Genomic expression profiling of mature soybean (Glycine max) pollen

Small but powerful: RALF peptides in plant adaptive and developmental responses

Plants live in a highly dynamic environment and require to rapidly respond to a plethora of environmental stimuli, so that to maintain their optimal growth and development. A small plant peptide, rapid alkalization factor (RALF), can rapidly increase the pH value of the extracellular matrix in plant cells. RALFs always function with its corresponding receptors. Mechanistically, effective amount of RALF is induced and released at the critical period of plant growth and development or under different external environmental factors. Recent studies also highlighted the role of RALF peptides as important regulators in plant intercellular communications, as well as their operation in signal perception and as ligands for different receptor kinases on the surface of the plasma membrane, to integrate various environmental cues. In this context, understanding the fine-print of above processes may be essential to solve the problems of crop adaptation to various harsh environments under current climate trends scenarios, by genetic means. This paper summarizes the current knowledge about the structure and diversity of RALF peptides and their roles in plant development and response to stresses, highlighting unanswered questions and problems to be solved.

Identifying long non-coding RNAs involved in heat stress response during wheat pollen development

Introduction

Wheat is a staple food crop for over one-third of the global population. However, the stability of wheat productivity is threatened by heat waves associated with climate change. Heat stress at the reproductive stage can result in pollen sterility and failure of grain development.

Methods

This study used transcriptome data analysis to explore the specific expression of long non-coding RNAs (lncRNAs) in response to heat stress during pollen development in four wheat cultivars.

Results and discussion

We identified 11,054 lncRNA-producing loci, of which 5,482 lncRNAs showed differential expression in response to heat stress. Heat-responsive lncRNAs could target protein-coding genes in cis and trans and in lncRNA-miRNA-mRNA regulatory networks. Gene ontology analysis predicted that target protein-coding genes of lncRNAs regulate various biological processes such as hormonal responses, protein modification and folding, response to stress, and biosynthetic and metabolic processes. We also noted some paired lncRNA/protein-coding gene modules and some lncRNA-miRNA-mRNA regulatory modules shared in two or more wheat cultivars. These modules were related to regulating plant responses to heat stress, such as heat-shock proteins and transcription factors, and protein domains, such as MADS-box, Myc-type, and Alpha crystallin/Hsp20 domain.

Conclusion

Our results provide the basic knowledge and molecular resources for future functional studies investigating wheat reproductive development under heat stress.

Genome-Wide Identification and Comparative Analysis of RALF Gene Family in Legume and Non-Legume Species

Rapid alkalinization factor (RALF) are small secreted peptide hormones that can induce rapid alkalinization in a medium. They act as signaling molecules in plants, playing a critical role in plant development and growth, especially in plant immunity. Although the function of RALF peptides has been comprehensively analyzed, the evolutionary mechanism of RALFs in symbiosis has not been studied. In this study, 41, 24, 17 and 12 RALFs were identified in Arabidopsis, soybean, Lotus and Medicago, respectively. A comparative analysis including the molecular characteristics and conserved motifs suggested that the RALF pre-peptides in soybean represented a higher value of isoelectric point and more conservative motifs/residues composition than other species. All 94 RALFs were divided into two clades according to the phylogenetic analysis. Chromosome distribution and synteny analysis suggested that the expansion of the RALF gene family in Arabidopsis mainly depended on tandem duplication, while segment duplication played a dominant role in legume species. The expression levels of most RALFs in soybean were significantly affected by the treatment of rhizobia. Seven GmRALFs are potentially involved in the release of rhizobia in the cortex cells. Overall, our research provides novel insights into the understanding of the role of the RALF gene family in nodule symbiosis.

How Do Pollen Allergens Sensitize?

Plant pollen is one of the main sources of allergens causing allergic diseases such as allergic rhinitis and asthma. Several allergens in plant pollen are panallergens which are also present in other allergen sources. As a result, sensitized individuals may also experience food allergies. The mechanism of sensitization and development of allergic inflammation is a consequence of the interaction of allergens with a large number of molecular factors that often are acting in a complex with other compounds, for example low-molecular-mass ligands, which contribute to the induction a type 2-driven response of immune system. In this review, special attention is paid not only to properties of allergens but also to an important role of their interaction with lipids and other hydrophobic molecules in pollen sensitization. The reactions of epithelial cells lining the nasal and bronchial mucosa and of other immunocompetent cells will also be considered, in particular the mechanisms of the activation of B and T lymphocytes and the formation of allergen-specific antibody responses.

Genome-Wide Identification and Analysis of Ariadne Gene Family Reveal Its Genetic Effects on Agronomic Traits of Brassica napus

E3 ligases promote protein ubiquitination and degradation, which regulate every aspect of eukaryotic life. The Ariadne (ARI) proteins of RBR (ring between ring fingers) protein subfamily has been discovered as a group of potential E3 ubiquitin ligases. Only a few available research studies show their role in plant adaptations processes against the external environment. Presently, the functions of ARI proteins are largely unknown in plants. Therefore, in this study, we performed genome-wide analysis to identify the ARI gene family and explore their potential importance in B. napus. A total of 39 ARI genes were identified in the B. napus genome and were classified into three subfamilies (A, B and C) based on phylogenetic analysis. The protein–protein interaction networks and enrichment analysis indicated that BnARI genes could be involved in endoreduplication, DNA repair, proteasome assembly, ubiquitination, protein kinase activity and stress adaptation. The transcriptome data analysis in various tissues provided us an indication of some BnARI genes’ functional importance in tissue development. We also identified potential BnARI genes that were significantly responsive towards the abiotic stresses. Furthermore, eight BnARI genes were identified as candidate genes for multiple agronomic traits through association mapping analysis in B. napus; among them, BnaA02g12100D, which is the ortholog of AtARI8, was significantly associated with ten agronomic traits. This study provided useful information on BnARI genes, which could aid targeted functional research and genetic improvement for breeding in B. napus.

Circular RNAs Repertoire and Expression Profile during Brassica rapa Pollen Development

Circular RNAs (circRNAs) are covalently closed RNA molecules generated by the back-splicing of exons from linear precursor mRNAs. Though various linear RNAs have been shown to play important regulatory roles in many biological and developmental processes, little is known about the role of their circular counterparts. In this study, we performed high-throughput RNA sequencing to delineate the expression profile and potential function of circRNAs during the five stages of pollen development in Brassica rapa. A total of 1180 circRNAs were detected in pollen development, of which 367 showed stage-specific expression patterns. Functional enrichment and metabolic pathway analysis showed that the parent genes of circRNAs were mainly involved in pollen-related molecular and biological processes such as mitotic and meiotic cell division, DNA processes, protein synthesis, protein modification, and polysaccharide biosynthesis. Moreover, by predicting the circRNA–miRNA network from our differentially expressed circRNAs, we found 88 circRNAs with potential miRNA binding sites, suggesting their role in post-transcriptional regulation of the genes. Finally, we confirmed the back-splicing sites of nine selected circRNAs using divergent primers and Sanger sequencing. Our study presents the systematic analysis of circular RNAs during pollen development and forms the basis of future studies for unlocking complex gene regulatory networks underpinning reproduction in flowering plants.

