Author: slquinlan

Appl Environ Microbiol. 2026 Sep 3:e0086526. doi: 10.1128/aem.00865-26. Online ahead of print.

ABSTRACT

Trichoderma reesei is known for its ability to secrete high amounts of cellulases, enzymes of fundamental importance in generating products from lignocellulosic biomass. Diverse signaling pathways and transcription factors (TFs) control the cellulolytic repertoire in T. reesei to ensure correct adaptation to the environment. Here, we analyzed RNA-Seq data and identified a new potential regulator of cellulase production in T. reesei: a novel TF named Nsd3, a homolog of NsdC from Aspergilli. Deletion of nsd3 reduced vegetative growth and conidiation on solid medium. Phenotypic characterization of the Δnsd3 strain showed that it is more sensitive to osmotic stress, but more resistant to cell wall and oxidative stresses. Our results showed that Nsd3 is a repressor of cellulase expression by directly regulating key genes in the cellulolytic pathway, an unreported role for this TF in fungi. Loss of nsd3 leads to a faster and more robust induction of cellulolytic genes, and higher cellulase and hemicellulase activities. Transcriptional profiling by RNA-Seq, chromatin accessibility profiling by ATAC-Seq, and protein-DNA interaction assays showed that sugar transporters are important targets of Nsd3 during cellulase expression regulation. Combined with microscopy and gene expression analyses, the ATAC-Seq data also highlighted Nsd3 as a central regulator of cell wall remodeling and organization. Furthermore, the transcriptomics also showed that Nsd3 regulates genes involved in secondary metabolism. These results showed that Nsd3 regulates several physiological processes and provide novel insights into the regulatory system of cellulases in T. reesei that can be used in the design of high-performance strains for biorefinery.IMPORTANCETrichoderma reesei is a key player in the production of hydrolytic enzymes for the degradation of lignocellulose biomass, and transcription factors are important targets for genetic engineering to construct cellulase-hyperproducing strains. Here, we identified the transcription factor Nsd3 and characterized its role as a regulator of cellulase production in T. reesei. We applied two powerful genomics methods (transcriptome sequencing and chromatin accessibility sequencing) to unravel the global role of Nsd3 and its regulatory mechanism. Nsd3 participates in various biological processes in T. reesei, including cell wall remodeling, calcium metabolism, and secondary metabolism, in addition to regulating the expression of sugar transporters. Protein-DNA interaction assays demonstrate that Nsd3 acts through important genes to regulate cellulase expression, including ace4, crt1, stp1, and cel1b. Our study provides mechanistic insights about how Nsd3 regulates diverse physiological processes in T. reesei. This work also applied ATAC-Seq for the first time to study chromatin accessibility in T. reesei.

PMID:42690075 | DOI:10.1128/aem.00865-26

mBio. 2026 Sep 1:e0183126. doi: 10.1128/mbio.01831-26. Online ahead of print.

ABSTRACT

Aspergillus fumigatus is a thermotolerant saprobe found in soils and plant debris worldwide and an important pathogen of humans, causing two million deaths annually. A. fumigatus makes abundant asexual spores (conidia), which are widely distributed by wind and can be inhaled from the environment. In susceptible individuals, inhaled conidia break dormancy, germinate, and grow in the lung, leading to serious disease. Recent work has shown that conidia made at 37°C and 50°C have different morphologies and germination kinetics. While the asexual cycle is well-characterized at 37°C, much less is known about the asexual cycle at 50°C. Here, we combine flow cytometry and transcriptomics to track morphology and gene expression in the hyphae, conidiophores, and conidia of A. fumigatus during asexual development at 37°C or 50°C. We show that the temperature during a narrow time window in late-stage conidiophore development dictates resulting conidial morphology, transcriptional program, and germination kinetics. As expected, conidiation at 37°C resulted in upregulation of brlA, encoding the master regulator of asexual development, and its downstream targets in conidiophores and conidia. Surprisingly, conidiation at 50°C resulted in upregulation of MAT1-1-1, encoding the master regulator of sexual development, and its downstream targets in conidiophores and conidia. Our findings suggest that temperature during late conidiophore development transcriptionally primes conidia for asexual, parasexual, or sexual development, enhancing chances of survival for progeny. Our findings are especially relevant for agricultural compost, where a wide gradient of temperatures exists, abundant A. fumigatus has been isolated, and resistance to antifungals is thought to evolve.IMPORTANCEThe human pathogen Aspergillus fumigatus has been found in natural and agricultural environments around the world. Disease is acquired when susceptible individuals inhale airborne asexual spores from the environment, which in agriculture generally includes proximity to compost and plant debris piles. This work shows that the environmental temperature when A. fumigatus spores are made determines the transcriptomes of those spores, priming them for future asexual or sexual development. The survival of asexual and sexual spores is very different at different temperatures, so these results are important for understanding how this pathogen survives in varied hostile environments. In addition, there are very few antifungal drugs with which to treat A. fumigatus infections, and resistance is increasing, driven in part by agricultural use of fungicides. These results suggest that higher temperatures during asexual spore formation can lead to increased sexual reproduction and greater chances to evolve antifungal resistance.

