Characterization of Arabidopsis MYB transcription factor gene AtMYB17 and its possible regulation by LEAFY and AGL15

The transcription factor RhMYB17 regulates the homeotic transformation of floral organs in rose (Rosa hybrida) under cold stress

Low temperatures affect flower development in rose (Rosa hybrida), increasing petaloid stamen number and reducing normal stamen number. We identified the low-temperature-responsive R2R3-MYB transcription factor RhMYB17, which is homologous to Arabidopsis MYB17 by similarity of protein sequences. RhMYB17 was up-regulated at low temperatures, and RhMYB17 transcripts accumulated in floral buds. Transient silencing of RhMYB17 by virus-induced gene silencing decreased petaloid stamen number and increased normal stamen number. According to the ABCDE model of floral organ identity, class A genes APETALA 1 (AP1) and AP2 contribute to sepal and petal formation. Transcription factor binding analysis identified RhMYB17 binding sites in the promoters of rose APETALA 2 (RhAP2) and APETALA 2-LIKE (RhAP2L). Yeast one-hybrid assays, dual-luciferase reporter assays, and electrophoretic mobility shift assays confirmed that RhMYB17 directly binds to the promoters of RhAP2 and RhAP2L, thereby activating their expression. RNA sequencing further demonstrated that RhMYB17 plays a pivotal role in regulating the expression of class A genes, and indirectly influences the expression of the class C gene. This study reveals a novel mechanism for the homeotic transformation of floral organs in response to low temperatures.

Characterisation of the R2R3 Myb subgroup 9 family of transcription factors in tomato

Tomato (Solanum lycopersicum) has many epidermal cell outgrowths including conical petal cells and multiple types of trichomes. These include the anther-specific trichome mesh which holds the anthers connate. The R2R3 Myb Subgroup 9 family of transcription factors is involved in development of epidermal cell outgrowths throughout the angiosperms. No previous study has examined all members of this transcription factor family in a single species. All 7 R2R3 Myb Subgroup 9 genes were isolated from tomato. They were ectopically expressed in tobacco to assess their ability to induce epidermal cell outgrowth. Endogenous expression patterns were examined by semi-quantitative RT-PCR at different stages of floral development relative to the development of anther trichomes. We report variation in the degree of epidermal cell outgrowth produced in transgenic tobacco by each ectopically expressed gene. Based on expression profile and ectopic activity, SlMIXTA-2 is likely involved in the production of leaf trichomes. SlMIXTA-2 is expressed most strongly in the leaves, and not expressed in the floral tissue. SlMYB17-2 is the best candidate for the regulation of the anther trichome mesh. SlMYB17-2 is expressed strongly in the floral tissue and produces a clear phenotype of epidermal cell outgrowths when ectopically expressed in tobacco. Analysis of the phenotypes of transgenic plants ectopically expressing all 7 genes has revealed the different extent to which members of the same transcription factor subfamily can induce cellular outgrowth.

A comparative full-length transcriptomic resource provides insight into the perennial monocarpic mass flowering

Perennial monocarpic mass flowering represents as a key developmental innovation in flowering time diversity in several biological and economical essential families, such as the woody bamboos and the shrubby Strobilanthes. However, molecular and genetic mechanisms underlying this important biodiversity remain poorly investigated. Here, we generated a full-length transcriptome resource incorporated into the BlueOmics database (http://blueomics.iflora.cn) for two Strobilanthes species, which feature contrasting flowering time behaviors. Using about 112 and 104 Gb Iso-seq reads together with ~185 and ~75 Gb strand-specific RNA seq data, we annotated 80 971 and 79 985 non-redundant full-length transcripts for the perennial polycarpic Strobilanthes tetrasperma and the perennial monocarpic Strobilanthes biocullata, respectively. In S. tetrasperma, we identified 8794 transcripts showing spatiotemporal expression in nine tissues. In leaves and shoot apical meristems at two developmental stages, 977 and 1121 transcripts were differentially accumulated in S. tetrasperma and S. biocullata, respectively. Interestingly, among the 33 transcription factors showing differential expression in S. tetrasperma but without differential expression in S. biocullata, three were involved potentially in the photoperiod and circadian-clock pathway of flowering time regulation (FAR1 RELATED SEQUENCE 12, FRS12; NUCLEAR FACTOR Y A1, NFYA1; PSEUDO-RESPONSE REGULATOR 5, PRR5), hence provides an important clue in deciphering the flowering diversity mechanisms. Our data serve as a key resource for further dissection of molecular and genetic mechanisms underpinning key biological innovations, here, the perennial monocarpic mass flowering.

MYB112 connects light and circadian clock signals to promote hypocotyl elongation in Arabidopsis

Ambient light and the endogenous circadian clock play key roles in regulating Arabidopsis (Arabidopsis thaliana) seedling photomorphogenesis. PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) acts downstream of both light and the circadian clock to promote hypocotyl elongation. Several members of the R2R3-MYB transcription factor (TF) family, the most common type of MYB TF family in Arabidopsis, have been shown to be involved in regulating photomorphogenesis. Nonetheless, whether R2R3-MYB TFs are involved in connecting the light and clock signaling pathways during seedling photomorphogenesis remains unknown. Here, we report that MYB112, a member of the R2R3-MYB family, acts as a negative regulator of seedling photomorphogenesis in Arabidopsis. The light signal promotes the transcription and protein accumulation of MYB112. myb112 mutants exhibit short hypocotyls in both constant light and diurnal cycles. MYB112 physically interacts with PIF4 to enhance the transcription of PIF4 target genes involved in the auxin pathway, including YUCCA8 (YUC8), INDOLE-3-ACETIC ACID INDUCIBLE 19 (IAA19), and IAA29. Furthermore, MYB112 directly binds to the promoter of LUX ARRHYTHMO (LUX), the central component of clock oscillators, to repress its expression mainly in the afternoon and relieve LUX-inhibited expression of PIF4. Genetic evidence confirms that LUX acts downstream of MYB112 in regulating hypocotyl elongation. Thus, the enhanced transcript accumulation and transcriptional activation activity of PIF4 by MYB112 additively promotes the expression of auxin-related genes, thereby increasing auxin synthesis and signaling and fine-tuning hypocotyl growth under diurnal cycles.