A Rapid Pipeline for Pollen- and Anther-Specific Gene Discovery Based on Transcriptome Profiling Analysis of Maize Tissues

Recently, crop breeders have widely adopted a new biotechnology-based process, termed Seed Production Technology (SPT), to produce hybrid varieties. The SPT does not produce nuclear male-sterile lines, and instead utilizes transgenic SPT maintainer lines to pollinate male-sterile plants for propagation of nuclear-recessive male-sterile lines. A late-stage pollen-specific promoter is an essential component of the pollen-inactivating cassette used by the SPT maintainers. While a number of plant pollen-specific promoters have been reported so far, their usefulness in SPT has remained limited. To increase the repertoire of pollen-specific promoters for the maize community, we conducted a comprehensive comparative analysis of transcriptome profiles of mature pollen and mature anthers against other tissue types. We found that maize pollen has much less expressed genes (>1 FPKM) than other tissue types, but the pollen grain has a large set of distinct genes, called pollen-specific genes, which are exclusively or much higher (100 folds) expressed in pollen than other tissue types. Utilizing transcript abundance and correlation coefficient analysis, 1215 mature pollen-specific (MPS) genes and 1009 mature anther-specific (MAS) genes were identified in B73 transcriptome. These two gene sets had similar GO term and KEGG pathway enrichment patterns, indicating that their members share similar functions in the maize reproductive process. Of the genes, 623 were shared between the two sets, called mature anther- and pollen-specific (MAPS) genes, which represent the late-stage pollen-specific genes of the maize genome. Functional annotation analysis of MAPS showed that 447 MAPS genes (71.7% of MAPS) belonged to genes encoding pollen allergen protein. Their 2-kb promoters were analyzed for cis-element enrichment and six well-known pollen-specific cis-elements (AGAAA, TCCACCA, TGTGGTT, [TA]AAAG, AAATGA, and TTTCT) were found highly enriched in the promoters of MAPS. Interestingly, JA-responsive cis-element GCC box (GCCGCC) and ABA-responsive cis-element-coupling element1 (ABRE-CE1, CCACC) were also found enriched in the MAPS promoters, indicating that JA and ABA signaling likely regulate pollen-specific MAPS expression. This study describes a robust and straightforward pipeline to discover pollen-specific promotes from publicly available data while providing maize breeders and the maize industry a number of late-stage (mature) pollen-specific promoters for use in SPT for hybrid breeding and seed production.

Plasma membrane H+ -ATPases-mediated cytosolic proton gradient regulates pollen tube growth

The polar growth of pollen tubes is essential for the delivery of sperm cells during fertilization in angiosperms. How this polar growth is regulated has been a long-standing question. An in vitro pharmacological assay previously implicated proton flux in pollen tube growth, although genetic and cellular supporting evidence was lacking. Here, we report that protons form a gradient from the pollen tube tip to the shank region and this gradient is generated by three members of Arabidopsis H⁺ -ATPases (AHAs). Genetic analysis suggested that these AHAs are essential for pollen tube growth, thus providing new insight into the regulation of polar growth.

Grape terpenoids: flavor importance, genetic regulation, and future potential

Terpenes significantly affect the flavor and quality of grapes and wine. This review summarizes recent research on terpenoids with regard to grape wine. Although, the grapevine terpene synthase gene family is the largest identified, genetic modifications involving terpenes to improve wine flavor have received little attention. Key enzyme modulation alters metabolite production. Over the last decade, the heterologous manipulation of grape glycosidase has been used to alter terpenoids, and cytochrome P450s may affect terpene synthesis. Metabolic and genetic engineering can further modify terpenoid metabolism, while using transgenic grapevines (trait transfer to the plant) could yield more flavorful wine. We also discuss traits involved in wine aroma quality, and the strategies that can be used to improve grapevine breeding technology.

Roy C, Munshi JL, A. Jahan MA. In vitro Micro Propagation of Soybean (Glycine max) BARI-5 Variety

Introduction:

The present research work was undertaken with a view to developing a suitable protocol for in vitro plant regeneration of economically important plant (Glycine max) (Bangladesh Agricultural Research Institute BARI- 5) variety, via both direct and indirect organogenesis from in vitro grown seedlings.

Methods:

For micropropagation explants were cultured on MS and half strength Murashige and Skoog (MS) medium supplemented with various plant growth regulators (cytokinins and auxins). In the present study for inducting of callus, among 3 different hormone combinations, the suitable medium was 3.32 mg/L 2, 4-D containing MS medium and the callus was deep green in color. Different type of media like MS, 1/2 MS and MS with different (6-Benzyl Amino Purine) BAP concentration was used for seed germination of Glycine max. 100% of seed germination was observed in MS +1 mg/L BAP containing the medium.

Results:

In the present investigation, different concentration of cytokinins and auxins{BAP, 2, 4-D, and Naphthalene Acetic Acid (NAA)} were used individually or in combinations with MS medium to observe their effect on multiple shoot regeneration from the cotyledonary nodal segment. 100% shoot formation from cotyledonary nodal segment was recorded in 1.5 mg/L BAP and 0.15 mg/L BAP + 0.025 mg/L NAA containing MS medium, the best number of shoot was 10.9±2.0 found in MS + 1.5 mg/L BAP containing medium and highest length of shoot was 2 cm recorded in 1.5 mg/L BAP + 0.3 mg/L (different concentrations of Giberrellic acid) GA3 containing MS medium. In addition, for root induction in vitro raised well developed and elongated shoots were excised and cultured on MS and 1/2 MS medium supplemented with various concentration of Indole-3-Butyric acid (IBA). It was observed that MS medium containing 0.1 mg/L IBA and 1/2 MS medium containing 0.25 mg/L IBA was optimal for root induction. In which 100% shoots rooted well within 13 days of culture. The highest average number of roots per shoot was 6 recorded in MS +0.5 mg/L IBA containing the medium and highest average length of root was 8 cm recorded in 0.1 mg/L IBA containing MS medium.

Conclusion:

The most effective surface sterilization treatment for explants of Glycine max has been found in 0.1% HgCl2 solution for 15 minutes.

Overlapping Patterns of Gene Expression Between Gametophyte and Sporophyte Phases in the Fern Polypodium amorphum (Polypodiales)

Ferns are unique among land plants in having sporophyte and gametophyte phases that are both free living and fully independent. Here, we examine patterns of sporophytic and gametophytic gene expression in the fern Polypodium amorphum, a member of the homosporous polypod lineage that comprises 80% of extant fern diversity, to assess how expression of a common genome is partitioned between two morphologically, ecologically, and nutritionally independent phases. Using RNA-sequencing, we generated transcriptome profiles for three replicates of paired samples of sporophyte leaf tissue and whole gametophytes to identify genes with significant differences in expression between the two phases. We found a nearly 90% overlap in the identity and expression levels of the genes expressed in both sporophytes and gametophytes, with less than 3% of genes uniquely expressed in either phase. We compare our results to those from similar studies to establish how phase-specific gene expression varies among major land plant lineages. Notably, despite having greater similarity in the identity of gene families shared between P. amorphum and angiosperms, P. amorphum has phase-specific gene expression profiles that are more like bryophytes and lycophytes than seed plants. Our findings suggest that shared patterns of phase-specific gene expression among seed-free plants likely reflect having relatively large, photosynthetic gametophytes (compared to the gametophytes of seed plants that are highly reduced). Phylogenetic analyses were used to further investigate the evolution of phase-specific expression for the phototropin, terpene synthase, and MADS-box gene families.

