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

Identification of the Optimal Quantitative RT-PCR Reference Gene for Paper Mulberry (Broussonetia papyrifera)

Paper Mulberry (Broussonetia papyrifera) possesses medicinal, economic, and ecological significance and is extensively used for feed production, papermaking, and ecological restoration due to its ease of propagation, rapid growth rate, and strong stress resistance. The recent completion of the sequencing of the Paper Mulberry genome has prompted further research into the genetic breeding and molecular biology of this important species. A highly stable reference gene is essential to enhance the quantitative analysis of functional genes in Paper Mulberry; however, none has been identified. Accordingly, in this study, the leaves, stems, roots, petioles, young fruits, and mature fruits of Paper Mulberry plants were selected as experimental materials, and nine candidate reference genes, namely, α-TUB1, α-TUB2, β-TUB, H2A, ACT, DnaJ, UBQ, CDC2, and TIP41, were identified by RT-qPCR. Their stability was assessed using the geNorm, Normfinder, Delta Ct, BestKeeper, and RefFinder algorithms, identifying ACT and UBQ as showing the greatest stability. The expression of BpMYB090, which regulates the production of trichomes, was examined in the leaves of plants of the wild type (which have more trichomes) and mutant (which have fewer trichomes) at various developmental stages to validate the results of this study. As a result, their identification addresses a critical gap in the field of Paper Mulberry research, providing a solid foundation for future research that will concentrate on the characterization of pertinent functional genes in this economically valuable species.

Hibiscus bullseyes reveal mechanisms controlling petal pattern proportions that influence plant-pollinator interactions

Colorful flower patterns are key signals to attract pollinators. To produce such motifs, plants specify boundaries dividing petals into subdomains where cells develop distinctive pigmentations, shapes, and textures. While some transcription factors and biosynthetic pathways behind these characteristics are well studied, the upstream processes restricting their activities to specific petal regions remain enigmatic. Here, we unveil that the petal surface of Hibiscus trionum, an emerging model featuring a bullseye on its corolla, is prepatterned as the bullseye boundary position is specified long before it becomes visible. Using a computational model, we explore how pattern proportions are maintained while petals experience a 100-fold size increase. Exploiting transgenic lines and natural variants, we show that plants can regulate boundary position during the prepatterning phase or modulate growth on either side of this boundary later in development to vary bullseye proportions. Such modifications are functionally relevant, as buff-tailed bumblebees can reliably identify food sources based on bullseye size and prefer certain pattern proportions.

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.

Mechanistic and structural insight into R2R3-MYB transcription factor in plants: molecular dynamics based binding free energy analysis

The MYB transcription factor (TF) family is essential for various plant growth and development processes, including responses to biotic and abiotic stresses. This study investigated the R2R3-MYB protein structure from five plants, including cereal crops. The R2R3-MYB protein structure was docked with the DNA structure, and the best complexes were selected for two runs of molecular dynamics (MD) simulations to investigate the key interacting residues and conformational changes in the R2R3-MYB proteins caused by DNA binding. The MM/PBSA method calculated the binding free energy for each R2R3-MYB protein-DNA complex, showing strong interaction. Hydrophobic and hydrogen bonds significantly stabilized the R2R3-MYB protein-DNA complexes. The principal component analysis showed high restrictions on the movement of protein atoms in the phase space. A similar MD simulation analysis was performed using the crystal structure of the R2R3-MYB protein-DNA complex from Arabidopsis thaliana, and the generated complexes resembled the X-ray crystal structure. This is the first detailed study on the R2R3-MYB protein-DNA complex in cereal crops, providing a cost-effective solution to identify the key interacting residues and analyze the conformational changes in the MYB domain before and after DNA binding.Communicated by Ramaswamy H. Sarma.

Genetic basis of nectar guide trichome variation between bumblebee- and self-pollinated monkeyflowers (Mimulus): role of the MIXTA-like gene GUIDELESS

Nectar guide trichomes play crucial ecological roles in bee-pollinated flowers, as they serve as footholds and guides for foraging bees to access the floral rewards. However, the genetic basis of natural variation in nectar guide trichomes among species remains poorly understood. In this study, we performed genetic analysis of nectar guide trichome variation between two closely related monkeyflower (Mimulus) species, the bumblebee-pollinated Mimulus lewisii and self-pollinated M. parishii. We demonstrate that a MIXTA-like R2R3-MYB gene, GUIDELESS, is a major contributor to the nectar guide trichome length variation between the two species. The short-haired M. parishii carries a recessive allele due to non-synonymous substitutions in a highly conserved motif among MIXTA-like MYB proteins. Furthermore, our results suggest that besides GUIDELESS, additional loci encoding repressors of trichome elongation also contribute to the transition from bumblebee-pollination to selfing. Taken together, these results suggest that during a pollination syndrome switch, changes in seemingly complex traits such as nectar guide trichomes could have a relatively simple genetic basis, involving just a few genes of large effects.

A eudicot MIXTA family ancestor likely functioned in both conical cells and trichomes

The MIXTA family of MYB transcription factors modulate the development of diverse epidermal features in land plants. This study investigates the evolutionary history and function of the MIXTA gene family in the early-diverging eudicot model lineage Thalictrum (Ranunculaceae), with R2R3 SBG9-A MYB transcription factors representative of the pre-core eudicot duplication and thus hereby referred to as "paleoMIXTA" (PMX). Cloning and phylogenetic analysis of Thalictrum paleoMIXTA (ThPMX) orthologs across 23 species reveal a genus-wide duplication coincident with a whole-genome duplication. Expression analysis by qPCR confirmed that the highest expression is found in carpels, while newly revealing high expression in leaves and nuanced differences between paralogs in representative polyploid species. The single-copy ortholog from the diploid species T. thalictroides (TthPMX, previously TtMYBML2), which has petaloid sepals with conical-papillate cells and trichomes on leaves, was functionally characterized by virus-induced gene silencing (VIGS), and its role in leaves was also assessed from heterologous overexpression in tobacco. Another ortholog from a species with conical-papillate cells on stamen filaments, TclPMX, was also targeted for silencing. Overexpression assays in tobacco provide further evidence that the paleoMIXTA lineage has the potential for leaf trichome function in a core eudicot. Transcriptome analysis by RNA-Seq on leaves of VIGS-treated plants suggests that TthPMX modulates leaf trichome development and morphogenesis through microtubule-associated mechanisms and that this may be a conserved pathway for eudicots. These experiments provide evidence for a combined role for paleoMIXTA orthologs in (leaf) trichomes and (floral) conical-papillate cells that, together with data from other systems, makes the functional reconstruction of a eudicot ancestor most likely as also having a combined function.

Function and molecular mechanism of a poplar placenta limited MIXTA gene in regulating differentiation of plant epidermal cells

The placenta in fruits of most plants either desiccate and shrink as the fruits mature or develop further to form the fleshy tissues. In poplars, placental epidermal cells protrude collectively to produce catkin fibers. In this study, three carpel limited MIXTA genes, PdeMIXTA02, PdeMIXTA03, PdeMIXTA04, were find to specifically expressed in carpel immediately after pollination. Heterologous expression of the three genes in Arabidopsis demonstrated that PdeMIXTA04 significantly promoted trichomes density and could restore trichomes in the trichomeless mutant. By contrast, such functions were not observed with PdeMIXTA02, PdeMIXTA03. In situ hybridization revealed that PdeMIXTA04 was explicitly expressed in poplar placental epidermal cells. We also confirmed trichome-specific expression of the PdeMIXTA04 promoter. Multiple experimental proofs have confirmed the interaction between PdeMIXTA04, PdeMYC and PdeWD40, indicating PdeMIXTA04 functioned through the MYB-bHLH-WD40 ternary complex. Our work provided distinctive understanding of the molecular mechanism triggering differentiation of poplar catkins.

