Temasek Life Sciences Laboratory

Ferroptotic death of the developing conidia is important for pathogenicity of the blast fungus Magnaporthe oryzae, yet its regulatory mechanism is not fully elucidated in fungal cell. In this study, we found that elevated indole-3-acetic acid (IAA) promoted iron and lipid peroxide accumulation, leading to a higher degree of ferroptotic death of conidia. By characterising the IAA biosynthesis mutant, tam1Δ, we found that conidial death was positively correlated with levels of endogenous IAA. Furthermore, we found an IAA-dependent lipid metabolism gene mutant ppoaΔ displayed deficiencies in conidial death and the consequent delay in appressorium formation, and reduced pathogenicity. Exogenous addition of two types of phosphatidylethanolamines (PEs), DOPE and SLPE, could at least partially restore such defects in both tam1Δ and ppoaΔ, indicating that IAA promotes ferroptosis by affecting lipid metabolism and/or peroxidation. Additionally, we found TAM1 affected autophagy by modulating transcription of the ATG8 gene. Overall, our study reveals that M. oryzae produces and uses IAA to promote pathogenicity through triggering ferroptotic conidial death during pathogenic development. Our results provide a theoretical basis for blast disease control using IAA synthesis inhibitors.

ABSTRACT Stomata are microscopic pores that play a vital role in transpiration and gaseous exchange from leaf surfaces in plants. The stomatal density and size directly influence photosynthesis and hydrodynamics capacity. Conventional approaches for counting and determining stomatal density is labour-intensive and lack scalability. Although there are several AI-based stomata finder tools that were published in the last decade, existing models were trained on model plants like wheat, barley and Arabidopsis . Stomata in such model plants are generally elliptical, but applying a universal model to all plant species is not feasible due to their diverse morphological characteristics. Previous studies have suggested using the stomatal index to quantify the ratio between epidermal cells and total stomatal count. However, this approach can be difficult to apply consistently, as epidermal cell shape and size vary across plant species. Instead, we propose measuring stomatal density based on the number of stomata per total imaged pixel area in the captured images. In this study, a comparison between YOLOv12 and RF-DETR models were made for real-time stomata detection in normal and difficult-to-image and out-of-focus occluded images. The in-house training dataset consisted of images of 300 rice,100 barley and 50 sugarcane leaves that were captured against a dark background. YOLOv12 outperformed RF-DETR with higher mAP50:95 score. The models were trained with image augmentation for 300 epochs and YOLOv12 achieved a peak mean average precision of 98.5% and exceled at detecting stomata across abaxial and adaxial surfaces of leaves of both monocot and dicot plants. StomaQuant has also been shown to be effective for both epidermal peel and ethanol decolorised samples. Thus, StomaQuant can be used to effectively and efficiently estimate the stomatal density and size in a wide range of host plant species.

Sex determination in vertebrates exhibits remarkable evolutionary plasticity, with diverse mechanisms and master sex-determining (MSD) genes arising independently across lineages. Among these, dmrt1, a dosage-sensitive gene, has repeatedly been recruited as an MSD gene through gene duplication or allelic diversification. However, the biochemical basis of such evolutionary transitions, particularly those driven by allelic diversification, remains largely unexplored. Here, we generated haplotype-resolved genome assemblies for both XX and XY black carp (Mylopharyngodon piceus) and identified a ∼40-kb region on chromosome 4, containing only dmrt1, as the candidate sex-determining locus. We discovered two Y-specific insertions in the dmrt1 promoter: a 13.4-kb highly repetitive element and an 11-bp motif. Functional assays revealed that these insertions act as enhancer and a promoter element, respectively, driving early, allele-specific upregulation of dmrt1 prior to gonadal differentiation. Notably, the 13.4-kb insertion contains transposable elements (TEs) functioning as cis-regulatory modules with transcription factor binding sites that mediate Y-specific activation. Our findings reveal a TE-mediated regulatory innovation that promoted dmrt1's evolution as a male-determining gene via allelic diversification, providing new insights into how mobile genetic elements drive the origin and diversification of sex-determining systems in vertebrates.

ABSTRACT China is the world's leading producer of red swamp crayfish ( Procambarus clarkii ). The aquaculture of P. clarkii and its related industry generated annual value over 458 billion Chinese yuan in 2022, contributing significantly to food security, livelihoods, and economic development. This review analyzes the status of the industry, highlighting its biological characteristics, farming practices, economic importance, and challenges. P. clarkii is adaptable and reproduces rapidly, but it is also invasive and disrupts native species diversity. Environmental concerns include water quality degradation and habitat loss. Disease outbreaks and regulatory issues pose additional challenges. Research is ongoing to improve broodstocks, seed production efficiency, and sustainability through breeding programs, better management practices, and technologies. China's crayfish aquaculture can achieve long‐term growth and contribute to a sustainable future. This can be done by overcoming challenges and embracing key innovations. These include selective breeding, genomic selection, monosex production, genome editing technologies, and improved production systems.