Combined analysis of microRNA and mRNA profiles provides insights into the pathogenic resistant mechanisms of the lotus rhizome rot

Lotus rhizome rot caused by Fusarium oxysporum is a common vascular fungal disease in plants that significantly impacts the yield. However, only a few studies have studied the mechanism of Nelumbo nucifera responding to lotus rhizome rot. Here, we investigated the pathogenic genes and miRNAs in lotus rhizome rot to uncover the pathogenic resistant mechanisms by transcriptome and small RNA sequencing of lotus roots after inoculation with Fusarium oxysporum. GO and KEGG functional enrichment analysis showed that differential miRNAs were mostly enriched in starch and sucrose metabolism, biosynthesis of secondary metabolites, glutathione metabolism, brassinosteroid biosynthesis and flavonoid biosynthesis pathways. Twenty-seven upregulated miRNAs, 19 downregulated miRNAs and their target genes were identified. Correlation analysis found that miRNAs negatively regulate target genes, which were also enriched in starch and sucrose metabolism and glutathione metabolism pathways. Their expression was measured by reverse transcription quantitative PCR (qRT-PCR), and the results were consistent with the transcriptome analysis, thus verifying the reliability of transcriptome data. We selected three miRNAs (miRNA858-y, miRNA171-z and a novel miRNA novel-m0005-5p) to test the relationship between miRNAs and their target genes. The activity of the GUS testing assay indicated that miRNA could decrease the GUS activity by inhibiting the expression of their target genes. Collectively, this study provides a comprehensive analysis of transcriptome and small RNA sequencing of lotus root after inoculation with Fusarium oxysporum, and we identified candidate miRNAs and their target genes for breeding strategies of Nelumbo nucifera.

Identification of the passion fruit (Passiflora edulis Sims) MYB family in fruit development and abiotic stress, and functional analysis of PeMYB87 in abiotic stresses

Environmental stresses are ubiquitous in agricultural cultivation, and they affect the healthy growth and development of edible tissues in passion fruit. The study of resistance mechanisms is important in understanding the adaptation and resistance of plants to environmental stresses. In this work, two differently resistant passion fruit varieties were selected, using the expression characteristics of the transcription factor MYB, to explore the resistance mechanism of the MYB gene under various environmental stresses. A total of 174 MYB family members were identified using high-quality passion fruit genomes: 98 2R-MYB, 5 3R-MYB, and 71 1R-MYB (MYB-relate). Their family information was systematically analyzed, including subcellular localization, physicochemical properties, phylogeny at the genomic level, promoter function, encoded proteins, and reciprocal regulation. In this study, bioinformatics and transcriptome sequencing were used to identify members of the PeMYB genes in passion fruit whole-genome data, and biological techniques, such as qPCR, gene clone, and transient transformation of yeast, were used to determine the function of the passion fruit MYB genes in abiotic stress tolerance. Transcriptomic data were obtained for differential expression characteristics of two resistant and susceptible varieties, three expression patterns during pulp development, and four induced expression patterns under abiotic stress conditions. We further focused on the resistance mechanism of PeMYB87 in environmental stress, and we selected 10 representative PeMYB genes for quantitative expression verification. Most of the genes were differentially induced by four abiotic stresses, among which PeMYB87 responded significantly to high-temperature-induced expression and overexpression of the PeMYB87 gene in the yeast system. The transgenic PeMYB87 in yeast showed different degrees of stress resistance under exposure to cold, high temperatures, drought, and salt stresses. These findings lay the foundation for further analysis of the biological functions of PeMYBs involved in stress resistance in passion fruit.

Genome-wide characterization and expression analysis of MYB transcription factors in Chrysanthemum nankingense

BACKGROUND

Chrysanthemum is a popular ornamental plant worldwide. MYB (v-myb avian myeloblastosis viral oncogene homolog) transcription factors play an important role in everything from stress resistance to plant growth and development. However, the MYB family of chrysanthemums has not been the subject of a detailed bioinformatics and expression investigation.

RESULTS

In this study, we examined 324 CnMYB transcription factors from Chrysanthemum nankingense genome data, which contained 122 Cn1R-MYB, 183 CnR2R3-MYB, 12 Cn3R-MYB, 2 Cn4R-MYB, and 5 atypical CnMYB. The protein motifs and classification of CnMYB transcription factors were analyzed. Among them, motifs 1, 2, 3, and 4 were found to encode the MYB DNA-binding domain in R2R3-MYB proteins, while in other-MYB proteins, the motifs 1, 2, 3, 4, 5, 6, 7, and 8 encode the MYB DNA-binding domain. Among all CnMYBs, 44 genes were selected due to the presence of CpG islands, while methylation is detected in three genes, including CnMYB9, CnMYB152, and CnMYB219. We analyzed the expression levels of each CnMYB gene in ray floret, disc floret, flower bud, leaf, stem, and root tissues. Based on phylogenetic analysis and gene expression analysis, three genes appeared likely to control cellulose and lignin synthesis in stem tissue, and 16 genes appeared likely to regulate flowering time, anther, pollen development, and flower color. Fifty-one candidate genes that may be involved in stress response were identified through phylogenetic, stress-responseve motif of promoter, and qRT-PCR analyses. According to genes expression levels under stress conditions, six CnMYB genes (CnMYB9, CnMYB172, CnMYB186, CnMYB199, CnMYB219, and CnMYB152) were identified as key stress-responsive genes.

CONCLUSIONS

This research provides useful information for further functional analysis of the CnMYB gene family in chrysanthemums, as well as offers candidate genes for further study of cellulose and lignin synthesis, flowering traits, salt and drought stress mechanism.

Silencing of SlMYB50 affects tolerance to drought and salt stress in tomato

High salinity and drought stresses often cause plants to produce ROS, including hydrogen peroxide (H₂O₂) and superoxide (O₂^-), which interfere with plant growth and affect crop yield. The transcription factors of the MYB family are involved in responses to biotic and abiotic stresses. Here, we isolated the R2R3-MYB transcription factor gene SlMYB50 and found that silencing of SlMYB50 increased resistance to PEG 6000, mannitol and salt. In addition, the resistance of transgenic tomatoes increased under high salt and drought stress. After stress treatment, the relative water content, chlorophyll content (critical for carbon fixation) and root vitality of the SlMYB50-RNAi lines were higher than those of the wild-type (WT). The opposite was true the water loss rate, relative conductivity, and MDA (as a sign of cell wall disruption). Under drought stress conditions, SlMYB50-silenced lines exhibited less H₂O₂ and less O₂^- accumulation, as well as higher CAT enzyme activity, than were exhibited by the WT. Notably, after stress treatment, the expression levels of chlorophyll-synthesis-related, flavonoid-synthesis-related, carotenoid-related, antioxidant-enzyme-related and ABA-biosynthesis-related genes were all upregulated in SlMYB50-silenced lines compared to those of WT. A dual-luciferase reporter system was used to verify that SlMYB50 could bind to the CHS1 promoter. In summary, this study identified essential roles for SlMYB50 in regulating drought and salt tolerance.