Regulation of capsule spine formation in castor

Castor (Ricinus communis L.) is a dicotyledonous oilseed crop that can have either spineless or spiny capsules. Spines are protuberant structures that differ from thorns or prickles. The developmental regulatory mechanisms governing spine formation in castor or other plants have remained largely unknown. Herein, using map-based cloning in 2 independent F2 populations, F2-LYY5/DL01 and F2-LYY9/DL01, we identified the RcMYB106 (myb domain protein 106) transcription factor as a key regulator of capsule spine development in castor. Haplotype analyses demonstrated that either a 4,353-bp deletion in the promoter or a single nucleotide polymorphism leading to a premature stop codon in the RcMYB106 gene could cause the spineless capsule phenotype in castor. Results of our experiments indicated that RcMYB106 might target the downstream gene RcWIN1 (WAX INDUCER1), which encodes an ethylene response factor known to be involved in trichome formation in Arabidopsis (Arabidopsis thaliana) to control capsule spine development in castor. This hypothesis, however, remains to be further tested. Nevertheless, our study reveals a potential molecular regulatory mechanism underlying the spine capsule trait in a nonmodel plant species.

Poplar coma morphogenesis and miRNA regulatory networks by combining ovary tissue sectioning and deep sequencing

Poplar coma, commonly referred to as "seed hairs", is a tuft of trichomes attached to the seed coat that helps seed dispersal. However, they can also trigger health impacts for humans, including sneezing, shortness of breath, and skin irritation. Despite efforts to study the regulatory mechanism of herbaceous trichome formation, poplar coma remains poorly understood. In this study, we showed that the epidermal cells of the funiculus and placenta are the origin of poplar coma based on observations of paraffin sections. Small RNA (sRNA) and degradome libraries were also constructed at three stages of poplar coma development, including initiation and elongation stages. Based on 7,904 miRNA-target pairs identified by small RNA and degradome sequencing, we constructed a miRNA-transcript factor and a stage-specific miRNA regulatory network. By combining paraffin section observation and deep sequencing, our research will provide greater insight into the molecular mechanisms of poplar coma development.

Flower transcriptional response to long term hot and cold environments in Antirrhinum majus

Short term experiments have identified heat shock and cold response elements in many biological systems. However, the effect of long-term low or high temperatures is not well documented. To address this gap, we grew Antirrhinum majus plants from two-weeks old until maturity under control (normal) (22/16°C), cold (15/5°C), and hot (30/23°C) conditions for a period of two years. Flower size, petal anthocyanin content and pollen viability obtained higher values in cold conditions, decreasing in middle and high temperatures. Leaf chlorophyll content was higher in cold conditions and stable in control and hot temperatures, while pedicel length increased under hot conditions. The control conditions were optimal for scent emission and seed production. Scent complexity was low in cold temperatures. The transcriptomic analysis of mature flowers, followed by gene enrichment analysis and CNET plot visualization, showed two groups of genes. One group comprised genes controlling the affected traits, and a second group appeared as long-term adaptation to non-optimal temperatures. These included hypoxia, unsaturated fatty acid metabolism, ribosomal proteins, carboxylic acid, sugar and organic ion transport, or protein folding. We found a differential expression of floral organ identity functions, supporting the flower size data. Pollinator-related traits such as scent and color followed opposite trends, indicating an equilibrium for rendering the organs for pollination attractive under changing climate conditions. Prolonged heat or cold cause structural adaptations in protein synthesis and folding, membrane composition, and transport. Thus, adaptations to cope with non-optimal temperatures occur in basic cellular processes.

Cuticle chemistry drives the development of diffraction gratings on the surface of Hibiscus trionum petals

Plants combine both chemical and structural means to appear colorful. We now have an extensive understanding of the metabolic pathways used by flowering plants to synthesize pigments, but the mechanisms remain obscure whereby cells produce microscopic structures sufficiently regular to interfere with light and create an optical effect. Here, we combine transgenic approaches in a novel model system, Hibiscus trionum, with chemical analyses of the cuticle, both in transgenic lines and in different species of Hibiscus, to investigate the formation of a semi-ordered diffraction grating on the petal surface. We show that regulating both cuticle production and epidermal cell growth is insufficient to determine the type of cuticular pattern produced. Instead, the chemical composition of the cuticle plays a crucial role in restricting the formation of diffraction gratings to the pigmented region of the petal. This suggests that buckling, driven by spatiotemporal regulation of cuticle chemistry, could pattern the petal surface at the nanoscale.

Characterization of anatomical features, developmental roadmaps, and key genes of bamboo leaf epidermis

The exact developmental roadmaps of bamboo leaf epidermis and the regulating genes are largely unknown. In this study, we comprehensively investigated the morphological features of the leaf epidermis of bamboo, Pseudosasa japonica. We also established the developmental roadmaps of the abaxial epidermis along the linearly growing leaf. A variant of P. japonica, P. japonica var. tsutsumiana, with smaller stomata and higher stomata density, was identified. Further analysis revealed that the higher stomata density of the variant was due to the abnormal increase in stomata columns within the single stomata band. This abnormal development of stomata bands was observed as early as the guard mother cell stage in the leaf division zone (DZ). Interestingly, the developmental pattern of the single stomata was similar in P. japonica and the variant. Molecular data showed that PjDLT (Dwarf and Low Tillering) was significantly downregulated in leaves DZ of the variant. Overexpression of PjDLT in Arabidopsis and rice results in smaller plants with lower stomata density, whereas downregulation or mutation of OsDLT results in increased stomata density. Our results highlight the morphological features and developmental schedule of the leaf epidermis of bamboo and provide evidence that DLT plays an important role in regulating stomata in bamboo and rice.

Conical petal epidermal cells, regulated by the MYB transcription factor MIXTA, have an ancient origin within the angiosperms

Conical epidermal cells occur on the tepals (perianth organs, typically petals and/or sepals) of the majority of animal-pollinated angiosperms, where they play both visual and tactile roles in pollinator attraction, providing grip to foraging insects, and enhancing colour, temperature, and hydrophobicity. To explore the evolutionary history of conical epidermal cells in angiosperms, we surveyed the tepal epidermis in representative species of the ANA-grade families, the early-diverging successive sister lineages to all other extant angiosperms, and analysed the function of a candidate regulator of cell outgrowth from Cabomba caroliniana (Nymphaeales). We identified conical cells in at least two genera from different families (Austrobaileya and Cabomba). A single SBG9 MYB gene was isolated from C. caroliniana and found to induce strong differentiation of cellular outgrowth, including conical cells, when ectopically expressed in Nicotiana tabacum. Ontogenetic analysis and quantitative reverse transcription-PCR established that CcSBG9A1 is spatially and temporally expressed in a profile which correlates with a role in conical cell development. We conclude that conical or subconical cells on perianth organs are ancient within the angiosperms and most probably develop using a common genetic programme initiated by a SBG9 MYB transcription factor.

