Author: slquinlan

Plant J. 2025 Aug;123(4):e70426. doi: 10.1111/tpj.70426.

ABSTRACT

Solanum verrucosum Schlechtendal (2x = 2n = 24) is unique among the clade 4 Solanum Sect Petota species. In addition to being one of the only fully self-compatible diploid potato species, S. verrucosum is the only clade 4 species that lacks prezygotic interspecific reproductive barriers. This allows S. verrucosum to accept pollen from a broad range of Solanum species and thereby serving as a genetic “bridge” between the cultivated or primary potato gene pool and distantly related wild relatives in the tertiary gene pool. The genetic mechanisms underlying self-compatibility in Solanum often underpin interspecific compatibility interactions, which in S. verrucosum, has been attributed to the lack of S-RNase expression. Using an interspecific F2 mapping population (n = 150), we investigated the genetic mechanisms responsible for the lack of interspecific reproductive barriers in S. verrucosum. This F2 population was evaluated for the ability to accept pollen from two clade 1, 1 EBN species (S. pinnatisectum and S. tarnii); from which two QTL for interspecific compatibility were identified on chromosomes 1 and 11, explaining 56.6% of the phenotypic variation observed. To identify the genetic basis of interspecific compatibility, we generated a chromosome-scale genome assembly of S. verrucosum MSII1813-2 and performed gene expression profiling of reproductive organs. Differential gene expression of S-RNase, located within the chromosome 1 QTL, confirmed the central role of the S-locus and specifically, S-RNase, in interspecific compatibility. Discovery of a non-S-locus QTL is consistent with previous findings that other non-S-locus factors are necessary for interspecific compatibility in S. verrucosum.

PMID:40836693 | DOI:10.1111/tpj.70426

New Phytol. 2025 Aug 20. doi: 10.1111/nph.70468. Online ahead of print.

ABSTRACT

Herbaceous plant species have been the focus of extensive, long-term research into climate change responses, but there has been little effort to synthesize results and predicted outlooks. This primer summarizes research on climate change responses for eight intensively studied herbaceous plant species. We establish generalities across species, examine limitations, and propose a path forward. Climate change has reduced fitness, caused maladaptation, and/or led to population declines in at least part of the range of all six forb species. Plasticity alone is likely not sufficient to allow adjustment to shifting climates. Most model species also have spatially restricted dispersal that may limit genetic and evolutionary rescue. These results are surprising, given that these species are generally widespread, span large elevation ranges, and have substantial genetic and phenotypic variation. The focal species have diverse life histories, reproductive strategies, and habitats, and most are native to North America. Thus, species that are rare, habitat specialists, or endemic to other parts of the world are poorly represented in this review. We encourage researchers to design demographic and field experiments that evaluate plant traits and fitness in contemporary and potential future conditions across the full life cycle, and that consider biotic interactions in climate change responses.

PMID:40836613 | DOI:10.1111/nph.70468

Proc Natl Acad Sci U S A. 2025 Aug 26;122(34):e2503491122. doi: 10.1073/pnas.2503491122. Epub 2025 Aug 20.

ABSTRACT

The chemical composition of wood plays a pivotal role in the adaptability and structural integrity of trees. However, few studies have investigated the environmental factors that determine lignin composition and its biological significance in plants. Here, we examined the lignin syringyl-to-guaiacyl (S/G) ratio in members of a Populus trichocarpa population sourced from their native habitat and conducted a genome wide association study to identify genes linked to lignin formation. Our results revealed many significant associations, suggesting that lignin biosynthesis is a complex polygenic trait. Additionally, we found an increase in the S/G ratio from northern to southern geographic origin of the trees sampled, along with a corresponding metabolic and transcriptional reprogramming of xylem cell wall biosynthesis. Further molecular analysis identified a mutation in a cell wall laccase genetically associated with higher S/G ratios that predominate in trees from warmer lower latitudes. Collectively, our findings suggest that lignin heterogeneity arises from an evolutionary process enabling poplar adaptation to different climatic challenges.

PMID:40833412 | DOI:10.1073/pnas.2503491122

China CDC Wkly. 2025 Aug 1;7(31):1031-1037. doi: 10.46234/ccdcw2025.175.

ABSTRACT

WHAT IS ALREADY KNOWN ABOUT THIS TOPIC?: Chronic diseases and multimorbidity impose substantial burdens on healthcare systems globally, particularly in aging populations, resulting in elevated healthcare utilization rates and increased expenditures.

WHAT IS ADDED BY THIS REPORT?: This study validates previous research findings using an extensive administrative database from a major city in South China. Additionally, it provides comprehensive estimates of annual hospitalization expenditures per patient associated with chronic diseases and multimorbidity patterns among older adults, elucidating the economic burden and cost variations across specific diseases and multimorbidity combinations. Cancer, cerebrovascular disease (CVD), and heart disease – whether occurring individually or in conjunction with other chronic conditions, particularly within complex multimorbidity patterns – were associated with substantial annual hospitalization expenditures and significant healthcare resource utilization.