Comparative Transcriptome Analysis Unveils the Molecular Mechanism Underlying Sepal Colour Changes under Acidic pH Substratum in Hydrangea macrophylla

The hydrangea (Hydrangea macrophylla (Thunb). Ser.), an ornamental plant, has good marketing potential and is known for its capacity to change the colour of its inflorescence depending on the pH of the cultivation media. The molecular mechanisms causing these changes are still uncertain. In the present study, transcriptome and targeted metabolic profiling were used to identify molecular changes in the RNAome of hydrangea plants cultured at two different pH levels. De novo assembly yielded 186,477 unigenes. Transcriptomic datasets provided a comprehensive and systemic overview of the dynamic networks of the gene expression underlying flower colour formation in hydrangeas. Weighted analyses of gene co-expression network identified candidate genes and hub genes from the modules linked closely to the hyper accumulation of Al³⁺ during different stages of flower development. F3'5'H, ANS, FLS, CHS, UA3GT, CHI, DFR, and F3H were enhanced significantly in the modules. In addition, MYB, bHLH, PAL6, PAL9, and WD40 were identified as hub genes. Thus, a hypothesis elucidating the colour change in the flowers of Al³⁺-treated plants was established. This study identified many potential key regulators of flower pigmentation, providing novel insights into the molecular networks in hydrangea flowers.

De novo transcriptome sequencing of Impatiens uliginosa and the analysis of candidate genes related to spur development

BACKGROUND

Spur, a structure capable of producing and storing nectar, not only plays a vital role in the pollination process but also promotes the rapid diversification of some plant lineages, which is considered a key innovation in plants. Spur is the focus of many studies, such as evolution and ecological hypothesis, but the current understanding of spur development is limited. High-throughput sequencing of Impatiens uliginosa was carried out to study the molecular mechanism of its spur development, which is believed to provide some insights into the spur development of Impatiens.

RESULTS

Transcriptomic sequencing and analysis were performed on spurs and limbs of I. uliginosa at three developmental stages. A total of 47.83 Gb of clean data were obtained, and 49,716 unigene genes were assembled. After comparison with NR, Swiss-Prot, Pfam, COG, GO and KEGG databases, a total of 27,686 genes were annotated successfully. Through comparative analysis, 19,356 differentially expressed genes were found and enriched into 208 GO terms and 146 KEGG pathways, among which plant hormone signal transduction was the most significantly enriched pathway. One thousand thirty-two transcription factors were identified, which belonged to 33 TF families such as MYB, bHLH and TCP. Twenty candidate genes that may be involved in spur development were screened and verified by qPCR, such as SBP, IAA and ABP.

CONCLUSIONS

Transcriptome data of different developmental stages of spurs were obtained, and a series of candidate genes related to spur development were identified. The importance of genes related to cell cycle, cell division, cell elongation and hormones in spur development was clarified. This study provided valuable information and resources for understanding the molecular mechanism of spur development in Impatiens.

Genome-wide analysis of R2R3-MYB transcription factors in Japanese morning glory

The R2R3-MYB transcription factor is one of the largest transcription factor families in plants. R2R3-MYBs play a variety of functions in plants, such as cell fate determination, organ and tissue differentiations, primary and secondary metabolisms, stress and defense responses and other physiological processes. The Japanese morning glory (Ipomoea nil) has been widely used as a model plant for flowering and morphological studies. In the present study, 127 R2R3-MYB genes were identified in the Japanese morning glory genome. Information, including gene structure, protein motif, chromosomal location and gene expression, were assigned to the InR2R3-MYBs. Phylogenetic tree analysis revealed that the 127 InR2R3-MYBs were classified into 29 subfamilies (C1-C29). Herein, physiological functions of the InR2R3-MYBs are discussed based on the functions of their Arabidopsis orthologues. InR2R3-MYBs in C9, C15, C16 or C28 may regulate cell division, flavonol biosynthesis, anthocyanin biosynthesis or response to abiotic stress, respectively. C16 harbors the known anthocyanin biosynthesis regulator, InMYB1 (INIL00g10723), and putative anthocyanin biosynthesis regulators, InMYB2 (INIL05g09650) and InMYB3 (INIL05g09651). In addition, INIL05g09649, INIL11g40874 and INIL11g40875 in C16 were suggested as novel anthocyanin biosynthesis regulators. We organized the R2R3-MYB transcription factors in the morning glory genome and assigned information to gene and protein structures and presuming their functions. Our study is expected to facilitate future research on R2R3-MYB transcription factors in Japanese morning glory.

Mapping of Two Major QTLs Controlling Flowering Time in Brassica napus Using a High-Density Genetic Map

Research on the flowering habit of rapeseed is important for the selection of varieties adapted to specific ecological environments. Here, quantitative trait loci (QTL) for the days-to-flowering trait were identified using a doubled haploid population of 178 lines derived from a cross between the winter type SGDH284 and the semi-winter type 158A. A linkage map encompassing 3268.01 cM was constructed using 2777 bin markers obtained from next-generation sequencing. The preliminary mapping results revealed 56 QTLs for the days to flowering in the six replicates in the three environments. Twelve consensus QTLs were identified by a QTL meta-analysis, two of which (cqDTF-C02 and cqDTF-C06) were designated as major QTLs. Based on the micro-collinearity of the target regions between B. napus and Arabidopsis, four genes possibly related to flowering time were identified in the cqDTF-C02 interval, and only one gene possibly related to flowering time was identified in the cqDTF-C06 interval. A tightly linked insertion-deletion marker for the cqFT-C02 locus was developed. These findings will aid the breeding of early maturing B. napus varieties.

Comparative analysis of R2R3-MYB transcription factors in the flower of Iris laevigata identifies a novel gene regulating tobacco cold tolerance

Breeding for flower cold resistance is a priority for flower breeding research in northern China. The identification of cold resistance genes will not only provide genetic resources for cold resistance breeding, but also form a basis for the study of plant cold resistance mechanisms. Based on the flower transcriptome of Iris laevigata, 20 R2R3-MYBs were identified and comprehensive analysis, including conservative domain, phylogenetic analyses and functional distribution, were performed for R2R3-MYBs. Expression patterns of the abiotic stress genes under cold stress were detected, the upregulated gene was genetically transformed into tobacco, and the related physiological indicators of the transgenic tobacco were measured. A novel cold resistance gene, IlMYB306, was obtained. qRT-PCR indicated that IlMYB306 was dramatically induced by cold stress and was significantly upregulated in roots. The free proline content, MDA, SOD and POD activity of the transgenic tobacco improved after cold stress, and the chlorophyll content decreased slowly. In addition, overexpression of IlMYB306 improved cold resistance of the seeds. SEM results showed leaves of transgenic tobacco had obvious folds, more grooves and bulges on the lower leaf surface. Overall, we report a novel cold resistance R2R3-MYB gene, IlMYB306, in the flower of I. laevigata, which could improve tobacco cold stress tolerance by thickening the waxy layer, increasing antioxidant activity and the content of proline.

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.

Comprehensive analysis of the MYB transcription factor gene family in Morus alba

BACKGROUND

The V-myb myeloblastosis viral oncogene homolog (MYB) family of proteins is large, containing functionally diverse transcription factors. However, MYBs in Morus are still poorly annotated and a comprehensive functional analysis of these transcription factors is lacking.

