Author: slquinlan

Proc Natl Acad Sci U S A. 2025 Aug 12;122(32):e2426650122. doi: 10.1073/pnas.2426650122. Epub 2025 Aug 6.

ABSTRACT

Cells accumulate mutations throughout development, contributing to cancer, aging, and evolution. Quantitative data on the abundance of de novo mutations within plants or animals are limited, as new mutations are often rare within a tissue and fall below the limits of current sequencing depths and error rates. Here, we show that mutations induced by the maize Mutator (Mu) transposon can be reliably quantified down to a detection limit of 1 part in 16,000. We measured the abundance of millions of de novo Mu insertions across four tissue types. Within a tissue, the distribution of de novo Mu allele frequencies was highly reproducible between plants, showing that, despite the stochastic nature of mutation, repeated statistical patterns of mutation abundance emerge. In contrast, there were significant differences in the allele frequency distribution between tissues. At the extremes, root was dominated by a small number of highly abundant de novo insertions, while endosperm was characterized by thousands of insertions at low allele frequencies. Finally, we used the measured pollen allele frequencies to reinterpret a classic genetic experiment, showing that evidence for late Mu activity in pollen is better explained by cell division statistics. These results provide insight into the complexity of mutation accumulation in multicellular organisms and a system to interrogate the factors that shape mutation abundance.

PMID:40768352 | DOI:10.1073/pnas.2426650122

Insects. 2025 Jun 24;16(7):653. doi: 10.3390/insects16070653.

ABSTRACT

Blueberry is a high-value fruit crop in the United States, with Georgia and Florida serving as important early-season production regions. In these areas, several thrips species (Thysanoptera: Thripidae), including Frankliniella tritici (Fitch), Frankliniella bispinosa (Morgan), and Scirtothrips dorsalis (Hood), have emerged as economically significant pests. While F. tritici and F. bispinosa primarily damage floral tissues, S. dorsalis targets young foliage. Their rapid reproduction, high mobility, and broad host range contribute to rapid population buildup and complicate the management programs. Species identification is often difficult due to overlapping morphological features and requires the use of molecular diagnostic tools for accurate identification. Although action thresholds, such as 2-6 F. tritici per flower cluster, are used to guide management decisions, robust economic thresholds based on yield loss remain undeveloped. Integrated pest management (IPM) practices include regular monitoring, cultural control (e.g., pruning, reflective mulch), biological control using Orius insidiosus (Say) and predatory mites, and chemical control. Reduced-risk insecticides like spinetoram and spinosad offer effective suppression while minimizing harm to pollinators and beneficial insects. However, the brief flowering period limits the establishment of biological control agents. Developing species-specific economic thresholds and phenology-based IPM strategies is critical for effective and sustainable thrips management in blueberry cropping systems.

PMID:40725285 | DOI:10.3390/insects16070653

BMC Microbiol. 2025 Jul 28;25(1):456. doi: 10.1186/s12866-025-04175-1.

ABSTRACT

BACKGROUND: The genus Enterobacter, in the family Enterobacteriaceae, is of both clinical and environmental importance. This genus has undergone frequent taxonomic changes, making it challenging to identify taxa even at genus level. This study aimed to design Enterobacter genus-specific primers that can be used for simple PCR identification of large sets of putative Enterobacter isolates.

RESULTS: Comparative genomic approaches were employed to identify genes that were universally present on Enterobacter genomes but absent from the genomes of other members of the family Enterobacteriaceae, based on an initial set of 89 genomes. The presence of these genes was further confirmed in 4,276 Enterobacter RefSeq genomes. While no strictly genus-specific genes were identified, the hpaB gene demonstrated a restricted distribution outside of the genus Enterobacter. Semi-nested primers were designed for hpaB and its flanking gene hpaC (hpaBC) and evaluated on 123 strains in single-tube PCR reactions. All taxa showing positive reactions belonged to the genus Enterobacter. For Enterobacter strains the PCR yielded two amplicons at 110 bp and at 370 bp, while strains only displaying the 110 bp amplicon were classified as Leclercia pneumoniae. A blind-test on 120 strains accessioned as Enterobacter sp. from the USDA-ARS culture collection (NRRL), revealed that one third of the strains had an incorrect genus assignment. Comparison of gene trees of the hpaBC fragment sequences with marker genes frequently used for single-gene barcoding or multi-locus sequence analysis (MLSA) further demonstrated its potential for preliminary species identification.

CONCLUSIONS: The nested PCR assay represents a rapid and cost-effective approach for preliminary identification of Enterobacter species. As the primer design was based on large-scale genomic comparison, including currently undescribed species clades, it will remain valid even after taxonomic changes within the genus.

PMID:40722002 | DOI:10.1186/s12866-025-04175-1

Front Plant Sci. 2025 Jul 11;16:1607733. doi: 10.3389/fpls.2025.1607733. eCollection 2025.

ABSTRACT

Maize (Zea mays L.) is the most widely produced crop in the world, and conventional production requires significant amounts of synthetic nitrogen fertilizer, which has negative economic and environmental consequences. Maize landraces from Oaxaca, Mexico, can acquire nitrogen from nitrogen-fixing bacteria that live in a mucilage secreted by aerial nodal roots. The development of these nodal roots is a characteristic traditionally associated with the juvenile vegetative stage of maize plants. However, mature Oaxacan landraces develop many more nodes with aerial roots than commercial maize varieties. Our study shows that Oaxacan landraces develop aerial roots during the juvenile and adult vegetative phases and even during early flowering under greenhouse and field conditions. Surprisingly, the development of these roots was only minimally affected by soil nitrogen and ambient humidity. These findings are an essential first step in developing maize varieties to reduce fertilizer needs in maize production across different environmental conditions.

PMID:40718026 | PMC:PMC12289584 | DOI:10.3389/fpls.2025.1607733

Plant Sci. 2025 Jul 23:112682. doi: 10.1016/j.plantsci.2025.112682. Online ahead of print.

ABSTRACT

Enhanced protein degradation, typically conducted by the coordinated action of proteases and the ubiquitin-proteasome system (UPS), is a common response to heat stress. It works by removing nonfunctional or damaged proteins to maintain normal cell function and to allow for the remobilization of nutrients, enabling plants to respond rapidly to environmental perturbation. Despite its crucial role, there has been limited research addressing proteolysis activities from both proteases and the UPS in grasses exposed to heat stress. This project aims to quantify activities of proteases and the UPS in different lines of creeping bentgrass (Agrostis stolonifera L.), a cool-season turfgrass that’s prized for its functional and aesthetic qualities, and detect changes in expression levels of known proteases and the UPS genes. Previously identified heat-tolerant and -sensitive creeping bentgrass lines were selected for this study. They were exposed to either control (20/15°C day/night) or heat stress (38/33°C day/night) treatments for 35 d. Protein degradation was enhanced under heat as demonstrated by significant increases in protease activity and the UPS activity over time. A more heat-tolerant line, S11 729-10, maintained lower activities of both protease and the UPS, contributing to its higher protein contents, and thereby greater thermotolerance. Additionally, gene expression was variable across lines, with heat sensitive Crenshaw having lower expression levels as heat stress progressed. This is the first time that the roles of protease activity and the UPS activity in heat stress were simultaneously analyzed in a perennial grass species. Such information will broaden the understanding of how protein degradation is regulated in response to heat stress, providing a deeper insight into thermotolerance mechanisms in creeping bentgrass.

PMID:40712792 | DOI:10.1016/j.plantsci.2025.112682

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