Sequence assembly of large and repeat-rich plant genomes has been challenging, requiring substantial computational resources and often several complementary sequence assembly and genome mapping ...approaches. The recent development of fast and accurate long-read sequencing by circular consensus sequencing (CCS) on the PacBio platform may greatly increase the scope of plant pan-genome projects. Here, we compare current long-read sequencing platforms regarding their ability to rapidly generate contiguous sequence assemblies in pan-genome studies of barley (Hordeum vulgare). Most long-read assemblies are clearly superior to the current barley reference sequence based on short-reads. Assemblies derived from accurate long reads excel in most metrics, but the CCS approach was the most cost-effective strategy for assembling tens of barley genomes. A downsampling analysis indicated that 20-fold CCS coverage can yield very good sequence assemblies, while even five-fold CCS data may capture the complete sequence of most genes. We present an updated reference genome assembly for barley with near-complete representation of the repeat-rich intergenic space. Long-read assembly can underpin the construction of accurate and complete sequences of multiple genomes of a species to build pan-genome infrastructures in Triticeae crops and their wild relatives.
Gln is a key player in plant metabolism. It is one of the major free amino acids that is transported into the developing seed and is central for nitrogen metabolism. However, Gln natural variation ...and its regulation and interaction with other metabolic processes in seeds remain poorly understood. To investigate the latter, we performed a metabolic genome-wide association study (mGWAS) of Gln-related traits measured from the dry seeds of the Arabidopsis (
) diversity panel using all potential ratios between Gln and the other members of the Glu family as traits. This semicombinatorial approach yielded multiple candidate genes that, upon further analysis, revealed an unexpected association between the aliphatic glucosinolates (GLS) and the Gln-related traits. This finding was confirmed by an independent quantitative trait loci mapping and statistical analysis of the relationships between the Gln-related traits and the presence of specific GLS in seeds. Moreover, an analysis of Arabidopsis mutants lacking GLS showed an extensive seed-specific impact on Gln levels and composition that manifested early in seed development. The elimination of GLS in seeds was associated with a large effect on seed nitrogen and sulfur homeostasis, which conceivably led to the Gln response. This finding indicates that both Gln and GLS play key roles in shaping the seed metabolic homeostasis. It also implies that select secondary metabolites might have key functions in primary seed metabolism. Finally, our study shows that an mGWAS performed on dry seeds can uncover key metabolic interactions that occur early in seed development.
Plants produce diverse metabolites to cope with the challenges presented by complex and ever-changing environments. These challenges drive the diversification of specialized metabolites within and ...between plant species. However, we are just beginning to understand how frequently new alleles arise controlling specialized metabolite diversity and how the geographic distribution of these alleles may be structured by ecological and demographic pressures. Here, we measure the variation in specialized metabolites across a population of 797 natural
accessions. We show that a combination of geography, environmental parameters, demography and different genetic processes all combine to influence the specific chemotypes and their distribution. This showed that causal loci in specialized metabolism contain frequent independently generated alleles with patterns suggesting potential within-species convergence. This provides a new perspective about the complexity of the selective forces and mechanisms that shape the generation and distribution of allelic variation that may influence local adaptation.
The population structure of crop pathogens such as Puccinia striiformis f. sp. tritici (Pst), the cause of wheat stripe rust, is of interest to researchers looking to understand these pathogens on a ...molecular level as well as those with an applied focus such as disease epidemiology. Cereal rusts can reproduce sexually or asexually, and the emergence of novel lineages has the potential to cause serious epidemics such as the one caused by the 'Warrior' lineage in Europe. In a global context, Pst lineages in Canada were not well-characterized and the origin of foreign incursions was not known. Additionally, while some Pst mating type genes have been identified in published genomes, there has been no rigorous assessment of mating type diversity and distribution across the species. We used a whole-genome/transcriptome sequencing approach for the Canadian Pst population to identify lineages in their global context and evidence tracing foreign incursions. More importantly: for the first time ever, we identified nine alleles of the homeodomain mating type locus in the worldwide Pst population and show that previously identified lineages exhibit a single pair of these alleles. Consistently with the literature, we find only two pheromone receptor mating type alleles. We show that the recent population shift from the 'PstS1' lineage to the 'PstS1-related' lineage is also associated with the introduction of a novel mating type allele (Pst-b3-HD) to the Canadian population. We also show evidence for high levels of mating type diversity in samples associated with the Himalayan center of diversity for Pst, including a single Canadian race previously identified as 'PstPr' (probable recombinant) which we identify as a foreign incursion, most closely related to isolates sampled from China circa 2015. These data describe a recent shift in the population of Canadian Pst field isolates and characterize homeodomain-locus mating type alleles in the global Pst population which can now be utilized in testing several research questions and hypotheses around sexuality and hybridization in rust fungi.
In the evolution of land plants, the plant immune system has experienced expansion in immune receptor and signaling pathways. Lineage-specific expansions have been observed in diverse gene families ...that are potentially involved in immunity but lack causal association. Here, we show that
Rps8
-mediated resistance in barley to the pathogen
Puccinia striiformis
f. sp.
tritici
(wheat stripe rust) is conferred by a genetic module:
Pur1
and
Exo70FX12
, which are together necessary and sufficient.
Pur1
encodes a leucine-rich repeat receptor kinase and is the ortholog of rice
Xa21
, and Exo70FX12 belongs to the Poales-specific Exo70FX clade. The Exo70FX clade emerged after the divergence of the Bromeliaceae and Poaceae and comprises from 2 to 75 members in sequenced grasses. These results demonstrate the requirement of a lineage-specific Exo70FX12 in Pur1-mediated immunity and suggest that the Exo70FX clade may have evolved a specialized role in receptor kinase signaling.