Identification and characterization of a novel gene involved in glandular trichome development in Nepeta tenuifolia

Nepeta tenuifolia is a medicinal plant rich in terpenoids and flavonoids with antiviral, immunoregulatory, and anti-inflammatory activities. The peltate glandular trichome (PGT) is a multicellular structure considered to be the primary storage organ for monoterpenes; it may serve as an ideal model for studying cell differentiation and the development of glandular trichomes (GTs). The genes that regulate the development of GTs have not yet been well studied. In this study, we identified NtMIXTA1, a GT development-associated gene from the R2R3 MYB SBG9 family. NtMIXTA1 overexpression in tobacco resulted in the production of longer and denser GTs. Virus-induced gene silencing of NtMIXTA1 resulted in lower PGT density, a significant reduction in monoterpene concentration, and the decreased expression of genes related to monoterpene biosynthesis. Comparative transcriptome and widely targeted metabolic analyses revealed that silencing NtMIXTA1 significantly influenced the expression of genes, and the production of metabolites involved in the biosynthesis of terpenoids, flavonoids, and lipids. This study provides a solid foundation describing a mechanism underlying the regulation of GT development. In addition, this study further deepens our understanding of the regulatory networks involved in GT development and GT development-associated metabolite flux, as well as provides valuable reference data for studying plants with a high medicinal value without genetic transformation.

Diversity, phylogeny, and adaptation of bryophytes: insights from genomic and transcriptomic data

Bryophytes including mosses, liverworts, and hornworts are among the earliest land plants, and occupy a crucial phylogenetic position to aid in the understanding of plant terrestrialization. Despite their small size and simple structure, bryophytes are the second largest group of extant land plants. They live ubiquitously in various habitats and are highly diversified, with adaptive strategies to modern ecosystems on Earth. More and more genomes and transcriptomes have been assembled to address fundamental questions in plant biology. Here, we review recent advances in bryophytes associated with diversity, phylogeny, and ecological adaptation. Phylogenomic studies have provided increasing supports for the monophyly of bryophytes, with hornworts sister to the Setaphyta clade including liverworts and mosses. Further comparative genomic analyses revealed that multiple whole-genome duplications might have contributed to the species richness and morphological diversity in mosses. We highlight that the biological changes through gene gain or neofunctionalization that primarily evolved in bryophytes have facilitated the adaptation to early land environments; among the strategies to adapt to modern ecosystems in bryophytes, desiccation tolerance is the most remarkable. More genomic information for bryophytes would shed light on key mechanisms for the ecological success of these 'dwarfs' in the plant kingdom.

Transcriptome mining of genes in Zanthoxylum armatum revealed ZaMYB86 as a negative regulator of prickly development

Zanthoxylum armatum DC. is an important economic tree species. Prickle is a type of trichome with special morphology, and there are a lot of prickles on the leaves of Z. armatum, which seriously restricts the development of Z. armatum industry. In this study, the leaves of Z. armatum cv. Zhuye (ZY) and its budding variety 'Rongchangwuci' (WC) (A less prickly mutant variety) at different developmental stages were used as materials, and the transcriptome sequencing data were analyzed. A total of 96,931 differentially expressed genes (DEGs) were identified among the samples, among which 1560 were candidate DEGs that might be involved in hormone metabolism. The contents of JA, auxin and CK phytohormones in ZY leaves were significantly higher than those in WC leaves. Combined with weighted gene co-expression network analysis, eight genes (MYC, IAA, ARF, CRE/AHK, PP2C, ARR-A, AOS and LOX) were identified, including 25 transcripts, which might affect the metabolism of the three hormones and indirectly participate in the formation of prickles. Combining with the proteins successfully reported in other plants to regulate trichome formation, ZaMYB86, a transcription factor of R2R3 MYB family, was identified through local Blast and phylogenetic tree analysis, which might regulate prickle formation of Z. armatum. Overexpression of ZaMYB86 in mutant A. thaliana resulted in the reduction of trichomes in A. thaliana leaves, which further verified that ZaMYB86 was involved in the formation of pickles. Yeast two-hybrid results showed that ZaMYB86 interacted with ZaMYB5. Furthermore, ZaMYB5 was highly homologous to AtMYB5, a transcription factor that regulated trichomes development, in MYB DNA binding domain. Taken together, these results indicated that ZaMYB86 and ZaMYB5 act together to regulate the formation of prickles in Z. armatum. Our findings provided a new perspective for revealing the molecular mechanism of prickly formation.

Characterisation of the Mentha canadensis R2R3-MYB transcription factor gene McMIXTA and its involvement in peltate glandular trichome development

BACKGROUND

Mentha canadensis L. has important economic value for the production of essential oils, which are synthesised, secreted and stored in peltate glandular trichomes. As a typical multicellular secretory trichome, glandular trichomes are important biological factories for the synthesis of some specialised metabolites. However, little is known about the molecular mechanism of glandular trichome development in M. canadensis.

RESULTS

In this study, the R2R3-MYB transcription factor gene McMIXTA was isolated to investigate its function in glandular trichome development. Bioinformatics analysis indicated that McMIXTA belonged to the subgroup 9 R2R3-MYB, with a R2R3 DNA-binding domain and conserved subgroup 9 motifs. A subcellular localisation assay indicated that McMIXTA was localised in the nucleus. Transactivation analysis indicated that McMIXTA was a positive regulator, with transactivation regions located between positions N253 and N307. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that McMIXTA formed a complex with McHD-Zip3, a trichome development-related HD-ZIP IV transcription factor. Overexpression of McMIXTA in Mentha × piperita L. caused an increase in peltate glandular trichomes density of approximately 25% on the leaf abaxial surface.

CONCLUSIONS

Our results demonstrated that the subgroup 9 R2R3-MYB transcription factor McMIXTA has a positive effect on regulating peltate glandular trichome development and the MIXTA/HD-ZIP IV complexes might be conserved regulators for glandular trichome initiation. These results provide useful information for revealing the regulatory mechanism of multicellular glandular trichome development.

Multi-Dimensional Molecular Regulation of Trichome Development in Arabidopsis and Cotton

Plant trichomes are specialized epidermal cells that are widely distributed on plant aerial tissues. The initiation and progression of trichomes are controlled in a coordinated sequence of multiple molecular events. During the past decade, major breakthroughs in the molecular understanding of trichome development were achieved through the characterization of various trichomes defective mutants and trichome-associated genes, which revealed a highly complex molecular regulatory network underlying plant trichome development. This review focuses on the recent millstone in plant trichomes research obtained using genetic and molecular studies, as well as 'omics' analyses in model plant Arabidopsis and fiber crop cotton. In particular, we discuss the latest understanding and insights into the underlying molecular mechanisms of trichomes formation at multiple dimensions, including at the chromatin, transcriptional, post-transcriptional, and post-translational levels. We summarize that the integration of multi-dimensional trichome-associated genes will enable us to systematically understand the molecular regulation network that landscapes the development of the plant trichomes. These advances will enable us to address the unresolved questions regarding the molecular crosstalk that coordinate concurrent and ordered the changes in cotton fiber initiation and progression, together with their possible implications for genetic improvement of cotton fiber.

