Perspective: Potatoes, Quality Carbohydrates, and Dietary Patterns.

Potatoes have long been a staple food in many cultures and cuisines, but they have gained a reputation as a low-quality carbohydrate source that should be avoided in the diet. Historically, this view has been justified by citing the glycemic index of potatoes as the main indicator of their quality. However, their nutrient composition should also be considered. The association of potatoes with energy-dense Western dietary patterns has also contributed to a perception that potatoes are inherently unhealthy. Although some studies have suggested an association between potato consumption and increased risk of health problems, such as type 2 diabetes, these associations may be confounded by fried potato intake and are strongest at intake levels higher than average consumption rates. Epidemiologic data suggest total potato intake is not a health risk in Eastern populations and can be consumed as part of a healthy diet. Furthermore, clinical trial data demonstrate that potatoes' health impact, irrespective of preparation, is similar to legumes and comparable with refined grains, with few deleterious effects found. These findings highlight the importance of moving beyond the glycemic index and adopting a more nuanced evaluation of the epidemiologic data to better understand the health impact of potato intake. Ultimately, the negative reputation of potatoes stems from an overinterpretation of their glycemic index and association with unhealthy Western dietary patterns, as well as oversimplification of the epidemiologic data. By considering carbohydrate quality, it becomes clear that potatoes can be part of a healthy diet given the proper consideration.

Defining Composition and Function of the Rhizosphere Microbiota of Barley Genotypes Exposed to Growth-Limiting Nitrogen Supplies.

The microbiota populating the rhizosphere, the interface between roots and soil, can modulate plant growth, development, and health. These microbial communities are not stochastically assembled from the surrounding soil, but their composition and putative function are controlled, at least partially, by the host plant. Here, we use the staple cereal barley as a model to gain novel insights into the impact of differential applications of nitrogen, a rate-limiting step for global crop production, on the host genetic control of the rhizosphere microbiota. Using a high-throughput amplicon sequencing survey, we determined that nitrogen availability for plant uptake is a factor promoting the selective enrichment of individual taxa in the rhizosphere of wild and domesticated barley genotypes. Shotgun sequencing and metagenome-assembled genomes revealed that this taxonomic diversification is mirrored by a functional specialization, manifested by the differential enrichment of multiple Gene Ontology terms, of the microbiota of plants exposed to nitrogen conditions limiting barley growth. Finally, a plant soil feedback experiment revealed that host control of the barley microbiota underpins the assembly of a phylogenetically diverse group of bacteria putatively required to sustain plant performance under nitrogen-limiting supplies. Taken together, our observations indicate that under nitrogen conditions limiting plant growth, host-microbe and microbe-microbe interactions fine-tune the host genetic selection of the barley microbiota at both taxonomic and functional levels. The disruption of these recruitment cues negatively impacts plant growth. IMPORTANCE The microbiota inhabiting the rhizosphere, the thin layer of soil surrounding plant roots, can promote the growth, development, and health of their host plants. Previous research indicated that differences in the genetic composition of the host plant coincide with variations in the composition of the rhizosphere microbiota. This is particularly evident when looking at the microbiota associated with input-demanding modern cultivated varieties and their wild relatives, which have evolved under marginal conditions. However, the functional significance of these differences remains to be fully elucidated. We investigated the rhizosphere microbiota of wild and cultivated genotypes of the global crop barley and determined that nutrient conditions limiting plant growth amplify the host control on microbes at the root-soil interface. This is reflected in a plant- and genotype-dependent functional specialization of the rhizosphere microbiota, which appears to be required for optimal plant growth. These findings provide novel insights into the significance of the rhizosphere microbiota for plant growth and sustainable agriculture.

Identifying plant genes shaping microbiota composition in the barley rhizosphere.

