Ontologies for increasing the FAIRness of plant research data

The importance of improving the FAIRness (findability, accessibility, interoperability, reusability) of research data is undeniable, especially in the face of large, complex datasets currently being produced by omics technologies. Facilitating the integration of a dataset with other types of data increases the likelihood of reuse, and the potential of answering novel research questions. Ontologies are a useful tool for semantically tagging datasets as adding relevant metadata increases the understanding of how data was produced and increases its interoperability. Ontologies provide concepts for a particular domain as well as the relationships between concepts. By tagging data with ontology terms, data becomes both human and machine interpretable, allowing for increased reuse and interoperability. However, the task of identifying ontologies relevant to a particular research domain or technology is challenging, especially within the diverse realm of fundamental plant research. In this review, we outline the ontologies most relevant to the fundamental plant sciences and how they can be used to annotate data related to plant-specific experiments within metadata frameworks, such as Investigation-Study-Assay (ISA). We also outline repositories and platforms most useful for identifying applicable ontologies or finding ontology terms.Comment: 34 pages, 4 figures, 1 table, 1 supplementary tabl

Quantification of Soluble Metabolites and Compound-Specific δ13C in Response to Water Availability and Developmental Stages in Field Grown Chickpea (Cicer arietinum L.)

Developing biomarkers and bio-indicators that will better indicate stress tolerance is crucial for plant breeding to increase crop resilience and productivity. However, complex interactions between water availability, light intensity, and temperature fluctuations make it difficult to develop standardised properties to monitor performance under field conditions. Sugar alcohols have been shown to function as stress metabolites, demonstrating considerable promise for use as bio-indicators of stress tolerance. This experiment monitored the accumulation of metabolites, including that of the sugar alcohol D-pinitol, in 3 chickpea genotypes grown under field conditions during reproductive stages of development. Further, compound specific carbon isotope abundance (δ13C) of these compounds was quantified to investigate the influence on predictions of water use efficiency. It was found that the magnitude of water deficit did not instigate significant responses in metabolite abundance, however, concentrations of D-pinitol increased significantly over reproductive stages, indicating the accumulation of this sugar alcohol may be under significant developmental control. Significant differences in the δ13C of D-pinitol compared to other metabolites indicate this compound imparts a substantial effect over concentration-weighted predictions of water use efficiency obtained from the soluble fraction of leaves, especially as its proportion in the soluble fraction increases with plant development

Physiological, chemical and molecular characterisation of sugar alcohol accumulation in Leguminosae

Sugar alcohols accumulate across a broad range of plant genera, often to concentrations exceeding that of soluble carbohydrates. While there is a general consensus on the function of sugar alcohols based on their physiochemical properties, gaps remain in understanding conditions that elicit sugar alcohol accumulation and its molecular control. Through a series of chemical, molecular, and physiological techniques, this thesis investigates the complexity of D-pinitol accumulation within the Leguminosae system and the transcriptional responses of key genes governing D-pinitol biosynthesis. In addition, naturally occurring compound specific carbon isotope abundances are used to evaluate the influence of D-pinitol synthesis on modelling water use efficiency. Assessing the chemical composition of the soluble leaf fraction found that DPinitol significantly increased over development in both chickpea (Cicer arietinum) grown in field and in soybean (Glycine max) grown under controlled environmental conditions. Compound specific carbon isotope abundance (δ13C) in samples collected from chickpea grown in field and soybean grown under elevated atmospheric CO2 established that concentrations of D-pinitol in the soluble fraction coupled with high Δ13C of the D-pinitol pool imparts a substantial influence over predictions of water use efficiency modelled from the leaf soluble fraction. Quantitative molecular investigations found that the inositol-1-phosphate synthase (INPS) gene is transcriptionally up regulated in response to a gradual water deficit in soybean grown in controlled conditions. While future studies must consider a wider range of legume species and genotypes when investigating sugar alcohol biosynthesis, the studies presented here suggest that the accumulation of D-pinitol in legumes is a good candidate for the improvement of plant performance and resilience

