Category: Pub Med

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

Am J Bot. 2026 Aug 7:e70246. doi: 10.1002/ajb2.70246. Online ahead of print.

ABSTRACT

PREMISE: Root hemiparasites form haustoria in belowground roots of hosts to extract nutrients and water from the surrounding hosts. Through parasitic symbiosis, these plants disproportionately affect plant communities relative to their abundance by reducing host size, altering nutrient flow, and eventually increasing local biodiversity. Their prevalence and potential as keystone species position hemiparasites as important drivers of community structure.

METHODS: In a 2-year study at the Rocky Mountain Biological Laboratory, we selected paired presence and absence plots for three species of hemiparasitic Castilleja across seven study sites to explore the association of Castilleja with differences in the structure of montane plant communities. Our objectives were to (1) observe the relationship between three hemiparasitic Castilleja species and plant community diversity and composition and (2) assess the host range and preference for each species in situ using direct and indirect sampling. Percentage cover of all species was recorded to assess the effect of Castilleja presence on plant community diversity and composition. To assess host range and preference and to support nearest-neighbor and indicator-species analyses, we excavated Castilleja individuals to observe haustorial connections.

RESULTS: Across sites, species, and years, the presence of Castilleja was consistently correlated with increased plant biodiversity and site-specific differences in community composition. Excavations suggested that Castilleja species are generalist hemiparasites with some preference for common, dominant hosts.

CONCLUSIONS: Our results identify a positive relationship between Castilleja presence and local plant community diversity and support the interpretation that these species act as generalist hemiparasites.

PMID:42563626 | DOI:10.1002/ajb2.70246

Int Microbiol. 2026 Aug 6. doi: 10.1007/s10123-026-00875-4. Online ahead of print.

ABSTRACT

Bacterial communities play important roles in the plant phyllosphere. Both microbial communities and their hosts exhibit endogenous circadian rhythms while simultaneously responding to environmental changes across the diurnal cycle. However, the interaction between the host and microbiome is still poorly understood. Here, we exploit paired sequencing data of host transcriptome and microbiome derived from diverse maize genotypes in field conditions and under two contrasting diurnal periods. Expression patterns of known maize circadian clock genes were consistent with the expected sampling phases. Groups of co-expressed genes that responded to diurnal periods were associated with nucleic acid-binding, heat stress responses, and photosynthesis. Microbiome analysis revealed only modest differences in alpha diversity between midday and midnight samples. However, beta diversity indicated a significant shift in community composition. Co-occurrence network analysis identified keystone taxa specific to each time point, suggesting time-dependent ecological roles within the phyllosphere microbiome. Cross-correlation analyses between host gene expression and bacterial taxon abundance revealed a greater number of host-microbe associations during the night. Several canonical circadian clock genes significantly correlated with microbial taxa. Our findings provide initial evidence for diurnal associations between host gene expression and leaf-associated bacteriome, suggesting that maize diurnal transcriptional dynamics, including the activity of circadian clock genes, may contribute to shaping the composition and functional potential of the phyllosphere microbiome.

PMID:42557505 | DOI:10.1007/s10123-026-00875-4

Microbiol Mol Biol Rev. 2026 Aug 5:e0001226. doi: 10.1128/mmbr.00012-26. Online ahead of print.

ABSTRACT

SUMMARYLiquid-liquid phase separation (LLPS) drives the formation of biomolecular condensates, a conserved phenomenon across eukaryotes. This process governs diverse cellular programs, from stress response and morphogenesis to disease pathology. Over the past two decades, the regulatory impact of biomolecular condensates in fungal biology has become increasingly recognized. In this review, we examine the fundamental molecular mechanisms driving LLPS, evaluate the current evidence for LLPS in macromolecular organization and cellular regulation in fungi, and outline the tools employed to study this phenomenon. Lastly, we highlight the challenges of bridging the gap between the in vitro behavior of biomolecular condensates and their complex regulatory functions in vivo within fungal biology.

PMID:42554499 | DOI:10.1128/mmbr.00012-26

G3 (Bethesda). 2026 Aug 5:jkag196. doi: 10.1093/g3journal/jkag196. Online ahead of print.

ABSTRACT

Accurate genotyping accelerates crop improvement, yet long-read sequencing remains underused in breeding due to cost. We present a scalable long-read low-pass (LRLP) sequencing framework for high-throughput variant discovery and trait mapping. Using PacBio HiFi reads in an allotetraploid peanut (Arachis hypogaea; AABB, 2n = 4x = 40) MAGIC population, we generated both LRLP and short-read low-pass (SRLP) data. At comparable depths, LRLP achieved substantially greater whole-genome and gene-space coverage than SRLP. Data were analyzed using both a single-reference genome and an 18-parent pangenome graph constructed with KhufuPan, a new tool for graph-based genotyping. Across analytical approaches, LRLP consistently identified more SNPs, indels (2-1,000 bp), and structural variants (>1 kb) than SRLP, improving genotype resolution and selection accuracy, particularly for large structural variants. By reducing cost barriers and increasing variant discovery in complex genomes, LRLP provides a practical path for deploying advanced genomics in under-resourced and orphan crops critical to global food security.

PMID:42552613 | DOI:10.1093/g3journal/jkag196