RESULTS

In the present study, a genome-wide identification of MYBs in Morus alba was performed. In total 166 MaMYBs were identified, including 103 R2R3-MYBs and four 3R-MaMYBs. Comprehensive analyses, including the phylogenetic analysis with putative functional annotation, motif and structure analysis, gene structure organization, promoter analysis, chromosomal localization, and syntenic relationships of R2R3-MaMYBs and 3R-MaMYBs, provided primary characterization for these MaMYBs. R2R3-MaMYBs covered the subgroups reported for R2R3-MYBs in Arabidopsis and Populus, and had two Morus-specific subgroups, indicating the high retention of MYBs in Morus. Motif analysis revealed high conservative residues at the start and end of each helix and residues consisting of the third helix in R2 and R3 repeats. Thirteen intron/exon patterns (a-m) were summarized, and the intron/exon pattern of two introns with phase numbers of 0 and 2 was the prevalent pattern for R2R3-MaMYBs. Various cis-elements in promoter regions were identified, and were mainly related to light response, development, phytohormone response, and abiotic and biotic stress response and secondary metabolite production. Expression patterns of R2R3-MaMYBs in different organs showed that MaMYBs involved in secondary cell wall components and stress responsiveness were preferentially expressed in roots or stems. R2R3-MaMYBs involved in flavonoid biosynthesis and anthocyanin accumulation were identified and characterized based on functional annotation and correlation of their expression levels with anthocyanin contents.

CONCLUSION

Based on a comprehensive analysis, this work provided functional annotation for R2R3-MYBs and an informative reference for further functional dissection of MYBs in Morus.

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.

Transcriptomic profiling suggests candidate molecular responses to waterlogging in cassava

Owing to climate change impacts, waterlogging is a serious abiotic stress that affects crops, resulting in stunted growth and loss of productivity. Cassava (Manihot esculenta Grantz) is usually grown in areas that experience high amounts of rainfall; however, little research has been done on the waterlogging tolerance mechanism of this species. Therefore, we investigated the physiological responses of cassava plants to waterlogging stress and analyzed global gene transcription responses in the leaves and roots of waterlogged cassava plants. The results showed that waterlogging stress significantly decreased the leaf chlorophyll content, caused premature senescence, and increased the activities of superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) in the leaves and roots. In total, 2538 differentially expressed genes (DEGs) were detected in the leaves and 13364 in the roots, with 1523 genes shared between the two tissues. Comparative analysis revealed that the DEGs were related mainly to photosynthesis, amino metabolism, RNA transport and degradation. We also summarized the functions of the pathways that respond to waterlogging and are involved in photosynthesis, glycolysis and galactose metabolism. Additionally, many transcription factors (TFs), such as MYBs, AP2/ERFs, WRKYs and NACs, were identified, suggesting that they potentially function in the waterlogging response in cassava. The expression of 12 randomly selected genes evaluated via both quantitative real-time PCR (qRT-PCR) and RNA sequencing (RNA-seq) was highly correlated (R² = 0.9077), validating the reliability of the RNA-seq results. The potential waterlogging stress-related transcripts identified in this study are representatives of candidate genes and molecular resources for further understanding the molecular mechanisms underlying the waterlogging response in cassava.

The underlying molecular conservation and diversification of dioecious flower and leaf buds provide insights into the development, dormancy breaking, flowering, and sex association of willows

As harbingers of bursting growth, flower buds and leaf buds generally show similar surface morphologies but different structural and functional changes. Dioecious plants further generate four types of Female/Male Flower/Leaf Buds (FFB, FLB, MFB, and MLB), showing a complex regulation. However, little is known about their underlying molecular mechanisms. Here, we exemplify the woody dioecious Salix linearistipularis to investigate their morphological characteristics and potential molecular mechanisms by combining cytological, physiological, phenological, and transcriptomic datasets. First, FFB and MFB have simultaneous development dynamics and so do FLB and MLB. Interestingly, FLB and MLB show very similar expression profiles preparing for photosynthesis and stress-tolerance, whereas FFB and MFB show great similarities but also striking sexual differences. Comparing flower buds and leaf buds after their revival from dormancy shows different cold- and vernalization-responsive genes (e.g. SliVRN1, SliAGL19, and SliAGL24), implying different programming processes for dormancy breaking between the buds. Moreover, except SliAP3, the expression of ABCDE model genes is consistent with their roles in the buds, suggesting a conserved mechanism of flower development between dioecious Salix and hermaphrodite Arabidopsis. Finally, considering sex-associated genes (e.g. SliCLE25, SliTPS21, and SliARR9) on Salix chromosomes and other reports, we hypothesize a dynamic model of sex determination on chromosomes 15 and 19 in the last ancestor of Salix and Populus but evolutionarily on 15 in Salix after their divergence. Together, our study provides new insights into the molecular mechanisms of dioecious four-type buds by showing the genes involved in their development, dormancy breaking, flowering, and sexual association.

MADS-box transcription factors MADS11 and DAL1 interact to mediate the vegetative-to-reproductive transition in pine

The reproductive transition is an important event that is crucial for plant survival and reproduction. Relative to the thorough understanding of the vegetative phase transition in angiosperms, a little is known about this process in perennial conifers. To gain insight into the molecular basis of the regulatory mechanism in conifers, we used temporal dynamic transcriptome analysis with samples from seven different ages of Pinus tabuliformis to identify a gene module substantially associated with aging. The results first demonstrated that the phase change in P. tabuliformis occurred as an unexpectedly rapid transition rather than a slow, gradual progression. The age-related gene module contains 33 transcription factors and was enriched in genes that belong to the MADS (MCMl, AGAMOUS, DEFICIENS, SRF)-box family, including six SOC1-like genes and DAL1 and DAL10. Expression analysis in P. tabuliformis and a late-cone-setting P. bungeana mutant showed a tight association between PtMADS11 and reproductive competence. We then confirmed that MADS11 and DAL1 coordinate the aging pathway through physical interaction. Overexpression of PtMADS11 and PtDAL1 partially rescued the flowering of 35S::miR156A and spl1,2,3,4,5,6 mutants in Arabidopsis (Arabidopsis thaliana), but only PtMADS11 could rescue the flowering of the ft-10 mutant, suggesting PtMADS11 and PtDAL1 play different roles in flowering regulatory networks in Arabidopsis. The PtMADS11 could not alter the flowering phenotype of soc1-1-2, indicating it may function differently from AtSOC1 in Arabidopsis. In this study, we identified the MADS11 gene in pine as a regulatory mediator of the juvenile-to-adult transition with functions differentiated from the angiosperm SOC1.

