Author: slquinlan

Front Genet. 2025 Nov 12;16:1731825. doi: 10.3389/fgene.2025.1731825. eCollection 2025.

ABSTRACT

[This corrects the article DOI: 10.3389/fgene.2025.1626083.].

PMID:41311856 | PMC:PMC12648043 | DOI:10.3389/fgene.2025.1731825

Nat Methods. 2025 Nov 27. doi: 10.1038/s41592-025-02900-2. Online ahead of print.

ABSTRACT

Single-cell RNA sequencing in plants requires the isolation of high-quality protoplasts-cells devoid of cell walls. However, many plant tissues and organs are resistant to enzymatic digestion, posing a significant barrier to advancing single-cell multi-omics in plant research. Furthermore, for field-grown crops, the lack of immediate laboratory facilities presents another major challenge for timely protoplast preparation. Here, to address these limitations, we developed FX-Cell and its derivatives, FXcryo-Cell and cryoFX-Cell, to enable single-cell RNA sequencing with both difficult-to-digest and cryopreserved plant samples. By optimizing the fixation buffer and minimizing RNA degradation, our approach ensures efficient cell wall digestion at high temperatures while maintaining high-quality single cells, even after long-term storage at -80 °C, and circumvents use of nuclei, which are not representative of the pool of translatable messenger RNAs. We successfully constructed high-quality cell atlases for rice tiller nodes, rhizomes of wild rice and maize crown roots grown under field conditions. Moreover, these methods enable the accurate reconstruction of plant acute wounding responses at single-cell resolution. Collectively, these advancements expand the applicability of plant single-cell genomics across a wider range of species and tissues, paving the way for comprehensive Plant Cell Atlases for plant species.

PMID:41310055 | DOI:10.1038/s41592-025-02900-2

Physiol Plant. 2025 Nov-Dec;177(6):e70655. doi: 10.1111/ppl.70655.

ABSTRACT

The use of microorganisms is a promising technique in agriculture to provide greater water and nutrient efficiency for crops. The objective of this study was to evaluate the effects of microbial inoculation on plant growth, fruit yield and fruit quality of cherry tomatoes (Solanum lycopersicum var. cerasiforme) in a protected environment. The experiment was arranged in a randomized block design with three treatments: (i) inoculation with Bacillus subtilis ATCC 23858; (ii) inoculation with Burkholderia seminalis TC3.4.2R3; and (iii) non-inoculation, with eight replications. The data were subjected to ANOVA using the F-test followed by the Tukey test (p < 0.05) and multivariate statistical analysis for principal component analysis. B. seminalis led to a higher germination rate, increased fruit yield (FY) by 4.3% and soluble solids content (SSC) of 12.33% compared to the non-inoculation treatment. B. subtilis increased plant height (PH) and root mass, FY by 9.56% and SSC by 9.25%. Inoculation increased the mechanical resistance of fruits in terms of compression and puncture. The results of this work indicated that the initial growth of cherry tomatoes was increased by inoculation with B. subtilis and B. seminalis, bringing new possibilities for the sustainable production of this crop since inoculation promoted plant growth, increased FY and improved fruit quality. The study suggests that inoculation with specific strains of B. subtilis and B. seminalis can be beneficial for cherry tomato cultivation in protected environments, highlighting the use of microorganisms in agriculture and their potential for sustainable and efficient crop management.

PMID:41292417 | DOI:10.1111/ppl.70655

Nucleic Acids Res. 2025 Nov 26:gkaf1287. doi: 10.1093/nar/gkaf1287. Online ahead of print.

ABSTRACT

Polyploidy and small-scale duplication have repeatedly reshaped plant genomes, making synteny and colinearity indispensable for evolutionary inference. We present PGDD 2.0 (accessible at chibba.agtec.uga.edu and pgdd2.org), a major update to the Plant Genome Duplication Database (PGDD) that now aggregates >120 complete telomere-to-telomere (T2T) assemblies, including many chromosome-scale genomes spanning all major Viridiplantae lineages. Each genome sequence is processed with a standardized pipeline to call intra- and intergenomic colinear (syntenic) blocks, estimate Ks, and block score metrics and age distributions. PGDD 2.0 introduces (i) interactive synteny networks for pattern discovery across taxa, (ii) a “riparian” or synteny alignment view for visualizing mesosynteny and rearrangements, and (iii) an embedded SynVisio module for rendering user-supplied or PGDD-downloaded MCScanX results directly in the browser. Together, these advances support tasks from resolving ancient whole-genome duplication signatures to tracing the postduplication fates of specific gene families with T2T-level precision and beyond. PGDD 2.0 delivers an up-to-date, uniform, and user-centered platform for plant comparative genomics, accelerating discovery regarding polyploidy, gene duplication, and genome evolution.

