Plant Gene Seeker -PGS
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RNA-seq and microarray complement each other in transcriptome profiling

RNA-seq and microarray complement each other in transcriptome profiling | Plant Gene Seeker -PGS | Scoop.it

Abstract (provisional)

Background

RNA-seq and microarray are the two popular methods employed for genome-wide transcriptome profiling. Current comparison studies have shown that transcriptome quantified by these two methods correlated well. However, none of them have addressed if they complement each other, considering the strengths and the limitations inherent with them. The pivotal requirement to address this question is the knowledge of a well known data set. In this regard, HrpX regulome from pathogenic bacteria serves as an ideal choice as the target genes of HrpX transcription factor are well studied due to their central role in pathogenicity.

Results

We compared the performance of RNA-seq and microarray in their ability to detect known HrpX target genes by profiling the transcriptome from the wild-type and the hrpX mutant strains of gamma-Proteobacterium Xanthomonas citri subsp. citri. Our comparative analysis indicated that gene expression levels quantified by RNA-seq and microarray well-correlated both at absolute as well as relative levels (Spearman correlation-coefficient, rs > 0.76). Further, the expression levels quantified by RNA-seq and microarray for the significantly differentially expressed genes (DEGs) also well-correlated with qRT-PCR based quantification (rs=0.58 to 0.94). Finally, in addition to the 55 newly identified DEGs, 72% of the already known HrpX target genes were detected by both RNA-seq and microarray, while, the remaining 28% could only be detected by either one of the methods.

Conclusions

This study has significantly advanced our understanding of the regulome of the critical transcriptional factor HrpX. RNA-seq and microarray together provide a more comprehensive picture of HrpX regulome by uniquely identifying new DEGs. Our study demonstrated that RNA-seq and microarray complement each other in transcriptome profiling.


Via Biswapriya Biswavas Misra
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Plant Gene Seeker -PGS
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Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives

Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives | Plant Gene Seeker -PGS | Scoop.it
There is a rapidly rising trend in the development and application of molecular marker assays for gene mapping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing (GBS) platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop molecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype–phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of (a) rapid development in gene discovery of important traits, (b) deepened understanding of quantitative traits through new analytical models and population designs, (c) integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and (d) improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.
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Plant Epigenomics

Plant Epigenomics | Plant Gene Seeker -PGS | Scoop.it
Epigenetic modifications contribute to phenotypic variation at multiple levels, from gene regulation, to development, stress response, and population-level phenotypic diversity and evolution. As sessile organisms, plants are particularly dependent on epigenetic mechanisms to express diverse phenotypic responses from the same genome sequence. Technological advances that allow genome-wide analysis of DNA or histone modifications coupled with new opportunities for editing the epigenome have the potential to reveal the functions of epigenetic regulation in plants. Here, Genome Biology highlights advances in our understanding of the functions of epigenetic modifications, and the application of this knowledge.
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New Phytologist - Virtual Issue - Root Traits

New Phytologist - Virtual Issue - Root Traits | Plant Gene Seeker -PGS | Scoop.it

New Phytologist has long been at the forefront of research on root biology, curating journal articles that have sought to advance our understanding and modeling of plant-mediated belowground processes, in special journal issues, and in sponsoring collaboration and discussion at symposia and workshops. This trend promises to continue for the foreseeable future; for example, the topic of plant roots will be highlighted in the upcoming 2017 Symposium, ‘Trait covariation: structural and functional relationships in plant ecology’. New Phytologist is now playing a prominent role in advancing the theme of root traits; the number of papers identified by a keyword search on ‘root traits’ in the journal has quintupled in the last 15 years. In a recently published Tansley insight, 2017 Tansley Medal winner Etienne Laliberté proposed six research frontiers for advancing belowground trait-based ecology: redefining fine roots, quantifying trait dimensionality, integrating mycorrhizas, broadening the suite of belowground traits, determining trait–environment linkages, and understanding ecosystem-level consequences. Research papers, Reviews, Letters, and Commentaries published in New Phytologist in recent years have all contributed to our understanding of these research frontiers, and we highlight this burgeoning ‘belowground movement’ in this Virtual Issue. Here, we present recent (2014–2017) papers in which root traits were the dominant focus, including papers describing the general concepts of root traits, how root traits can be harnessed by terrestrial biosphere models, and the relationships among root traits and root function, mycorrhizas, and ecosystem properties.

