Author: slquinlan

Fungal Biol. 2025 Aug;129(5):101590. doi: 10.1016/j.funbio.2025.101590. Epub 2025 May 6.

ABSTRACT

The Fifth International Symposium on Fungal Stress (ISFUS) brought together in Brazil many of the leaders in the field of fungal stress responses, from fourteen countries, for four days of outstanding science ranging from basic research to studies with agricultural, medical, industrial, and environmental significance. In addition to the excellent oral and poster presentations, the Symposium organisers ensured that all participants had ample opportunity to engage, socialise, and network to exchange ideas and share research. The conference was enhanced by the world-class venue near Iguazu Falls, probably the greatest natural phenomenon in South America.

PMID:40707112 | DOI:10.1016/j.funbio.2025.101590

Mol Ecol Resour. 2025 Jul 22:e70012. doi: 10.1111/1755-0998.70012. Online ahead of print.

ABSTRACT

Yellow monkeyflowers (Mimulus guttatus complex, Phrymaceae) are a powerful system for studying ecological adaptation, reproductive variation, and genome evolution. To initiate pan-genomics in this group, we present four chromosome-scale assemblies and annotations of accessions spanning a broad evolutionary spectrum: two from a single M. guttatus population, one from the closely related selfing species M. nasutus, and one from a more divergent species M. tilingii. All assemblies are highly complete and resolve centromeric and repetitive regions. Comparative analyses reveal such extensive structural variation in repeat-rich, gene-poor regions that large portions of the genome are unalignable across accessions. As a result, this Mimulus pan-genome is primarily informative in genic regions, underscoring limitations of resequencing approaches in such polymorphic taxa. We document gene presence-absence, investigate the recombination landscape using high-resolution linkage data, and quantify nucleotide diversity. Surprisingly, pairwise differences at fourfold synonymous sites are exceptionally high-even in regions of very low recombination-reaching ~3.2% within a single M. guttatus population, ~7% within the interfertile M. guttatus species complex (approximately equal to SNP divergence between great apes and Old World monkeys), and ~7.4% between that complex and the reproductively isolated M. tilingii. Genome-wide patterns of nucleotide variation show little evidence of linked selection, and instead suggest that the concentration of genes (and likely selected sites) in high-recombination regions may buffer diversity loss. These assemblies, annotations, and comparative analyses provide a robust genomic foundation for Mimulus research and offer new insights into the interplay of recombination, structural variation, and molecular evolution in highly diverse plant genomes.

PMID:40693537 | DOI:10.1111/1755-0998.70012

Plant Physiol. 2025 Jul 3;198(3):kiaf294. doi: 10.1093/plphys/kiaf294.

ABSTRACT

Minimal native and synthetic Polymerase III promoters enable efficient and customizable CRISPR multiplexing in plants, expanding genome engineering capabilities

PMID:40673482 | PMC:PMC12268498 | DOI:10.1093/plphys/kiaf294

Plant J. 2025 Jul;123(2):e70294. doi: 10.1111/tpj.70294.

ABSTRACT

Advances in engineering of bioenergy crops were driven over the past years by adapting technological breakthroughs and accelerating conventional applications but also exposed intriguing challenges. New tools revealed rich interconnectivity in the exponentially growing and dynamic ‘big’ omics data’ of metabolomes, transcriptomes, and genomes at previously inaccessible magnitude (global, cross-species, meta-) and resolution (single cell). Insights enabled fresh hypotheses and stimulated disciplines such as functional genomics with discovery of broad regulatory networks and their determinants, that is, DNA parts, including promoters, regulatory elements, and transcription factors. Their rational design, assembly into increasingly complex blueprints, and installation into diverse chassis is an existing frontier that may benefit from emerging technologies to address bottlenecks. Interweaving nature-inspired to fully synthetic parts has already allowed building of fine-tuned regulatory circuits, or new-to-nature metabolic routes insulated from the biological context of the chassis species. Similarly, developments and the evolving need for unifying principles in plant transformation and species-agnostic technologies highlight future opportunities for engineering the next generation of bioenergy plants.

PMID:40674648 | DOI:10.1111/tpj.70294

Mol Ecol. 2025 Jul 17:e70033. doi: 10.1111/mec.70033. Online ahead of print.