MYB117 is a negative regulator of flowering time in Arabidopsis

Plant flowering is crucial for the onset and progression of reproduction processes. The control of flowering time is a sophisticated system with multiple known regulatory mechanisms in plants. Here, we show that MYB117 participates in the flowering time regulation in Arabidopsis as myb117 mutants exhibited early flowering phenotypes under long-day condition. Transcriptome analysis of myb117 mutants revealed 410 differentially expressed genes between wild type and myb117-1 mutants, where selective genes including the Flowering Locus T (FT) were further confirmed by qRT-PCR analysis. Further, in vivo dual-luciferase and chromatin immunoprecipitation quantitative PCR (ChIP-qPCR) assays showed that MYB117 directly binds to the promoter of FT to suppress its expression. Taken together, we have revealed the transcriptome profile of myb117 mutants and identified MYB117 as a negative regulator in controlling flowering time through regulating the expression of FT in Arabidopsis.

Genome-Wide Identification and Expression Analysis of MYB Transcription Factors and Their Responses to Abiotic Stresses in Woodland Strawberry (Fragaria vesca)

Woodland strawberry (Fragaria vesca) is a diploid strawberry that is widely used as a model of cultivated octoploid strawberry (Fragaria × ananassa). It has also been used as a model for Rosaceae fruits, non-climacteric fruits, and stolons. The MYB superfamily is the largest transcription factor family in plants, and its members play important roles in plant growth and development. However, the complete MYB superfamily in woodland strawberry has not been studied. In this study, a total of 217 MYB genes were identified in woodland strawberry and classified into four groups: one 4R-MYB protein, five 3R-MYB proteins, 113 2R-MYB proteins, and 98 1R-MYB proteins. The phylogenetic relationship of each MYB subgroup was consistent in terms of intron/exon structure and conserved motif composition. The MYB genes in woodland strawberry underwent loss and expansion events during evolution. The transcriptome data revealed that most FveMYB genes are expressed in several organs, whereas 15 FveMYB genes exhibit organ-specific expression, including five genes (FveMYB101, -112, -44, and -8; FveMYB1R81) in roots, two genes (FveMYB62 and -77) in stolon tips, three genes (FveMYB99 and -35; FveMYB1R96) in open flowers, and five genes (FveMYB76 and -100; FveMYB1R4, -5, and -86) in immature fruits. During fruit ripening of woodland strawberry, the expression levels of 84 FveMYB genes were decreased, of which five genes (FveMYB4, -22, -50, and -66; FveMYB1R57) decreased more than 10-fold, whereas those 18 FveMYB genes were increased, especially FveMYB10 and FveMYB74 increased more than 30-fold. In addition, the expression levels of 36, 68, 52, and 62 FveMYB genes were altered by gibberellic acid, abscisic acid, cold, and heat treatments, respectively, and among them, several genes exhibited similar expression patterns for multiple treatments, suggesting possible roles in the crosstalk of multiple signaling pathways. This study provides candidate genes for the study of stolon formation, fruit development and ripening, and abiotic stress responses.

Differential regulation of triterpene biosynthesis induced by an early failure in cuticle formation in apple

Waxy apple cuticles predominantly accumulate ursane-type triterpenes, but the profile shifts with the induction of skin russeting towards lupane-type triterpenes. We previously characterised several key enzymes in the ursane-type and lupane-type triterpene pathways, but this switch in triterpene metabolism associated with loss of cuticle integrity is not fully understood. To analyse the relationship between triterpene biosynthesis and russeting, we used microscopy, RNA-sequencing and metabolite profiling during apple fruit development. We compared the skin of three genetically-close clones of 'Golden Delicious' (with waxy, partially russeted and fully russeted skin). We identified a unique molecular profile for the russet clone, including low transcript abundance of multiple cuticle-specific metabolic pathways in the early stages of fruit development. Using correlation analyses between gene transcription and metabolite concentration we found MYB transcription factors strongly associated with lupane-type triterpene biosynthesis. We showed how their transcription changed with the onset of cuticle cracking followed by russeting and that one factor, MYB66, was able to bind the promoter of the oxidosqualene cyclase OSC5, to drive the production of lupeol derivatives. These results provide insights into the breakdown of cuticle integrity leading to russet and how this drives MYB-regulated changes to triterpene biosynthesis.

Genome-Wide Analysis of MYB Gene Family in Chinese Bayberry (Morella rubra) and Identification of Members Regulating Flavonoid Biosynthesis

Chinese bayberry (Morella rubra), the most economically important fruit tree in the Myricaceae family, is a rich source of natural flavonoids. Recently the Chinese bayberry genome has been sequenced, and this provides an opportunity to investigate the organization and evolutionary characteristics of MrMYB genes from a whole genome view. In the present study, we performed the genome-wide analysis of MYB genes in Chinese bayberry and identified 174 MrMYB transcription factors (TFs), including 122 R2R3-MYBs, 43 1R-MYBs, two 3R-MYBs, one 4R-MYB, and six atypical MYBs. Collinearity analysis indicated that both syntenic and tandem duplications contributed to expansion of the MrMYB gene family. Analysis of transcript levels revealed the distinct expression patterns of different MrMYB genes, and those which may play important roles in leaf and flower development. Through phylogenetic analysis and correlation analyses, nine MrMYB TFs were selected as candidates regulating flavonoid biosynthesis. By using dual-luciferase assays, MrMYB12 was shown to trans-activate the MrFLS1 promoter, and MrMYB39 and MrMYB58a trans-activated the MrLAR1 promoter. In addition, overexpression of 35S:MrMYB12 caused a significant increase in flavonol contents and induced the expression of NtCHS, NtF3H, and NtFLS in transgenic tobacco leaves and flowers and significantly reduced anthocyanin accumulation, resulting in pale-pink or pure white flowers. This indicates that MrMYB12 redirected the flux away from anthocyanin biosynthesis resulting in higher flavonol content. The present study provides valuable information for understanding the classification, gene and motif structure, evolution and predicted functions of the MrMYB gene family and identifies MYBs regulating different aspects of flavonoid biosynthesis in Chinese bayberry.

Ectopic expression of a R2R3 MYB transcription factor of dove tree (Davidia involucrata) aggravates seed abortion in Arabidopsis thaliana

Serious seed abortion of dove tree (Davidia involucrate Baill.) is one of the critical factors leading to the low fecundity of this species. Seed abortion is a complicated process and various factors have been verified to synergistically determine the fate of seeds. To reveal the mechanism of seed abortion in D. involucrata, we performed transcriptome analysis in normal and abortive seeds of D. involucrata. According to the transcriptome data, we noticed that most of the genes encoding a MYB transcription factor were predominantly expressed in abortive seeds. Among these, a gene named DiMYB1 was selected and its function was validated in this study. Overexpression of DiMYB1 resulted in obviously reduced viability of transgenic seeds and seedlings, and caused a significantly higher seed abortion rate. The vegetative growth of transgenic plants was hindered, resulting in an earlier flowering time. In addition, colour changes occurred in transgenic plants. Some transgenic sprouts, stems and pods appeared purple instead of green in colour. Our finding demonstrated that DiMYB1 participates in multiple plant developmental processes, especially in seed development in Arabidopsis thaliana (L.) Heynh., which indicated the similar role of this gene in D. involucrata.