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Nitrogen nutrition in plants: rapid progress and new challenges

Nitrogen nutrition in plants: rapid progress and new challenges | Plant Gene Seeker -PGS | Scoop.it
As a main feature of plant autotrophy, assimilation of inorganic nitrogen is not only of fundamental scientific interest, but also a crucial factor in crop productivity. In its broad sense – from root uptake of various forms of N in the soil to allocation of N assimilates to different organs – it involves a wide range of physiological processes whose mechanisms are far from being fully understood. The aim of this special issue is to provide a wide overview of recent progress in this field, and to draw an interdisciplinary picture of the prospects for future research.
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Developmental transitions: integrating environmental cues with hormonal signaling in the chromatin landscape in plants

Developmental transitions: integrating environmental cues with hormonal signaling in the chromatin landscape in plants | Plant Gene Seeker -PGS | Scoop.it
Plant development is predominantly postembryonic and tuned in to respond to environmental cues. All living plant cells can be triggered to de-differentiate, assume different cell identities, or form a new organism. This developmental plasticity is thought to be an adaptation to the sessile lifestyle of plants. Recent discoveries have advanced our understanding of the orchestration of plant developmental switches by transcriptional master regulators, chromatin state changes, and hormone response pathways. Here, we review these recent advances with emphasis on the earliest stages of plant development and on the switch from pluripotency to differentiation in different plant organ systems.
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The common transcriptional subnetworks of the grape berry skin in the late stages of ripening

The common transcriptional subnetworks of the grape berry skin in the late stages of ripening | Plant Gene Seeker -PGS | Scoop.it
Wine grapes are important economically in many countries around the world. Defining the optimum time for grape harvest is a major challenge to the grower and winemaker. Berry skins are an important source of flavor, color and other quality traits in the ripening stage. Senescent-like processes such as chloroplast disorganization and cell death characterize the late ripening stage. To better understand the molecular and physiological processes involved in the late stages of berry ripening, RNA-seq analysis of the skins of seven wine grape cultivars (Cabernet Franc, Cabernet Sauvignon, Merlot, Pinot Noir, Chardonnay, Sauvignon Blanc and Semillon) was performed. RNA-seq analysis identified approximately 2000 common differentially expressed genes for all seven cultivars across four different berry sugar levels (20 to 26 °Brix). Network analyses, both a posteriori (standard) and a priori (gene co-expression network analysis), were used to elucidate transcriptional subnetworks and hub genes associated with traits in the berry skins of the late stages of berry ripening. These independent approaches revealed genes involved in photosynthesis, catabolism, and nucleotide metabolism. The transcript abundance of most photosynthetic genes declined with increasing sugar levels in the berries. The transcript abundance of other processes increased such as nucleic acid metabolism, chromosome organization and lipid catabolism. Weighted gene co-expression network analysis (WGCNA) identified 64 gene modules that were organized into 12 subnetworks of three modules or more and six higher order gene subnetworks. Some gene subnetworks were highly correlated with sugar levels and some subnetworks were highly enriched in the chloroplast and nucleus. The petal R package was utilized independently to construct a true small-world and scale-free complex gene co-expression network model. A subnetwork of 216 genes with the highest connectivity was elucidated, consistent with the module results from WGCNA. Hub genes in these subnetworks were identified including numerous members of the core circadian clock, RNA splicing, proteolysis and chromosome organization. An integrated model was constructed linking light sensing with alternative splicing, chromosome remodeling and the circadian clock. A common set of differentially expressed genes and gene subnetworks from seven different cultivars were examined in the skin of the late stages of grapevine berry ripening. A densely connected gene subnetwork was elucidated involving a complex interaction of berry senescent processes (autophagy), catabolism, the circadian clock, RNA splicing, proteolysis and epigenetic regulation. Hypotheses were induced from these data sets involving sugar accumulation, light, autophagy, epigenetic regulation, and fruit development. This work provides a better understanding of berry development and the transcriptional processes involved in the late stages of ripening.
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Frontiers | Abiotic Stress Tolerance in Plants: Myriad Roles of Ascorbate Peroxidase | Plant Science