PMID:42678159 | DOI:10.1128/mbio.01831-26

J Evol Biol. 2026 Aug 26:voag075. doi: 10.1093/jeb/voag075. Online ahead of print.

ABSTRACT

Abiotic and biotic factors interact to shape the expression of traits and fitness. In contemporary environments, species must respond not only to novel climates but also to altered biotic interactions, and these pressures likely differ across the landscape, which affects population persistence and range limits. Here, we tested the interactive effects of soil microbial communities and temperature variation on plant traits and fitness. We predict that plants are locally adapted to their home soil communities and temperatures, and that local soil microbes could mitigate stresses associated with exposure to elevated temperatures. We conducted a growth chamber experiment using a perennial plant native to the southeastern U.S.A., Elephantopus tomentosus (Asteraceae, L.), in which we exposed accessions from populations in the center of the range and the northern range edge to a fully factorial combination of three soil communities and two temperature levels, reflecting the current average temperature in the central portion of the range vs. potential future climates (+ 4°C). To test whether plants are adapted to their local soil microbial community, we inoculated pots with field soils collected from the center of the range, the range-edge, or with a sterilized control. Plants experienced a greater reduction in reproductive fitness under elevated temperatures when exposed to sterile soil than when grown in live soil. Additionally, plants in central soils had greater fecundity at elevated temperatures than those in northern range-edge soils, which is congruent with expectations and with the finding that seeds sourced from northern populations exhibited a greater reduction in fecundity under elevated temperatures than those sourced from the warmer central populations. Central soil communities increased the growth rate of both accessions, likely due to central-range specific microbes. Our study revealed that plant fitness varied with both temperature and soil microbes, highlighting the importance of accounting for biotic interactions in studies of the biological evolution to climate change.

PMID:42642040 | DOI:10.1093/jeb/voag075

Pest Manag Sci. 2026 Aug 25. doi: 10.1002/ps.71226. Online ahead of print.

ABSTRACT

BACKGROUND: Managing viruses transmitted by the sweet-potato whitefly (Bemisia tabaci Gennadius) is challenging as no single tactic provides adequate and consistent efficacy. These viruses are commonly found as a mixed infection in squash (Cucurbita pepo) plants; hence, they are collectively termed as the ‘whitefly-transmitted virus complex’ (WTVC) in this manuscript. While some tactics for managing WTVC are available, the relative impact of each management tactic in reducing disease severity is not known. This study aimed to quantify the relative importance of key management practices and develop a data-driven risk assessment framework to support integrated pest management (IPM) decisions.

RESULTS: Utilizing data from 14 field trials (n = 14) conducted over 3 years (2020-2022) in southern Georgia, United States, a random forest model was applied to evaluate the influence of five management variables on WTVC severity. Planting date and use of row cover were identified as the most influential factors, followed by squash type, planting material, and mulch type. A risk assessment index was developed based on variable importance scores. The cumulative risk-point values showed significant positive correlations with standardized area under the disease progress curve (sAUDPC) in both training (r = 0.58, P < 0.001) and testing (r = 0.50, P < 0.001) datasets. Early planting, particularly yellow squash, the use of seedlings and the row covers were associated with reduced WTVC severity.

CONCLUSIONS: Planting squash before the seasonal peak in whitefly populations, using row covers, and seedlings were associated with the lower WTVC risk. In our study, the resulting risk index and SquashRx application provided pre-season decision support for fall squash production in southern Georgia. As the index was developed and validated using data from this region, it should be validated before use elsewhere. © 2026 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

PMID:42642918 | DOI:10.1002/ps.71226

Mol Ecol. 2026 Aug;35(16):e70522. doi: 10.1111/mec.70522.