A novel role of the soybean clock gene LUX ARRHYTHMO in male reproductive development

The evening complex of ELF4-ELF3-LUX proteins is an integral component of a plant circadian clock. LUX ARRHYTHMO (LUX) is one of the key components of the evening complex, and that play a key role in circadian rhythms and flowering. Here, we report that diverged soybean LUX has the additional role in male reproductive development. We studied diurnal and circadian rhythms of soybean LUX (GmLUXa, GmLUXb, and GmLUXc) using qRT-PCR, and show its nuclear localisation by particle bombardment. Yeast-two hybrid (Y2H) studies indicate that both GmLUXb and GmLUXc form an evening complex with GmELF4b and GmELF3a, respectively. Ectopic expression of GmLUXb in Arabidopsis lux mutants can complement functions of AtLUX, whereas GmLUXc generates novel phenotypes of serrated leaves, stunted plants, shortened anther filament, and low seed set. Overall, our results suggest that the LUX gene has diverged in soybean where GmLUXb and GmLUXc share the role to control flowering time, but GmLUXc has evolved to regulate anther filament growth and seed set by regulating the Gibberellin hormone biosynthesis pathway.

In Vitro Plant Regeneration from Commercial Cultivars of Soybean

Soybean, a major legume crop, is the source of vegetable oil and protein. There is a need for transgenic approaches to breeding superior soybean varieties to meet future climate challenges. Efficient plant regeneration is a prerequisite for successful application of genetic transformation technology. Soybean cultivars are classified into different maturity groups based on photoperiod requirements. In this study, nine soybean varieties belonging to different maturity group were regenerated successfully from three different explants: half split hypocotyl, complete hypocotyl, and cotyledonary node. All the genotypes and explant types responded by producing adventitious shoots. Shoot induction potential ranged within 60-87%, 50-100%, and 75-100%, and regeneration rate ranged within 4.2-10, 2.7-4.2, and 2.6-10.5 shoots per explant using half split hypocotyl, complete hypocotyl, and cotyledonary explants, respectively, among all the tested genotypes. Bunya variety showed the best regeneration response using half split and complete hypocotyl explants and the PNR791 with cotyledonary node. The regenerated shoots were successfully rooted and acclimatized to glasshouse conditions. This study shows that commercial varieties of soybean are amenable to shoot regeneration with high regeneration frequencies and could be exploited for genetic transformation. Further, our results show no correlation between shoots regeneration capacity with the maturity grouping of the soybean cultivars tested.

Transcriptomes of Plant Gametophytes Have a Higher Proportion of Rapidly Evolving and Young Genes than Sporophytes

Reproductive traits in plants tend to evolve rapidly due to various causes that include plant-pollinator coevolution and pollen competition, but the genomic basis of reproductive trait evolution is still largely unknown. To characterize evolutionary patterns of genome wide gene expression in reproductive tissues in the gametophyte and to compare them to developmental stages of the sporophyte, we analyzed evolutionary conservation and genetic diversity of protein-coding genes using microarray-based transcriptome data from three plant species, Arabidopsis thaliana, rice (Oryza sativa), and soybean (Glycine max). In all three species a significant shift in gene expression occurs during gametogenesis in which genes of younger evolutionary age and higher genetic diversity contribute significantly more to the transcriptome than in other stages. We refer to this phenomenon as "evolutionary bulge" during plant reproductive development because it differentiates the gametophyte from the sporophyte. We show that multiple, not mutually exclusive, causes may explain the bulge pattern, most prominently reduced tissue complexity of the gametophyte, a varying extent of selection on reproductive traits during gametogenesis as well as differences between male and female tissues. This highlights the importance of plant reproduction for understanding evolutionary forces determining the relationship of genomic and phenotypic variation in plants.

Digital Gene Expression Analysis of Populus simonii × P. nigra Pollen Germination and Tube Growth

Pollen tubes are an ideal model for the study of cell growth and morphogenesis because of their extreme elongation without cell division; however, the genetic basis of pollen germination and tube growth remains largely unknown. Using the Illumina/Solexa digital gene expression system, we identified 13,017 genes (representing 28.3% of the unigenes on the reference genes) at three stages, including mature pollen, hydrated pollen, and pollen tubes of Populus simonii × P. nigra. Comprehensive analysis of P. simonii × P. nigra pollen revealed dynamic changes in the transcriptome during pollen germination and pollen tube growth (PTG). Gene ontology analysis of differentially expressed genes showed that genes involved in functional categories such as catalytic activity, binding, transporter activity, and enzyme regulator activity were overrepresented during pollen germination and PTG. Some highly dynamic genes involved in pollen germination and PTG were detected by clustering analysis. Genes related to some key pathways such as the mitogen-activated protein kinase signaling pathway, regulation of the actin cytoskeleton, calcium signaling, and ubiquitin-mediated proteolysis were significantly changed during pollen germination and PTG. These data provide comprehensive molecular information toward further understanding molecular mechanisms underlying pollen germination and PTG.

Bioinformatics resources for pollen

Bioinformatics for Pollen. Pollen plays a key role in crop production, and its development is the most delicate phase in reproduction. Different metabolic pathways are involved in pollen development, and changes in the level of some metabolites, as well as responses to stress, are correlated with the reduction in pollen viability, leading consequently to a decrease in the fruit production. However, studies on pollen may be hard because gamete development and fertilization are complex processes that occur during a short window of time. The rise of the so-called -omics sciences provided key strategies to promote molecular research in pollen tissues, starting from model organisms and moving to increasing number of species. An integrated multi-level approach based on investigations from genomics, transcriptomics, proteomics and metabolomics appears now feasible to clarify key molecular processes in pollen development and viability. To this aim, bioinformatics has a fundamental role for data production and analysis, contributing varied and ad hoc methodologies, endowed with different sensitivity and specificity, necessary for extracting added-value information from the large amount of molecular data achievable. Bioinformatics is also essential for data management, organization, distribution and integration in suitable resources. This is necessary to catch the biological features of the pollen tissues and to design effective approaches to identifying structural or functional properties, enabling the modeling of the major involved processes in normal or in stress conditions. In this review, we provide an overview of the available bioinformatics resources for pollen, ranging from raw data collections to complete databases or platforms, when available, which include data and/or results from -omics efforts on the male gametophyte. Perspectives in the fields will also be described.

Acclimation to high temperature during pollen development

KEY MESSAGE

Pollen heat acclimation. As a consequence of global warming, plants have to face more severe and more frequently occurring periods of high temperature stress. While this affects the whole plant, development of the male gametophyte, the pollen, seems to be the most sensitive process. Given the great importance of functioning pollen for the plant life cycle and for agricultural production, it is necessary to understand this sensitivity. While changes in temperature affect different components of all cells and require a cellular response and acclimation, high temperature effects and responses in developing pollen are distinct from vegetative tissues at several points. This could be related to specific physiological characteristics of developing pollen and supporting tissues which make them vulnerable to high temperature, or its derived effects such as ROS accumulation and carbohydrate starvation. But also expression of heat stress-responsive genes shows unique patterns in developing pollen when compared to vegetative tissues that might explain the failure to withstand high temperatures. As an alternative to viewing pollen failure under high temperature as a result of inherent sensitivity of a specific developmental process, we end by discussing whether it might actually be an adaptation.