PMID:41296551 | DOI:10.1093/nar/gkaf1287

Proc Natl Acad Sci U S A. 2025 Dec 2;122(48):e2514194122. doi: 10.1073/pnas.2514194122. Epub 2025 Nov 26.

ABSTRACT

The rate and spectrum of somatic mutations can diverge from that of germline mutations. This is because somatic tissues experience different mutagenic processes than germline tissues. Here, we use nanorate sequencing (NanoSeq) to identify somatic mutations in Arabidopsis shoots with high sensitivity. We report a somatic mutation rate of 3.6 × 10^-8 mutations/bp, ~2 to 7× measured germline mutation rates. Somatic mutations displayed elevated signatures consistent with oxidative damage, UV damage, and transcription-coupled nucleotide excision repair. Both somatic and germline mutations were enriched in transposable elements and depleted in genes, but this depletion was greater in germline mutations. Somatic mutation rate correlated with proximity to the centromere, DNA methylation, chromatin accessibility, and gene/TE content, properties which were also largely true of germline mutations. We note that DNA methylation and chromatin accessibility have different predicted effects on mutation rate for genic and nongenic regions; DNA methylation associates with a greater increase in mutation rate when in nongenic regions, and accessible chromatin associates with a lower mutation rate in nongenic regions but a higher mutation rate in genic regions. Together, these results characterize key differences and similarities in the genomic distribution of somatic and germline mutations.

PMID:41296725 | DOI:10.1073/pnas.2514194122

Nucleic Acids Res. 2025 Nov 26;53(22):gkaf1201. doi: 10.1093/nar/gkaf1201.

ABSTRACT

The SNF2 family chromatin remodeler HELLS has emerged as an important regulator of cell proliferation, genome stability, and several cancer pathways. Significant upregulation of HELLS has been reported in 33 human cancer types. While HELLS has been implicated in DNA damage response, its function in DNA repair is poorly understood. Here, we report a new regulatory link between HELLS and single-strand break (SSB) repair in cellular responses to DNA alkylation damage. We found that loss of HELLS impairs SSB repair and selectively sensitizes cells to DNA alkylating agents and PARP inhibitors (PARPi). Our data reveal non-epistatic interactions between HELLS and PARP1 and suggest that HELLS functionally compensates for PARP1 deficiency in promoting cell survival in response to DNA alkylation damage. Furthermore, we found that HELLS is co-expressed with PARP1 in cancer cells, and its loss is synthetic lethal with homologous recombination deficiency (HRD). This work unveils new functions of HELLS in modulating SSB repair and responses to clinically relevant DNA alkylation damage, thus offering new insights into the potential therapeutic value of targeting HELLS in cancer.

PMID:41297801 | DOI:10.1093/nar/gkaf1201

Appl Environ Microbiol. 2025 Nov 25:e0164325. doi: 10.1128/aem.01643-25. Online ahead of print.

ABSTRACT

Pseudomonas alliivorans is an important emerging pathogen affecting numerous crops. The species is closely related to Pseudomonas viridiflava, with which P. alliivorans strains were often misidentified in the past. Here, we investigated the genetic and pathogenic characteristics of P. alliivorans strains isolated primarily from onions and weeds in Georgia, USA, using whole-genome sequencing, comparative genomics, and functional assays. We delineated the core genome and genetic diversity of these isolates, assessed their pathogenicity on onion foliage and red onion scales, and examined the roles of key virulence determinants (Hrp1-type III secretion system [T3SS], rhizobium-T3SS, type II secretion systems [T2SSs], and thiosulfinate [allicin]-tolerance alt cluster). Our results showed that the Hrp1-T3SS is pivotal for pathogenicity in P. alliivorans, whereas the rhizobium-T3SS, T2SSs, and alt cluster do not contribute to symptom development on red onion scales. Notably, the alt cluster confers in vitro thiosulfinate tolerance, supporting bacterial survival against onion-derived antimicrobial compounds. Additionally, homologous recombination in P. alliivorans occurs infrequently (at approximately one-tenth the rate of point mutations) and involves divergent DNA segments. The alt cluster is acquired through horizontal gene transfer, as evidenced by its lower GC content and the presence of adjacent transposases. In summary, our research provides valuable insights into the genetic diversity, evolutionary dynamics, and virulence mechanisms of P. alliivorans strains from Georgia, USA.IMPORTANCEPseudomonas alliivorans is an emerging plant pathogen that threatens onion and other plants of economic importance. This study identifies key traits that help this bacterium cause disease, such as a specific secretion system critical for infecting onions, and a gene cluster that aids bacterial survival in onion tissues. Beyond highlighting weed as a potential inoculum source and supporting better weed management, the findings of this research open avenues for more targeted disease menegement. By unraveling the genetics of this pathogen, we can develop improved ways to detect, prevent, and reduce its impact, protecting crop health and yields.