Specificity of MYB interactions relies on motifs in ordered and disordered contexts

Physical interactions between members of the MYB and bHLH transcription factor (TF) families regulate many important biological processes in plants. Not all reported MYB–bHLH interactions can be explained by the known binding sites in the R3 repeat of the MYB DNA-binding domain. Noteworthy, most of the sequence diversity of MYB TFs lies in their non-MYB regions, which contain orphan small subgroup-defining motifs not yet linked to molecular functions. Here, we identified the motif mediating interaction between MYB TFs from subgroup 12 and their bHLH partners. Unlike other known MYB–bHLH interactions, the motif locates to the centre of the predicted disordered non-MYB region. We characterised the core motif, which enabled accurate prediction of previously unknown bHLH-interacting MYB TFs in Arabidopsis thaliana, and we confirmed its functional importance in planta. Our results indicate a correlation between the MYB–bHLH interaction affinity and the phenotypic output controlled by the TF complex. The identification of an interaction motif outside R3 indicates that MYB–bHLH interactions must have arisen multiple times, independently and suggests many more motifs of functional relevance to be harvested from subgroup-specific studies.

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.

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.

Effects of vitro sucrose on quality components of tea plants (Camellia sinensis) based on transcriptomic and metabolic analysis

BACKGROUND

Tea plants [Camellia sinensis (L.) O. Kuntze] can produce one of the three most widely popular non-alcoholic beverages throughout the world. Polyphenols and volatiles are the main functional ingredients determining tea's quality and flavor; however, the biotic or abiotic factors affecting tea polyphenol biosynthesis are unclear. This paper focuses on the molecular mechanisms of sucrose on polyphenol biosynthesis and volatile composition variation in tea plants.

RESULTS

Metabolic analysis showed that the total content of anthocyanins, catechins, and proanthocyanidins(PAs) increased with sucrose, and they accumulated most significantly after 14 days of treatment. Transcriptomic analysis revealed 8384 and 5571 differentially expressed genes in 2-day and 14-day sucrose-treated tea plants compared with control-treated plants. Most of the structural genes and transcription factors (TFs) involved in polyphenol biosynthesis were significantly up-regulated after 2d. Among these transcripts, the predicted genes encoding glutathione S-transferase (GST), ATP-binding cassette transporters (ABC transporters), and multidrug and toxic compound extrusion transporters (MATE transporters) appeared up regulated. Correspondingly, ultra-performance liquid chromatography-triple quadrupole mass spectrometry (UPLC-QQQ-MS/MS) analysis revealed that the content of non-galloylated catechins and oligomeric PAs decreased in the upper-stem and increased in the lower-stem significantly, especially catechin (C), epicatechin (EC), and their oligomeric PAs. This result suggests that the related flavonoids were transported downward in the stem by transporters. GC/MS data implied that four types of volatile compounds, namely terpene derivatives, aromatic derivatives, lipid derivatives, and others, were accumulated differently after in vitro sucrose treatment.

CONCLUSIONS

Our data demonstrated that sucrose regulates polyphenol biosynthesis in Camellia sinensis by altering the expression of transcription factor genes and pathway genes. Additionally, sucrose promotes the transport of polyphenols and changes the aroma composition in tea plant.

Genome-Wide Analysis and Expression Profiles of the MYB Genes in Brachypodium distachyon

MYB transcription factors are widespread in plants and play key roles in plant development. Although MYB transcription factors have been thoroughly characterized in many plants, genome-wide analysis of the MYB gene family has not yet been undertaken in Brachypodium distachyon. In this study, 122 BdMYB transcription factors were identified, comprising 85 MYB-R2R3, 34 MYB-related and three MYB-R1R2R3. Phylogenetic analysis showed that BdMYBs, OsMYBs and AtMYBs with similar functions were clustered in the same subgroup, and the phylogenetic relationships of BdMYB transcription factors were supported by highly conserved motifs and gene structures. Two cis-elements were found in the promoters of BdMYB genes. One is related to plant growth/development, the other is related to stress responses. Gene Ontology (GO) analysis indicated that most of the BdMYB genes are involved in various biological processes. The chromosome distribution pattern strongly indicated that genome-wide tandem and segment duplication mainly contributed to the expansion of the BdMYB gene family. Synteny analysis showed that 56, 58 and 61 BdMYB genes were orthologous to rice, maize and sorghum, respectively. We further demonstrated that BdMYB genes have evolved under strong purifying selection. The expression profiles indicated that most BdMYB genes might participate in floral development and respond to abiotic stresses. Additionally, 338 pairs of proteins were predicted to interact by constructing the interaction network. This work laid the foundation and provided clues for understanding the biological functions of these transcription factors.

Identification and expression analysis under abiotic stress of the R2R3-MYB genes in Ginkgo biloba L

The R2R3-MYB gene family is the largest MYB subfamily in plants and is involved in the regulation of plant secondary metabolism and specific morphogenesis, as well as the response to biotic and abiotic stress. However, a systematic identification and characterization of this gene family has not been carried out in Ginkgo biloba. In this study, we performed a transcriptome-wide survey from four tissues of G. biloba to determine the genetic variation and expression pattern of the R2R3-MYB genes. We analyzed 45 GbMYBs and identified 42 with a complete coding sequence via conserved motif searches. The MYB domain and other motifs in GbMYBs are highly conserved with Arabidopsis thaliana AtMYBs. Phylogenetic analysis of the GbMYBs and AtMYBs categorized the R2R3-MYBs into 26 subgroups, of which 11 subgroups included proteins from both G. biloba and Arabidopsis, and 1 subgroup was specific to G. biloba. Moreover, the GbMYBs expression patterns were analyzed in different tissues and abiotic stress conditions. The results revealed that GbMYBs were differentially expressed in various tissues and following abiotic stresses and phytohormone treatments, indicating their possible roles in biological processes and abiotic stress tolerance and adaptation. Our study demonstrated the functional diversity of the GbMYBs and will provide a foundation for future research into their biological and molecular functions.

The draft genome of Ruellia speciosa (Beautiful Wild Petunia: Acanthaceae)

The genus Ruellia (Wild Petunias; Acanthaceae) is characterized by an enormous diversity of floral shapes and colours manifested among closely related species. Using Illumina platform, we reconstructed the draft genome of Ruellia speciosa, with a scaffold size of 1,021 Mb (or ∼1.02 Gb) and an N50 size of 17,908 bp, spanning ∼93% of the estimated genome (∼1.1 Gb). The draft assembly predicted 40,124 gene models and phylogenetic analyses of four key enzymes involved in anthocyanin colour production [flavanone 3-hydroxylase (F3H), flavonoid 3'-hydroxylase (F3'H), flavonoid 3',5'-hydroxylase (F3'5'H), and dihydroflavonol 4-reductase (DFR)] found that most angiosperms here sampled harboured at least one copy of F3H, F3'H, and DFR. In contrast, fewer than one-half (but including R. speciosa) harboured a copy of F3'5'H, supporting observations that blue flowers and/or fruits, which this enzyme is required for, are less common among flowering plants. Ka/Ks analyses of duplicated copies of F3'H and DFR in R. speciosa suggested purifying selection in the former but detected evidence of positive selection in the latter. The genome sequence and annotation of R. speciosa represents only one of only four families sequenced in the large and important Asterid clade of flowering plants and, as such, will facilitate extensive future research on this diverse group, particularly with respect to floral evolution.

