New technologies accelerate the exploration of non-coding RNAs in horticultural plants.

Non-coding RNAs (ncRNAs), that is, RNAs not translated into proteins, are crucial regulators of a variety of biological processes in plants. While protein-encoding genes have been relatively well-annotated in sequenced genomes, accounting for a small portion of the genome space in plants, the universe of plant ncRNAs is rapidly expanding. Recent advances in experimental and computational technologies have generated a great momentum for discovery and functional characterization of ncRNAs. Here we summarize the classification and known biological functions of plant ncRNAs, review the application of next-generation sequencing (NGS) technology and ribosome profiling technology to ncRNA discovery in horticultural plants and discuss the application of new technologies, especially the new genome-editing tool clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems, to functional characterization of plant ncRNAs

Third-codon transversion rate-based _Nymphaea_ basal angiosperm phylogeny -- concordance with developmental evidence

Flowering plants (angiosperms) appeared on Earth rather suddenly approximately 130 million years ago and underwent a massive expansion in the subsequent 10-12 million years. Current molecular phylogenies have predominantly identified _Amborella_, followed by _Nymphaea_ (water lilies) or _Amborella_ plus _Nymphaea_, in the ANITA clade (_Amborella_, Nymphaeales, Illiciaceae, Trimeniaceae and Austrobaileyaceae) as the earliest angiosperm. However, developmental studies suggest that the earliest angiosperm had a 4-cell/4-nucleus female gametophyte and a diploid endosperm represented by _Nymphaea_, suggesting that _Amborella_, having an 8-cell/9-nucleus female gametophyte and a triploid endosperm, cannot be representative of the basal angiosperm. This evolution-development discordance is possibly caused by erroneous inference based on phylogenetic signals with low neutrality and/or high saturation. Here we show that the 3rd codon transversion (P3Tv), with high neutrality and low saturation, is a robust high-resolution phylogenetic signal for such divergences and that the P3Tv-based land plant phylogeny cautiously identifies _Nymphaea_, followed by _Amborella_, as the most basal among the angiosperm species examined in this study. This P3Tv-based phylogeny contributes insights to the origin of angiosperms with concordance to fossil and stomata development evidence

MicroSyn: A user friendly tool for detection of microsynteny in a gene family

<p>Abstract</p> <p>Background</p> <p>The traditional phylogeny analysis within gene family is mainly based on DNA or amino acid sequence homologies. However, these phylogenetic tree analyses are not suitable for those "non-traditional" gene families like microRNA with very short sequences. For the normal protein-coding gene families, low bootstrap values are frequently encountered in some nodes, suggesting low confidence or likely inappropriateness of placement of those members in those nodes.</p> <p>Results</p> <p>We introduce MicroSyn software as a means of detecting microsynteny in adjacent genomic regions surrounding genes in gene families. MicroSyn searches for conserved, flanking colinear homologous gene pairs between two genomic fragments to determine the relationship between two members in a gene family. The colinearity of homologous pairs is controlled by a statistical distance function. As a result, gene duplication history can be inferred from the output independent of gene sequences. MicroSyn was designed for both experienced and non-expert users with a user-friendly graphical-user interface. MicroSyn is available from: <url>http://fcsb.njau.edu.cn/microsyn/</url>.</p> <p>Conclusions</p> <p>Case studies of the microRNA167 genes in plants and Xyloglucan ndotransglycosylase/Hydrolase family in <it>Populus trichocarpa </it>were presented to show the utility of the software. The easy using of MicroSyn in these examples suggests that the software is an additional valuable means to address the problem intrinsic in the computational methods and sequence qualities themselves in gene family analysis.</p

Comparative Genomics Analysis Provides New Insight Into Molecular Basis of Stomatal Movement in Kalanchoë fedtschenkoi

CO2 uptake and water loss in plants are regulated by microscopic pores on the surface of leaves, called stomata. This enablement of gas exchange by the opening and closing of stomata is one of the most essential processes in plant photosynthesis and transpiration, affecting water-use efficiency (WUE) and thus drought susceptibility. In plant species with crassulacean acid metabolism (CAM) photosynthesis, diel stomatal movement pattern is inverted relative to C3 and C4 photosynthesis species, resulting in much higher WUE and drought tolerance. However, little is known about the molecular basis of stomatal movement in CAM species. The goal of this study is to identify candidate genes that could play a role in stomatal movement in an obligate CAM species, Kalanchoë fedtschenkoi. By way of a text-mining approach, proteins were identified in various plant species, spanning C3, C4, and CAM photosynthetic types, which are orthologous to proteins known to be involved in stomatal movement. A comparative analysis of diel time-course gene expression data was performed between K. fedtschenkoi and two C3 species (i.e., Arabidopsis thaliana and Solanum lycopersicum) to identify differential gene expression between the dusk and dawn phases of the 24-h cycle. A rescheduled catalase gene known to be involved in stomatal movement was identified, suggesting a role for H2O2 in CAM-like stomatal movement. Overall, these results provide new insights into the molecular regulation of stomatal movement in CAM plants, facilitating genetic improvement of drought resistance in agricultural crops through manipulation of stomata-related genes

Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa

<p>Abstract</p> <p>Background</p> <p>Auxin/Indole-3-Acetic Acid (Aux/IAA) and Auxin Response Factor (ARF) transcription factors are key regulators of auxin responses in plants. We identified the suites of genes in the two gene families in <it>Populus </it>and performed comparative genomic analysis with <it>Arabidopsis </it>and rice.</p> <p>Results</p> <p>A total of 35 <it>Aux/IAA </it>and 39 <it>ARF </it>genes were identified in the <it>Populus </it>genome. Comparative phylogenetic analysis revealed that several Aux/IAA and ARF subgroups have differentially expanded or contracted between the two dicotyledonous plants. Activator <it>ARF </it>genes were found to be two fold-overrepresented in the <it>Populus </it>genome. <it>PoptrIAA </it>and <it>PoptrARF </it>gene families appear to have expanded due to high segmental and low tandem duplication events. Furthermore, expression studies showed that genes in the expanded <it>PoptrIAA3 </it>subgroup display differential expression.</p> <p>Conclusion</p> <p>The present study examines the extent of conservation and divergence in the structure and evolution of <it>Populus Aux/IAA </it>and <it>ARF </it>gene families with respect to <it>Arabidopsis </it>and rice. The gene-family analysis reported here will be useful in conducting future functional genomics studies to understand how the molecular roles of these large gene families translate into a diversity of biologically meaningful auxin effects.</p

Conservation and Diversification of Circadian Rhythmicity Between a Model Crassulacean Acid Metabolism Plant Kalanchoë fedtschenkoi and a Model C3 Photosynthesis Plant Arabidopsis thaliana

Crassulacean acid metabolism (CAM) improves photosynthetic efficiency under limited water availability relative to C3 photosynthesis. It is widely accepted that CAM plants have evolved from C3 plants and it is hypothesized that CAM is under the control of the internal circadian clock. However, the role that the circadian clock plays in the evolution of CAM is not well understood. To identify the molecular basis of circadian control over CAM evolution, rhythmic gene sets were identified in a CAM model plant species (Kalanchoë fedtschenkoi) and a C3 model plant species (Arabidopsis thaliana) through analysis of diel time-course gene expression data using multiple periodicity detection algorithms. Based on protein sequences, ortholog groups were constructed containing genes from each of these two species. The ortholog groups were categorized into five gene sets based on conservation and diversification of rhythmic gene expression. Interestingly, minimal functional overlap was observed when comparing the rhythmic gene sets of each species. Specifcally, metabolic processes were enriched in the gene set under circadian control in K. fedtschenkoi and numerous genes were found to have retained or gained rhythmic expression in K. fedtsechenkoi. Additonally, several rhythmic orthologs, including CAM-related orthologs, displayed phase shifts between species. Results of this analysis point to several mechanisms by which the circadian clock plays a role in the evolution of CAM. These genes provide a set of testable hypotheses for future experiments

Mechanisms of cadmium toxicity and tolerance in Populus

Abstract ID#: 26642&#xd;&#xa;Background and Methods:&#xd;&#xa;&#xd;&#xa;Cadmium (Cd), ranked the 7th most hazardous substance, is one of the most widespread pollutants of soil and water in industrialized nations. Its increased movement in soil-plant systems is posing a serious threat to human health. Cd, without any known functions in plants, was found to be toxic even at minute concentrations, leading to the development of symptoms such as leaf roll, chlorosis and root and shoot growth reduction. Phytoremediation is an emerging cost-effective and environment friendly technology that utilizes high biomass producing plants including Populus plants to remove, transform or stabilize contaminants in soils. The objectives of our study were to record phenotypic variation in a Populus pedigree to Cd exposure, to identify Cd tolerant and susceptible genotypes of Populus, to map QTLs (Quantitative Trait Loci - genomic regions responsible) for Cd tolerance and accumulation in Populus and to predict a mechanism for Cd toxicity and tolerance in susceptible and tolerant Populus genotypes.&#xd;&#xa;&#xd;&#xa;QTL mapping was accomplished by conducting a greenhouse hydroponic study in which 252 genotypes of a Populus pseudo-backcross progeny were grown for 40 days and treated with 25 &#xb5;M Cd. Phenotypic variation in total dry weight was recorded on these genotypes and was used for identifying QTL for Cd tolerance. We identified genotypes with contrasting responses to the Cd treatment and conducted a microarray study to identify potential Cd tolerance mechanisms based on gene expression patterns.&#xd;&#xa;&#xd;&#xa; &#xd;&#xa;&#xd;&#xa;Results/Conclusions:&#xd;&#xa;&#xd;&#xa;Significant variation was observed among genotypes in response to Cd treatment based on changes in total dry weight. Cd tolerant and susceptible genotypes were identified based on the least square mean differences (Control-Cd treated for each genotype) among all the genotypes. Three QTLs were identified for Cd tolerance and they accounted for approximately 25% of the phenotypic variation in Cd tolerance measured as total dry weights.&#xd;&#xa;&#xd;&#xa;In the microarray study, the Cd-susceptible genotype had higher expression of Fe-transporters compared to the tolerant genotypes, and Cd and Fe levels were significantly different in foliage. Even the susceptible genotype controls had higher, though not significant, Fe levels than tolerant genotype controls. We therefore hypothesize that part of the mechanism for Cd tolerance is determined by the differences in the activity of Fe transporters in genotypes with differential Fe homeostasis

Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon

Abstract Background Glycoside hydrolases cleave the bond between a carbohydrate and another carbohydrate, a protein, lipid or other moiety. Genes encoding glycoside hydrolases are found in a wide range of organisms, from archea to animals, and are relatively abundant in plant genomes. In plants, these enzymes are involved in diverse processes, including starch metabolism, defense, and cell-wall remodeling. Glycoside hydrolase genes have been previously cataloged for Oryza sativa (rice), the model dicotyledonous plant Arabidopsis thaliana, and the fast-growing tree Populus trichocarpa (poplar). To improve our understanding of glycoside hydrolases in plants generally and in grasses specifically, we annotated the glycoside hydrolase genes in the grasses Brachypodium distachyon (an emerging monocotyledonous model) and Sorghum bicolor (sorghum). We then compared the glycoside hydrolases across species, at the levels of the whole genome and individual glycoside hydrolase families. Results We identified 356 glycoside hydrolase genes in Brachypodium and 404 in sorghum. The corresponding proteins fell into the same 34 families that are represented in rice, Arabidopsis, and poplar, helping to define a glycoside hydrolase family profile which may be common to flowering plants. For several glycoside hydrolase familes (GH5, GH13, GH18, GH19, GH28, and GH51), we present a detailed literature review together with an examination of the family structures. This analysis of individual families revealed both similarities and distinctions between monocots and eudicots, as well as between species. Shared evolutionary histories appear to be modified by lineage-specific expansions or deletions. Within GH families, the Brachypodium and sorghum proteins generally cluster with those from other monocots. Conclusions This work provides the foundation for further comparative and functional analyses of plant glycoside hydrolases. Defining the Brachypodium glycoside hydrolases sets the stage for Brachypodium to be a grass model for investigations of these enzymes and their diverse roles in planta. Insights gained from Brachypodium will inform translational research studies, with applications for the improvement of cereal crops and bioenergy grasses

Sphagnum physiology in the context of changing climate: emergent influences of genomics, modelling and host-microbiome interactions on understanding ecosystem function.

Peatlands harbour more than one-third of terrestrial carbon leading to the argument that the bryophytes, as major components of peatland ecosystems, store more organic carbon in soils than any other collective plant taxa. Plants of the genus Sphagnum are important components of peatland ecosystems and are potentially vulnerable to changing climatic conditions. However, the response of Sphagnum to rising temperatures, elevated CO2 and shifts in local hydrology have yet to be fully characterized. In this review, we examine Sphagnum biology and ecology and explore the role of this group of keystone species and its associated microbiome in carbon and nitrogen cycling using literature review and model simulations. Several issues are highlighted including the consequences of a variable environment on plant-microbiome interactions, uncertainty associated with CO2 diffusion resistances and the relationship between fixed N and that partitioned to the photosynthetic apparatus. We note that the Sphagnum fallax genome is currently being sequenced and outline potential applications of population-level genomics and corresponding plant photosynthesis and microbial metabolic modelling techniques. We highlight Sphagnum as a model organism to explore ecosystem response to a changing climate and to define the role that Sphagnum can play at the intersection of physiology, genetics and functional genomics

Fungal Endophytes of Populus trichocarpa Alter Host Phenotype, Gene Expression, and Rhizobiome Composition.

Mortierella and Ilyonectria genera include common species of soil fungi that are frequently detected as root endophytes in many plants, including Populus spp. However, the ecological roles of these and other endophytic fungi with respect to plant growth and function are still not well understood. The functional ecology of two key taxa from the P. trichocarpa rhizobiome, M. elongata PMI93 and I. europaea PMI82, was studied by coupling forest soil bioassays with environmental metatranscriptomics. Using soil bioassay experiments amended with fungal inoculants, M. elongata was observed to promote the growth of P. trichocarpa. This response was cultivar independent. In contrast, I. europaea had no visible effect on P. trichocarpa growth. Metatranscriptomic studies revealed that these fungi impacted rhizophytic and endophytic activities in P. trichocarpa and induced shifts in soil and root microbial communities. Differential expression of core genes in P. trichocarpa roots was observed in response to both fungal species. Expression of P. trichocarpa genes for lipid signaling and nutrient uptake were upregulated, and expression of genes associated with gibberellin signaling were altered in plants inoculated with M. elongata, but not I. europaea. Upregulation of genes for growth promotion, downregulation of genes for several leucine-rich repeat receptor kinases, and alteration of expression of genes associated with plant defense responses (e.g., jasmonic acid, salicylic acid, and ethylene signal pathways) also suggest that M. elongata manipulates plant defenses while promoting plant growth