ABSTRACT

Hybridization is a powerful force shaping the evolutionary trajectories of species, yet its outcomes are highly variable both across taxa and within a pair of species. In this study, we examine the processes shaping variation in the extent of hybrid ancestry, both among populations and across the genome. We use low-coverage sequencing data to infer local ancestry across the genome for 782 individuals from multiple populations across two geographic regions within the broadly overlapping range of Mimulus guttatus and Mimulus nasutus. We find that the extent of hybrid ancestry is variable across populations, supporting disparate historical patterns of hybridization. However, genomic patterns of hybrid ancestry are correlated across groups, indicating they are shaped by parallel processes. Correlations are highest in geographically proximal populations, including between sympatric and allopatric locations, providing evidence that introgression is not locally constrained but spreads via migration across the landscape. We find that features of the genome are predictive of hybrid ancestry and its correlations among populations. However, contrary to findings in some other species, these patterns are likely not driven by simple linked selection against hybrid ancestry. Genomic outliers for high hybrid ancestry are often shared among populations, suggesting a role for parallel positive selection on ancestry. However, known loci associated with reproductive isolation are poor predictors of ancestry variation across populations, indicating that selection acting in natural hybrid populations is highly polygenic and that the underlying genetic architecture varies across space. Overall, this study demonstrates how ecological, demographic and genomic features all interact to shape the outcomes of hybridization.

PMID:42639733 | DOI:10.1111/mec.70522

Int J Biol Macromol. 2026 Aug 21:154166. doi: 10.1016/j.ijbiomac.2026.154166. Online ahead of print.

ABSTRACT

Pectin is a complex plant cell wall polysaccharide whose galacturonic acid residues can be acetylated at O-2 and/or O-3 positions. The degree of acetylation is regulated by pectin acetyl esterase (PAE, EC 3.1.1.6). However, the structure and function of plant PAEs is unclear, impairing our understanding of the role of the fine-tuning of pectin acetylation in the control of plant development. This study highlights the importance of AtPAE11 from Arabidopsis thaliana in fine tuning of pectin acetylation. AtPAE11 was heterologously expressed in HEK cells and purified by affinity chromatography. AtPAE11 exhibited activity across a broad pH range (3.5-7.5), with an optimal temperature of 30 °C. Nuclear magnetic resonance spectroscopy, supported by molecular docking, indicated a specific activity toward O-3 acetylated homogalacturonan (HG), with reduced activity on methylesterified HG. Mass spectrometry analyses showed no AtPAE11 activity on lyase-treated HG. Enzymatic pretreatment of pectin using pectin methylesterase and AtPAE11 slightly enhanced the oligogalacturonides formation by HG lyase activity, indicating a sequential degradation mechanism. Additionally, AtPAE11 treatment improved the stiffness of sugar beet pectin gel, opening new possibilities for pectin valorization. These findings provide new insights into the function of plant PAEs in plants and identify AtPAE11 as a highly specific enzyme.

PMID:42628858 | DOI:10.1016/j.ijbiomac.2026.154166

Proc Natl Acad Sci U S A. 2026 Sep;123(35):e2606323123. doi: 10.1073/pnas.2606323123. Epub 2026 Aug 21.

ABSTRACT

Geophytes are plants that produce underground storage organs such as tubers, rhizomes, and bulbs, to facilitate asexual reproduction and withstand a myriad of environmental challenges. While the potato (Solanum tuberosum L.) serves as the primary model for studying tuberization, the genetic mechanisms encoding this trait across diverse angiosperm lineages remains unclear. This study utilized a phylogenomic-transcriptomic approach to compare tuber development across nine tuberizing species with five nontuberizing sister taxa. We identified orthologs of key potato tuberization genes that exhibit similar expression in the stolons or tubers of these distant relatives. In nontuberizing species, these orthologs exhibit distinct expression profiles and are primarily expressed in the stem. This suggests that the independent evolution of tubers across angiosperms resulted from shifts in the expression of preexisting genes that led to their co-option. This process, also known as exaptation, occurs when existing genetic suites are recruited for entirely new biological functions. This mechanism stands in contrast to the repeated loss or gain of genes, which has been associated with the origin of other adaptive plant traits. Furthermore, the co-option of the same genes was observed in species with other stem-derived storage organs, such as rhizomes and runners. These findings reveal a conserved evolutionary model for the development of stem-derived geophyte organs that evolved independently across the flowering plants over the past 160 My.

PMID:42627842 | DOI:10.1073/pnas.2606323123

Theor Appl Genet. 2026 Aug 20;139(9):237. doi: 10.1007/s00122-026-05346-y.