A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere, the interface between roots and soil. Here, we use metagenomics information as an external quantitative phenotype to map the host genetic determinants of the rhizosphere microbiota in wild and domesticated genotypes of barley, the fourth most cultivated cereal globally. We identify a small number of loci with a major effect on the composition of rhizosphere communities. One of those, designated the QRMC-3HS, emerges as a major determinant of microbiota composition. We subject soil-grown sibling lines harbouring contrasting alleles at QRMC-3HS and hosting contrasting microbiotas to comparative root RNA-seq profiling. This allows us to identify three primary candidate genes, including a Nucleotide-Binding-Leucine-Rich-Repeat (NLR) gene in a region of structural variation of the barley genome. Our results provide insights into the footprint of crop improvement on the plant's capacity of shaping rhizosphere microbes.

WHIRLY1 functions in the nucleus to regulate barley leaf development and associated metabolite profiles.

The WHIRLY (WHY) DNA/RNA binding proteins fulfil multiple but poorly characterised functions in leaf development. Here, we show that WHY1 transcript levels were highest in the bases of 7-day old barley leaves. Immunogold labelling revealed that the WHY1 protein was more abundant in the nuclei than the proplastids of the leaf bases. To identify transcripts associated with leaf development we conducted hierarchical clustering of differentially abundant transcripts along the developmental gradient of wild-type leaves. Similarly, metabolite profiling was employed to identify metabolites exhibiting a developmental gradient. A comparative analysis of transcripts and metabolites in barley lines (W1-1 and W1-7) lacking WHY1, which show delayed greening compared with the wild type revealed that the transcript profile of leaf development was largely unchanged in W1-1 and W1-7 leaves. However, there were differences in levels of several transcripts encoding transcription factors associated with chloroplast development. These include a barley homologue of the Arabidopsis GATA transcription factor that regulates stomatal development, greening and chloroplast development, NAC1; two transcripts with similarity to Arabidopsis GLK1 and two transcripts encoding ARF transcriptions factors with functions in leaf morphogenesis and development. Chloroplast proteins were less abundant in the W1-1 and W1-7 leaves than the wild type. The levels of tricarboxylic acid cycle metabolites and GABA were significantly lower in WHY1 knockdown leaves than the wild type. This study provides evidence that WHY1 is localised in the nuclei of leaf bases, contributing the regulation of nuclear-encoded transcripts that regulate chloroplast development.

Applications of the indole-alkaloid gramine modulate the assembly of individual members of the barley rhizosphere microbiota.

Microbial communities proliferating at the root-soil interface, collectively referred to as the rhizosphere microbiota, represent an untapped beneficial resource for plant growth, development and health. Integral to a rational manipulation of the microbiota for sustainable agriculture is the identification of the molecular determinants of these communities. In plants, biosynthesis of allelochemicals is centre stage in defining inter-organismal relationships in the environment. Intriguingly, this process has been moulded by domestication and breeding selection. The indole-alkaloid gramine, whose occurrence in barley (Hordeum vulgare L.) is widespread among wild genotypes but has been counter selected in several modern varieties, is a paradigmatic example of this phenomenon. This prompted us to investigate how exogenous applications of gramine impacted on the rhizosphere microbiota of two, gramine-free, elite barley varieties grown in a reference agricultural soil. High throughput 16S rRNA gene amplicon sequencing revealed that applications of gramine interfere with the proliferation of a subset of soil microbes with a relatively broad phylogenetic assignment. Strikingly, growth of these bacteria appeared to be rescued by barley plants in a genotype- and dosage-independent manner. In parallel, we discovered that host recruitment cues can interfere with the impact of gramine application in a host genotype-dependent manner. Interestingly, this latter effect displayed a bias for members of the phyla Proteobacteria. These initial observations indicate that gramine can act as a determinant of the prokaryotic communities inhabiting the root-soil interface.

Draft genome assemblies for tree pathogens Phytophthora pseudosyringae and Phytophthora boehmeriae.

