Canada has made significant contributions to the field of plant biochemistry, with numerous researchers actively focusing on elucidating the biosynthetic pathways of plant specialized metabolites and producing these compounds in heterologous systems, such as bacteria, yeast, or other plant species. The review aims to highlight the strengths of Canadian research in this domain over the last three decades. It will describe advances in pathway elucidation, enzyme characterization, and production of enzymes and metabolites in heterologous systems, particularly in the areas of alkaloids, terpenoids, and phenolic compounds. Canadian researchers have not only made pivotal scientific discoveries but have also ensured the continuity of scientific excellence by mentoring new generations of principal investigators in plant specialized metabolites. These advances warrant recognition and financial support to retain future talent and to maintain Canada’s leadership in scientific progress on the global stage.

In recent times, microalgae have emerged as powerful hosts for biotechnological applications, ranging from the production of lipids and specialized metabolites (SMs) of pharmaceutical interest to biofuels, nutraceutical supplements, and more. SM synthesis through bioengineered pathways relies on the availability of aromatic amino acids (AAAs) as an essential precursor. AAAs, phenylalanine, tyrosine, and tryptophan are also the building blocks of proteins, maintaining the structural and functional integrity of cells. Hence, they are crucial intermediates linking the primary and specialized metabolism. The biosynthesis pathway of AAAs in microbes and plants has been studied for decades, but not much is known about microalgae. The allosteric control present in this pathway has been targeted for metabolic engineering in microbes. This review focuses on the biosynthesis of AAAs in eukaryotic microalgae and engineering techniques for enhanced production. All the putative genes involved in AAA pathways in the model microalgae Chlamydomonas reinhardtii and Phaeodactylum tricornutum are listed in this review.

The integration of artificial intelligence (AI) into academia has revolutionized the way research and education are conducted. Two AI tools that have received significant attention are ChatGPT (https://chatgpt.com), a large language model (LLM), and DALL-E (https://openai.com/index/dall-e-3), a text-to-image model, both developed by OpenAI. These tools offer immense opportunities for enhancing academic productivity, creativity, and accessibility. They can help researchers to overcome language barriers, streamline administrative tasks, and improve the clarity and readability of academic writing. For instance, researchers who are non-native English speakers can use AI tools to correct grammar and enhance the readability of their manuscripts, thereby increasing their chances of publication in the journals of their choice. However, these tools also pose several challenges, particularly concerning scientific integrity and ethical use. This editorial explores the uses of ChatGPT and DALL-E in academia by highlighting the opportunities they present, the challenges linked to them, and discusses strategies for maintaining scientific integrity while utilizing them.

The utilization of alternate treatments to enhance the quality and safety of fresh produce has become a challenge for food industries and scientists. Cold plasma (CP) is an emerging technology that involves the generation of reactive gases, which through the generation of reactive species interact with microbial loads and lead chemical reactions to induce bioactive components. Despite the many applications of this technology, the mechanisms of action still need to be fully understood. The definition of CP involves several types of treatments and sources, providing the potential to develop adaptations within the parameters to reach optimal results. The scalability of these treatments to laboratory conditions, however, requires a deeper understanding. The use of CP to reduce pathogen loads such as Listeria monocytogenes, E. coli O157:H7 and Salmonella has been described; besides, the enhancement of bioactive constituents such as anthocyanins, phenols and carotenoids is also probed. Furthermore, the mechanisms of action of CP treatments are described. At the moment, CP treatments require further development and study to achieve their full range of industrial applications. These treatments can also be key for postharvest handling and research, mainly to preserve quality and prolong the shelf life of produce.