ABSTRACT

In sunflower (Helianthus annuus L.), the composition of fatty acids in the seeds, primarily oleic, linoleic, stearic and palmitic acid, is of utmost importance for oil quality. Despite this, the genetic basis of this trait and its interaction with the environment is poorly understood. Understanding this interaction is critical to improvement of sunflower within the context of climate change. In this work, we incorporated fatty acid composition measurements from the sunflower SAM population and eight environments across an extensive geographic cline into GWAS. The SAM panel consists of 287 varieties representing approximately 90% of sunflower diversity, for which 2.2 million high-quality SNPs with a MAF > 5% are available. For increased power, multivariate GWAS was performed with four different inputs: (i) mean fatty acid composition within each environment, (ii) mean fatty acid composition within each environment omitting high oleic varieties, (iii) trait stability within environments quantified by standard errors among replicate samples (α stability) and (iv) Eberhart and Russell’s β, which quantifies trait stabilities across environments (β stability). All four analyses yielded highly significantly associated SNPs. We found that high oleic varieties exhibited high β trait stability, resulting in substantial overlap in markers between analyses (i) and (iv), with signals being fairly consistent between environments in analysis (i). For analyses (ii) and (iii), significant markers tended to vary between trials. For significant SNPs across all analyses, 147 candidate genes were identified, including promising candidates such as 15 fatty acid metabolism genes, 6 heat shock proteins and 22 transcription factors. Lastly, a large introgression consisting of two flanking inverted sequences on Chromosome 5 was found to coincide with α stability in the Georgia trial, suggesting a role in FA composition stability under high heat conditions.

PMID:42622697 | DOI:10.1007/s00122-026-05346-y

Proc Natl Acad Sci U S A. 2026 Aug 25;123(34):e2610136123. doi: 10.1073/pnas.2610136123. Epub 2026 Aug 18.

ABSTRACT

Extensive selection for yield and disease resistance during tomato crop improvement has led to flavor loss in modern commercial tomatoes in comparison with heirloom varieties. To investigate the chemical and genetic architecture of tomato flavor through both domestication and improvement, we analyzed flavor-related chemicals across 558 globally collected accessions comprising wild relatives, semidomesticated and domesticated populations, including uncharacterized Latin American accessions. Key flavor volatiles exhibit major differences across accessions. A genome-wide association study was used to detect associations between genetic loci and flavor-related chemical contents, including sugars, acids, and volatiles. Multiple genetic loci linked to known genes encoding flavor metabolism enzymes, as well as many new loci, were identified. Among the newly identified loci, a gene encoding a previously uncharacterized lipase (Sl-LIP100) was experimentally proven to have an important role in synthesis of lipid-derived flavor volatiles. This enzyme is responsible for synthesis of several important five- and six-carbon flavor volatiles. In sum, this study provides chemical and genetic insights into the evolution of tomato flavor during domestication and subsequent improvement, identifying the complexity of genetic control of fruit flavor chemicals as well as a number of new alleles that can be used to improve the contents of flavor-linked chemicals.

PMID:42611996 | DOI:10.1073/pnas.2610136123

Front Plant Sci. 2026 Jul 23;17:1870120. doi: 10.3389/fpls.2026.1870120. eCollection 2026.

ABSTRACT

Tall fescue (Festuca arundinacea Schreb.) is a cool-season, allohexaploid perennial grass used for forage, soil conservation, and turf. In the United States, it is mainly adapted to the transition zone between the temperate North and mild South, with broad distribution in central and eastern regions. Forage yield depends on genotype, fertilization, and environmental conditions. As the performance of genotypes for tall fescue biomass yield is significantly affected by genotype-by-environment interaction (G×E), we evaluated biomass yield and its stability for 14 tall fescue genotypes across eight location-year combinations in the United States and Canada using 434 observations from a multi-environment trial. We analyzed data using additive main effects and multiplicative interaction (AMMI), genotype plus G×E (GGE) biplot, and restricted maximum likelihood (REML)-based mixed models to estimate best linear unbiased predictions (BLUPs). AMMI analysis revealed significant genotype, environment, and G×E effects (P < 0.001), with the first two interaction principal component axes together explaining a total of 81.8% of the interaction variance. The GGE biplot corroborated environment-specific genotype performance, supported mega-environment delineation, and identified winning genotypes (g2t and k21) within environmental clusters. Mean vs. stability and ideal genotype analyses indicated that k21 and jmx were among the most favorable genotypes for combined yield performance and stability across environments. Mixed-model BLUP estimates and probability-based ranking further supported these findings under partially unbalanced data. For simultaneous selection for productivity and stability, a Yield Weighted Stability Index (YWSI) was calculated by integrating BLUP-predicted yield with AMMI-based stability, providing a composite criterion for comparative evaluation of genotype performance. The YWSI results were consistent with those obtained from the other analytical approaches. The combined use of AMMI, GGE, BLUP, and YWSI provided a comprehensive framework for characterizing G×E patterns and facilitating genotype evaluation across diverse environments.

PMID:42564454 | PMC:PMC13442827 | DOI:10.3389/fpls.2026.1870120