The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention. We survey 141 sequenced plant genomes to elucidate consequences of gene and genome duplication, processes central to the evolution of biodiversity. We develop a pipeline named DupGen_finder to identify different modes of gene duplication in plants. Genes derived from whole-genome, tandem, proximal, transposed, or dispersed duplication differ in abundance, selection pressure, expression divergence, and gene conversion rate among genomes. The number of WGD-derived duplicate genes decreases exponentially with increasing age of duplication events—transposed duplication- and dispersed duplication-derived genes declined in parallel. In contrast, the frequency of tandem and proximal duplications showed no significant decrease over time, providing a continuous supply of variants available for adaptation to continuously changing environments. Moreover, tandem and proximal duplicates experienced stronger selective pressure than genes formed by other modes and evolved toward biased functional roles involved in plant self-defense. The rate of gene conversion among WGD-derived gene pairs declined over time, peaking shortly after polyploidization. To provide a platform for accessing duplicated gene pairs in different plants, we constructed the Plant Duplicate Gene Database. We identify a comprehensive landscape of different modes of gene duplication across the plant kingdom by comparing 141 genomes, which provides a solid foundation for further investigation of the dynamic evolution of duplicate genes.

/pdf/gene-duplication-and-evolution-in-recurring-polyploidization-1tk6fsc37e.pdf

Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants.

Pathogenesis of Pseudoperonospora cubensis causing downy mildew of cucumber resulted in changes in the metabolic processes within cucumber leaves including the transpiration rate. Due to the negative correlation between transpiration rate and leaf temperature, digital infrared thermography permitted a non-invasive monitoring and an indirect visualization of downy mildew development. Depending on the stage of pathogenesis and the topology of chloroses and necroses, infection resulted in a typical temperature pattern. Spatial heterogeneity of the leaf temperature could be quantified by the maximum temperature difference (MTD) within a leaf. The MTD increased during pathogenesis with the formation of necrotic tissue and was related to disease severity as described by linear and quadratic regression curves. Under controlled conditions, changes in temperature of infected leaves allowed the discrimination between healthy and infected areas in thermograms, even before visible symptoms of downy mildew appeared. Environmental conditions during thermographic measurement, in particular air temperature and humidity, as well as water content and age of the leaf influenced the temperature of its surface. Conditions enhancing the transpiration rate facilitated the detection of changes in leaf temperature of infected leaves at early stages of infection. As modified by environmental conditions, MTD alone is not suitable for the quantification of downy mildew severity in the field.

Thermal imaging of cucumber leaves affected by downy mildew and environmental conditions

A major problem facing humanity is that our numbers are growing but the availability of land and fresh water for agriculture is not. This problem is being exacerbated by climate change-induced increases in drought, and other abiotic stresses. Stress-resistant crops are needed to ensure yield stability under stress conditions and to minimize the environmental impacts of crop production. Evolution has created thousands of species of naturally stress-resistant plants (NSRPs), some of which have already been subjected to human domestication and are considered minor crops. Broader cultivation of these minor crops will diversify plant agriculture and the human diet, and will therefore help improve global food security and human health. More research should be directed toward understanding and utilizing NSRPs. Technologies are now available that will enable researchers to rapidly improve the genetics of NSRPs, with the goal of increasing NSRP productivity while retaining NSRP stress resistance and nutritional value. There are multiple strategies to fortify crop nutrition and support global food security and sustainable agriculture. Here the authors propose to increase the diversity of crops by devoting more efforts to studying minor crops that are naturally stress resistant.

Developing naturally stress-resistant crops for a sustainable agriculture.

R2R3-MYB transcription factors (TFs) belong to a large and functionally diverse protein superfamily in plants. In this study, we explore the evolution and function of this family in grapevine (Vitis vinifera L.), a high-value fruit crop. We identified and manually curated 134 genes using RNA-Seq data, and named them systematically according to the Super-Nomenclature Committee. We identified novel genes, splicing variants and grapevine/woody-specific duplicated subgroups, suggesting possible neo- and sub-functionalization events. Regulatory network analysis ascribed biological functions to uncharacterized genes and validated those of known genes (e.g. secondary cell wall biogenesis and flavonoid biosynthesis). A comprehensive analysis of different MYB binding motifs in the promoters of co-expressed genes predicted grape R2R3-MYB binding preferences and supported evidence for putative downstream targets. Enrichment of cis-regulatory motifs for diverse TFs reinforced the notion of transcriptional coordination and interaction between MYBs and other regulators. Analysis of the network of Subgroup 2 showed that the resveratrol-related VviMYB14 and VviMYB15 share common co-expressed STILBENE SYNTHASE genes with the uncharacterized VviMYB13. These regulators have distinct expression patterns within organs and in response to biotic and abiotic stresses, suggesting a pivotal role of VviMYB13 in regulating stilbene accumulation in vegetative tissues and under biotic stress conditions.