R2R3-MYB genes coordinate conical cell development and cuticular wax biosynthesis in Phalaenopsis aphrodite

Petals of the monocot Phalaenopsis aphrodite (Orchidaceae) possess conical epidermal cells on their adaxial surfaces, and a large amount of cuticular wax is deposited on them to serve as a primary barrier against biotic and abiotic stresses. It has been widely reported that subgroup 9A members of the R2R3-MYB gene family, MIXTA and MIXTA-like in eudicots, act to regulate the differentiation of conical epidermal cells. However, the molecular pathways underlying conical epidermal cell development and cuticular wax biosynthesis in monocot petals remain unclear. Here, we characterized two subgroup 9A R2R3-MYB genes, PaMYB9A1 and PaMYB9A2 (PaMYB9A1/2), from P. aphrodite through the transient overexpression of their coding sequences and corresponding chimeric repressors in developing petals. We showed that PaMYB9A1/2 function to coordinate conical epidermal cell development and cuticular wax biosynthesis. In addition, we identified putative targets of PaMYB9A1/2 through comparative transcriptome analyses, revealing that PaMYB9A1/2 acts to regulate the expression of cell wall-associated and wax biosynthetic genes. Furthermore, a chemical composition analysis of cuticular wax showed that even-chain n-alkanes and odd-chain primary alcohols are the main chemical constituents of cuticular wax deposited on petals, which is inconsistent with the well-known biosynthetic pathways of cuticular wax, implying a distinct biosynthetic pathway occurring in P. aphrodite flowers. These results reveal that the function of subgroup 9A R2R3-MYB family genes in regulating the differentiation of epidermal cells is largely conserved in monocots and dicots. Furthermore, both PaMYB9A1/2 have evolved additional functions controlling the biosynthesis of cuticular wax.

Two zinc-finger roteins control the initiation and elongation of long stalk trichomes in tomato

Plant glandular trichomes are epidermal secretory structures that are important for plant resistance to pests. Although several regulatory genes have been characterized in trichome development, the molecular mechanisms conferring glandular trichome morphogenesis are unclear. We observed the differences in trichomes in cultivated tomato cv. 'Moneymaker' (MM) and the wild species Solanum pimpinellifolium PI365967 (PP), and used a recombinant inbred line (RIL) population to identify the genes that control trichome development in tomato. We found that the genomic variations in two genes, H and SH, contribute to the trichome differences between MM and PP. H and SH encode two paralogous C2H2 zinc-finger proteins that function redundantly in regulating trichome formation. Loss-of-function h/sh double mutants exhibited a significantly decreased number of Type I trichomes and complete loss of long stalk trichomes. Molecular and genetic analyses further indicate that H and SH act upstream of ZFP5. Overexpression of ZFP5 partially restored the trichome defects in NIL-h^PPsh^PP. Moreover, H and SH expression is induced by high temperatures, and their mutations inhibit the elongation of trichomes that reduce the plant repellent to whiteflies. Our findings confirm that H and SH are two vital transcription factors controlling initiation and elongation of Type I and III multicellular trichomes in tomato.

An HD-ZIP-MYB complex regulates glandular secretory trichome initiation in Artemisia annua

Plant glandular secretory trichomes (GSTs) produce various specialized metabolites. Increasing GST density represents a strategy to enhance the yield of these chemicals; however, the gene regulatory network that controls GST initiation remains unclear. In a previous study of Artemisia annua L., we found that a HD-ZIP IV transcription factor, AaHD1, promotes GST initiation by directly regulating AaGSW2. Here, we identified two AaHD1-interacting transcription factors, namely AaMIXTA-like 2 (AaMYB16) and AaMYB5. Through the generation and characterization of transgenic plants, we found that AaMYB16 is a positive regulator of GST initiation, whereas AaMYB5 has the opposite effect. Notably, neither of them regulates GST formation independently. Rather, they act competitively, by interacting and modulating AaHD1 promoter binding activity. Additionally, the phytohormone jasmonic acid (JA) was shown to be associated with the AaHD1-AaMYB16/AaMYB5 regulatory network through transcriptional regulation via a JASMONATE-ZIM DOMAIN (JAZ) protein repressor. These results bring new insights into the mechanism of GST initiation through regulatory complexes, which appear to have similar functions in a range of vascular plant taxa.

The land plant-specific MIXTA-MYB lineage is implicated in the early evolution of the plant cuticle and the colonization of land

The evolution of a lipid-based cuticle on aerial plant surfaces that protects against dehydration is considered a fundamental innovation in the colonization of the land by the green plants. However, key evolutionary steps in the early regulation of cuticle synthesis are still poorly understood, owing to limited studies in early-diverging land plant lineages. Here, we characterize a land plant specific subgroup 9 R2R3 MYB transcription factor MpSBG9, in the early-diverging land plant model Marchantia polymorpha, that is homologous to MIXTA proteins in vascular plants. The MpSBG9 functions as a key regulator of cuticle biosynthesis by preferentially regulating expression of orthologous genes for cutin formation, but not wax biosynthesis genes. The MpSBG9 also promotes the formation of papillate cells on the adaxial surface of M. polymorpha, which is consisitent with its canonical role in vascular plants. Our observations imply conserved MYB transcriptional regulation in the control of the cutin biosynthesis pathway as a core genetic network in the common ancestor of all land plants, implicating the land plant-specific MIXTA MYB lineage in the early origin and evolution of the cuticle.

MIXTAs and phytohormones orchestrate cotton fiber development

Cotton is the largest source of natural fiber for textile industry in the world. Cotton fibers are seed trichomes that make cotton unique among plants. Cotton fibers originate from ovule epidermal cells and serve as an excellent model to study the process of cell differentiation in plants. Characterization of factors contributing to fiber development will help to reveal general mechanisms of cell differentiation in plants. Transcription factors (TFs), especially MYB-MIXTA-like (MML) factors, appear to have evolved unique roles in fiber development. In addition, phytohormones including brassinosteroids, jasmonic acid, GA and auxin also play an important role in regulating fiber development. Here, we summarize the mechanisms of MIXTAs and phytohormones orchestrating cotton fiber development. The progress in understanding molecular basis of fiber development will facilitate future genetic engineering and breeding to improve cotton fiber quality and yield.

An R2R3-MYB Transcription Factor Positively Regulates the Glandular Secretory Trichome Initiation in Artemisia annua L

Artemisia annua L. is known for its specific product "artemisinin" which is an active ingredient for curing malaria. Artemisinin is secreted and accumulated in the glandular secretory trichomes (GSTs) on A. annua leaves. Earlier studies have shown that increasing GST density is effective in increasing artemisinin content. However, the mechanism of GST initiation is not fully understood. To this end, we isolated and characterized an R2R3-MYB gene, AaMYB17, which is expressed specifically in the GSTs of shoot tips. Overexpression of AaMYB17 in A. annua increased GST density and enhanced the artemisinin content, whereas RNA interference of AaMYB17 resulted in the reduction of GST density and artemisinin content. Additionally, neither overexpression lines nor RNAi lines showed an abnormal phenotype in plant growth and the morphology of GSTs. Our study demonstrates that AaMYB17 is a positive regulator of GSTs' initiation, without influencing the trichome morphology.