Role of Lipid Metabolism in Plant Pollen Exine Development

Pollen plays important roles in the life cycle of angiosperms plants. It acts as not only a biological protector of male sperms but also a communicator between the male and the female reproductive organs, facilitating pollination and fertilization. Pollen is produced within the anther, and covered by the specialized outer envelope, pollen wall. Although the morphology of pollen varies among different plant species, the pollen wall is mainly comprised of three layers: the pollen coat, the outer exine layer, and the inner intine layer. Except the intine layer, the other two layers are basically of lipidic nature. Particularly, the outer pollen wall layer, the exine, is a highly resistant biopolymer of phenylpropanoid and lipidic monomers covalently coupled by ether and ester linkages. The precise molecular mechanisms underlying pollen coat formation and exine patterning remain largely elusive. Herein, we summarize the current genetic, phenotypic and biochemical studies regarding to the pollen exine development and underlying molecular regulatory mechanisms mainly obtained from monocot rice (Oryza sativa) and dicot Arabidopsis thaliana, aiming to extend our understandings of plant male reproductive biology. Genes, enzymes/proteins and regulatory factors that appear to play conserved and diversified roles in lipid biosynthesis, transportation and modification during pollen exine formation, were highlighted.

Exploration of rice pistil responses during early post-pollination through a combined proteomic and transcriptomic analysis

Pollen-stigma interaction is a multi-step and complex physiological process which contains different signaling and biochemical pathways. However, little is known about the molecular mechanism underlying this process in rice (Oryza sativa). In this study, the changes of gene expression were investigated through a combination study of transcriptome and proteome profiles in rice pistil during pollination. Totally, 1117 differentially expressed genes were identified, among which 962 and 167 were detected at transcriptional and protein level respectively. Functional categorization analysis showed that the genes involved in central metabolism were up-regulated, which can lead to the enhancement of these metabolisms. The reactive oxygen species (ROS) were over-accumulated in the stigma. In response to this, the proteins or transcripts involved in redox homeostasis regulation were differentially expressed. Furthermore, significant changes of protein ubiquitination and its related genes or proteins, especially some E3 ligases encoding genes, indicate that protein ubiquitination might play important roles in cell signal transduction during the pollination process. Our study sheds some lights on gene and protein expression profiles of rice pistil pollination process, and gives us a comprehensive understanding of the basic molecular mechanisms controlling pollination in rice.

BIOLOGICAL SIGNIFICANCE

Using RNA-seq, 2-DE and iTRAQ assays, we have generated the large-scale transcriptomic and proteomic data containing abundant information on genes involved in pollen and pistil interaction. Our results showed that ROS were significantly accumulated in stigma after pollination, and the abundance of genes involve in redox homeostasis system were changed variously. We also show that, changes of some E3 ligases encoding genes might indicate that protein ubiquitination play important roles in cell signal transduction during the pollination process. Data in this study might be helpful to deeply understand the pollination in rice.

A decade of pollen transcriptomics

KEY MESSAGE

Overview of pollen transcriptome studies. Pollen development is driven by gene expression, and knowledge of the molecular events underlying this process has undergone a quantum leap in the last decade through studies of the transcriptome. Here, we outline historical evidence for male haploid gene expression and review the wealth of pollen transcriptome data now available. Knowledge of the transcriptional capacity of pollen has progressed from genetic studies to the direct analysis of RNA and from gene-by-gene studies to analyses on a genomic scale. Microarray and/or RNA-seq data can now be accessed for all phases and cell types of developing pollen encompassing 10 different angiosperms. These growing resources have accelerated research and will undoubtedly inspire new directions and the application of system-based research into the mechanisms that govern the development, function and evolution of angiosperm pollen.

De novo sequencing and analysis of the lily pollen transcriptome: an open access data source for an orphan plant species

Pollen grains of Lilium longiflorum are a long-established model system for pollen germination and tube tip growth. Due to their size, protein content and almost synchronous germination in synthetic media, they provide a simple system for physiological measurements as well as sufficient material for biochemical studies like protein purifications, enzyme assays, organelle isolation or determination of metabolites during germination and pollen tube elongation. Despite recent progresses in molecular biology techniques, sequence information of expressed proteins or transcripts in lily pollen is still scarce. Using a next generation sequencing strategy (RNAseq), the lily pollen transcriptome was investigated resulting in more than 50 million high quality reads with a length of 90 base pairs. Sequenced transcripts were assembled and annotated, and finally visualized with MAPMAN software tools and compared with other RNAseq or genome data including Arabidopsis pollen, Lilium vegetative tissues and the Amborella trichopoda genome. All lily pollen sequence data are provided as open access files with suitable tools to search sequences of interest.

The male germline of angiosperms: repertoire of an inconspicuous but important cell lineage

The male germline of flowering plants constitutes a specialized lineage of diminutive cells initiated by an asymmetric division of the initial microspore cell that sequesters the generative cell from the pollen vegetative cell. The generative cell subsequently divides to form the two male gametes (non-motile sperm cells) that fuse with the two female gametophyte target cells (egg and central cells) to form the zygote and endosperm. Although these male gametes can be as little as 1/800th of the volume of their female counterpart, they encode a highly distinctive and rich transcriptome, translate proteins, and display a novel suite of gamete-distinctive control elements that create a unique chromatin environment in the male lineage. Sperm-expressed transcripts also include a high proportion of transposable element-related sequences that may be targets of non-coding RNA including miRNA and silencing elements from peripheral cells. The number of sperm-encoded transcripts is somewhat fewer than the number present in the egg cell, but are remarkably distinct compared to other cell types according to principal component and other analyses. The molecular role of the male germ lineage cells is just beginning to be understood and appears more complex than originally anticipated.

Proteomics Advances in the Understanding of Pollen-Pistil Interactions

The first key point to the successful pollination and fertilization in plants is the pollen-pistil interaction, referring to the cellular and molecular levels, which mainly involve the haploid pollen and the diploid pistil. The process is defined as “siphonogamy”, which starts from the capture of pollen by the epidermis of stigma and ends up with the fusion of sperm with egg. So far, the studies of the pollen-pistil interaction have been explicated around the self-compatibility and self-incompatibility (SI) process in different species from the molecular genetics and biochemistry to cellular and signal levels, especially the mechanism of SI system. Among them, numerous proteomics studies based on the advanced technologies from gel-system to gel-free system were conducted, focusing on the interaction, in order to uncover the mechanism of the process. The current review mainly focuses on the recent developments in proteomics of pollen-pistil interaction from two aspects: self-incompatible and compatible pollination. It might provide a comprehensive insight on the proteins that were involved in the regulation of pollen-pistil interaction.

Analysis of phosphoproteome in rice pistil

As the female reproductive part of a flower, the pistil consists of the ovary, style, and stigma, and is a critical organ for the process from pollen recognition to fertilization and seed formation. Previous studies on pollen-pistil interaction mainly focused on gene expression changes with comparative transcriptomics or proteomics method. However, studies on protein PTMs are still lacking. Here we report a phosphoproteomic study on mature pistil of rice. Using IMAC enrichment, hydrophilic interaction chromatography fraction and high-accuracy MS instrument (TripleTOF 5600), 2347 of high-confidence (Ascore ≥ 19, p ≤ 0.01), phosphorylation sites corresponding to 1588 phosphoproteins were identified. Among them, 1369 phosphorylation sites within 654 phosphoproteins were newly identified; 41 serine phosphorylation motifs, which belong to three groups: proline-directed, basophilic, and acidic motifs were identified after analysis by motif-X. Two hundred and one genes whose phosphopeptides were identified here showed tissue-specific expression in pistil based on information mining of previous microarray data. All MS data have been deposited in the ProteomeXchange with identifier PXD000923 (http://proteomecentral.proteomexchange.org/dataset/PXD000923). This study will help us to understand pistil development and pollination on the posttranslational level.