Frontiers | Abiotic Stress Tolerance in Plants: Myriad Roles of Ascorbate Peroxidase | Plant Science | Plant Gene Seeker -PGS | Scoop.it
One of the most significant manifestations of environmental stress in plants is the increased production of Reactive Oxygen Species (ROS). These ROS, if allowed to accumulate unchecked, can lead to cellular toxicity. A battery of antioxidant molecules is present in plants for keeping ROS levels under check and to maintain the cellular homeostasis under stress. Ascorbate peroxidase (APX) is a key antioxidant enzyme of such scavenging systems. It catalyses the conversion of H2O2 into H2O, employing ascorbate as an electron donor. The expression of APX is differentially regulated in response to environmental stresses and during normal plant growth and development as well. Different isoforms of APX show differential response to environmental stresses, depending upon their sub-cellular localization and the presence of specific regulatory elements in the upstream regions of the respective genes. The present review delineates role of APX isoforms with respect to different types of abiotic stresses and its importance as a key antioxidant enzyme in maintaining cellular homeostasis.
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Improvements in Genomic Technologies: Application to Crop Genomics

Improvements in Genomic Technologies: Application to Crop Genomics | Plant Gene Seeker -PGS | Scoop.it
Second-generation sequencing (SGS) has advanced the study of crop genomes and has provided insights into diversity and evolution. However, repetitive DNA sequences in crops often lead to incomplete or erroneous assemblies because SGS reads are too short to fully resolve these repeats. To overcome some of these challenges, long-read sequencing and optical mapping have been developed to produce high-quality assemblies for complex genomes. Previously, high error rates, low throughput, and high costs have limited the adoption of long-read sequencing and optical mapping. However, with recent improvements and the development of novel algorithms, the application of these technologies is increasing. We review the development of long-read sequencing and optical mapping, and assess their application in crop genomics for breeding improved crops.
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Plant, Cell & Environment - Special Issue on Water Transport 

Plant, Cell & Environment - Special Issue on Water Transport  | Plant Gene Seeker -PGS | Scoop.it
Outstanding articles on water transport and regulation, plus effects on Carbon dioxide, stomatal responses, drought.
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Technology: The Future of Agriculture : Nature 

Technology: The Future of Agriculture : Nature  | Plant Gene Seeker -PGS | Scoop.it
A technological revolution in farming led by advances in robotics and sensing technologies looks set to disrupt modern practice.
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Malate-dependent Fe accumulation is a critical checkpoint in the root developmental response to low phosphate

Malate-dependent Fe accumulation is a critical checkpoint in the root developmental response to low phosphate | Plant Gene Seeker -PGS | Scoop.it

Low phosphate (Pi) availability constrains plant development and seed production in both natural and agricultural ecosystems. When Pi is scarce, modifications of root system architecture (RSA) enhance the soil exploration ability of the plant and lead to an increase in Pi uptake. In Arabidopsis, an iron-dependent mechanism reprograms primary root growth in response to low Pi availability. This program is activated upon contact of the root tip with low-Pi media and induces premature cell differentiation and the arrest of mitotic activity in the root apical meristem, resulting in a short-root phenotype. However, the mechanisms that regulate the primary root response to Pi-limiting conditions remain largely unknown. Here we report on the isolation and characterization of two low-Pi insensitive mutants (lpi5 and lpi6), which have a long-root phenotype when grown in low-Pi media. Cellular, genomic, and transcriptomic analysis of low-Pi insensitive mutants revealed that the genes previously shown to underlie Arabidopsis Al tolerance via root malate exudation, known as SENSITIVE TO PROTON RHIZOTOXICITY (STOP1) and ALUMINUM ACTIVATED MALATE TRANSPORTER 1 (ALMT1), represent a critical checkpoint in the root developmental response to Pi starvation in Arabidopsis thaliana. Our results also show that exogenous malate can rescue the long-root phenotype of lpi5 and lpi6. Malate exudation is required for the accumulation of Fe in the apoplast of meristematic cells, triggering the differentiation of meristematic cells in response to Pi deprivation.