Interactions between various microbial pathogens including viruses, bacteria, fungi, oomycetes and their plant hosts have traditionally been the focus of phytopathology. In recent years, a significant and growing interest in the study of eukaryotic microorganisms not classified among fungi or oomycetes has emerged. Many of these protists establish complex interactions with photosynthetic hosts, and understanding these interactions is crucial in understanding the dynamics of these parasites within traditional and emerging types of farming, including marine aquaculture. Many phytopathogenic protists are biotrophs with complex polyphasic life cycles, which makes them difficult or impossible to culture, a fact reflected in a wide gap in the availability of comprehensive genomic data when compared to fungal and oomycete plant pathogens. Furthermore, our ability to use available genomic resources for these protists is limited by the broad taxonomic distance that these organisms span, that makes comparisons with other genomic datasets difficult. The current rapid progress in genomics and computational tools for the prediction of protein functions and interactions is revolutionising the landscape in plant pathology. This is also opening novel possibilities, specifically for a deeper understanding of protist effectors. Tools such as Alphafold enable better and more targeted functional predictions of divergent protein sequences. In turn this allows to ask better biological questions and, coupled with innovative experimental strategies, will lead into a new era of effector research, especially for protists, to expand our knowledge on these elusive pathogens and their interactions with photosynthetic hosts.

Climate change has facilitated the introduction, establishment, and movement of invasive species in northern regions, enabling the colonization of previously unsuitable areas. While the responses of insects to these changes have been increasingly studied, our understanding of how such alterations impact trophic interactions still requires further research to make reliable predictions about the spread of diseases in a warming world. Phytoplasmas, a group of obligate parasitic unculturable Mollicutes, primarily rely on leafhoppers (Hemiptera: Cicadellidae) for transmission, spread, and survival. Phytoplasmas are associated with over 600 diseases affecting more than 1,000 plant species, including berries, grapevines, and other small fruits. In North America, diseases such as grapevine yellows, blueberry stunt, and strawberry green petal diseases have been linked to phytoplasma strains transmitted by known leafhopper species. However, the number of phytoplasma diseases has significantly increased in North America over the past decade, suggesting the presence of unidentified vectors or an abundance of leafhopper vectors. This short review provides an overview of the current knowledge on leafhoppers as vectors of phytoplasmas to berries, focusing on the last decade’s research in Canada. This paper also explores the potential implications of climate change on this pathosystem, including the anticipated range expansion of leafhopper species, changes in phytoplasma acquisition and transmission, and the risk of new leafhopper-transmitted plant-pathogen introductions through the arrival of new leafhopper species.

Genome-wide association studies (GWAS) have allowed the discovery of marker–trait associations in crops over recent decades. However, their power is hampered by a number of limitations, with the key one among them being an overreliance on single-nucleotide polymorphisms (SNPs) as molecular markers. Indeed, SNPs represent only one type of genetic variation and are usually derived from alignment to a single genome assembly that may be poorly representative of the population under study. To overcome this, k-mer-based GWAS approaches have recently been developed. k-mer-based GWAS provide a universal way to assess variation due to SNPs, insertions/deletions, and structural variations without having to specifically detect and genotype these variants. In addition, k-mer-based analyses can be used in species that lack a reference genome. However, the use of k-mers for GWAS presents challenges such as data size and complexity, lack of standard tools, and potential detection of false associations. Nevertheless, efforts are being made to overcome these challenges and a general analysis workflow has started to emerge. We identify the priorities for k-mer-based GWAS in years to come, notably in the development of user-friendly programs for their analysis and approaches for linking significant k-mers to sequence variation.

In the 18th century, Carolus Linnaeus created a formalized system of classification of living organisms based on their anatomic relationships, which we know as taxonomic nomenclature. Historically, the genus Cannabis has been described three ways under this system: Cannabis sativa by C. Linnaeus in 1753, Cannabis indica by J.B. Lamarck in 1785, and Cannabis ruderalis by D.E. Janischewsky in 1924, with these taxonomic classifications having been derived from physical, morphological, chemical, and geographical data. Today, this confusing taxonomy has led to an ongoing debate about whether the genus Cannabis consists of a single species or multiple distinct species or subspecies. Recently, genome sequencing and bioinformatics have provided greater resolution of taxonomic assignments at the species level. As a result, some previously discussed classification frameworks have been brought into question. The aim of this review is to provide a historical context for the confusion surrounding the taxonomy of the genus Cannabis and highlight recent research on genomics-based taxonomical approaches to clarify the question of Cannabis taxonomy. We suggest that the latest evidence shifts away from the previous multiple species framework and points towards the genus Cannabis consisting of a highly diverse monotypic species.