The wheat stripe rust resistance gene
Rps8
is encoded by two genes: a receptor kinase and Poales-specific Exo70.
Ammonia (NH3) dissociation, oxidation, and associated nitric oxide (NO) emission in a vertical cylindrical quartz reactor is investigated to establish the effect of temperature (1000 K–1400 K), ...initial NH3 concentration (2%, 4%, 6%, 8%, 10%) and flowrate (250 mL/min, 500 mL/min, 750 mL/min). Ammonia oxidation experiments also examine the effect of equivalence ratio (ɸ = 0.8, 0.9, 1.0, 1.1). The NH3 and O2 conversions, N2 yield, and NO emission are determined by analysing the reactor effluent compositions. Ammonia dissociation of <6% is observed for all conditions tested. Ammonia oxidation is initiated at ∼1100 K, with majority of NH3 conversion occurring at 1200 K–1300 K before completion at ∼1325 K. NO emission becomes significant at temperatures >1300 K for ɸ ≤ 1.0 and increases with decreasing equivalence ratio. Under fuel-lean conditions, increasing initial NH3 concentration increases NO emission. Fuel-rich conditions return negligible NO, attributed to the reductive effect of excessive NH3.
•NH3 dissociation, oxidation and NO emission in a flow reactor are carefully studied.•NH3 dissociation of <6% is observed under all conditions examined.•NH3 oxidation initiates at 1100 K, becomes significant at 1200 K, completes at 1300 K.•NO emission is negligible under fuel-rich but significant at fuel-lean conditions.•NO formation precedes NO reduction by (locally) available NH3.
This paper conducted an extensive set of gravity-driven filtration simulations using the discrete element method (DEM). The simulations were used to statistically analyse the inherent variability in ...filter performance due to variations in initial particle position using one-way ANOVA for repeated measures tests. The simulations accounted for group effects associated with the interaction of base particles within the voids of the filter particles, and considered a size ratio that captured the complete range of filtration behaviour. The simulations were performed in a highly controlled manner, such that the sole difference between the base-filter realisations was initial particle position. Four filtration characteristics, based on filter efficiency and filling degree, were considered to define filter performance. One-way ANOVA for repeated measures tests conclusively showed that initial filter particle position had a statistically significant effect on filter performance for all four characteristics. Significant variability was observed with normalised ranges up to 16.0%. Increasing the domain width did not eradicate the observed statistically significant differences in filter performance. These observations highlighted the importance of considering multiple stochastically generated base-filter realisations in DEM studies before drawing conclusions about the performance of filters due to the inherent variability of the particle-scale mechanisms underlying the filtration process.
Shadows are prevalent in urban environments, introducing high uncertainties to fine-scale urban land-cover mapping. In this study, we developed a Recurrent Shadow Attention Model (RSAM), capitalizing ...on state-of-the-art deep learning architectures, to retrieve fine-scale land-cover classes within cast and self shadows along the urban-rural gradient. The RSAM differs from the other existing shadow removal models by progressively refining the shadow detection result with two attention-based interacting modules – Shadow Detection Module (SDM) and Shadow Classification Module (SCM). To facilitate model training and validation, we also created a Shadow Semantic Annotation Database (SSAD) using the 1 m resolution (National Agriculture Imagery Program) NAIP aerial imagery. The SSAD comprises 103 image patches (500 × 500 pixels each) containing various types of shadows and six major land-cover classes – building, tree, grass/shrub, road, water, and farmland. Our results show an overall accuracy of 90.6% and Kappa of 0.82 for RSAM to extract the six land-cover classes within shadows. The model performance was stable along the urban-rural gradient, although it was slightly better in rural areas than in urban centers or suburban neighborhoods. Findings suggest that RSAM is a robust solution to eliminate the effects in high-resolution mapping both from cast and self shadows that have not received equal attention in previous studies.
•We propose a model to retrieve fine-scale land-cover classes within shadows.•We developed a shadow semantic annotation database comprising 103 image patches.•The model is a robust solution to eliminate the effects from cast and self shadows.•The model performance is stable along the urban-rural gradient.
Maize (Zea mays) seeds are a good source of protein, despite being deficient in several essential amino acids. However, eliminating the highly abundant but poorly balanced seed storage proteins has ...revealed that the regulation of seed amino acids is complex and does not rely on only a handful of proteins. In this study, we used two complementary omics-based approaches to shed light on the genes and biological processes that underlie the regulation of seed amino acid composition. We first conducted a genome-wide association study to identify candidate genes involved in the natural variation of seed protein-bound amino acids. We then used weighted gene correlation network analysis to associate protein expression with seed amino acid composition dynamics during kernel development and maturation. We found that almost half of the proteome was significantly reduced during kernel development and maturation, including several translational machinery components such as ribosomal proteins, which strongly suggests translational reprogramming. The reduction was significantly associated with a decrease in several amino acids, including lysine and methionine, pointing to their role in shaping the seed amino acid composition. When we compared the candidate gene lists generated from both approaches, we found a nonrandom overlap of 80 genes. A functional analysis of these genes showed a tight interconnected cluster dominated by translational machinery genes, especially ribosomal proteins, further supporting the role of translation dynamics in shaping seed amino acid composition. These findings strongly suggest that seed biofortification strategies that target the translation machinery dynamics should be considered and explored further.
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