High-Resolution Transcriptome Atlas and Improved Genome Assembly of Common Buckwheat, Fagopyrum esculentum

Common buckwheat (Fagopyrum esculentum) is an important non-cereal grain crop and a prospective component of functional food. Despite this, the genomic resources for this species and for the whole family Polygonaceae, to which it belongs, are scarce. Here, we report the assembly of the buckwheat genome using long-read technology and a high-resolution expression atlas including 46 organs and developmental stages. We found that the buckwheat genome has an extremely high content of transposable elements, including several classes of recently (0.5-1 Mya) multiplied TEs ("transposon burst") and gradually accumulated TEs. The difference in TE content is a major factor contributing to the three-fold increase in the genome size of F. esculentum compared with its sister species F. tataricum. Moreover, we detected the differences in TE content between the wild ancestral subspecies F. esculentum ssp. ancestrale and buckwheat cultivars, suggesting that TE activity accompanied buckwheat domestication. Expression profiling allowed us to test a hypothesis about the genetic control of petaloidy of tepals in buckwheat. We showed that it is not mediated by B-class gene activity, in contrast to the prediction from the ABC model. Based on a survey of expression profiles and phylogenetic analysis, we identified the MYB family transcription factor gene tr_18111 as a potential candidate for the determination of conical cells in buckwheat petaloid tepals. The information on expression patterns has been integrated into the publicly available database TraVA: http://travadb.org/browse/Species=Fesc/. The improved genome assembly and transcriptomic resources will enable research on buckwheat, including practical applications.

The MIXTA-LIKE transcription factor CsMYB6 regulates fruit spine and tubercule formation in cucumber

Cucumber fruit wart composed of tubercule and spine (trichome on fruit) is not only an important fruit quality trait in cucumber production, but also a well-studied model for plant cell-fate determination. The development of spine is closely related to the initiation and formation of tubercule. The spine differentiation regulator CsGL1 has been proved to be epistatic to the tubercule initiation factor CsTu, which is the only connection to be identified between spine and tubercule formations. Our previous studies found that the MIXTA-LIKE transcription factor CsMYB6 can suppress fruit spine initiation, which is independent of CsGL1. How the formation of spine and tubercule is regulated at the molecular level by CsMYB6 remains poorly understood. In this study, we characterized cucumber 35S:CsMYB6 transgenic plants, which displayed an obvious reduction in the number and size of fruit spines and tubecules. Molecular analyses showed that CsMYB6 directly interacted with the key spine formation factor CsTTG1 in regulating the formation of fruit spine, and CsTu in regulating the initiation of fruit tubercule, respectively. Based on these evidences, a novel regulatory network is proposed by which CsMYB6/CsTTG1 and CsMYB6/CsTu complexes play an important role in regulating epidermal development, including spine formation and tubercule initiation in cucumber.

EgMIXTA1, a MYB-Type Transcription Factor, Promotes Cuticular Wax Formation in Eustoma grandiflorum Leaves

In the aerial plant organs, cuticular wax forms a hydrophobic layer that can protect cells from dehydration, repel pathogen attacks, and prevent organ fusion during development. The MIXTA gene encodes an MYB-like transcription factor, which is associated with epicuticular wax biosynthesis to increase the wax load on the surface of leaves. In this study, the AmMIXTA-homologous gene EgMIXTA1 was functionally characterized in the Eustoma grandiflorum. EgMIXTA1 was ubiquitously, but highly, expressed in leaves and buds. We identified the Eustoma MIXTA homolog and developed the plants for overexpression. EgMIXTA1-overexpressing plants had more wax crystal deposition on the leaf surface compared to wild-type and considerably more overall cuticular wax. In the leaves of the overexpression line, the cuticular transpiration occurred more slowly than in those of non-transgenic plants. Analysis of gene expression indicated that several genes, such as EgCER3, EgCER6, EgCER10, EgKCS1, EgKCR1, and EgCYP77A6, which are known to be involved in wax biosynthesis, were induced by EgMIXTA1-overexpression lines. Expression of another gene, WAX INDUCER1/SHINE1, encoding a transcription factor that stimulates the production of cutin, was also significantly higher in the overexpressors than in wild-type. However, the expression of a lipid-related gene, EgABCG12, did not change relative to the wild-type. These results suggest that EgMIXTA1 is involved in the biosynthesis of cuticular waxes.

The R2R3-MYB gene family in banana (Musa acuminata): Genome-wide identification, classification and expression patterns

The R2R3-MYB genes comprise one of the largest transcription factor gene families in plants, playing regulatory roles in plant-specific developmental processes, defense responses and metabolite accumulation. To date MYB family genes have not yet been comprehensively identified in the major staple fruit crop banana. In this study, we present a comprehensive, genome-wide analysis of the MYB genes from Musa acuminata DH-Pahang (A genome). A total of 285 R2R3-MYB genes as well as genes encoding three other classes of MYB proteins containing multiple MYB repeats were identified and characterised with respect to structure and chromosomal organisation. Organ- and development-specific expression patterns were determined from RNA-Seq data. For 280 M. acuminata MYB genes for which expression was found in at least one of the analysed samples, a variety of expression patterns were detected. The M. acuminata R2R3-MYB genes were functionally categorised, leading to the identification of seven clades containing only M. acuminata R2R3-MYBs. The encoded proteins may have specialised functions that were acquired or expanded in Musa during genome evolution. This functional classification and expression analysis of the MYB gene family in banana establishes a solid foundation for future comprehensive functional analysis of MaMYBs and can be utilized in banana improvement programmes.

The transcription factor MML4_D12 regulates fiber development through interplay with the WD40-repeat protein WDR in cotton

In planta, a vital regulatory complex, MYB-basic helix-loop-helix (bHLH)-WD40 (MBW), is involved in trichome development and synthesis of anthocyanin and proanthocyanin in Arabidopsis. Usually, WD40 proteins provide a scaffold for protein-protein interaction between MYB and bHLH proteins. Members of subgroup 9 of the R2R3 MYB transcription factors, which includes MYBMIXTA-Like (MML) genes important for plant cell differentiation, are unable to interact with bHLH. In this study, we report that a cotton (Gossypium hirsutum) seed trichome or lint fiber-related GhMML factor, GhMML4_D12, interacts with a diverged WD40 protein (GhWDR) in a process similar to but different from that of the MBW ternary complex involved in Arabidopsis trichome development. Amino acids 250-267 of GhMML4_D12 and the first and third WD40 repeat domains of GhWDR determine their interaction. GhWDR could rescue Arabidopsis ttg1 to its wild type, confirming its orthologous function in trichome development. Our findings shed more light towards understanding the key role of the MML and WD40 families in plants and in the improvement of cotton fiber production.

Genetic Control of Glandular Trichome Development

Plant glandular trichomes are epidermal secretory structures producing various specialized metabolites. These metabolites are involved in plant adaptation to its environment and many of them have remarkable properties exploited by fragrance, flavor, and pharmaceutical industries. The identification of genes controlling glandular trichome development is of high interest to understand how plants produce specialized metabolites. Our knowledge about this developmental process is still limited, but genes controlling glandular trichome initiation and morphogenesis have recently been identified. In particular, R2R3-MYB and HD-ZIP IV transcription factors appear to play essential roles in glandular trichome initiation in Artemisia annua and tomato. In this review, we focus on the results obtained in these two species and we propose genetic regulation models integrating these data.

Colourful cones: how did flower colour first evolve?

Angiosperms that are biotically pollinated typically produce flowers with bright and contrasting colours that help to attract pollinators and hence contribute to the reproductive success of the species. This colourful array contrasts with the much less multicoloured reproductive structures of the four living gymnosperm lineages, which are mostly wind pollinated, though cycads and Gnetales are predominantly pollinated by insects that feed on surface fluids from the pollination drops. This review examines the possible evolutionary pathways and cryptic clues for flower colour in both living and fossil seed plants. It investigates how the ancestral flowering plants could have overcome the inevitable trade-off that exists between attracting pollinators and minimizing herbivory, and explores the possible evolutionary and biological inferences from the colours that occur in some living gymnosperms. The red colours present in the seed-cone bracts of some living conifers result from accumulation of anthocyanin pigments; their likely primary function is to help protect the growing plant tissues under particular environmental conditions. Thus, the visual cue provided by colour in flower petals could have first evolved as a secondary effect, probably post-dating the evolution of bee colour vision but occurring before the subsequent functional accumulation of a range of different flower pigments.