Plasmodiophora brassicae Wor., the clubroot pathogen, is the perfect example of an “atypical” plant pathogen. This soil-borne protist and obligate biotrophic parasite infects the roots of cruciferous crops, inducing galls or clubs that lead to wilting, loss of productivity, and plant death. Unlike many other agriculturally relevant pathosystems, research into the molecular mechanisms that underlie clubroot disease and Plasmodiophora-host interactions is limited. After release of the first P. brassicae genome sequence and subsequent availability of transcriptomic data, the clubroot research community have implicated the involvement of phytohormones during the clubroot pathogen’s manipulation of host development. Herein we review the main events leading to the formation of root galls and describe how modulation of select phytohormones may be key to modulating development of the plant host to the benefit of the pathogen. Effector-host interactions are at the base of different strategies employed by pathogens to hijack plant cellular processes. This is how we suspect the clubroot pathogen hijacks host plant metabolism and development to induce nutrient-sink roots galls, emphasizing a need to deepen our understanding of this master manipulator.

RNA viruses are the most common class of pathogens responsible for the emergence of new human diseases, with two to three newly identified viruses annually. The recent 2019 coronavirus disease pandemic (Covid-19) underscores the importance of discovering new and effective antiviral agents. Alkaloids are a class of heterocyclic organic molecules bearing one or more nitrogen atoms and exhibiting a wide variety of structures. Several plant alkaloids are known for their extensive therapeutic properties. The objective of this review is to highlight the antiviral potential of alkaloids from Amaryllidaceae and from other types of plants against several families of RNA viruses, such as Flaviviruses, coronaviruses, Alphaviruses, Alphainfluenzaviruses and also against human immunodeficiency virus type 1 (HIV-1). Alkaloids act against viruses using several strategies and target both viral and cellular proteins. These molecules are bioactive agents that offer attractive prospects in the search for new antiviral drugs.

Nitrogen (N), a common chemical element in the atmosphere (78% of our atmosphere) yet less common within the Earth’s crust (less than 2%), is a crucial nutrient for life. It is an essential constituent of many cells, such as amino acids, proteins, chlorophyll, and even DNA, and is involved in various processes, such as photosynthesis, energy transfer, growth and reproduction. Up to 90% of the N in surface soils is organic in nature and is contained in soil organic matter (SOM). N cycling is complex, with numerous interacting controlling factors. Scientists around the world have been working for many decades now to understand, model and predict the soil’s capacity to supply N to plants in different ecosystems, whether agricultural, forest, grassland or urban. Plant available nitrogen (PAN) is a pillar of the functioning and productivity of any ecosystem.

The evolutionary fitness of plants to changing environments has been a continuous effort of stimulatory or adaptive responses to stress-induced hormesis; it is somewhat considered transgenerational. Recently, stress-induced hormesis in produce has recently drawn much attention, and various abiotic stressors have been tested successfully. The beneficial effects of hormesis in harvested crops include delayed senescence, disease resistance and enhanced abundance of secondary metabolites. This review attempts to give an overview of the importance of postharvest hormesis, the possible existence of such phenomenon in various stressors, possible underlying mechanisms involved, and finally provide some perspectives for its future application.

Artificial intelligence (AI) has revolutionized numerous fields, including genomics, where it has significantly impacted variant calling, a crucial process in genomic analysis. Variant calling involves the detection of genetic variants such as single nucleotide polymorphisms (SNPs), insertions/deletions (InDels), and structural variants from high-throughput sequencing data. Traditionally, statistical approaches have dominated this task, but the advent of AI led to the development of sophisticated tools that promise higher accuracy, efficiency, and scalability. This review explores the state-of-the-art AI-based variant calling tools, including DeepVariant, DNAscope, DeepTrio, Clair, Clairvoyante, Medaka, and HELLO. We discuss their underlying methodologies, strengths, limitations, and performance metrics across different sequencing technologies, alongside their computational requirements, focusing primarily on SNP and InDel detection. By comparing these AI-driven techniques with conventional methods, we highlight the transformative advancements AI has introduced and its potential to further enhance genomic research.