Expression of the floral repressor miRNA156 is positively regulated by the AGAMOUS-like proteins AGL15 and AGL18

The regulation of flowering time has crucial implications for plant fitness. MicroRNA156 (miR156) represses the floral transition in Arabidopsis thaliana, but the mechanisms regulating its transcription remain unclear. Here, we show that two AGAMOUS-like proteins, AGL15 and AGL18, act as positive regulators of the expression of MIR156. Small RNA northern blot analysis revealed a significant decrease in the levels of mature miR156 in agl15 agl18 double mutants, but not in the single mutants, suggesting that AGL15 and AGL18 co-regulate miR156 expression. Histochemical analysis further indicated that the double mutants showed a reduction in MIR156 promoter strength. The double mutants also showed reduced abundance of pri-miR156a and pri-miR156c, two of the primary transcripts from MIR156 genes. Electrophoretic mobility shift assays demonstrated that AGL15 directly associated with the CArG motifs in the MIR156a/c promoters. AGL18 did not show binding affinity to the CArG motifs, but pull-down and yeast two-hybrid assays showed that AGL18 forms a heterodimer with AGL15. GFP reporter assays and bimolecular fluorescence complementation (BiFC) showed that AGL15 and AGL18 co-localize in the nucleus and confirmed their in vivo interaction. Overexpression of miR156 did not affect the levels of AGL15 and AGL18 transcripts. Taking these data together, we present a model for the transcriptional regulation of MIR156. In this model, AGL15 and AGL18 may form a complex along with other proteins, and bind to the CArG motifs of the promoters of MIR156 to activate the MIR156 expression.

RNA-seq analysis of transcriptome and glucosinolate metabolism in seeds and sprouts of broccoli (Brassica oleracea var. italic)

BACKGROUND

Broccoli (Brassica oleracea var. italica), a member of Cruciferae, is an important vegetable containing high concentration of various nutritive and functional molecules especially the anticarcinogenic glucosinolates. The sprouts of broccoli contain 10-100 times higher level of glucoraphanin, the main contributor of the anticarcinogenesis, than the edible florets. Despite the broccoli sprouts' functional importance, currently available genetic and genomic tools for their studies are very limited, which greatly restricts the development of this functionally important vegetable.

RESULTS

A total of ∼85 million 251 bp reads were obtained. After de novo assembly and searching the assembled transcripts against the Arabidopsis thaliana and NCBI nr databases, 19,441 top-hit transcripts were clustered as unigenes with an average length of 2,133 bp. These unigenes were classified according to their putative functional categories. Cluster analysis of total unigenes with similar expression patterns and differentially expressed unigenes among different tissues, as well as transcription factor analysis were performed. We identified 25 putative glucosinolate metabolism genes sharing 62.04-89.72% nucleotide sequence identity with the Arabidopsis orthologs. This established a broccoli glucosinolate metabolic pathway with high colinearity to Arabidopsis. Many of the biosynthetic and degradation genes showed higher expression after germination than in seeds; especially the expression of the myrosinase TGG2 was 20-130 times higher. These results along with the previous reports about these genes' studies in Arabidopsis and the glucosinolate concentration in broccoli sprouts indicate the breakdown products of glucosinolates may play important roles in the stage of broccoli seed germination and sprout development.

CONCLUSION

Our study provides the largest genetic resource of broccoli to date. These data will pave the way for further studies and genetic engineering of broccoli sprouts and will also provide new insight into the genomic research of this species and its relatives.

An emerging picture of the seed desiccome: confirmed regulators and newcomers identified using transcriptome comparison

Desiccation tolerance (DT) is the capacity to withstand total loss of cellular water. It is acquired during seed filling and lost just after germination. However, in many species, a germinated seed can regain DT under adverse conditions such as osmotic stress. The genes, proteins and metabolites that are required to establish this DT is referred to as the desiccome. It includes both a range of protective mechanisms and underlying regulatory pathways that remain poorly understood. As a first step toward the identification of the seed desiccome of Medicago truncatula, using updated microarrays we characterized the overlapping transcriptomes associated with acquisition of DT in developing seeds and the re-establishment of DT in germinated seeds using a polyethylene glycol treatment (-1.7 MPa). The resulting list contained 740 and 2829 transcripts whose levels, respectively, increased and decreased with DT. Fourty-eight transcription factors (TF) were identified including MtABI3, MtABI5 and many genes regulating flowering transition and cell identity. A promoter enrichment analysis revealed a strong over-representation of ABRE elements together with light-responsive cis-acting elements. In Mtabi5 Tnt1 insertion mutants, DT could no longer be re-established by an osmotic stress. Transcriptome analysis on Mtabi5 radicles during osmotic stress revealed that 13 and 15% of the up-regulated and down-regulated genes, respectively, are mis-regulated in the mutants and might be putative downstream targets of MtABI5 implicated in the re-establishment of DT. Likewise, transcriptome comparisons of the desiccation sensitive Mtabi3 mutants and hairy roots ectopically expressing MtABI3 revealed that 35 and 23% of the up-regulated and down-regulated genes are acting downstream of MtABI3. Our data suggest that ABI3 and ABI5 have complementary roles in DT. Whether DT evolved by co-opting existing pathways regulating flowering and cellular phase transition and cell identity is discussed.

MYB transcription factor genes as regulators for plant responses: an overview

Regulation of gene expression at the level of transcription controls many crucial biological processes. Transcription factors (TFs) play a great role in controlling cellular processes and MYB TF family is large and involved in controlling various processes like responses to biotic and abiotic stresses, development, differentiation, metabolism, defense etc. Here, we review MYB TFs with particular emphasis on their role in controlling different biological processes. This will provide valuable insights in understanding regulatory networks and associated functions to develop strategies for crop improvement.

Molecular cloning and characterization of a gene regulating flowering time from Alfalfa (Medicago sativa L.)