Species of Phytophthora, plant pathogenic eukaryotic microbes, can cause disease on many tree species. Genome sequencing of species from this genus has helped to determine components of their pathogenicity arsenal. Here, we sequenced genomes for two widely distributed species, Phytophthora pseudosyringae and Phytophthora boehmeriae, yielding genome assemblies of 49 and 40 Mb, respectively. We identified more than 270 candidate disease promoting RXLR effector coding genes for each species, and hundreds of genes encoding candidate plant cell wall degrading carbohydrate active enzymes (CAZymes). These data boost genome sequence representation across the Phytophthora genus, and form resources for further study of Phytophthora pathogenesis.

Haustorium formation and a distinct biotrophic transcriptome characterize infection of Nicotiana benthamiana by the tree pathogen Phytophthora kernoviae.

Phytophthora species cause some of the most serious diseases of trees and threaten forests in many parts of the world. Despite the generation of genome sequence assemblies for over 10 tree-pathogenic Phytophthora species and improved detection methods, there are many gaps in our knowledge of how these pathogens interact with their hosts. To facilitate cell biology studies of the infection cycle we examined whether the tree pathogen Phytophthora kernoviae could infect the model plant Nicotiana benthamiana. We transformed P. kernoviae to express green fluorescent protein (GFP) and demonstrated that it forms haustoria within infected N. benthamiana cells. Haustoria were also formed in infected cells of natural hosts, Rhododendron ponticum and European beech (Fagus sylvatica). We analysed the transcriptome of P. kernoviae in cultured mycelia, spores, and during infection of N. benthamiana, and detected 12,559 transcripts. Of these, 1,052 were predicted to encode secreted proteins, some of which may function as effectors to facilitate disease development. From these, we identified 87 expressed candidate RXLR (Arg-any amino acid-Leu-Arg) effectors. We transiently expressed 12 of these as GFP fusions in N. benthamiana leaves and demonstrated that nine significantly enhanced P. kernoviae disease progression and diversely localized to the cytoplasm, nucleus, nucleolus, and plasma membrane. Our results show that N. benthamiana can be used as a model host plant for studying this tree pathogen, and that the interaction likely involves suppression of host immune responses by RXLR effectors. These results establish a platform to expand the understanding of Phytophthora tree diseases.

Chitosan primes plant defence mechanisms against Botrytis cinerea, including expression of Avr9/Cf-9 rapidly elicited genes.

Current crop protection strategies against the fungal pathogen Botrytis cinerea rely on a combination of conventional fungicides and host genetic resistance. However, due to pathogen evolution and legislation in the use of fungicides, these strategies are not sufficient to protect plants against this pathogen. Defence elicitors can stimulate plant defence mechanisms through a phenomenon known as defence priming. Priming results in a faster and/or stronger expression of resistance upon pathogen recognition by the host. This work aims to study defence priming by a commercial formulation of the elicitor chitosan. Treatments with chitosan result in induced resistance (IR) in solanaceous and brassicaceous plants. In tomato plants, enhanced resistance has been linked with priming of callose deposition and accumulation of the plant hormone jasmonic acid (JA). Large-scale transcriptomic analysis revealed that chitosan primes gene expression at early time-points after infection. In addition, two novel tomato genes with a characteristic priming profile were identified, Avr9/Cf-9 rapidly elicited protein 75 (ACRE75) and 180 (ACRE180). Transient and stable over-expression of ACRE75, ACRE180 and their Nicotiana benthamiana homologs, revealed that they are positive regulators of plant resistance against B. cinerea. This provides valuable information in the search for strategies to protect Solanaceae plants against B. cinerea.

Student's satisfaction and intercultural competence development from a short study abroad programs: A multiple cross-sectional study.