Marine specialized metabolites (MSM) represent a fascinating realm of chemical diversity with multifaceted functions across the spectrum of life on Earth. These metabolites serve as weapons, metal transporters, regulatory agents, and more. The conservation of genes responsible for their production over extensive evolutionary timescales underscores their selective advantage. Recent decades have witnessed an upsurge in MSM studies, driven by advancements in analytical techniques and the ever-growing accessibility of the aquatic environment. Marine macro and microorganisms offer a rich tapestry of specialized metabolites, some exhibiting potent activities in diverse domains, including medicine. The study of MSM presents several challenges, reflecting the need to separate complex mixtures into individual bioactive metabolites and utilize state-of-the-art extraction methods. Comprehensive structural analysis relies on advanced spectroscopic approaches, including nuclear magnetic resonance and mass spectrometry. These tools are instrumental in unravelling the chemical diversity of MSM and understanding their potential applications. While bioprospecting offers enormous potential, it raises critical challenges concerning sustainability, conservation, and equitable benefit-sharing. International protocols like the Nagoya Protocol seeks to regulate access to and share benefits from genetic resources, with considerable implications for marine bioprospecting. The convergence of advanced metabolomics, metagenomics, and synthetic biology offers promising avenues for accelerating the discovery and sustainable production of MSM, shaping the future of this field. This comprehensive review provides a deep dive into the challenges, methodologies, and emerging trends in studying marine-derived natural products, underscoring the immense potential of MSM for advancing chemical sciences and their transformative applications in diverse areas such as food, medicine, biotechnology, and environmental conservation. By bridging multiple disciplines, the continued exploration and sustainable utilization of these metabolites hold the promise of unlocking new innovations for society's benefit.

Food loss and waste occur throughout the food supply chain and represent food security and environmental, economic, and societal problems. Fresh fruit and vegetables contribute to over 40% of global food loss and waste. A significant portion of fruit and vegetables loss takes place on the farm during postharvest handling in developing countries, which is linked to smallholders’ financial and geographic constraints in purchasing modern postharvest handling technologies. While in developed countries, waste is the main problem identified at the retail and consumption levels because of inadequate logistics management, storage, and consumer behavior. The loss and waste deprive the population of a significant quantity of healthy food. To address this challenge, cost-effective, easy-to-use, and affordable approaches could be supplied to stakeholders. These strategies encompass the utilization of shading, low-cost packaging, porous evaporative cooling, zero-energy cooling chambers, and pot-in-pot coolers, for reductions in loss in developing countries. Meanwhile, in developed countries, biosensors, 1-methylcyclopropene, and imaging processing are employed to assess the quality of fresh fruit and vegetables at both retail and consumer levels. By exploring these methods, the review aims to provide smallholders, retailers, and consumers with efficient methods for improving produce operating techniques, resulting in reduced losses and waste and higher income.

Amaryllidaceae alkaloid (AAs) biosynthesis has garnered significant attention in recent years, particularly with the commercialisation of galanthamine as a treatment for the symptoms of Alzheimer‟s disease. A significant amount of research work over the last 8 decades has focused on the understanding of AA biosynthesis, starting from early radiolabelling studies to recent multi-omics analysis with modern biotechnological advancements. Those studies enabled the identification of hundreds of metabolites, the characterisation of biochemical pathway, an understanding of the environmental stimuli, and of the molecular regulation of these pharmaceutically and agriculturally important metabolites. Despite the numerous works there remain significant gaps in understanding their biosynthesis in Amaryllidaceae plants. As such, further research is needed to fully elucidate the metabolic pathway and facilitate their production. This review aims to provide a comprehensive overall summary of the current state of knowledge on AAs biosynthesis, from elicitation of transcription factors expression in the cell nucleus to alkaloid transport in the apoplast, and to highlight the challenges that need to be overcome for further advancement.