The Dynamic Genetic-Hormonal Regulatory Network Controlling the Trichome Development in Leaves

Plant trichomes are outgrowths developed from an epidermal pavement cells of leaves and other organs. Trichomes (also called 'hairs') play well-recognized roles in defense against insect herbivores, forming a physical barrier that obstructs insect movement and mediating chemical defenses. In addition, trichomes can act as a mechanosensory switch, transducing mechanical stimuli (e.g., insect movement) into physiological signals, helping the plant to respond to insect attacks. Hairs can also modulate plant responses to abiotic stresses, such as water loss, an excess of light and temperature, and reflect light to protect plants against UV radiation. The structure of trichomes is species-specific and this trait is generally related to their function. These outgrowths are easily analyzed and their origin represents an outstanding subject to study epidermal cell fate and patterning in plant organs. In leaves, the developmental control of the trichomatous complement has highlighted a regulatory network based on four fundamental elements: (i) genes that activate and/or modify the normal cell cycle of epidermal pavement cells (i.e., endoreduplication cycles); (ii) transcription factors that create an activator/repressor complex with a central role in determining cell fate, initiation, and differentiation of an epidermal cell in trichomes; (iii) evidence that underlines the interplay of the aforesaid complex with different classes of phytohormones; (iv) epigenetic mechanisms involved in trichome development. Here, we reviewed the role of genes in the development of trichomes, as well as the interaction between genes and hormones. Furthermore, we reported basic studies about the regulation of the cell cycle and the complexity of trichomes. Finally, this review focused on the epigenetic factors involved in the initiation and development of hairs, mainly on leaves.

Synteny-based mapping of causal point mutations relevant to sand rice (Agriophyllum squarrosum) trichomeless1 mutant by RNA-sequencing

Sand rice (Agriophyllum squarrosum), a diploid Amaranthaceae species within the order Caryophyllalles, has potential as a crop in response to concerns about ongoing climate change and future food security. Modifying the weedy traits, such as dense trichomes, is important for the domestication of sand rice. In this study, an ethyl methanesulfonate (EMS) induced Agriophyllum squarrosum trichomeless mutant (astcl1) was isolated and genetic analysis revealed that this mutant was controlled by a single recessive locus. RNA sequencing was employed to analyze sequence variations between the mutant and wild-type individuals based on allele frequencies. Synteny-based mapping against two closely related and sequenced species finally delimited the causal mutations into an approximately 18.97 mega base pair (Mb) interval on the top portion of the chromosome 6 (Bv6) of sugar beet (Beta vulgaris) and two intervals (5.56 and 2.69 Mb) on the chromosomes 14 (CqA14) and 6 (CqB06) of quinoa (Chenopodium quinoa). These two quinoa intervals were located in the orthologous chromosomal regions against sugar beet Bv6. Differential expression analysis revealed that the astcl1 mutation only affects the expression of a small subset of genes. Most significantly, 17 lipid transport and metabolism related genes, such as GDSL esterases and very-long-chain 3-oxoacyl-CoA reductase 1, and two R2R3 MYB genes, MYB39 and RAX3, were down-regulated in astcl1 mutants. These results imply that the Astcl1 protein coordinately regulates trichome initiation and cuticle biosynthesis in sand rice.

Evolution of ALOG gene family suggests various roles in establishing plant architecture of Torenia fournieri

BACKGROUND

ALOG (Arabidopsis LSH1 and Oryza G1) family with a conserved domain widely exists in plants. A handful of ALOG members have been functionally characterized, suggesting their roles as key developmental regulators. However, the evolutionary scenario of this gene family during the diversification of plant species remains largely unclear.

METHODS

Here, we isolated seven ALOG genes from Torenia fournieri and phylogenetically analyzed them with different ALOG members from representative plants in major taxonomic clades. We further examined their gene expression patterns by RT-PCR, and regarding the protein subcellular localization, we co-expressed the candidates with a nuclear marker. Finally, we explored the functional diversification of two ALOG members, TfALOG1 in euALOG1 and TfALOG2 in euALOG4 sub-clades by obtaining the transgenic T. fournieri plants.

RESULTS

The ALOG gene family can be divided into different lineages, indicating that extensive duplication events occurred within eudicots, grasses and bryophytes, respectively. In T. fournieri, seven TfALOG genes from four sub-clades exhibit distinct expression patterns. TfALOG1-6 YFP-fused proteins were accumulated in the nuclear region, while TfALOG7-YFP was localized both in nuclear and cytoplasm, suggesting potentially functional diversification. In the 35S:TfALOG1 transgenic lines, normal development of petal epidermal cells was disrupted, accompanied with changes in the expression of MIXTA-like genes. In 35S:TfALOG2 transgenic lines, the leaf mesophyll cells development was abnormal, favoring functional differences between the two homologous proteins. Unfortunately, we failed to observe any phenotypical changes in the TfALOG1 knock-out mutants, which might be due to functional redundancy as the case in Arabidopsis.

CONCLUSION

Our results unraveled the evolutionary history of ALOG gene family, supporting the idea that changes occurred in the cis regulatory and/or nonconserved coding regions of ALOG genes may result in new functions during the establishment of plant architecture.

Disentangling historical signal and pollinator selection on the micromorphology of flowers: an example from the floral epidermis of the Nymphaeaceae

The family Nymphaeaceae includes most of the diversity among the ANA-grade angiosperms. Among the species of this family, floral structures and pollination strategies vary. The genus Victoria, as well as subgenera Lotos and Hydrocallis in Nymphaea, present night-blooming, scented flowers pollinated by scarab beetles. Such similar pollination strategies have led to macromorphological similarities among the flowers of these species, which could be interpreted as homologies or convergences based on different phylogenetic hypotheses about the relationships of these groups. We employed scanning electron microscopy of floral epidermis for seven species of the Nymphaeaceae with contrasting pollination biology to identify the main characters of the floral organs and the potential homologous nature of the structures involved in pollinator attraction. Moreover, we used transmission electron microscopy to observe ultrastructure of papillate-conical epidermis in the stamen of Victoria cruziana. We then tested the phylogenetic or ecological distribution of these traits using both consensus network approaches and ancestral state reconstruction on fixed phylogenies. Our results show that the night-blooming flowers present different specialisations in their epidermis, with V. cruziana presenting the most elaborate floral anatomy. We also identify for the first time the presence of conical-papillate cells in the order Nymphaeales. The epidermal characters tend to reflect phylogenetic relationships more than convergence due to pollinator selection. These results point to an independent and parallel evolution of scarab pollination in Nymphaeaceae and demonstrate the promise of floral anatomy as a phylogenetic marker. Moreover, they indicate a degree of sophistication in the anatomical basis of cantharophilous flowers in the Nymphaeales that diverges from the most simplistic views of floral evolution in the angiosperms.