A pollen-specific calmodulin-binding protein, NPG1, interacts with putative pectate lyases

Previous genetic studies have revealed that a pollen-specific calmodulin-binding protein, No Pollen Germination 1 (NPG1), is required for pollen germination. However, its mode of action is unknown. Here we report direct interaction of NPG1 with pectate lyase-like proteins (PLLs). A truncated form of AtNPG1 lacking the N-terminal tetratricopeptide repeat 1 (TPR1) failed to interact with PLLs, suggesting that it is essential for NPG1 interaction with PLLs. Localization studies with AtNPG1 fused to a fluorescent reporter driven by its native promoter revealed its presence in the cytosol and cell wall of the pollen grain and the growing pollen tube of plasmolyzed pollen. Together, our data suggest that the function of NPG1 in regulating pollen germination is mediated through its interaction with PLLs, which may modify the pollen cell wall and regulate pollen tube emergence and growth.

The meiotic transcriptome architecture of plants

Although a number of genes that play key roles during the meiotic process have been characterized in great detail, the whole process of meiosis is still not completely unraveled. To gain insight into the bigger picture, large-scale approaches like RNA-seq and microarray can help to elucidate the transcriptome landscape during plant meiosis, discover co-regulated genes, enriched processes, and highly expressed known and unknown genes which might be important for meiosis. These high-throughput studies are gaining more and more popularity, but their beginnings in plant systems reach back as far as the 1960's. Frequently, whole anthers or post-meiotic pollen were investigated, while less data is available on isolated cells during meiosis, and only few studies addressed the transcriptome of female meiosis. For this review, we compiled meiotic transcriptome studies covering different plant species, and summarized and compared their key findings. Besides pointing to consistent as well as unique discoveries, we finally draw conclusions what can be learned from these studies so far and what should be addressed next.

A new link between stress response and nucleolar function during pollen development in Arabidopsis mediated by AtREN1 protein

Heat shock transcription factors (Hsfs) are involved in multiple aspects of stress response and plant growth. However, their role during male gametophyte development is largely unknown, although the generative phase is the most sensitive and critical period in the plant life cycle. Based on a wide screen of T-DNA mutant lines, we identified the atren1 mutation (restricted to nucleolus1) in early male gametophytic gene At1g77570, which has the closest homology to HSFA5 gene, the member of a heat shock transcription factor (HSF) gene family. The mutation causes multiple defects in male gametophyte development in both structure and function. Because the mutation disrupts an early acting (AtREN1) gene, these pollen phenotype abnormalities appear from bicellular pollen stage to pollen maturation. Moreover, the consequent progamic phase is compromised as well as documented by pollen germination defects and limited transmission via male gametophyte. In addition, atren1/- plants are defective in heat stress (HS) response and produce notably higher proportion of aberrant pollen grains. AtREN1 protein is targeted specifically to the nucleolus that, together with the increased size of the nucleolus in atren1 pollen, suggests that it is likely to be involved in ribosomal RNA biogenesis or other nucleolar functions.

Dynamic adaption of metabolic pathways during germination and growth of lily pollen tubes after inhibition of the electron transport chain

Investigation of the metabolome and the transcriptome of pollen of lily (Lilium longiflorum) gave a comprehensive overview of metabolic pathways active during pollen germination and tube growth. More than 100 different metabolites were determined simultaneously by gas chromatography coupled to mass spectrometry, and expressed genes of selected metabolic pathways were identified by next-generation sequencing of lily pollen transcripts. The time-dependent changes in metabolite abundances, as well as the changes after inhibition of the mitochondrial electron transport chain, revealed a fast and dynamic adaption of the metabolic pathways in the range of minutes. The metabolic state prior to pollen germination differed clearly from the metabolic state during pollen tube growth, as indicated by principal component analysis of all detected metabolites and by detailed observation of individual metabolites. For instance, the amount of sucrose increased during the first 60 minutes of pollen culture but decreased during tube growth, while glucose and fructose showed the opposite behavior. Glycolysis, tricarbonic acid cycle, glyoxylate cycle, starch, and fatty acid degradation were activated, providing energy during pollen germination and tube growth. Inhibition of the mitochondrial electron transport chain by antimycin A resulted in an immediate production of ethanol and a fast rearrangement of metabolic pathways, which correlated with changes in the amounts of the majority of identified metabolites, e.g. a rapid increase in γ-aminobutyric acid indicated the activation of a γ-aminobutyric acid shunt in the tricarbonic acid cycle, while ethanol fermentation compensated the reduced ATP production after inhibition of the oxidative phosphorylation.

Selection is no more efficient in haploid than in diploid life stages of an angiosperm and a moss

The masking hypothesis predicts that selection is more efficient in haploids than in diploids, because dominant alleles can mask the deleterious effects of recessive alleles in diploids. However, gene expression breadth and noise can potentially counteract the effect of masking on the rate at which genes evolve. Land plants are ideal to ask whether masking, expression breadth, or expression noise dominate in their influence on the rate of molecular evolution, because they have a biphasic life cycle in which the duration and complexity of the haploid and diploid phase varies among organisms. Here, we generate and compile genome-wide gene expression, sequence divergence, and polymorphism data for Arabidopsis thaliana and for the moss Funaria hygrometrica to show that the evolutionary rates of haploid- and diploid-specific genes contradict the masking hypothesis. Haploid-specific genes do not evolve more slowly than diploid-specific genes in either organism. Our data suggest that gene expression breadth influence the evolutionary rate of phase-specific genes more strongly than masking. Our observations have implications for the role of haploid life stages in the purging of deleterious mutations, as well as for the evolution of ploidy.

Pollen transcriptome analysis of Solanum tuberosum (2n = 4x = 48), S. demissum (2n = 6x = 72), and their reciprocal F1 hybrids

Pollen mRNAs were different in reciprocal F 1 hybrids, which were probably caused by a cytoplasm-nuclear chromosomal genes interaction. We have found reciprocal differences in crossability between F1 hybrids of Solanum tuberosum (T) and a Mexican wild potato species S. demissum (D). When the reciprocal hybrids were crossed as pollen parents with S. demissum, a significantly higher berry-setting rate was obtained in TD compared with DT. In this study, we performed a whole-genome transcript analysis of the pollen mRNA using a high-throughput sequencer. We obtained 12.6 billion bases that were aligned into 13,020 transcripts with 9,366 loci. All possible genetic modes were observed between the parents and their progeny, where over-dominance and under-recessive types were relatively frequent (15.7 and 15.3 %, respectively). We found that 59.1 % of transcripts were more abundant in TD and over fourfold higher transcription levels were found in 66 TD transcripts and three DT transcripts. A higher proportion of over-dominance and a lower proportion of under-recessive transcription types were also observed in TD. The percentage contributions of multiple transcripts at the same locus varied greatly and were transcribed differently between species. In the new allelic combinations created by hybridization, approximately three-fourth of the transcripts had intermediate percentage contributions between the parents but no differential transcription patterns were apparent between the reciprocal hybrids. A broad spectrum of functionally different nuclear genes was over-represented in TD pollen, some of which were directly related to pollen behavior. Since TD and DT pollen had the same composition of nuclear genes, a cytoplasm-nuclear chromosomal genes interaction is suggested for the cause of transcriptional and phenotypic differences between reciprocal hybrids.