Nurses should be culturally competent to care appropriately to all patient groups. Whilst there are many opportunities to obtain clinical experiences, there are less curriculum-based opportunities to develop cultural competencies. This multiple cross-sectional study aimed to explore the development of intercultural awareness, knowledge, and competence in two different nursing students' groups (2016 and 2017 program edition) during a one-week study abroad program hosted by a European network of 14 higher education institutions. A questionnaire was designed specifically for the study and reliability established. Factor analysis confirmed three dimensions: perceived benefits, satisfaction, and acquisition of learning outcomes. Fifty-eight students (71.6%) completed the questionnaire for the April 2016 group, and 60 (88.2%) from the April 2017 group. There were minimal differences in responses between the two groups which suggested perceived benefits were retained one year later. Ratings were high for perceived satisfaction, perceived benefits; and the learning outcomes with regard to cultural competencies. Overall, the one-week program was considered a success and students would recommend it to others. This study concludes that a short, one-week study abroad program enabled nursing students to develop individually as well as develop cultural competencies in healthcare.

Escherichia coli O157:H7 F9 Fimbriae Recognize Plant Xyloglucan and Elicit a Response in Arabidopsis thaliana.

Fresh produce is often a source of enterohaemorrhagic Escherichia coli (EHEC) outbreaks. Fimbriae are extracellular structures involved in cell-to-cell attachment and surface colonisation. F9 (Fml) fimbriae have been shown to be expressed at temperatures lower than 37 °C, implying a function beyond the mammalian host. We demonstrate that F9 fimbriae recognize plant cell wall hemicellulose, specifically galactosylated side chains of xyloglucan, using glycan arrays. E. coli expressing F9 fimbriae had a positive advantage for adherence to spinach hemicellulose extract and tissues, which have galactosylated oligosaccharides as recognized by LM24 and LM25 antibodies. As fimbriae are multimeric structures with a molecular pattern, we investigated whether F9 fimbriae could induce a transcriptional response in model plant Arabidopsis thaliana, compared with flagella and another fimbrial type, E. coli common pilus (ECP), using DNA microarrays. F9 induced the differential expression of 435 genes, including genes involved in the plant defence response. The expression of F9 at environmentally relevant temperatures and its recognition of plant xyloglucan adds to the suite of adhesins EHEC has available to exploit the plant niche.

Ingested but not perceived: Response to satiety cues disrupted by perceptual load.

Selective attention research has shown that when perceptual demand is high, unattended sensory information is filtered out at early stages of processing. We investigated for the first time whether the sensory and nutrient cues associated with becoming full (satiety) would be filtered out in a similar manner. One-hundred and twenty participants consumed either a low-satiety (75 kcal) or high-satiety (272 kcal plus thicker texture) beverage, delivered via an intra-oral infusion device while participants simultaneously completed a task which was either low or high in perceptual demand. Among participants who performed the low perceptual load task, ingestion of the high-satiety beverage increased rated satiety and reduced consumption at a subsequent snack test. However, both effects were eliminated by the high perceptual load task. Therefore, the processing of satiety cues was dependent on the availability of attention, identifying a novel perceptual load mechanism of inattentive eating and supporting more recent cognitive models of appetite control.

Hedonic contrast and the short-term stimulation of appetite.

Hedonic contrast describes how liking for one item is influenced by the recent experience of other items which differ in hedonic valence. In the context of food stimuli, there is abundant evidence that hedonic contrast alters liking, but limited information on its impact on intake, and the aim here was to further clarify how hedonic impact modifies intake. Participants (96 female volunteers) rated and consumed ad libitum a sequence of four bowls of a snack (potato crisps) in one of three conditions. In the Palatable (salted crisps) and Bland (unsalted crisps) conditions, all four bowls were the same. In the Contrast condition participants alternated between salted and unsalted crisps. In total, significantly more was consumed in the Palatable (35.0 ± 2.6 g) than Bland (26.6 ± 2.4 g) condition, but most was consumed in the Contrast condition (37.0 ± 1.6 g). The impact of hedonic contrast was seen in the third serving, where those in the Contrast condition consumed the most of any serving, and significantly more than in Palatable or Bland conditions, and at the final serving, when those in the Contrast condition consumed significantly less than in Bland or Palatable conditions. Rated liking for the foods showed a similar pattern, with liking decreasing across servings in Palatable and Bland conditions. However, liking was influenced by the preceding serving in the Contrast condition, and the change in liking produced by contrast predicted subsequent intake. Overall, these data provide clear evidence that hedonic contrast can influence consumption, with intake driven by this adjusted liking.