WHAT ARE THE IMPLICATIONS FOR PUBLIC HEALTH PRACTICE?: Disease burden studies provide critical evidence for prioritizing public health policies and targeted interventions. Policymakers should implement comprehensive prevention strategies, evidence-based interventions, appropriate reimbursement policies, and integrated management approaches to control disease progression and reduce healthcare expenditures.

PMID:40831617 | PMC:PMC12360313 | DOI:10.46234/ccdcw2025.175

Nat Plants. 2025 Aug 8. doi: 10.1038/s41477-025-02079-6. Online ahead of print.

ABSTRACT

The hexaploid sweetpotato (Ipomoea batatas [L.] Lam.) is a globally important stable crop that plays a key role in biofortification. Its high resilience and adaptability provide distinct advantages in addressing food security and climate challenges. Here we report a haplotype-resolved chromosome-level genome assembly of an African cultivar, ‘Tanzania’, revealing mosaic genomic origins along haplotype-phased chromosomes. The wild tetraploid I. aequatoriensis, currently found in coastal Ecuador, contributes to a substantial fraction of the sweetpotato genome. Another large proportion of the genome shows a closer genetic relationship to the wild tetraploid I. batatas 4×, distributed in Central America. The sequences contributed by different wild species are not distributed in typical subgenomes but are intertwined along chromosomes, possibly owing to the known non-preferential recombination among sweetpotato haplotypes. This study improves our understanding of sweetpotato origin and genome architecture and provides valuable genomic resources to accelerate sweetpotato breeding.

PMID:40781486 | DOI:10.1038/s41477-025-02079-6

Plant Dis. 2025 Aug 6. doi: 10.1094/PDIS-12-24-2589-SR. Online ahead of print.

ABSTRACT

Gummy stem blight (GSB), caused by three Stagonosporopsis species, S. citrulli, S. cucurbitacearum and S. caricae, is one of the most economically important diseases hindering watermelon production worldwide. Since there is no commercial resistance to GSB in watermelon cultivars, its management depends on cultural practices and preventative fungicides. Therefore, efficient methods for the detection of Stagonosporopsis species that could aid management decisions are required. To help achieve this, a loop-mediated isothermal amplification (LAMP) assay specific to S. citrulli (SCIT850) was developed under two detection formats: fluorescence quantification and endpoint colorimetric detection. The SCIT850 assay was determined to be specific to its target species and exhibited a consistent sensitivity of 1 pg of genomic DNA under both formats. The assay can be combined with a previously reported LAMP assay for the collective detection of the three Stagonosporopsis spp. (STAGY), which have comparable sensitivity to SCIT850 and can aid in species discrimination. A field diagnostic system for GSB-causing Stagonosporopsis was developed by coupling the SCIT850 and STAGY assays to quick DNA extraction protocols. Two DNA extraction methods were tested: one from leaves using cellulose dipsticks, and one from steel rods (typical of spore traps) using Chelex100. With the dipstick method, we detected pathogen DNA in inoculated asymptomatic, mildly infected, and severely infected plants, while with the Chelex100 we detected pathogen DNA from rods infested with as few as 500 spores. The SCIT850 and STAGY assays coupled with these quick sample processing methods could be adapted for field deployment, which would allow growers to make efficient and timely management decisions based on detection of the actual Stagonosporopsis species present in the field.

PMID:40767855 | DOI:10.1094/PDIS-12-24-2589-SR

Sci Data. 2025 Aug 5;12(1):1362. doi: 10.1038/s41597-025-05131-4.

ABSTRACT

Biological nitrogen fixation (BNF) is the main natural source of new nitrogen inputs in terrestrial ecosystems, supporting terrestrial productivity, carbon uptake, and other Earth system processes. We assembled a comprehensive global dataset of field measurements of BNF in all major N-fixing niches across natural terrestrial biomes derived from the analysis of 376 BNF studies. The dataset comprises 32 variables, including site location, biome type, N-fixing niche, sampling year, quantification method, BNF rate (kg N ha^-1 y^-1), the percentage of nitrogen derived from the atmosphere (%N_dfa), N fixer or N-fixing substrate abundance, BNF rate per unit of N fixer abundance, and species identity. Overall, the dataset combines 1,207 BNF rates for trees, shrubs, herbs, soil, leaf litter, woody litter, dead wood, mosses, lichens, and biocrusts, 152 herb %N_dfa values, 1,005 measurements of N fixer or N-fixing substrate abundance, and 762 BNF rates per unit of N fixer abundance for a total of 424 species across 66 countries. This dataset facilitates synthesis, meta-analysis, upscaling, and model benchmarking of BNF fluxes at multiple spatial scales.

PMID:40764484 | DOI:10.1038/s41597-025-05131-4

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