Molecular and immunological characterization of ragweed (Ambrosia artemisiifolia L.) pollen after exposure of the plants to elevated ozone over a whole growing season

Climate change and air pollution, including ozone is known to affect plants and might also influence the ragweed pollen, known to carry strong allergens. We compared the transcriptome of ragweed pollen produced under ambient and elevated ozone by 454-sequencing. An enzyme-linked immunosorbent assay (ELISA) was carried out for the major ragweed allergen Amb a 1. Pollen surface was examined by scanning electron microscopy and attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR), and phenolics were analysed by high-performance liquid chromatography. Elevated ozone had no influence on the pollen size, shape, surface structure or amount of phenolics. ATR-FTIR indicated increased pectin-like material in the exine. Transcriptomic analyses showed changes in expressed-sequence tags (ESTs), including allergens. However, ELISA indicated no significantly increased amounts of Amb a 1 under elevated ozone concentrations. The data highlight a direct influence of ozone on the exine components and transcript level of allergens. As the total protein amount of Amb a 1 was not altered, a direct correlation to an increased risk to human health could not be derived. Additional, the 454-sequencing contributes to the identification of stress-related transcripts in mature pollen that could be grouped into distinct gene ontology terms.

Gene, protein, and network of male sterility in rice

Rice is one of the most important model crop plants whose heterosis has been well-exploited in commercial hybrid seed production via a variety of types of male-sterile lines. Hybrid rice cultivation area is steadily expanding around the world, especially in Southern Asia. Characterization of genes and proteins related to male sterility aims to understand how and why the male sterility occurs, and which proteins are the key players for microspores abortion. Recently, a series of genes and proteins related to cytoplasmic male sterility (CMS), photoperiod-sensitive male sterility, self-incompatibility, and other types of microspores deterioration have been characterized through genetics or proteomics. Especially the latter, offers us a powerful and high throughput approach to discern the novel proteins involving in male-sterile pathways which may help us to breed artificial male-sterile system. This represents an alternative tool to meet the critical challenge of further development of hybrid rice. In this paper, we reviewed the recent developments in our understanding of male sterility in rice hybrid production across gene, protein, and integrated network levels, and also, present a perspective on the engineering of male-sterile lines for hybrid rice production.

Comparative proteomic analyses reveal the changes of metabolic features in soybean (Glycine max) pistils upon pollination

Siphonogamy is a critical process in plant reproductive growth, during which numerous cell-cell interaction events occur between pistil and pollen. Previous studies in Solanaceae, Papaveraceae, and Brassicaceae focusing on pollen-stigma recognition in self-incompatible systems have provided many important views. In this study, we profiled the proteome in soybean mature pistils before and after pollination. Comparative analyses of two-dimensional gel electrophoresis maps from un-pollinated and pollinated pistils were conducted. The results showed that 22 proteins were increased and 36 proteins decreased after pollination. Functional categorization showed that most of them were metabolism- and redox-related proteins. The enhancement of primary metabolism, biosynthesis of pollen tube guidance compounds, and adjustment of redox homeostasis system might be helpful for a successful pollination. Quantitative reverse transcript-polymerase chain reaction analysis implied that the regulation of gene expression might happen at both transcriptional and posttranscriptional levels during pollination. This study will enhance our understanding of pollen-stigma interaction in plant sexual reproductive growth.

Brachypodium distachyon as a model for defining the allergen potential of non-prolamin proteins

Epitope databases and the protein sequences of published plant genomes are suitable to identify some of the proteins causing food allergies and sensitivities. Brachypodium distachyon, a diploid wild grass with a sequenced genome and low prolamin content, is the closest relative of the allergen cereals, such as wheat or barley. Using the Brachypodium genome sequence, a workflow has been developed to identify potentially harmful proteins which may cause either celiac disease or wheat allergy-related symptoms. Seed tissue-specific expression of the potential allergens has been determined, and intact epitopes following an in silico digestion with several endopeptidases have been identified. Molecular function of allergen proteins has been evaluated using Gene Ontology terms. Biologically overrepresented proteins and potentially allergen protein families have been identified.

Evolution of the RALF Gene Family in Plants: Gene Duplication and Selection Patterns

Rapid alkalinization factors (RALFs) are plant small peptides that could induce a rapid pH increase in the medium of plant cell suspension culture and play a critical role in plant development. The evolutionary process of the RALF gene family remains unclear. To obtain details of the phylogeny of these genes, this study characterized RALF genes in Arabidopsis, rice, poplar and maize. Phylogenetic trees, evolutionary patterns and molecular evolutionary rates were used to elucidate the evolutionary process of this gene family. In addition, the different signatures of selection, expression patterns, and subcellular localization of RALFs were also analyzed. We found that the RALF gene family had a rapid birth process after the separation of the eudicot and monocot species about 145 million years ago, that tandem duplication played a dominant role in the expansion of Arabidopsis and rice RALF gene family, and that RALFs were under purifying selection according to estimations of the substitution rates of these genes. We also identified a diverse expression pattern of RALF genes and predominant extracellular localization feature of RALF proteins. Our findings shed light on several key differences in RALF gene family evolution among the plant species, which may provide a scaffold for future functional analysis of this family.

Analysis of plant germline development by high-throughput RNA profiling: technical advances and new insights

Reproduction is a crucial step in the life cycle of plants. The male and female germline lineages develop in the reproductive organs of the flower, which in higher plants are the anthers and ovules, respectively. Development of the germline lineage initiates from a dedicated sporophytic cell that undergoes meiosis to form spores that subsequently give rise to the gametophytes through mitotic cell divisions. The mature male and female gametophytes harbour the male (sperm cells) and female gametes (egg and central cell), respectively. Those unite during double fertilization to initiate embryo and endosperm development in sexually reproducing higher plants. While cytological changes involved in development of the germline lineages have been well characterized in a number of species, investigation of the transcriptional basis underlying their development and the specification of the gametes proved challenging. This is largely due to the inaccessibility of the cells constituting the germline lineages, which are enclosed by sporophytic tissues. Only recently, these technical limitations could be overcome by combining new methods to isolate the relevant cells with powerful transcriptional profiling methods, such as microarrays or high-throughput sequencing of RNA. This review focuses on these technical advances and the new insights gained from them concerning the transcriptional basis and molecular mechanisms underlying germline development.

Comprehensive analysis of tobacco pollen transcriptome unveils common pathways in polar cell expansion and underlying heterochronic shift during spermatogenesis

BACKGROUND

Many flowering plants produce bicellular pollen. The two cells of the pollen grain are destined for separate fates in the male gametophyte, which provides a unique opportunity to study genetic interactions that govern guided single-cell polar expansion of the growing pollen tube and the coordinated control of germ cell division and sperm cell fate specification. We applied the Agilent 44 K tobacco gene chip to conduct the first transcriptomic analysis of the tobacco male gametophyte. In addition, we performed a comparative study of the Arabidopsis root-hair trichoblast transcriptome to evaluate genetic factors and common pathways involved in polarized cell-tip expansion.

RESULTS

Progression of pollen grains from freshly dehisced anthers to pollen tubes 4 h after germination is accompanied with > 5,161 (14.9%) gametophyte-specific expressed probes active in at least one of the developmental stages. In contrast, > 18,821 (54.4%) probes were preferentially expressed in the sporophyte. Our comparative approach identified a subset of 104 pollen tube-expressed genes that overlap with root-hair trichoblasts. Reverse genetic analysis of selected candidates demonstrated that Cu/Zn superoxide dismutase 1 (CSD1), a WD-40 containing protein (BP130384), and Replication factor C1 (NtRFC1) are among the central regulators of pollen-tube tip growth. Extension of our analysis beyond the second haploid mitosis enabled identification of an opposing-dynamic accumulation of core regulators of cell proliferation and cell fate determinants in accordance with the progression of the germ cell cycle.