Genes that regulate flowering time play crucial roles in plant development and biomass formation. Based on the cDNA sequence of Medicago truncatula (accession no. AY690425), the LFY gene of alfalfa was cloned. Sequence similarity analysis revealed high homology with FLO/LFY family genes of other plants. When fused to the green fluorescent protein, MsLFY protein was localized in the nucleus of onion (Allium cepa L.) epidermal cells. The RT-qPCR analysis of MsLFY expression patterns showed that the expression of MsLFY gene was at a low level in roots, stems, leaves and pods, and the expression level in floral buds was the highest. The expression of MsLFY was induced by GA3 and long photoperiod. Plant expression vector was constructed and transformed into Arabidopsis by the agrobacterium-mediated methods. PCR amplification with the transgenic Arabidopsis genome DNA indicated that MsLFY gene had integrated in Arabidopsis genome. Overexpression of MsLFY specifically caused early flowering under long day conditions compared with non-transgenic plants. These results indicated MsLFY played roles in promoting flowering time.

Evolutionary analysis of the MIXTA gene family highlights potential targets for the study of cellular differentiation

Differentiated epidermal cells such as trichomes and conical cells perform numerous essential functions in plant biology and are important for our understanding of developmental patterning and cell shape regulation. Many are also commercially significant, such as cotton fibers and trichomes that secrete pharmaceutically useful or herbivore-deterring compounds. Here, we focus on the phylogeny and evolution of the subgroup 9 R2R3 MYB gene transcription factors, which include the MIXTA gene, and that are important for the specification and regulation of plant cellular differentiation. We have sequenced 49 subgroup 9 R2R3 MYB genes from key experimental taxa and combined these sequences with those identified by an exhaustive bioinformatic search, to compile a data set of 223 subgroup 9 R2R3 MYB genes. Our phylogenetic analyses demonstrate, for the first time, the complex evolutionary history of the subgroup 9 R2R3 MYB genes. A duplication event is inferred before the origin of seed plants giving rise to two major gene lineages, here termed SBG9-A and SBG9-B. The evolutionary conservation of the SBG9-B gene lineage has not been previously recognized and its role in cellular differentiation is unknown, thus an entire clade of potential candidate genes for epidermal cell regulation remains to be explored. Using a heterologous transformation bioassay, we provide functional data that implicate members of the SBG9-B lineage in the specification of epidermal projections. Furthermore, we reveal numerous putative duplication events in both SBG9-A and SBG9-B lineages, resolving uncertainty about orthology and paralogy among the subgroup 9 R2R3 MYB genes. Finally, we provide a robust framework over which to interpret existing functional data and to direct ongoing comparative genetic research into the evolution of plant cellular diversity.

LATE MERISTEM IDENTITY2 acts together with LEAFY to activate APETALA1

The switch from producing vegetative structures (branches and leaves) to producing reproductive structures (flowers) is a crucial developmental transition that significantly affects the reproductive success of flowering plants. In Arabidopsis, this transition is in large part controlled by the meristem identity regulator LEAFY (LFY). The molecular mechanisms by which LFY orchestrates a precise and robust switch to flower formation is not well understood. Here, we show that the direct LFY target LATE MERISTEM IDENTITY2 (LMI2) has a role in the meristem identity transition. Like LFY, LMI2 activates AP1 directly; moreover, LMI2 and LFY interact physically. LFY, LMI2 and AP1 are connected in a feed-forward and positive feedback loop network. We propose that these intricate regulatory interactions not only direct the precision of this crucial developmental transition in rapidly changing environmental conditions, but also contribute to its robustness and irreversibility.

The transcription factor EMISSION OF BENZENOIDS II activates the MYB ODORANT1 promoter at a MYB binding site specific for fragrant petunias

Fragrance production in petunia flowers is highly regulated. Two transcription factors, ODORANT1 (ODO1) and EMISSION OF BENZENOIDS II (EOBII) have recently been identified as regulators of the volatile benzenoid/phenylpropanoid pathway in petals. Unlike the non-fragrant Petunia hybrida cultivar R27, the fragrant cultivar Mitchell highly expresses ODO1. Using stable reporter lines, we identified the 1.2-kbp ODO1 promoter from Mitchell that is sufficient for tissue-specific, developmental and rhythmic expression. This promoter fragment can be activated in non-fragrant R27 petals, indicating that the set of trans-acting factors driving ODO1 expression is conserved in these two petunias. Conversely, the 1.2-kbp ODO1 promoter of R27 is much less active in Mitchell petals. Transient transformation of 5' deletion and chimeric Mitchell and R27 ODO1 promoter reporter constructs in petunia petals identified an enhancer region, which is specific for the fragrant Mitchell cultivar and contains a putative MYB binding site (MBS). Mutations in the MBS of the Mitchell promoter decreased overall promoter activity by 50%, highlighting the importance of the enhancer region. We show that EOBII binds and activates the ODO1 promoter via this MBS, establishing a molecular link between these two regulators of floral fragrance biosynthesis in petunia.

A glutathione S-transferase regulated by light and hormones participates in the modulation of Arabidopsis seedling development

Glutathione S-transferases (GSTs) have been well documented to be involved in diverse aspects of biotic and abiotic stresses, especially detoxification processes. Whether they regulate plant development remains unclear. Here, we report on our isolation by reverse transcription-polymerase chain reaction of a plant GST, AtGSTU17, from Arabidopsis (Arabidopsis thaliana) and demonstrate that its expression is regulated by multiple photoreceptors, especially phytochrome A (phyA) under all light conditions. Further physiological studies indicated that AtGSTU17 participates in various aspects of seedling development, including hypocotyl elongation, anthocyanin accumulation, and far-red light-mediated inhibition of greening with a requirement of functional phyA. The loss-of-function mutant of AtGSTU17 (atgstu17) resulted in reduced biomass of seedlings and number of lateral roots in the presence of auxin, as well as insensitivity to abscisic acid (ABA)-mediated inhibition of root elongation, with similarity to different phyA mutant alleles. Moreover, the root phenotype conferred by atgstu17 was reflected by histochemical β-glucuronidase staining of AtGSTU17 promoter activity with the addition of auxin or ABA. Further microarray analysis of wild-type Columbia and atgstu17 seedlings treated with far-red irradiation or ABA revealed that AtGSTU17 might modulate hypocotyl elongation by positively regulating some light-signaling components and negatively regulating a group of auxin-responsive genes and modulate root development by negatively controlling an auxin transport protein in the presence of ABA. Therefore, our data reveal that AtGSTU17 participates in light signaling and might modulate various aspects of Arabidopsis development by affecting glutathione pools via a coordinated regulation with phyA and phytohormones.

MYB transcription factors in Arabidopsis

The MYB family of proteins is large, functionally diverse and represented in all eukaryotes. Most MYB proteins function as transcription factors with varying numbers of MYB domain repeats conferring their ability to bind DNA. In plants, the MYB family has selectively expanded, particularly through the large family of R2R3-MYB. Members of this family function in a variety of plant-specific processes, as evidenced by their extensive functional characterization in Arabidopsis (Arabidopsis thaliana). MYB proteins are key factors in regulatory networks controlling development, metabolism and responses to biotic and abiotic stresses. The elucidation of MYB protein function and regulation that is possible in Arabidopsis will provide the foundation for predicting the contributions of MYB proteins to the biology of plants in general.