Amaryllidaceae alkaloids (AAs) are a unique class of specialized metabolites containing heterocyclic nitrogen bridging that play a distinct role in higher plants. Irrespective of their diverse structures, most AAs are biosynthesized via intramolecular oxidative coupling. The complex organization of biosynthetic pathways is constantly enlightened by new insights owing to the advancement of natural product chemistry, synthetic organic chemistry, biochemistry, systems and synthetic biology tools and applications. These promote novel compound identification, trace-level metabolite quantification, synthesis, and characterization of enzymes engaged in AA catalysis, enabling the recognition of biosynthetic pathways. A complete understanding of the pathway benefits biotechnological applications in the long run. This review emphasizes the structural diversity of the AA specialized metabolites involved in biogenesis although the process is not entirely defined yet. Moreover, this work underscores the pivotal role of synthetic and enantioselective studies in justifying biosynthetic conclusions. Their prospective candidacy as lead constituents for antiviral drug discovery has also been established. However, a complete understanding of the pathway requires further interdisciplinary efforts in which antiviral studies address the structure–activity relationship. This review presents current knowledge on the topic.

One widely recognized climate change mitigation strategy in agriculture is enhancing soil carbon (C) sequestration – the process of capturing atmospheric carbon dioxide and storing it in the soil. By adopting natural climate solutions (NCS) such as cover crops, reduced tillage, and diverse crop rotations, farmers can increase soil C sequestration and co-benefits such as biodiversity. Canada is increasingly interested in better positioning farmers to adopt NCS via government cost-share programs, ecosystem marketplaces, and outreach and education initiatives. Given the policy and market driven interest in soil C sequestration in agriculture, there is a need to advance the science policy interface, ensuring foundational science, NCS implementation, and approaches to promote NCS are aligned. Herein, the objective is to present insights from multiple disciplines that can help build connections between soil carbon sequestration science and policy relevant to Canada's croplands. The method is a review of literature on soil and pedoclimate science, agricultural NCS adoption, agricultural NCS governance, and science policy interfaces to achieve this objective. From this review, key insights underline that Canadian cropland soils do not have a homogenous history in NCS adoption and production type, nor are all regions influenced by the same contextual factors, have the same potential in C storage or exist within the same agri-environmental conditions. Therefore, it is emphasized herein that policies that aim to enhance soil organic carbon in croplands should consider local context and C sequestration potential. Policies and programs implemented locally to enhance C sequestration across Canada should be complemented by nationally scalable measuring and monitoring to ensure outcomes are accounted for against climate goals. This review aims to contribute to building a common understanding of soil C sequestration in Canada’s croplands and its science policy interface. Efforts to further strengthen the science policy interface for soil C sequestration in Canada’s croplands might include greater integration and utilization of science and data from multiple disciplines, co-design and collaborative opportunities, and establishing on-the-ground test projects to explore innovation in policy and market design.

As green chemical factories, medicinal plants contain a wide range of bioactive compounds crucial for biomaterial industries. Despite their high economic value, medicinal plants are in the last ring of domestication syndrome and have been neglected for many years by plant breeders. In recent years, plant scientists have tried to compensate for these shortages by developing different strategies, especially faster biotechnology-based methods (BBMs) to conserve and improve these valuable but neglected plants. For the first step, the information and awareness of endangered medicinal plants is very important. Kakkar et al. reviewed all available information related to the nomenclature and classification, endangerment, plant morphology, ploidy, secondary metabolites, drug pharmacokinetics, conservation, and omics-based computational studies in Aconitum genus. The presented information is very valuable in terms of conservation of endangered economically important poisonous mountainous medicinal plant species in this genus.The assessment of the genetic background of valuable medicinal plants is the second step to improve medicinal plants and schedule efficient breeding programs. In this context, the research article by Wei et al. applied the complete chloroplast genome sequencing and phylogenetic study to distinguish three Gaoben-related medicinal plants, including Ligusticum sinense, L. jeholense, and Conioselinum vaginatum, which are similar in morphology and are difficult t