A footprint of plant eco-geographic adaptation on the composition of the barley rhizosphere bacterial microbiota.

The microbiota thriving in the rhizosphere, the thin layer of soil surrounding plant roots, plays a critical role in plant's adaptation to the environment. Domestication and breeding selection have progressively differentiated the microbiota of modern crops from the ones of their wild ancestors. However, the impact of eco-geographical constraints faced by domesticated plants and crop wild relatives on recruitment and maintenance of the rhizosphere microbiota remains to be fully elucidated. Here we performed a comparative 16S rRNA gene survey of the rhizosphere of 4 domesticated and 20 wild barley (Hordeum vulgare) genotypes grown in an agricultural soil under controlled environmental conditions. We demonstrated the enrichment of individual bacteria mirrored the distinct eco-geographical constraints faced by their host plants. Unexpectedly, Elite varieties exerted a stronger genotype effect on the rhizosphere microbiota when compared with wild barley genotypes adapted to desert environments with a preferential enrichment for members of Actinobacteria. Finally, in wild barley genotypes, we discovered a limited, but significant, correlation between microbiota diversity and host genomic diversity. Our results revealed a footprint of the host's adaptation to the environment on the assembly of the bacteria thriving at the root-soil interface. In the tested conditions, this recruitment cue layered atop of the distinct evolutionary trajectories of wild and domesticated plants and, at least in part, is encoded by the barley genome. This knowledge will be critical to design experimental approaches aimed at elucidating the recruitment cues of the barley microbiota across a range of soil types.

A high-throughput genomic screen identifies a role for the plasmid-borne type II secretion system of Escherichia coli O157:H7 (Sakai) in plant-microbe interactions.

Shiga-toxigenic Escherichia coli (STEC) is often transmitted into food via fresh produce plants, where it can cause disease. To identify early interaction factors for STEC on spinach, a high-throughput positive-selection system was used. A bacterial artificial chromosome (BAC) clone library for isolate Sakai was screened in four successive rounds of short-term (2 h) interaction with spinach roots, and enriched loci identified by microarray. A Bayesian hierarchical model produced 115 CDS credible candidates, comprising seven contiguous genomic regions. Of the two candidate regions selected for functional assessment, the pO157 plasmid-encoded type two secretion system (T2SS) promoted interactions, while a chaperone-usher fimbrial gene cluster (loc6) did not. The T2SS promoted bacterial binding to spinach and appeared to involve the EtpD secretin protein. Furthermore, the T2SS genes, etpD and etpC, were expressed at a plant-relevant temperature of 18 °C, and etpD was expressed in planta by E. coli Sakai on spinach plants.

Dataset of Escherichia coli O157: H7 genes enriched in adherence to spinach root tissue.

A high-throughput positive-selection approach was taken to generate a dataset of Shigatoxigenic Escherichia coli (STEC) O157:H7 genes enriched in adherence to plant tissue. The approach generates a differential dataset based on BAC clones enriched in the output, after adherence, compared to the inoculum used as the input. A BAC clone library derived from STEC isolate 'Sakai' was used since this isolate is associated with a very large-scale outbreak of human disease from consumption of contaminated fresh produce; white radish sprouts. Spinach was used for the screen since it is associated with STEC outbreaks, and the roots provide a suitable site for bacterial colonisation. Four successive of rounds of Sakai BAC clone selection and amplification were applied for spinach root adherence, in parallel to a non-plant control. Genomic DNA was obtained from a total of 7.17 × 108 cfu/ml of bacteria from the plant treatment and 1.13 × 109 cfu/ml of bacteria from the no-plant control. Relative gene abundance of the output compared to the input pools was obtained using an established E. coli DNA microarray chip for STEC. The dataset enables screening for genes enriched under the treatment condition and informs on genes that may play a role in plant-microbe interactions.

