbr MYB members in subgroup C1 were identified as important candidate genes in the regulation of lignin synthesis by quantitative real-time PCR analysis. Further correlation analysis revealed that six PbrMYBs were significantly correlated with five structural gene families (F5H, HCT, CCR, POD and C3'H) in the lignin pathway. The phylogenetic, evolution and expression analyses of the MYB gene family in Chinese white pear establish a solid foundation for future comprehensive functional analysis of Pbr MYB genes.

Genome-Wide Identification of R2R3-MYB Genes and Expression Analyses During Abiotic Stress in Gossypium raimondii

The R2R3-MYB is one of the largest families of transcription factors, which have been implicated in multiple biological processes. There is great diversity in the number of R2R3-MYB genes in different plants. However, there is no report on genome-wide characterization of this gene family in cotton. In the present study, a total of 205 putative R2R3-MYB genes were identified in cotton D genome (Gossypium raimondii), that are much larger than that found in other cash crops with fully sequenced genomes. These GrMYBs were classified into 13 groups with the R2R3-MYB genes from Arabidopsis and rice. The amino acid motifs and phylogenetic tree were predicted and analyzed. The sequences of GrMYBs were distributed across 13 chromosomes at various densities. The results showed that the expansion of the G. Raimondii R2R3-MYB family was mainly attributable to whole genome duplication and segmental duplication. Moreover, the expression pattern of 52 selected GrMYBs and 46 GaMYBs were tested in roots and leaves under different abiotic stress conditions. The results revealed that the MYB genes in cotton were differentially expressed under salt and drought stress treatment. Our results will be useful for determining the precise role of the MYB genes during stress responses with crop improvement.

Genome-Wide Identification, Characterization and Expression Analysis of the Chalcone Synthase Family in Maize

Members of the chalcone synthase (CHS) family participate in the synthesis of a series of secondary metabolites in plants, fungi and bacteria. The metabolites play important roles in protecting land plants against various environmental stresses during the evolutionary process. Our research was conducted on comprehensive investigation of CHS genes in maize (Zea mays L.), including their phylogenetic relationships, gene structures, chromosomal locations and expression analysis. Fourteen CHS genes (ZmCHS01-14) were identified in the genome of maize, representing one of the largest numbers of CHS family members identified in one organism to date. The gene family was classified into four major classes (classes I-IV) based on their phylogenetic relationships. Most of them contained two exons and one intron. The 14 genes were unevenly located on six chromosomes. Two segmental duplication events were identified, which might contribute to the expansion of the maize CHS gene family to some extent. In addition, quantitative real-time PCR and microarray data analyses suggested that ZmCHS genes exhibited various expression patterns, indicating functional diversification of the ZmCHS genes. Our results will contribute to future studies of the complexity of the CHS gene family in maize and provide valuable information for the systematic analysis of the functions of the CHS gene family.

MYB Transcription Factors in Chinese Pear (Pyrus bretschneideri Rehd.): Genome-Wide Identification, Classification, and Expression Profiling during Fruit Development

The MYB family is one of the largest families of transcription factors in plants. Although, some MYBs were reported to play roles in secondary metabolism, no comprehensive study of the MYB family in Chinese pear (Pyrus bretschneideri Rehd.) has been reported. In the present study, we performed genome-wide analysis of MYB genes in Chinese pear, designated as PbMYBs, including analyses of their phylogenic relationships, structures, chromosomal locations, promoter regions, GO annotations, and collinearity. A total of 129 PbMYB genes were identified in the pear genome and were divided into 31 subgroups based on phylogenetic analysis. These PbMYBs were unevenly distributed among 16 chromosomes (total of 17 chromosomes). The occurrence of gene duplication events indicated that whole-genome duplication and segmental duplication likely played key roles in expansion of the PbMYB gene family. Ka/Ks analysis suggested that the duplicated PbMYBs mainly experienced purifying selection with restrictive functional divergence after the duplication events. Interspecies microsynteny analysis revealed maximum orthology between pear and peach, followed by plum and strawberry. Subsequently, the expression patterns of 20 PbMYB genes that may be involved in lignin biosynthesis according to their phylogenetic relationships were examined throughout fruit development. Among the 20 genes examined, PbMYB25 and PbMYB52 exhibited expression patterns consistent with the typical variations in the lignin content previously reported. Moreover, sub-cellular localization analysis revealed that two proteins PbMYB25 and PbMYB52 were localized to the nucleus. All together, PbMYB25 and PbMYB52 were inferred to be candidate genes involved in the regulation of lignin biosynthesis during the development of pear fruit. This study provides useful information for further functional analysis of the MYB gene family in pear.