Clubroot is a devastating disease affecting cruciferous crops worldwide, caused by the obligate parasite Plasmodiophora brassicae. Currently, the use of clubroot resistant cultivars is the best strategy to stop the spreading of the disease and avoid millionaire loses experienced by the industry every year. Unfortunately, after decades of research, clubroot resistance is being overcome by new pathotypes and the mechanisms behind this remain unknown. Here we discuss how we can advance our understanding of the pathogen and the host through genomics. However, this multilayered strategy needs to be concerted to find a stable solution for growers.

Phytophthora sojae, the agent responsible for stem and root rot, is one of the most damaging plant pathogens of soybean. To establish a compatible-interaction, P. sojae secretes a wide array of effector proteins into the host cell. These effectors have been shown to act either in the apoplastic area or the cytoplasm of the cell to manipulate the host cellular processes in favor of the development of the pathogen. Deciphering effector-plant interactions is important for understanding the role of P. sojae effectors in disease progression and developing approaches to prevent infection. Here, we review the subcellular localization, the host proteins, and the processes associated with P. sojae effectors. We also discuss the emerging topic of effectors in the context of effector-resistance genes interaction, as well as model systems and recent developments in resources and techniques that may provide a better understanding of the soybean-P. sojae interaction.

Background: Plasmodiophora brassicae is the causal agent of clubroot disease of cru-ciferous plants and one of the biggest threats to the rapeseed (Brassica napus) and brassica vegetable industry worldwide.

Disease symptoms: In the advanced stages of clubroot disease wilting, stunting, yel-lowing, and redness are visible in the shoots. However, the typical symptoms of the disease are the presence of club-shaped galls in the roots of susceptible hosts that block the absorption of water and nutrients.

Host range: Members of the family Brassicaceae are the primary host of the patho-gen, although some members of the family, such as Bunias orientalis, Coronopus squa-matus, and Raphanus sativus, have been identified as being consistently resistant to P. brassicae isolates with variable virulence profile.

Taxonomy: Class: Phytomyxea; Order: Plasmodiophorales; Family: Plasmodiophoraceae; Genus: Plasmodiophora; Species: Plasmodiophora brassicae (Woronin, 1877).

Distribution: Clubroot disease is spread worldwide, with reports from all continents except Antarctica. To date, clubroot disease has been reported in more than 80 countries.

Pathotyping: Based on its virulence on different hosts, P. brassicae is classified into pathotypes or races. Five main pathotyping systems have been developed to under-stand the relationship between P. brassicae and its hosts. Nowadays, the Canadian clubroot differential is extensively used in Canada and has so far identified 36 differ-ent pathotypes based on the response of a set of 13 hosts.

Effectors and resistance: After the identification and characterization of the clubroot pathogen SABATH-type methyltransferase PbBSMT, several other effectors have been characterized. However, no avirulence gene is known, hindering the functional characterization of the five intercellular nucleotide- binding (NB) site leucine- rich- repeat (LRR) receptors (NLRs) clubroot resistance genes validated to date.

Amaryllidaceae alkaloids (AAs) are plant specialized metabolites with therapeutic properties exclusively produced by the Amaryllidaceae plant family. The two most studied representatives of the family are galanthamine, an acetylcholinesterase inhibitor used as a treatment of Alzheimer’s disease, and lycorine, displaying potent in vitro and in vivo cytotoxic and antiviral properties. Unfortunately, the variable level of AAs’ production in planta restricts most of the pharmaceutical applications. Several biotechnological alternatives, such as in vitro culture or synthetic biology, are being developed to enhance the production and fulfil the increasing demand for these AAs plant-derived drugs. In this review, current biotechnological approaches to produce different types of bioactive AAs are discussed.