Intraspecific variation in the petal epidermal cell morphology of Vicia faba L. (Fabaceae)

At a microscopic scale, the shape and fine cell relief of the petal epidermal cells of a flower play a key role in its interaction with pollinators. In particular, conical shaped petal epidermal cells have been shown to have an important function in providing grip on the surface of bee-pollinated flowers and can influence bee visitation rates. Previous studies have explored interspecific variation in this trait within genera and families, but naturally-occurring intraspecific variation has not yet been comprehensively studied. Here, we investigate petal epidermal cell morphology in 32 genotypes of the crop Vicia faba, which has a yield highly dependent on pollinators. We hypothesise that conical cells may have been lost in some genotypes as a consequence of selective sweeps or genetic drift during breeding programmes. We find that 13% of our lines have a distribution of conical petal epidermal cells that deviates from that normally seen in V. faba flowers. These abnormal phenotypes were specific to the ad/abaxial side of petals, suggesting that these changes are the result of altered gene expression patterns rather than loss of gene function.

Genetics and evolution of MIXTA genes regulating cotton lint fiber development

Cotton, with cellulose-enriched mature fibers, is the largest source of natural textiles. Through a map-based cloning strategy, we isolated an industrially important lint fiber development gene (Li₃ ) that encodes an MYB-MIXTA-like transcription factor (MML) on chromosome D12 (GhMML4_D12). Virus-induced gene silencing or decreasing the expression of the GhMML4_D12 gene in n₂ NSM plants resulted in a significant reduction in epidermal cell prominence and lint fiber production. GhMML4_D12 is arranged in tandem with GhMML3, another MIXTA gene responsible for fuzz fiber development. These two very closely related MIXTA genes direct fiber initiation production in two specialized cell forms: lint and fuzz fibers. They may control the same metabolic pathways in different cell types. The MIXTAs expanded in Malvaceae during their evolution and produced a Malvaceae-specific family that regulates epidermal cell differentiation, different from the gene family that regulates leaf hair trichome development. Cotton has developed a unique transcriptional regulatory network for fiber development. Characterization of target genes regulating fiber production has provided insights into the molecular mechanisms underlying cotton fiber development and has allowed the use of genetic engineering to increase lint yield by inducing more epidermal cells to develop into lint rather than fuzz fibers.

The roles of AaMIXTA1 in regulating the initiation of glandular trichomes and cuticle biosynthesis in Artemisia annua

The glandular secretory trichomes (GSTs) on Artemisia annua leaves have the capacity to secrete and store artemisinin, a compound which is the most effective treatment for uncomplicated malaria. An effective strategy to improve artemisinin content is therefore to increase the density of GSTs in A. annua. However, the formation mechanism of GSTs remains poorly understood. To explore the mechanisms of GST initiation in A. annua, we screened myeloblastosis (MYB) transcription factor genes from a GST transcriptome database and identified a MIXTA transcription factor, AaMIXTA1, which is expressed predominantly in the basal cells of GST in A. annua. Overexpression and repression of AaMIXTA1 resulted in an increase and decrease, respectively, in the number of GSTs as well as the artemisinin content in transgenic plants. Transcriptome analysis and cuticular lipid profiling showed that AaMIXTA1 is likely to be responsible for activating cuticle biosynthesis. In addition, dual-luciferase reporter assays further demonstrated that AaMIXTA1 could directly activate the expression of genes related to cuticle biosynthesis. Taken together, AaMIXTA1 regulated cuticle biosynthesis and prompted GST initiation without any abnormal impact on the morphological structure of the GSTs and so provides a new way to improve artemisinin content in this important medicinal plant.

TRANSPARENT TESTA GLABRA 1-Dependent Regulation of Flavonoid Biosynthesis

The flavonoid composition of various tissues throughout plant development is of biological relevance and particular interest for breeding. Arabidopsis thaliana TRANSPARENT TESTA GLABRA 1 (AtTTG1) is an essential regulator of late structural genes in flavonoid biosynthesis. Here, we provide a review of the regulation of the pathway's core enzymes through AtTTG1-containing R2R3-MYELOBLASTOSIS-basic HELIX-LOOP-HELIX-WD40 repeat (MBW(AtTTG1)) complexes embedded in an evolutionary context. We present a comprehensive collection of A. thalianattg1 mutants and AtTTG1 orthologs. A plethora of MBW(AtTTG1) mechanisms in regulating the five major TTG1-dependent traits is highlighted.

Candidate regulators of Early Leaf Development in Maize Perturb Hormone Signalling and Secondary Cell Wall Formation When Constitutively Expressed in Rice

All grass leaves are strap-shaped with a series of parallel veins running from base to tip, but the distance between each pair of veins, and the cell-types that develop between them, differs depending on whether the plant performs C₃ or C₄ photosynthesis. As part of a multinational effort to introduce C₄ traits into rice to boost crop yield, candidate regulators of C₄ leaf anatomy were previously identified through an analysis of maize leaf transcriptomes. Here we tested the potential of 60 of those candidate genes to alter leaf anatomy in rice. In each case, transgenic rice lines were generated in which the maize gene was constitutively expressed. Lines grouped into three phenotypic classes: (1) indistinguishable from wild-type; (2) aberrant shoot and/or root growth indicating possible perturbations to hormone homeostasis; and (3) altered secondary cell wall formation. One of the genes in class 3 defines a novel monocot-specific family. None of the genes were individually sufficient to induce C₄-like vein patterning or cell-type differentiation in rice. A better understanding of gene function in C₄ plants is now needed to inform more sophisticated engineering attempts to alter leaf anatomy in C₃ plants.

Diversification of R2R3-MYB Transcription Factors in the Tomato Family Solanaceae

MYB transcription factors play an important role in regulating key plant developmental processes involving defense, cell shape, pigmentation, and root formation. Within this gene family, sequences containing an R2R3 MYB domain are the most abundant type and exhibit a wide diversity of functions. In this study, we identify 559 R2R3 MYB genes using whole genome data from four species of Solanaceae and reconstruct their evolutionary relationships. We compare the Solanaceae R2R3 MYBs to the well-characterized Arabidopsis thaliana sequences to estimate functional diversity and to identify gains and losses of MYB clades in the Solanaceae. We identify numerous R2R3 MYBs that do not appear closely related to Arabidopsis MYBs, and thus may represent clades of genes that have been lost along the Arabidopsis lineage or gained after the divergence of Rosid and Asterid lineages. Despite differences in the distribution of R2R3 MYBs across functional subgroups and species, the overall size of the R2R3 subfamily has changed relatively little over the roughly 50 million-year history of Solanaceae. We added our information regarding R2R3 MYBs in Solanaceae to other data and performed a meta-analysis to trace the evolution of subfamily size across land plants. The results reveal many shifts in the number of R2R3 genes, including a 54 % increase along the angiosperm stem lineage. The variation in R2R3 subfamily size across land plants is weakly positively correlated with genome size and strongly positively correlated with total number of genes. The retention of such a large number of R2R3 copies over long evolutionary time periods suggests that they have acquired new functions and been maintained by selection. Discovering the nature of this functional diversity will require integrating forward and reverse genetic approaches on an -omics scale.