Background/Objectives: The presence of multi-drug-resistant (MDR) bacteria in healthy individuals poses a significant public health concern, as these strains may contribute to or even facilitate the dissemination of antibiotic resistance genes (ARGs) and virulence factors. In this study, we investigated the genomic features of antimicrobial-producing Escherichia coli strains from the gut microbiota of healthy individuals in Singapore. Methods: Using a large-scale screening approach, we analyzed 3107 E. coli isolates from 109 fecal samples for inhibitory activity against E. coli DH5α and performed whole-genome sequencing on 37 representative isolates. Results: Our findings reveal genetically diverse strains, with isolates belonging to five phylogroups (A, B1, B2, D, and F) and 23 unique sequence types (STs). Bacteriocin gene clusters were widespread (92% of isolates carried one or more bacteriocin gene clusters), with colicins and microcins dominating the profiles. Notably, we identified an hcp-et3-4 gene cluster encoding an effector linked to a Type VI secretion system. Approximately 40% of the sequenced isolates were MDR, with resistance for up to eight antibiotic classes in one strain (strain D96). Plasmids were the primary vehicles for ARG dissemination, but chromosomal resistance determinants were also detected. Additionally, over 55% of isolates were classified as potential extraintestinal pathogenic E. coli (ExPEC), raising concerns about their potential pathogenicity outside the intestinal tract. Conclusions: Our study highlights the co-occurrence of bacteriocin genes, ARGs, and virulence genes in gut-residing E. coli, underscoring their potential role in shaping microbial dynamics and antibiotic resistance. While bacteriocin-producing strains show potential as probiotic alternatives, careful assessment of their safety and genetic stability is necessary for therapeutic applications.

Abstract The presence of multi-drug-resistant (MDR) bacteria in healthy individuals poses a significant public health concern, as these strains may contribute to or even facilitate the dissemination of antibiotic resistance genes (ARGs) and virulence factors. In this study, we investigated the genomic features of antimicrobial-producingEscherichia colistrains from the gut microbiota of healthy individuals in Singapore. Using a large-scale screening approach, we analyzed 3,107E. coliisolates from 109 fecal samples for inhibitory activity againstE. coliDH5α and performed whole-genome sequencing on 37 representative isolates.Our findings reveal genetically diverse strains, with isolates belonging to five phylogroups (A, B1, B2, D, and F) and 23 unique sequence types (STs). Bacteriocin gene clusters were widespread, with colicins and microcins dominating the profiles. Notably, we identified a hcp-et3-4 gene cluster, encoding an effector linked to Type VI secretion system. Approximately 40% of the sequenced isolates were MDR, with resistance for up to eight antibiotic classes in one strain. Plasmids were the primary vehicles for ARG dissemination, but chromosomal resistance determinants were also detected. Additionally, over 55% of isolates were classified as potential extraintestinal pathogenicE. coli(ExPEC), raising concerns about their potential pathogenicity outside the intestinal tract.Our study highlights the co-occurrence of bacteriocins, ARGs, and virulence genes in gut-residingE. coli, underscoring their potential role in shaping microbial dynamics and antibiotic resistance. While bacteriocin-producing strains show potential as probiotic alternatives, careful assessment of their safety and genetic stability is necessary for therapeutic applications.ImportanceThis study provides genomic insights into the diverse repertoire of potential bacteriocin production inE. colistrains isolated from a cohort of healthy human subjects in Southeast Asia. Our findings suggest that the co-occurrence of bacteriocin genes with multiple antibiotic resistance and virulence genes is a common feature among non-clinical isolates. This genetic linkage could contribute to the increased abundance of multi-drug-resistant and virulent strains within individual hosts. Moreover, this co-occurrence may facilitate the host colonization with strains carrying antibiotic resistance and virulence determinants, potentially also contributing to the dissemination of resistant and pathogenic strains within the local population and beyond.

ABSTRACTOrnamental aquaculture and fishkeeping are very popular with millions of enthusiasts worldwide. The number of newly imported fish species for ornamental purposes grew slowly from World War I until the 1980s. It then exponentially increased until now with more than 7900 species and a large number of scientifically undescribed morphotypes. Here we present the first comprehensive review of freshwater and brackish fish importations during the boom of ornamental fish keeping at the turn of the Millennium and discuss this with a cultural and socio‐economic lens in the European context. The increase in imports accelerated following the availability of air transport and the end of the Cold War. From the list of traded species, the largest number of species imported for ornamental purposes was found in the following groups: armored loricariid catfish (family Loricariidae), cory catfish (family Callichthyidae, subfamily Callichthyinae), cichlids of African Great Lakes (order Cichliformes), killifish (egg‐laying species of the order Cyprinodontiformes), and characids (order Characiformes). These taxa represent ca. 74% of all fresh and brackish water ornamental fish species. The species of fish with the ability to absorb atmospheric oxygen (e.g., Belontidae, including gouramis and bettas) have dominated the market, but their ratio to the other species has declined during the modern era of ornamental aquaculture (after the end of WWI). By identifying the most popular aquarium species traded through the history of the aquarium trade, our findings aim to guide present‐day management of ornamental aquaculture and better inform invasion risk assessments.