CONCLUSIONS

The current study provides a foundation to isolate conserved regulators of cell tip expansion and those that are unique for pollen tube growth to the female gametophyte. A transcriptomic data set is presented as a benchmark for future functional studies using developing pollen as a model. Our results demonstrated previously unknown functions of certain genes in pollen-tube tip growth. In addition, we highlighted the molecular dynamics of core cell-cycle regulators in the male gametophyte and postulated the first genetic model to account for the differential timing of spermatogenesis among angiosperms and its coordination with female gametogenesis.

Identification and exploration of pollen tube small proteins encoded by pollination-induced transcripts

Pollination is composed of cell-cell communication and complicated signaling cascades that regulate pollen tube growth and guidance toward the ovules for double fertilization, and is critical for successful sexual reproduction. Exploring expression profiles of in vivo grown pollen tubes is important. Nevertheless, it is difficult to obtain accessible pollen tubes for profiling studies in most model plants. By taking advantage of the hollow styles of lily (Lilium longiflorum), in vivo pollen tubes harvested from pollinated styles which had been cut open were used here to study their protein and transcript profiles. Pollination quantitatively and qualitatively altered the total protein composition of elongating pollen tubes. cDNAs generated and amplified from total RNAs of 24 h in vivo grown and 12 h in vitro cultured pollen tubes were used for suppression subtractive hybridization analyses and preparation of home-made array chips. Microarray analyses conducted with different probe sets revealed 16 transcripts specifically present and/or enriched in in vivo pollen tubes. Reverse transcription-PCR (RT-PCR), in situ hybridization and Northern blotting were applied to validate their unique pollination-induced expression features. Interestingly, several transcripts were simultaneously detected on the stylar transmitting tract epidermis, where in vivo pollen tubes tightly adhered during pollination. Their deduced amino acid sequences showed that most of them encoded small proteins and could be classified into several families. Transient assay revealed filament-like structures decorated by these proteins and one probably localized in the generative cell. These small peptides might be critical for pollen tube growth during pollination, and further exploration of their biological functions and mechanisms of action are of great interest.

Interspecific reproductive barriers in the tomato clade: opportunities to decipher mechanisms of reproductive isolation

The tomato clade within the genus Solanum has numerous advantages for mechanistic studies of reproductive isolation. Its thirteen closely related species, along with four closely allied Solanum species, provide a defined group with diverse mating systems that display complex interspecific reproductive barriers. Several kinds of pre- and postzygotic barriers have already been identified within this clade. Well-developed genetic maps, introgression lines, interspecific bridging lines, and the newly available draft genome sequence of the domesticated tomato (Solanum lycopersicum) are valuable tools for the genetic analysis of interspecific reproductive barriers. The excellent chromosome morphology of these diploid species allows detailed cytological analysis of interspecific hybrids. Transgenic methodologies, well developed in the Solanaceae, allow the functional testing of candidate reproductive barrier genes as well as live imaging of pollen rejection events through the use of fluorescently tagged proteins. Proteomic and transcriptomics approaches are also providing new insights into the molecular nature of interspecific barriers. Recent progress toward understanding reproductive isolation mechanisms using these molecular and genetic tools is assessed in this review.

Computational identification of root hair-specific genes in Arabidopsis

Activated cortical domains (ACDs) are regions of the plant cell cortex performing localized membrane turnover, delimited by concerted action of the cortical cytoskeleton and endomembrane compartments. Arabidopsis thaliana rhizodermis consists of two cell types differing by a single ACD (trichoblasts, carrying tip-growing root hairs, and hairless atrichoblasts), providing a model for the study of ACD determination. We compiled a set of genes specifically upregulated in root hairs from published transcriptome data, and compared it with a "virtual Arabidopsis root hair proteome", i.e. a list of computationally identified homologs of proteins from the published soybean root hair proteome. Both data sets were enriched in genes and proteins associated with root hairs in functional studies, but there was little overlap between the transcriptome and the proteome: the former captured gene products specific to root hairs, while the latter selected those abundant in root hairs but not necessarily specific to them. Decisive steps in ACD specification may be performed by signaling proteins of high expression specifity and low abundance. Nevertheless, 73 genes specifically transcribed in Arabidopsis trichoblasts or root hairs encode homologs of abundant root hair proteins from soybean. Most of them encode "housekeeping" proteins required for rapid tip growth. However, among the "candidates" is also a generative actin isoform, ACT11. Preliminary characterization of an act11 mutant allele indeed suggests a hitherto unexpected role for this gene in root and root hair development.

Diversification and Specialization of Plant RBR Ubiquitin Ligases

Background

RBR ubiquitin ligases are components of the ubiquitin-proteasome system present in all eukaryotes. They are characterized by having the RBR (RING – IBR – RING) supradomain. In this study, the patterns of emergence of RBR genes in plants are described.

Methodology/Principal Findings

Phylogenetic and structural data confirm that just four RBR subfamilies (Ariadne, ARA54, Plant I/Helicase and Plant II) exist in viridiplantae. All of them originated before the split that separated green algae from the rest of plants. Multiple genes of two of these subfamilies (Ariadne and Plant II) appeared in early plant evolution. It is deduced that the common ancestor of all plants contained at least five RBR genes and the available data suggest that this number has been increasing slowly along streptophyta evolution, although losses, especially of Helicase RBR genes, have also occurred in several lineages. Some higher plants (e. g. Arabidopsis thaliana, Oryza sativa) contain a very large number of RBR genes and many of them were recently generated by tandem duplications. Microarray data indicate that most of these new genes have low-level and sometimes specific expression patterns. On the contrary, and as occurs in animals, a small set of older genes are broadly expressed at higher levels.

Conclusions/Significance

The available data suggests that the dynamics of appearance and conservation of RBR genes is quite different in plants from what has been described in animals. In animals, an abrupt emergence of many structurally diverse RBR subfamilies in early animal history, followed by losses of multiple genes in particular lineages, occurred. These patterns are not observed in plants. It is also shown that while both plants and animals contain a small, similar set of essential RBR genes, the rest evolves differently. The functional implications of these results are discussed.

Dramatic change in function and expression pattern of a gene duplicated by polyploidy created a paternal effect gene in the Brassicaceae

New gene formation by polyploidy has been an ongoing process during the evolution of various eukaryotes that has contributed greatly to the large number of genes in their genomes. After duplication, some genes that are retained can acquire new functions or expression patterns, or subdivide their functions or expression patterns between duplicates. Here, we show that SHORT SUSPENSOR (SSP) and Brassinosteroid Kinase 1 (BSK1) are paralogs duplicated by a polyploidy event that occurred in the Brassicaceae family about 23 Ma. SSP is involved in paternal control of zygote elongation in Arabidopsis thaliana by transcription in the sperm cells of pollen and then translation in the zygote, whereas BSK1 is involved in brassinosteroid signal transduction. Comparative analysis of expression in 63 different organs and developmental stages revealed that BSK1 and SSP have opposite expression patterns in pollen compared with all other parts of the plant. We determined that BSK1 retains the ancestral expression pattern and function. Thus, SSP has diverged in function after duplication from a component of the brassinosteroid signaling pathway to a paternal regulator of the timing of zygote elongation. The ancestral function of SSP was lost by deletions in the kinase domain. Our sequence rate analysis revealed that SSP but not BSK1 has experienced a greatly accelerated rate of amino acid sequence changes and relaxation of purifying selection. In addition, SSP has been duplicated to create a new gene (SSP-like1) with a completely different expression pattern, a shorter coding sequence that has lost a critical functional domain, and a greatly accelerated rate of amino acid sequence evolution along with evidence for positive selection, together indicative of neofunctionalization. This study illustrates two dramatic examples of neofunctionalization following gene duplication by complete changes in expression pattern and function. In addition, our findings indicate that paternal control of zygote elongation by SSP is an evolutionarily recent innovation in the Brassicaceae family.