PMID:41288358 | DOI:10.1128/aem.01643-25

Proc Natl Acad Sci U S A. 2025 Dec 2;122(48):e2514628122. doi: 10.1073/pnas.2514628122. Epub 2025 Nov 24.

ABSTRACT

CO₂ fertilization of the terrestrial biosphere is limited by nitrogen. Biological nitrogen fixation (BNF) is the dominant natural nitrogen source to the terrestrial biosphere and can alleviate nitrogen limitation but is poorly constrained in Earth system models (ESMs). Here, we compare terrestrial BNF from an ensemble of ESMs of the 6th Coupled Model Intercomparison Project to a new global synthesis of observations across natural and agricultural biomes. We find that compared to observations, ESMs underestimate agricultural BNF but overestimate natural BNF in the present day by over 50%. Natural BNF is overestimated in the most productive ecosystems that contribute most to the terrestrial carbon sink (forests and grasslands). ESMs with different BNF representations yield a range of BNF responses to CO₂ enrichment. Some ESMs with phenomenological representations of BNF predict a natural BNF increase in response to a doubling of CO₂ that aligns with a meta-analysis of CO₂ enrichment experiments (31% increase) but fail to account for the substantial carbon cost of BNF. In contrast, ESMs with mechanistic representations of BNF account for its carbon cost as well as its regulation by nitrogen limitation but overestimate the BNF response to a doubling of CO₂ (135% increase). Overall, all current BNF representations in ESMs fall short of fully capturing its response to rising atmospheric CO₂. Finally, we find a positive correlation between modeled present-day natural BNF and the CO₂ fertilization effect across ESMs, suggesting that overestimated natural BNF translates to an exaggerated CO₂ fertilization effect of approximately 11% in ESMs.

PMID:41284886 | DOI:10.1073/pnas.2514628122

Cell Rep. 2025 Nov 22;44(12):116603. doi: 10.1016/j.celrep.2025.116603. Online ahead of print.

ABSTRACT

In the human fungal pathogen Cryptococcus deneoformans, sexual reproduction facilitates evolution and adaptation. This fungus can undergo two sexual modes: α × a sexual reproduction and unisexual reproduction (without mating partner cooperation), with α-unisexual reproduction predominating. However, the mechanism driving commitment to α-unisexual reproduction has remained elusive. Here, through a multilayered genetic screen of transfer DNA (T-DNA) insertional mutants, we identified several mutants with enhanced unisexual reproduction but impaired α × a heterothallic mating. Genome sequencing of these mutants revealed that the T-DNA insertions are enriched in genes involved in respiration. Consistently, pharmacological inhibition of respiration recapitulated this phenotype. This respiratory-inhibition-prompted selection for unisexual development requires the filamentation activator Znf2, which directly inhibits the cyclin Cln1, resulting in cell-cycle arrest in the G2/M phase, which promotes unisexual development but functionally excludes α × a heterothallic mating. Collectively, our findings uncover a mechanism that commits unisexual reproduction through respiratory inhibition.

PMID:41275490 | DOI:10.1016/j.celrep.2025.116603

Science. 2025 Nov 20;390(6775):786-787. doi: 10.1126/science.aec7902. Epub 2025 Nov 20.

ABSTRACT

Chromosome engineering produces a reduced eight-chromosome karyotype in Arabidopsis thaliana.

PMID:41264719 | DOI:10.1126/science.aec7902