ABSTRACT

Endemic pathogens continue to pose threats of recurring outbreaks, especially in agricultural settings. How these outbreaks unfold and what drives the variability in disease epidemics is less understood. We addressed this question in the Xanthomonas-tomato pathosystem by developing an integrated approach that linked the within-field quantitative signature of local pathogen diversity to climatic conditions to explain variable bacterial disease epidemics across fields. Using strain-resolved metagenomics, we found that pathogen heterogeneity with multiple co-occurring lineages is common. Higher disease severity was associated with higher pathogen diversity. Considering these observations, we used response-specific regression models to investigate the role of environmental variables in driving differences in disease and strain dynamics. Abrupt and frequent changes in environmental factors explained the variability of disease severity. We observed variable lineage dynamics across fields, but at least two lineages with divergent, climate-dependent fitness strategies coexisted throughout the growing season without either of them taking the lead. We further profiled the dynamics of single-nucleotide polymorphism variants in the pathogen population and observed that some alleles are temporarily favoured by specific climatic conditions encountered throughout the growing season, leading to oscillating seasonal patterns of allelic frequencies. These alleles can be referred to as seasonal alleles. Overall, our study revealed that the seasonal fluctuations in pathogen strain composition, diversity and climate-influenced pathogen fitness play a significant role in shaping the severity and variability of bacterial spot disease outbreaks.

PMID:40673408 | DOI:10.1111/mec.70033

Nat Chem Biol. 2025 Jul 16. doi: 10.1038/s41589-025-01970-9. Online ahead of print.

ABSTRACT

Monoterpene indole alkaloids (MIAs) are a large, structurally diverse class of bioactive natural products. These compounds are biosynthetically derived from a stereoselective Pictet-Spengler condensation that generates a tetrahydro-β-carboline scaffold characterized by a 3S stereocenter. However, a subset of MIAs contains a noncanonical 3R stereocenter. Here we report the basis for 3R-MIA biosynthesis in Mitragyna speciosa (kratom). We discover the presence of the iminium species (20S)-3-dehydrocorynantheidine, which supports isomerization of 3S to 3R via oxidation and stereoselective reduction downstream of the initial Pictet-Spengler condensation. Isotopologue feeding experiments identify the sites for downstream MIA pathway biosynthesis as well as the oxidase/reductase pair that catalyzes this epimerization. This oxidase/reductase pair has broad substrate specificity, suggesting that this pathway may be responsible for the formation of many 3R-MIAs and downstream spirooxindole alkaloids in kratom. The elucidation of this epimerization mechanism allows biocatalytic access to a range of pharmacologically active spirooxindole alkaloid compounds.

PMID:40670688 | DOI:10.1038/s41589-025-01970-9

Nature. 2025 Jul;643(8072):705-711. doi: 10.1038/s41586-025-09201-w. Epub 2025 Jul 16.

ABSTRACT

Biological nitrogen fixation (BNF) is the largest natural source of new nitrogen (N) that supports terrestrial productivity^1,2, yet estimates of global terrestrial BNF remain highly uncertain^3,4. Here we show that this uncertainty is partly because of sampling bias, as field BNF measurements in natural terrestrial ecosystems occur where N fixers are 17 times more prevalent than their mean abundances worldwide. To correct this bias, we develop new estimates of global terrestrial BNF by upscaling field BNF measurements using spatially explicit abundances of all major biogeochemical N-fixing niches. We find that natural biomes sustain lower BNF, 65 (52-77) Tg N yr^-1, than previous empirical bottom-up estimates^3,4, with most BNF occurring in tropical forests and drylands. We also find high agricultural BNF in croplands and cultivated pastures, 56 (54-58) Tg N yr^-1. Agricultural BNF has increased terrestrial BNF by 64% and total terrestrial N inputs from all sources by 60% over pre-industrial levels. Our results indicate that BNF may impose stronger constraints on the carbon sink in natural terrestrial biomes and represent a larger source of agricultural N than is generally considered in analyses of the global N cycle^5,6, with implications for proposed safe operating limits for N use^7,8.

PMID:40670639 | DOI:10.1038/s41586-025-09201-w

PLoS Genet. 2025 Jul 16;21(7):e1011742. doi: 10.1371/journal.pgen.1011742. Online ahead of print.