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Prospect on Ionomic Signatures for the Classification of Grapevine Berries According to Their Geographical Origin | Plant Science

Prospect on Ionomic Signatures for the Classification of Grapevine Berries According to Their Geographical Origin | Plant Science | Plant Gene Seeker -PGS | Scoop.it
The determination of food geographical origin has been an important subject of study over the past decade, with an increasing number of analytical techniques being developed to determine the provenance of agricultural products. Agricultural soils can differ for the composition and the relative quantities of mineral nutrients and trace elements whose bioavailability depends on soil properties. Therefore, the ionome of fruits, vegetables and derived products can reflect the mineral composition of the growth substrate. Multi-elemental analysis has been successfully applied to trace the provenance of wines from different countries or different wine-producing regions. However, winemaking process and environmental and cultural conditions may affect a geographical fingerprint. In this article, we discuss the possibility of applying ionomics in wines classification on a local scale and also by exploiting grape berry analyses. In this regard, we present the ionomic profile of grapevine berries grown within an area of approximately 300 km2 and the subsequent application of chemometric methods for the assignment of their geographical origin. The best discrimination was obtained by using a dataset composed only of rare earth elements (REEs). Considering the experiences reported in the literature and our results, we concluded that sample representativeness and the application of a preliminary Principal Component Analysis, as pattern recognition techniques, might represent two necessary starting points for the geographical determination of the geographical origin of grape berries; therefore, on the basis of these observations we also include some recommendations to be considered for future application of these techniques for grape and wines classification.
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Genome Editing of Plants

Genome Editing of Plants | Plant Gene Seeker -PGS | Scoop.it
Genome editing in organisms via random mutagenesis is a naturally occurring phenomenon. As a technology, genome editing has evolved from the use of chemical and physical mutagenic agents capable of altering DNA sequences to biological tools such as designed sequence-specific nucleases (SSN) to produce knock-out (KO) or knock-in (KI) edits and Oligonucleotide Directed Mutagenesis (ODM) where specific nucleotide changes are made in a directed manner resulting in custom single nucleotide polymorphisms (SNPs). Cibus' SU Canola™, which the US Department of Agriculture (USDA) views as non-genetically modified (non-GM), is Cibus' first commercial product arising from plant genome editing and had its test launch in 2014. Regulatory aspects of the various genome editing tools will be discussed.
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Root Tip Shape Governs Root Elongation Rate under Increased Soil Strength

Root Tip Shape Governs Root Elongation Rate under Increased Soil Strength | Plant Gene Seeker -PGS | Scoop.it
Increased soil strength due to soil compaction or soil drying is a major limitation to root growth and crop productivity. Roots need to exert higher penetration force, resulting in increased penetration stress when elongating in soils of greater strength. This study aimed to quantify how the genotypic diversity of root tip geometry and root diameter influences root elongation under different levels of soil strength and to determine the extent to which roots adjust to increased soil strength. Fourteen wheat (Triticum aestivum) varieties were grown in soil columns packed to three bulk densities representing low, moderate, and high soil strength. Under moderate and high soil strength, smaller root tip radius-to-length ratio was correlated with higher genotypic root elongation rate, whereas root diameter was not related to genotypic root elongation. Based on cavity expansion theory, it was found that smaller root tip radius-to-length ratio reduced penetration stress, thus enabling higher root elongation rates in soils with greater strength. Furthermore, it was observed that roots could only partially adjust to increased soil strength. Root thickening was bounded by a maximum diameter, and root tips did not become more acute in response to increased soil strength. The obtained results demonstrated that root tip geometry is a pivotal trait governing root penetration stress and root elongation rate in soils of greater strength. Hence, root tip shape needs to be taken into account when selecting for crop varieties that may tolerate high soil strength.
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Leaf Hydraulic Architecture and Stomatal Conductance: A Functional Perspective

Leaf Hydraulic Architecture and Stomatal Conductance: A Functional Perspective | Plant Gene Seeker -PGS | Scoop.it
The structure of leaf vasculature viewed over a broad phylogenetic scale from lycophytes to eudicots correlates with stomatal conductance, providing the basis for the hypothesis that increasing vein density drove the evolution of high fluxes in angiosperms. Yet, the relationship between vascular
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Life behind the wall: sensing mechanical cues in plants

Life behind the wall: sensing mechanical cues in plants | Plant Gene Seeker -PGS | Scoop.it
There is increasing evidence that all cells sense mechanical forces in order to perform their functions. In animals, mechanotransduction has been studied during the establishment of cell polarity, fate, and division in single cells, and increasingly is studied in the context of a multicellular tissue. What about plant systems? Our goal in this review is to summarize what is known about the perception of mechanical cues in plants, and to provide a brief comparison with animals.
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Identification of Putative Transmembrane Proteins Involved in Salinity Tolerance in Chenopodium quinoa by Integrating Physiological Data, RNAseq, and SNP Analyses | Plant Science