Evolution and divergence of SBP-box genes in land plants

Background

Squamosa promoter binding protein (SBP)-box family genes encode plant-specific transcription factors that control many important biological functions, including phase transition, inflorescence branching, fruit ripening, and copper homeostasis. Nevertheless, the evolutionary patterns of SBP-box genes and evolutionary forces driving them are still not well understood.

Methods

104 SBP-box gene candidates of five representative land plants were obtained from Phytozome database (v10.3). Phylogenetic combined with gene structure analyses were used to identify SBP-box gene lineages in land plants. Gene copy number and the sequence and structure features were then compared among these different SBP-box lineages. Selection analysis, relative rate tests and expression divergence were finally used to interpret the evolutionary relationships and divergence of SBP-box genes in land plants.

Results

We investigated 104 SBP-box genes from moss, Arabidopsis, poplar, rice, and maize. These genes are divided into group I and II, and the latter is further divided into two subgroups (subgroup II-1 and II-2) based on phylogenetic analysis. Interestingly, subgroup II-1 genes have similar sequence and structural features to group I genes, whereas subgroup II-2 genes exhibit intrinsic differences on these features, including high copy numbers and the presence of miR156/miR529 regulation. Further analyses indicate that subgroup II-1 genes are constrained by stronger purifying selection and evolve at a lower substitution rate than II-2 genes, just as group I genes do when compared to II genes. Among subgroup II-2 genes, miR156 targets evolve more rapidly than miR529 targets and experience comparatively relaxed purifying selection. These results suggest that group I and subgroup II-1 genes under strong selective constraint are conserved. By contrast, subgroup II-2 genes evolve under relaxed purifying selection and have diversified through gene copy duplications and changes in miR156/529 regulation, which might contribute to morphological diversifications of land plants.

Conclusions

Our results indicate that different evolutionary rates and selection strengths lead to differing evolutionary patterns in SBP-box genes in land plants, providing a guide for future functional diversity analyses of these genes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1998-y) contains supplementary material, which is available to authorized users.

Identification and Characterization of 40 Isolated Rehmannia glutinosa MYB Family Genes and Their Expression Profiles in Response to Shading and Continuous Cropping

The v-myb avian myeloblastosis viral oncogene homolog (MYB) superfamily constitutes one of the most abundant groups of transcription factors (TFs) described in plants. To date, little is known about the MYB genes in Rehmannia glutinosa. Forty unique MYB genes with full-length cDNA sequences were isolated. These 40 genes were grouped into five categories, one R1R2R3-MYB, four TRFL MYBs, four SMH MYBs, 25 R2R3-MYBs, and six MYB-related members. The MYB DNA-binding domain (DBD) sequence composition was conserved among proteins of the same subgroup. As expected, most of the closely related members in the phylogenetic tree exhibited common motifs. Additionally, the gene structure and motifs of the R. glutinosa MYB genes were analyzed. MYB gene expression was analyzed in the leaf and the tuberous root under two abiotic stress conditions. Expression profiles showed that most R. glutinosa MYB genes were expressed in the leaf and the tuberous root, suggesting that MYB genes are involved in various physiological and developmental processes in R. glutinosa. Seven MYB genes were up-regulated in response to shading in at least one tissue. Two MYB genes showed increased expression and 13 MYB genes showed decreased expression in the tuberous root under continuous cropping. This investigation is the first comprehensive study of the MYB gene family in R. glutinosa.