Small interfering RNAs from bidirectional transcripts of GhMML3_A12 regulate cotton fiber development

Natural antisense transcripts (NATs) are commonly observed in eukaryotic genomes, but only a limited number of such genes have been identified as being involved in gene regulation in plants. In this research, we investigated the function of small RNA derived from a NAT in fiber cell development. Using a map-based cloning strategy for the first time in tetraploid cotton, we cloned a naked seed mutant gene (N1 ) encoding a MYBMIXTA-like transcription factor 3 (MML3)/GhMYB25-like in chromosome A12, GhMML3_A12, that is associated with fuzz fiber development. The extremely low expression of GhMML3_A12 in N1 is associated with NAT production, driven by its 3' antisense promoter, as indicated by the promoter-driven histochemical staining assay. In addition, small RNA deep sequencing analysis suggested that the bidirectional transcriptions of GhMML3_A12 form double-stranded RNAs and generate 21-22 nt small RNAs. Therefore, in a fiber-specific manner, small RNA derived from the GhMML3_A12 locus can mediate GhMML3_A12 mRNA self-cleavage and result in the production of naked seeds followed by lint fiber inhibition in N1 plants. The present research reports the first observation of gene-mediated NATs and siRNA directly controlling fiber development in cotton.

Gene networks controlling petal organogenesis

One of the biggest unanswered questions in developmental biology is how growth is controlled. Petals are an excellent organ system for investigating growth control in plants: petals are dispensable, have a simple structure, and are largely refractory to environmental perturbations that can alter their size and shape. In recent studies, a number of genes controlling petal growth have been identified. The overall picture of how such genes function in petal organogenesis is beginning to be elucidated. This review will focus on studies using petals as a model system to explore the underlying gene networks that control organ initiation, growth, and final organ morphology.

Adaptation in flower form: a comparative evodevo approach

Evolutionary developmental biology (evodevo) attempts to explain how the process of organismal development evolves, utilizing a comparative approach to investigate changes in developmental pathways and processes that occur during the evolution of a given lineage. Evolutionary genetics uses a population approach to understand how organismal changes in form or function are linked to underlying genetics, focusing on changes in gene and genotype frequencies within populations and the fixation of genotypic variation into traits that define species or evoke speciation events. Microevolutionary processes, including mutation, genetic drift, natural selection and gene flow, can provide the foundation for macroevolutionary patterns observed as morphological evolution and adaptation. The temporal element linking microevolutionary processes to macroevolutionary patterns is development: an organism's genotype is converted to phenotype by ontogenetic processes. Because selection acts upon the phenotype, the connection between evolutionary genetics and developmental evolution becomes essential to understanding adaptive evolution in organismal form and function. Here, we discuss how developmental genetic studies focused on key developmental processes could be linked within a comparative framework to study the developmental genetics of adaptive evolution, providing examples from research on two key processes of plant evodevo - floral symmetry and organ fusion - and their role in the adaptation of floral form.

The Phenotypic and Genetic Underpinnings of Flower Size in Polemoniaceae

Corolla length is a labile flower feature and has strong implications for pollinator success. However, the phenotypic and genetic bases of corolla elongation are not well known, largely due to a lack of good candidate genes for potential genetic exploration and functional work. We investigate both the cellular phenotypic differences in corolla length, as well as the genetic control of this trait, in Saltugilia (Polemoniaceae). Taxa in this clade exhibit a large range of flower sizes and differ dramatically in pollinator guilds. Flowers of each species were collected from multiple individuals during four stages of flower development to ascertain if cell number or cell size is more important in determining flower size. In Saltugilia, increased flower size during development appears to be driven more by cell size than cell number. Differences in flower size between species are governed by both cell size and cell number, with the large-flowered S. splendens subsp. grantii having nearly twice as many cells as the small-flowered species. Fully mature flowers of all taxa contain jigsaw cells similar to cells seen in sepals and leaves; however, these cells are not typically found in the developing flowers of most species. The proportion of this cell type in mature flowers appears to have substantial implications, comprising 17-68% of the overall flower size. To identify candidate genes responsible for differences in cell area and cell type, transcriptomes were generated for two individuals of the species with the smallest (S. australis) and largest (S. splendens subsp. grantii) flowers across the same four developmental stages visualized with confocal microscopy. Analyses identified genes associated with cell wall formation that are up-regulated in the mature flower stage compared to mid-stage flowers (75% of mature size). This developmental change is associated with the origin of jigsaw cells in the corolla tube of mature flowers. Further comparisons between mature flowers in the two species revealed 354 transcripts that are up-regulated in the large-flowered S. splendens subsp. grantii compared to the small-flowered S. australis. These results are likely broadly applicable to Polemoniaceae, a clade of nearly 400 species, with extensive variation in floral form and shape.

Genome-wide identification and characterisation of R2R3-MYB genes in sugar beet (Beta vulgaris)

BACKGROUND

The R2R3-MYB genes comprise one of the largest transcription factor gene families in plants, playing regulatory roles in plant-specific developmental processes, metabolite accumulation and defense responses. Although genome-wide analysis of this gene family has been carried out in some species, the R2R3-MYB genes in Beta vulgaris ssp. vulgaris (sugar beet) as the first sequenced member of the order Caryophyllales, have not been analysed heretofore.

RESULTS

We present a comprehensive, genome-wide analysis of the MYB genes from Beta vulgaris ssp. vulgaris (sugar beet) which is the first species of the order Caryophyllales with a sequenced genome. A total of 70 R2R3-MYB genes as well as genes encoding three other classes of MYB proteins containing multiple MYB repeats were identified and characterised with respect to structure and chromosomal organisation. Also, organ specific expression patterns were determined from RNA-seq data. The R2R3-MYB genes were functionally categorised which led to the identification of a sugar beet-specific clade with an atypical amino acid composition in the R3 domain, putatively encoding betalain regulators. The functional classification was verified by experimental confirmation of the prediction that the R2R3-MYB gene Bv_iogq encodes a flavonol regulator.

CONCLUSIONS

This study provides the first step towards cloning and functional dissection of the role of MYB transcription factor genes in the nutritionally and evolutionarily interesting species B. vulgaris. In addition, it describes the flavonol regulator BvMYB12, being the first sugar beet R2R3-MYB with an experimentally proven function.

Gene regulation networks generate diverse pigmentation patterns in plants

The diversity of pigmentation patterns observed in plants occurs due to the spatial distribution and accumulation of colored compounds, which may also be associated with structural changes to the tissue. Anthocyanins are flavonoids that provide red/purple/blue coloration to plants, often forming complex patterns such as spots, stripes, and vein-associated pigmentation, particularly in flowers. These patterns are determined by the activity of MYB-bHLH-WDR (MBW) transcription factor complexes, which activate the anthocyanin biosynthesis genes, resulting in anthocyanin pigment accumulation. Recently, we established that the MBW complex controlling anthocyanin synthesis acts within a gene regulation network that is conserved within at least the Eudicots. This network involves hierarchy, reinforcement, and feedback mechanisms that allow for stringent and responsive regulation of the anthocyanin biosynthesis genes. The gene network and mobile nature of the WDR and R3-MYB proteins provide exciting new opportunities to explore the basis of pigmentation patterning, and to investigate the evolutionary history of the MBW components in land plants.

Bulk segregant analysis of an induced floral mutant identifies a MIXTA-like R2R3 MYB controlling nectar guide formation in Mimulus lewisii

The genetic and developmental basis of many ecologically important floral traits (e.g., carotenoid pigmentation, corolla tube structure, nectar volume, pistil and stamen length) remains poorly understood. Here we analyze a chemically induced floral mutant of Mimulus lewisii through bulk segregant analysis and transgenic experiments and identify a MIXTA-like R2R3 MYB gene that controls nectar guide formation in M. lewisii flowers, which involves epidermal cell development and carotenoid pigmentation.