Identification of Putative Transmembrane Proteins Involved in Salinity Tolerance in Chenopodium quinoa by Integrating Physiological Data, RNAseq, and SNP Analyses | Plant Science | Plant Gene Seeker -PGS | Scoop.it
Chenopodium quinoa (quinoa) is an emerging crop that produces nutritious grains with the potential to contribute to global food security. Quinoa can also grow on marginal lands, such as soils affected by high salinity. To identify candidate salt tolerance genes in the recently sequenced quinoa genome, we used a multifaceted approach integrating RNAseq analyses with comparative genomics and topology prediction. We identified 219 candidate genes by selecting those that were differentially expressed in response to salinity, were specific to or overrepresented in quinoa relative to other Amaranthaceae species, and had more than one predicted transmembrane domain. To determine whether these genes might underlie variation in salinity tolerance in quinoa and its close relatives, we compared the response to salinity stress in a panel of 21 Chenopodium accessions (14 C. quinoa, 5 C. berlandieri and 2 C. hircinum). We found large variation in salinity tolerance, with one C. hircinum displaying the highest salinity tolerance. Using genome re-sequencing data from these accessions, we investigated single nucleotide polymorphisms and copy number variation in the 219 candidate genes in accessions of contrasting salinity tolerance, and identified 15 genes that could contribute to the differences in salinity tolerance of these Chenopodium accessions.
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Polymorphisms and minihaplotypes in the VvNAC26 gene associate with berry size variation in grapevine

Polymorphisms and minihaplotypes in the VvNAC26 gene associate with berry size variation in grapevine | Plant Gene Seeker -PGS | Scoop.it
Domestication and selection of Vitis vinifera L. for table and wine grapes has led to a large level of berry size diversity in current grapevine cultivars. Identifying the genetic basis for this natural variation is paramount both for breeding programs and for elucidating which genes contributed to crop evolution during domestication and selection processes. The gene VvNAC26, which encodes a NAC domain-containing transcription factor, has been related to the early development of grapevine flowers and berries. It was selected as candidate gene for an association study to elucidate its possible participation in the natural variation of reproductive traits in cultivated grapevine.

Methods
A grapevine collection of 114 varieties was characterized during three consecutive seasons for different berry and bunch traits. The promoter and coding regions of VvNAC26 gene (VIT_01s0026g02710) were sequenced in all the varieties of the collection, and the existing polymorphisms (SNP and INDEL) were detected. The corresponding haplotypes were inferred and used for a phylogenetic analysis. The possible associations between genotypic and phenotypic data were analyzed independently for each season data, using different models and significance thresholds.

Results
A total of 30 non-rare polymorphisms were detected in the VvNAC26 sequence, and 26 different haplotypes were inferred. Phylogenetic analysis revealed their clustering in two major haplogroups with marked phenotypic differences in berry size between varieties harboring haplogroup-specific alleles. After correcting the statistical models for the effect of the population genetic stratification, we found a set of polymorphisms associated with berry size explaining between 8.4 and 21.7 % (R2) of trait variance, including those generating the differentiation between both haplogroups. Haplotypes built from only three polymorphisms (minihaplotypes) were also associated with this trait (R2: 17.5 – 26.6 %), supporting the involvement of this gene in the natural variation for berry size.

Conclusions
Our results suggest the participation of VvNAC26 in the determination of the grape berry final size. Different VvNAC26 polymorphisms and their combination showed to be associated with different features of the fruit. The phylogenetic relationships between the VvNAC26 haplotypes and the association results indicate that this nucleotide variation may have contributed to the differentiation between table and wine grapes.
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Introduction to a Virtual Issue on root traits

Introduction to a Virtual Issue on root traits | Plant Gene Seeker -PGS | Scoop.it

Plant traits – ‘morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs’ (Kattge et al., 2011) – are increasingly being harnessed by empiricists and modelers as a framework to understand patterns in the structure and function of species across the globe. Trait-based ecology, which emphasizes functional traits over the taxonomical relationships among organisms (Laliberté, 2017), promises to improve generality, synthesis, and predictive ability across ecological scales (Shipley et al., 2016).

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State of the World's Plants | Royal Botanic Gardens, Kew

State of the World's Plants | Royal Botanic Gardens, Kew | Plant Gene Seeker -PGS | Scoop.it
Annual cutting-edge horizon scan of global plant status. Produced by Royal Botanic Gardens Kew - Science.