Testing a load theory framework for food-related cognition.

The way we process rewarding stimuli is widely held to play a key role in normal and abnormal behavior. Biased processing of food-arguably the most primal form of reward-has been strongly implicated in the obesity crisis. Paradoxically, however, existing evidence suggests that both too much and too little attention can potentially lead to overeating. Here we sought to explain this contradiction within the framework of the load theory of attention, while also elucidating the relatively understudied role of memory biases. In 3 experiments, we presented food and nonfood images as irrelevant distractors during a letter search task with high and low levels of perceptual load, followed by a forced choice recognition task. As predicted, increasing perceptual load consistently powerfully reduced distraction by food and nonfood images alike. Similarly, food images encountered under high perceptual load were less likely to be recognized in a surprise memory test. Unexpectedly, however, there was a striking absence of attentional bias to food above and beyond salient nonfood stimuli, either within-subjects or in relation to traits implicated in food-biases. By contrast, a food memory bias was consistently observed across participants, and appeared independent of attentional biases. Food memory was consistently heightened in individuals with high levels of trait disinhibition (a measure of opportunistic eating). Our findings suggest that attention and memory for food and nonfood are similarly impacted by perceptual load. We discuss implications of the load theory framework for the wider literature on food-related cognition and for real world eating behaviors. (PsycInfo Database Record (c) 2020 APA, all rights reserved).

A high perceptual load task reduces thoughts about chocolate, even while hungry.

Intrusive thoughts about food can trigger cravings and result in unhealthy eating behaviour. Here we tested whether Load Theory of attention can be applied to the eating behaviour literature and reduce intrusive appetitive-related thoughts. Load Theory predicts that high levels of perceptual load in a task exhaust attentional capacity and so reduces interference from a range of stimuli, including intrusive thoughts. Therefore, this study aimed to test whether perceptual load reduced appetitive-related intrusive thoughts about chocolate. Sixty female participants were first given a chocolate bar to interact with for 2 min, before rating their levels of hunger, craving and liking for chocolate. They were then asked to avoid thinking about chocolate and instead focus attention on a visual search task. Perceptual load was manipulated within-subjects by varying the search set size. Appetitive-related thoughts were measured using both self-caught and probe-caught measures, allowing us to index load effects at varying levels of meta-awareness. Across subjects, the level of appetitive-related thoughts seen in the high load condition was significantly reduced, to less than half the level seen in the low load condition, on both probe and self-caught measures. Furthermore, self-reported hunger, craving and liking for the chocolate were positively correlated with appetitive-related thoughts under low load, but high perceptual load eliminated these state individual differences. Therefore, engaging in perceptually demanding tasks may be a worthwhile strategy for those wanting to disrupt the cycle of craving at the earliest stage.

Physiological, Biochemical, and Transcriptional Responses to Single and Combined Abiotic Stress in Stress-Tolerant and Stress-Sensitive Potato Genotypes.

Potato production is often constrained by abiotic stresses such as drought and high temperatures which are often present in combination. In the present work, we aimed to identify key mechanisms and processes underlying single and combined abiotic stress tolerance by comparative analysis of tolerant and susceptible cultivars. Physiological data indicated that the cultivars Desiree and Unica were stress tolerant while Agria and Russett Burbank were stress susceptible. Abiotic stress caused a greater reduction of photosynthetic carbon assimilation in the susceptible cultivars which was associated with a lower leaf transpiration rate. Oxidative stress, as estimated by the accumulation of malondialdehyde was not induced by stress treatments in any of the genotypes with the exception of drought stress in Russett Burbank. Stress treatment resulted in increases in ascorbate peroxidase activity in all cultivars except Agria which increased catalase activity in response to stress. Transcript profiling highlighted a decrease in the abundance of transcripts encoding proteins associated with PSII light harvesting complex in stress tolerant cultivars. Furthermore, stress tolerant cultivars accumulated fewer transcripts encoding a type-1 metacaspase implicated in programmed cell death. Stress tolerant cultivars exhibited stronger expression of genes associated with plant growth and development, hormone metabolism and primary and secondary metabolism than stress susceptible cultivars. Metabolite profiling revealed accumulation of proline in all genotypes following drought stress that was partially suppressed in combined heat and drought. On the contrary, the sugar alcohols inositol and mannitol were strongly accumulated under heat and combined heat and drought stress while galactinol was most strongly accumulated under drought. Combined heat and drought also resulted in the accumulation of Valine, isoleucine, and lysine in all genotypes. These data indicate that single and multiple abiotic stress tolerance in potato is associated with a maintenance of CO2 assimilation and protection of PSII by a reduction of light harvesting capacity. The data further suggests that stress tolerant cultivars suppress cell death and maintain growth and development via fine tuning of hormone signaling, and primary and secondary metabolism. This study highlights potential targets for the development of stress tolerant potato cultivars.