/pdf/a-systems-oriented-analysis-of-the-grapevine-r2r3-myb-4i88zcldhq.pdf

A systems-oriented analysis of the grapevine R2R3-MYB transcription factor family uncovers new insights into the regulation of stilbene accumulation

Emerging insights in buckwheat molecular genetics allow the integration of genomics driven breeding to revive this ancient crop of immense nutraceutical potential from Asia. Out of several thousand known edible plant species, only four crops-rice, wheat, maize and potato provide the largest proportion of daily nutrition to billions of people. While these crops are the primary supplier of carbohydrates, they lack essential amino acids and minerals for a balanced nutrition. The overdependence on only few crops makes the future cropping systems vulnerable to the predicted climate change. Diversifying food resources through incorporation of orphan or minor crops in modern cropping systems is one potential strategy to improve the nutritional security and mitigate the hostile weather patterns. One such crop is buckwheat, which can contribute to the agricultural sustainability as it grows in a wide range of environments, requires relatively low inputs and possess balanced amino acid and micronutrient profiles. Additionally, gluten-free nature of protein and nutraceutical properties of secondary metabolites make the crop a healthy alternative of wheat-based diet in developed countries. Despite enormous potential, efforts for the genetic improvement of buckwheat are considerably lagged behind the conventional cereal crops. With the draft genome sequences in hand, there is a great scope to speed up the progress of genetic improvement of buckwheat. This article outlines the state of the art in buckwheat research and provides concrete perspectives how modern breeding approaches can be implemented to accelerate the genetic gain. Our suggestions are transferable to many minor and underutilized crops to address the issue of limited genetic gain and low productivity.

Revisiting the versatile buckwheat: reinvigorating genetic gains through integrated breeding and genomics approach.

Buckwheat (Fagopyrum esculentum Moench; 2n = 2x = 16) is a nutritionally dense annual crop widely grown in temperate zones. To accelerate molecular breeding programmes of this important crop, we generated a draft assembly of the buckwheat genome using short reads obtained by next-generation sequencing (NGS), and constructed the Buckwheat Genome DataBase. After assembling short reads, we determined 387,594 scaffolds as the draft genome sequence (FES_r1.0). The total length of FES_r1.0 was 1,177,687,305 bp, and the N50 of the scaffolds was 25,109 bp. Gene prediction analysis revealed 286,768 coding sequences (CDSs; FES_r1.0_cds) including those related to transposable elements. The total length of FES_r1.0_cds was 212,917,911 bp, and the N50 was 1,101 bp. Of these, the functions of 35,816 CDSs excluding those for transposable elements were annotated by BLAST analysis. To demonstrate the utility of the database, we conducted several test analyses using BLAST and keyword searches. Furthermore, we used the draft genome as a reference sequence for NGS-based markers, and successfully identified novel candidate genes controlling heteromorphic self-incompatibility of buckwheat. The database and draft genome sequence provide a valuable resource that can be used in efforts to develop buckwheat cultivars with superior agronomic traits.

/pdf/assembly-of-the-draft-genome-of-buckwheat-and-its-pn31xuqbwh.pdf

Assembly of the draft genome of buckwheat and its applications in identifying agronomically useful genes.

Leaf browning induced at sites distant from wounds in Acanthaceae and Gesneriaceae plants

To evaluate the effect of wounding on the incidence of leaf browning to a sudden temperature drop, Ruellia macrantha, cuttings of a highly wound-sensitive Acanthaceae species, were briefly immersed in water (3-9°C lower than the leaf temperature for 3 sec). Leaf browning occurred in wounded plants but not in intact ones. The incidence and the severity of leaf browning increased with decreased temperatures, but even the immersion in 25°C water induced leaf browning in injured plants (25°C). These responses indicate that the water stimulates leaf browning in a wounded plant, whereas the reduced temperature intensifies the responsiveness. This wound-induced increase in sensitivity to water stimulus is referred to as hypersensitivity. Injuring the leaf, petiole, stem or root by cutting or crushing induced hypersensitivity only in young expanded leaves above the wound site. The hypersensitivity reached maximum 2 or 3 min after wounding and disappeared after 30 min. In addition, cutting the shoot a short distance from the apex resulted in severe leaf browning, indicating that the distance from young expanded leaves to the site of wounding affects the level of hypersensitivity. Our data indicate that a wound signal is rapidly translocated to the unwounded leaves to play a role in inducing hypersensitive responses to mechanical stimuli, such as water stimulus and sudden temperature drop.

Wounding enhances rapid-browning responsiveness of distal unwounded leaves to water stimulus in Ruellia macrantha

Hypersensitivity is induced in many species of Acanthaceae and Gesneriaceae by local mechanical wounding. Once a plant of these species sustains a wounded leaf, it exhibits a temporary hypersensitive state and severe injury easily occurrs even in unwounded leaves. Locally wounded African violet (Saintpaulia sp.) plants sometimes show severe injury even at a noninjurious temperature for this species. This study was aimed to clarify changes in the temperature sensitivity of hypersensitivity-induced African violet plants by local wounding. The basal leaves of African violet ‘Ritali’ plants were cut as a local wounding treatment. The locally wounded plants were transferred to growth chambers at various temperatures and we evaluated the degree of leaf injury using an analysis software. In locally wounded plants, temperature sensitivity increased and leaf injury was observed even at 11°C, which is a noninjurious temperature for unwounded African violet. Such a wound-induced sensitivity to low temperature treatment (7°C for 1 h) quantitatively increased with local wounding severity. For the investigation of time-course changes in the hypersensitive state (wounding memory) of locally wounded plants, the plants were transferred to low temperature conditions at various intervals after the wounding treatment. The wounding memory was short-lived, that is, it was generally observed immediately after local wounding and then almost disappeared 30 min after. In conclusion, the low temperature sensitivity of African violet plants was enhanced by prewounding treatment.

Low temperature sensitivity enhanced by local wounding in Saintpaulia

Leaf Injury Induced by Temperature Drop Shock in Gesneriaceae and Acanthaceae Plants

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