Transcriptomes of the desiccation-tolerant resurrection plant Craterostigma plantagineum

Studies of the resurrection plant Craterostigma plantagineum have revealed some of the mechanisms which these desiccation-tolerant plants use to survive environments with extreme dehydration and restricted seasonal water. Most resurrection plants are polyploid with large genomes, which has hindered efforts to obtain whole genome sequences and perform mutational analysis. However, the application of deep sequencing technologies to transcriptomics now permits large-scale analyses of gene expression patterns despite the lack of a reference genome. Here we use pyro-sequencing to characterize the transcriptomes of C. plantagineum leaves at four stages of dehydration and rehydration. This reveals that genes involved in several pathways, such as those required for vitamin K and thiamin biosynthesis, are tightly regulated at the level of gene expression. Our analysis also provides a comprehensive picture of the array of cellular responses controlled by gene expression that allow resurrection plants to survive desiccation.

Genome-scale analysis and comparison of gene expression profiles in developing and germinated pollen in Oryza sativa

Background

Pollen development from the microspore involves a series of coordinated cellular events, and the resulting mature pollen has a specialized function to quickly germinate, produce a polar-growth pollen tube derived from the vegetative cell, and deliver two sperm cells into the embryo sac for double fertilization. The gene expression profiles of developing and germinated pollen have been characterised by use of the eudicot model plant Arabidopsis. Rice, one of the most important cereal crops, has been used as an excellent monocot model. A comprehensive analysis of transcriptome profiles of developing and germinated pollen in rice is important to understand the conserved and diverse mechanism underlying pollen development and germination in eudicots and monocots.

Results

We used Affymetrix GeneChip^® Rice Genome Array to comprehensively analyzed the dynamic changes in the transcriptomes of rice pollen at five sequential developmental stages from microspores to germinated pollen. Among the 51,279 transcripts on the array, we found 25,062 pollen-preferential transcripts, among which 2,203 were development stage-enriched. The diversity of transcripts decreased greatly from microspores to mature and germinated pollen, whereas the number of stage-enriched transcripts displayed a "U-type" change, with the lowest at the bicellular pollen stage; and a transition of overrepresented stage-enriched transcript groups associated with different functional categories, which indicates a shift in gene expression program at the bicellular pollen stage. About 54% of the now-annotated rice F-box protein genes were expressed preferentially in pollen. The transcriptome profile of germinated pollen was significantly and positively correlated with that of mature pollen. Analysis of expression profiles and coexpressed features of the pollen-preferential transcripts related to cell cycle, transcription, the ubiquitin/26S proteasome system, phytohormone signalling, the kinase system and defense/stress response revealed five expression patterns, which are compatible with changes in major cellular events during pollen development and germination. A comparison of pollen transcriptomes between rice and Arabidopsis revealed that 56.6% of the rice pollen preferential genes had homologs in Arabidopsis genome, but 63.4% of these homologs were expressed, with a small proportion being expressed preferentially, in Arabidopsis pollen. Rice and Arabidopsis pollen had non-conservative transcription factors each.

Conclusions

Our results demonstrated that rice pollen expressed a set of reduced but specific transcripts in comparison with vegetative tissues, and the number of stage-enriched transcripts displayed a "U-type" change during pollen development, with the lowest at the bicellular pollen stage. These features are conserved in rice and Arabidopsis. The shift in gene expression program at the bicellular pollen stage may be important to the transition from earlier cell division to later pollen maturity. Pollen at maturity pre-synthesized transcripts needed for germination and early pollen tube growth. The transcription regulation associated with pollen development would have divergence between the two species. Our results also provide novel insights into the molecular program and key components of the regulatory network regulating pollen development and germination.

Haploids in flowering plants: origins and exploitation

The first haploid angiosperm, a dwarf form of cotton with half the normal chromosome complement, was discovered in 1920, and in the ninety years since then such plants have been identified in many other species. They can occur either spontaneously or can be induced by modified pollination methods in vivo, or by in vitro culture of immature male or female gametophytes. Haploids represent an immediate, one-stage route to homozygous diploids and thence to F(1) hybrid production. The commercial exploitation of heterosis in such F(1) hybrids leads to the development of hybrid seed companies and subsequently to the GM revolution in agriculture. This review describes the range of techniques available for the isolation or induction of haploids and discusses their value in a range of areas, from fundamental research on mutant isolation and transformation, through to applied aspects of quantitative genetics and plant breeding. It will also focus on how molecular methods have been used recently to explore some of the underlying aspects of this fascinating developmental phenomenon.

Cloning and expression analysis of a pollen preferential rapid alkalinization factor gene, BoRALF1, from broccoli flowers

Rapid alkalinization factors (RALFs) are recently reported active peptide hormones and are considered to play important roles in plant development. We previously identified a differentially expressed cDNA fragment between cabbage flower buds of sterility lines and its maintainer line, which showed significant homology to Arabidopsis RALFL9. The novel RALF cDNA (BoRALF1) was isolated from broccoli flower buds by EST assembly. The open reading frame (ORF) comprises 240 bp, encoding a small putative preprotein of 79 amino acids (molecular weight of 8.72 kDa and a pI of 7.8), which contains the mature polypeptide at its C terminus. BoRALF1 shares 70.3% identity with Arabidopsis RALFL9, but has only moderate similarity with functionally characterized RALFs (ranging from 16.2% to 38.0%). BoRALF1 shows typical features of RALFs, including the 28-aa signal peptide, typical arrangement of four position conserved cysteines, the YIXY motif and a similar secondary structure. RT-PCR studies of different tissues and promoter-GUS fusions confirmed that BoRALF1 is expressed strictly in mature pollen grains and in the anther cells around the loculi. Based on in vivo transient assays, we found that BoRALF1 appears to be largely localized in the plasma membrane. Although the function of BoRALF1 remains to be determined, our experiments confirm the presence of RALF peptide in broccoli, and suggest it could have a role in anther or pollen development.

Floral initiation process at the soybean shoot apical meristem may involve multiple hormonal pathways

Flowering and seed set underpin most of the agriculture production. In the 57 Issue of The Plant Journal, we analysed the gene expression changes in the shoot apical meristem (SAM) during the transition from vegetative to flowering phase in soybean, an important legume crop. We identified a number of genes that are actively transcribed or repressed during the transition to flowering and the annotation of which have allowed us to infer the involvement of at least three hormonal pathways: those that involve abscisic acid (ABA), auxin and jasmonic acid (JA) in the regulation of floral initiation process in soybean. Intriguingly, the induction of known floral homeiotic transcript that includes APETALA1 in the SAM occurred after the induction of these hormonal transcripts adding a likely novel biochemical dimension to the current understanding of floral regulatory pathways. In view of recent studies, a cross-regulatory mechanism involving these hormones is proposed to operate at the SAM to initiate flowering.