Barley Anther and Meiocyte Transcriptome Dynamics in Meiotic Prophase I.

In flowering plants, successful germinal cell development and meiotic recombination depend upon a combination of environmental and genetic factors. To gain insights into this specialized reproductive development program we used short- and long-read RNA-sequencing (RNA-seq) to study the temporal dynamics of transcript abundance in immuno-cytologically staged barley (Hordeum vulgare) anthers and meiocytes. We show that the most significant transcriptional changes in anthers occur at the transition from pre-meiosis to leptotene-zygotene, which is followed by increasingly stable transcript abundance throughout prophase I into metaphase I-tetrad. Our analysis reveals that the pre-meiotic anthers are enriched in long non-coding RNAs (lncRNAs) and that entry to meiosis is characterized by their robust and significant down regulation. Intriguingly, only 24% of a collection of putative meiotic gene orthologs showed differential transcript abundance in at least one stage or tissue comparison. Argonautes, E3 ubiquitin ligases, and lys48 specific de-ubiquitinating enzymes were enriched in prophase I meiocyte samples. These developmental, time-resolved transcriptomes demonstrate remarkable stability in transcript abundance in meiocytes throughout prophase I after the initial and substantial reprogramming at meiosis entry and the complexity of the regulatory networks involved in early meiotic processes.

BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq.

BACKGROUND: The time required to analyse RNA-seq data varies considerably, due to discrete steps for computational assembly, quantification of gene expression and splicing analysis. Recent fast non-alignment tools such as Kallisto and Salmon overcome these problems, but these tools require a high quality, comprehensive reference transcripts dataset (RTD), which are rarely available in plants. RESULTS: A high-quality, non-redundant barley gene RTD and database (Barley Reference Transcripts - BaRTv1.0) has been generated. BaRTv1.0, was constructed from a range of tissues, cultivars and abiotic treatments and transcripts assembled and aligned to the barley cv. Morex reference genome (Mascher et al. Nature; 544: 427-433, 2017). Full-length cDNAs from the barley variety Haruna nijo (Matsumoto et al. Plant Physiol; 156: 20-28, 2011) determined transcript coverage, and high-resolution RT-PCR validated alternatively spliced (AS) transcripts of 86 genes in five different organs and tissue. These methods were used as benchmarks to select an optimal barley RTD. BaRTv1.0-Quantification of Alternatively Spliced Isoforms (QUASI) was also made to overcome inaccurate quantification due to variation in 5' and 3' UTR ends of transcripts. BaRTv1.0-QUASI was used for accurate transcript quantification of RNA-seq data of five barley organs/tissues. This analysis identified 20,972 significant differentially expressed genes, 2791 differentially alternatively spliced genes and 2768 transcripts with differential transcript usage. CONCLUSION: A high confidence barley reference transcript dataset consisting of 60,444 genes with 177,240 transcripts has been generated. Compared to current barley transcripts, BaRTv1.0 transcripts are generally longer, have less fragmentation and improved gene models that are well supported by splice junction reads. Precise transcript quantification using BaRTv1.0 allows routine analysis of gene expression and AS.