Via Loïc Lepiniec
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The Tea Tree Genome Provides Insights into Tea Flavor and Independent Evolution of Caffeine Biosynthesis

The Tea Tree Genome Provides Insights into Tea Flavor and Independent Evolution of Caffeine Biosynthesis | Plant Gene Seeker -PGS | Scoop.it
Tea is the world's oldest and most popular caffeine-containing beverage with immense economic, medicinal, and cultural importance. Here, we present the first high-quality nucleotide sequence of the repeat-rich (80.9%), 3.02-Gb genome of the cultivated tea tree Camellia sinensis. We show that an extraordinarily large genome size of tea tree is resulted from the slow, steady, and long-term amplification of a few LTR retrotransposon families. In addition to a recent whole-genome duplication event, lineage-specific expansions of genes associated with flavonoid metabolic biosynthesis were discovered, which enhance catechin production, terpene enzyme activation, and stress tolerance, important features for tea flavor and adaptation. We demonstrate an independent and rapid evolution of the tea caffeine synthesis pathway relative to cacao and coffee. A comparative study among 25 Camellia species revealed that higher expression levels of most flavonoid- and caffeine- but not theanine-related genes contribute to the increased production of catechins and caffeine and thus enhance tea-processing suitability and tea quality. These novel findings pave the way for further metabolomic and functional genomic refinement of characteristic biosynthesis pathways and will help develop a more diversified set of tea flavors that would eventually satisfy and attract more tea drinkers worldwide.
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Nutrition: A world of insecurity: Nature Research

Nutrition: A world of insecurity: Nature Research | Plant Gene Seeker -PGS | Scoop.it
Malnutrition is a global problem. With population and consumption set to rise over the coming decades, achieving food security will require action on many fronts.
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Unique Physiological and Transcriptional Shifts under Combinations of Salinity, Drought, and Heat

Unique Physiological and Transcriptional Shifts under Combinations of Salinity, Drought, and Heat | Plant Gene Seeker -PGS | Scoop.it
Climate-change-driven stresses such as extreme temperatures, water deficit, and ion imbalance are projected to exacerbate and jeopardize global food security. Under field conditions, these stresses usually occur simultaneously and cause damages that exceed single stresses. Here, we investigated the transcriptional patterns and morpho-physiological acclimations of Brachypodium dystachion to single salinity, drought, and heat stresses, as well as their double and triple stress combinations. Hierarchical clustering analysis of morpho-physiological acclimations showed that several traits exhibited a gradually aggravating effect as plants were exposed to combined stresses. On the other hand, other morphological traits were dominated by salinity, while some physiological traits were shaped by heat stress. Response patterns of differentially expressed genes, under single and combined stresses (i.e. common stress genes), were maintained only among 37% of the genes, indicating a limited expression consistency among partially overlapping stresses. A comparison between common stress genes and genes that were uniquely expressed only under combined stresses (i.e. combination unique genes) revealed a significant shift from increased intensity to antagonistic responses, respectively. The different transcriptional signatures imply an alteration in the mode of action under combined stresses and limited ability to predict plant responses as different stresses are combined. Coexpression analysis coupled with enrichment analysis revealed that each gene subset was enriched with different biological processes. Common stress genes were enriched with known stress response pathways, while combination unique-genes were enriched with unique processes and genes with unknown functions that hold the potential to improve stress tolerance and enhance cereal productivity under suboptimal field conditions.
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An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations | Plant Gene Seeker -PGS | Scoop.it

Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNA-seq and Pacific Biosciences (PacBio) full-length cDNAs to identify 104,091 high-confidence protein-coding genes and 10,156 noncoding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop.

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The interaction of human population, food production, and biodiversity protection

Research suggests that the scale of human population and the current pace of its growth contribute substantially to the loss of biological diversity. Although technological change and unequal consumption inextricably mingle with demographic impacts on the environment, the needs of all human beings—especially for food—imply that projected population growth will undermine protection of the natural world. Numerous solutions have been proposed to boost food production while protecting biodiversity, but alone these proposals are unlikely to staunch biodiversity loss. An important approach to sustaining biodiversity and human well-being is through actions that can slow and eventually reverse population growth: investing in universal access to reproductive health services and contraceptive technologies, advancing women’s education, and achieving gender equality.
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