ABSTRACT

Meiotic drive elements are regions of the genome that are transmitted to progeny at frequencies that exceed Mendelian expectations, often to the detriment of the organism. In maize there are three prevalent chromosomal drive elements known as Abnormal chromosome 10 (Ab10), K10L2, and the B chromosome. There has been much speculation about how these drivers might interact with each other and the environment in traditional maize landraces and their teosinte ancestors. Here we used genotype-by-sequencing data to score more than 10,000 maize and teosinte lines for the presence or absence of each driver. Fewer than ~0.5% of modern inbred lines carry chromosomal drivers. In contrast, among individuals from 5331 open-pollinated landraces, 6.32% carried Ab10, 5.16% carried K10L2, and 12.28% carried at least one B chromosome. These frequencies are consistent with those reported in previous studies. Using a GWAS approach we identified unlinked loci that associate with the presence or absence of the selfish genetic elements. Many significant SNPs are positively associated with the drivers, suggesting that there may have been selection for alleles that ameliorate their negative fitness consequences. We then assessed the contributions of population structure, associated loci, and the environment on the distribution of each chromosomal driver. There was no significant relationship between any chromosomal driver and altitude, contrary to conclusions based on smaller studies. Our data suggest that the distribution of the major chromosomal drivers is primarily influenced by neutral processes and the deleterious fitness consequences of the drivers themselves. While each driver has a unique relationship to genetic background and the environment, they are largely unconstrained by either.

PMID:40668866 | DOI:10.1371/journal.pgen.1011742

Mol Ecol. 2025 Jul 15:e70024. doi: 10.1111/mec.70024. Online ahead of print.

ABSTRACT

Understanding the impact of domestication on deleterious mutations has fascinated evolutionary biologists and breeders alike. A ‘cost of domestication’ has been reported for some organisms through accumulation of gene disruptions or radical amino acid changes. However, recent evidence paints a more complex picture of this phenomenon in different domesticated species. In this study, we used genomic sequences of 253 tomato accessions to investigate the evolution of deleterious mutations and genomic structural variants (SVs) through tomato domestication history. We apply phylogeny-based methods to identify deleterious mutations in the domesticated tomato as well as its semi-wild and wild relatives. Our results implicate a downward trend throughout domestication in the number of genetic variants, regardless of their functional impact. This suggests that demographic factors have reduced overall genetic diversity, leading to lower deleterious load and SVs as well as loss of some beneficial alleles during tomato domestication. However, we detected an increase in proportions of nonsynonymous and deleterious alleles (relative to synonymous and neutral nonsynonymous alleles, respectively) during the initial stage of tomato domestication in Ecuador. Additionally, deleterious alleles in the commonly cultivated tomato seem to be more frequent than expected under a neutral hypothesis of molecular evolution. Our analyses also revealed frequent deleterious alleles in several well-studied tomato genes, probably involved in response to biotic and abiotic stress as well as fruit development and flavour regulation. To provide a practical guide for breeding experiments, we created TomDel, a public searchable database of 21,162 potentially deleterious alleles identified in this study (hosted on the Solanaceae Genomic Network; https://solgenomics.net/).

PMID:40662302 | DOI:10.1111/mec.70024

Front Plant Sci. 2025 Jun 30;16:1588485. doi: 10.3389/fpls.2025.1588485. eCollection 2025.

ABSTRACT

Pearl millet [Cenchrus americanus (L.) Morrone, formerly Pennisetum glaucum (L.) R. Br.] is the sixth most important cereal globally and is used for forage and feed in the U.S. To identify genomic regions governing important physiological, agronomic and yield related traits, a recombinant inbred line population derived from the cross between Tift 99D₂B_{1 ×} Tift 454 was phenotyped in the field in 2006, 2007 and 2013. In addition, the population was phenotyped for root-knot nematode resistance in the greenhouse during 2009. Using a previously generated genetic map containing 505 single nucleotide polymorphism markers and composite interval mapping, we identified 45 QTLs for eight traits (plant height, stem diameter, days to heading, panicle diameter, panicle length, 1000 seed weight, Pyricularia leaf spot disease, and root-knot nematode egg mass) across almost all linkage groups. These QTLs explained 6.31 to 32.51% of phenotypic variance for each trait and were consistently detected over different environments. Plant height and days to heading were colocalized on LG2 and LG5 showing maturity and plant height are linked and influence each other, similarly to other cereal crops. Interestingly, 5 of 19 QTLs linked to plant height, stem diameter, panicle diameter, and panicle length colocalized to the same locations on LG3, indicating breeding for one trait could simultaneously improve the other. The markers and genes identified in the present study can be used in developing high yielding pearl millet varieties using marker-assisted selection.

PMID:40661761 | PMC:PMC12256767 | DOI:10.3389/fpls.2025.1588485