Water Deficit Elicits a Transcriptional Response of Genes Governing <span style="font-variant: small-caps">d</span>-pinitol Biosynthesis in Soybean (<i>Glycine max</i>)

d-pinitol is the most commonly accumulated sugar alcohol in the Leguminosae family and has been observed to increase significantly in response to abiotic stress. While previous studies have identified genes involved in d-pinitol synthesis, no study has investigated transcript expression in planta. The present study quantified the expression of several genes involved in d-pinitol synthesis in different plant tissues and investigated the accumulation of d-pinitol, myo-inositol and other metabolites in response to a progressive soil drought in soybean (Glycine max). Expression of myo-inositol 1-phosphate synthase (INPS), the gene responsible for the conversion of glucose-6-phosphate to myo-inositol-1-phosphate, was significantly up regulated in response to a water deficit for the first two sampling weeks. Expression of myo-inositol O-methyl transferase (IMT1), the gene responsible for the conversion of myo-inositol into d-ononitol was only up regulated in stems at sampling week 3. Assessment of metabolites showed significant changes in their concentration in leaves and stems. d-Pinitol concentration was significantly higher in all organs sampled from water deficit plants for all three sampling weeks. In contrast, myo-inositol, had significantly lower concentrations in leaf samples despite up regulation of INPS suggesting the transcriptionally regulated flux of carbon through the myo-inositol pool is important during water deficit

Metabolic adaptation and allocation of metabolites to phloem transport and regulation under stress

Metabolic adjustment by plants in response to changes in their environment underpin a range of morphological and physiological adaptations. Allocation of compounds to phloem-mediated transport has a major influence over plant scale processes. In fully expanded leaves, over 90% of recently fixed carbon can be exported to the phloem stream. Despite this, the use of phloem contents as indicators of plant health has not received significant attention in part due to the difficulties in sample collection. Here we outline how metabolic shifts in the allocation of carbon among selected solute pools observed in phloem contents may be used as bio-indicators of plant health and vigor

Oxford Nanopore Sequencing: New opportunities for plant genomics?

DNA sequencing was dominated by Sanger’s chain-termination method until the mid-2000s, when it was progressively supplanted by new sequencing technologies that can generate much larger quantities of data in a shorter time. At the forefront of these developments, long-read sequencing technologies (third-generation sequencing) can produce reads that are several kilobases in length. This greatly improves the accuracy of genome assemblies by spanning the highly-repetitive segments that cause difficulty for second-generation short-read technologies. Third-generation sequencing is especially appealing for plant genomes, which can be extremely large with long stretches of highly-repetitive DNA. Until recently, the low basecalling accuracy of third-generation technologies meant that accurate genome assembly required expensive, highcoverage sequencing followed by computational analysis to correct for errors. However, today’s long-read technologies are more accurate and less expensive, making them the method of choice for the assembly of complex genomes. Oxford Nanopore Technologies (ONT), a thirdgeneration platform for the sequencing of native DNA strands, is particularly suitable for the generation of high-quality assemblies of highly-repetitive plant genomes. Here we discuss the benefits of ONT, especially for the plant science community, and describe the issues that remain to be addressed when using ONT for plant genome sequencing

Morphological and Physiological Traits Associated with Yield under Reduced Irrigation in Chilean Coastal Lowland Quinoa

Quinoa (Chenopodium quinoa Willd.) is a genetically diverse crop that has gained popularity in recent years due to its high nutritional content and ability to tolerate abiotic stresses such as salinity and drought. Varieties from the coastal lowland ecotype are of particular interest due to their insensitivity to photoperiod and their potential to be cultivated in higher latitudes. We performed a field experiment in the southern Atacama Desert in Chile to investigate the responses to reduced irrigation of nine previously selected coastal lowland self-pollinated (CLS) lines and the commercial cultivar Regalona. We found that several lines exhibited a yield and seed size superior to Regalona, also under reduced irrigation. Plant productivity data were analyzed together with morphological and physiological traits measured at the visible inflorescence stage to estimate the contribution of these traits to differences between the CLS lines and Regalona under full and reduced irrigation. We applied proximal sensing methods and found that thermal imaging provided a promising means to estimate variation in plant water use relating to yield, whereas hyperspectral imaging separated lines in a different way, potentially related to photosynthesis as well as water use

Identification and Characterization of the Haloperoxidase VPO-RR from Rhodoplanes roseus by Genome Mining and Structure-Based Catalytic Site Mapping

Halogenating enzymes have evolved in considerable mechanistic diversity. The apparent need for secondary metabolism coincides with the current need to introduce halogens in synthetic products. The potential of halogenating enzymes and, especially, vanadate-dependent haloperoxidases has been insufficiently exploited for synthetic purposes. In this work, we identified potential halogenase sequences by screening algal, fungal, and protobacterial sequence databases, structural modeling of putative halogenases, and mapping and comparing active sites. In a final step, individual haloperoxidases were expressed and kinetically characterized. A vanadate-dependent haloperoxidase from Rhodoplanes roseus was heterologously expressible by E. coli and could be purified to homogeneity. The kinetic data revealed a higher turnover number than the known VClPO-CI and no inhibitory effect from bromide, rendering this enzyme a promising biocatalyst. Other predicted haloperoxidases were not expressed successfully yet but these enzymes were predicted to be present in a wide taxonomic variety