Author: slquinlan

Int J Mol Sci. 2026 Jun 26;27(13):5760. doi: 10.3390/ijms27135760.

ABSTRACT

Seashore paspalum (Paspalum vaginatum), a salinity-tolerant turfgrass, lacks well-characterized viral profiles. This study reports the discovery of a novel virus, tentatively named Paspalum latent virus (PaLV), representing a new taxon within the Alphaflexiviridae. Using high-throughput sequencing and RACE PCR, the 6995 nt genome was determined, revealing five open reading frames. Notably, PaLV lacks the AlkB domain and exhibits unique features, including overlapping start-stop codons (ORF4/ORF5) and a second in-frame AUG in the coat protein (CP) region. Phylogenetic analysis of the replicase placed PaLV in a distinct clade, separate from Potexvirus and Lolavirus. Despite low sequence identity, AlphaFold2 revealed conserved CP structural domains. Genetic analysis of 11 isolates showed low diversity and strong purifying selection. Pathogenicity assays through mechanical transmission demonstrated a broad but latent host range, including Zea mays and Sorghum spp. These findings suggest PaLV represents a novel species within a putatively new genus, Paspalovirus. Given its 90% incidence rate and latent profile, the RT-PCR assay developed here is vital for routine molecular diagnostics in turfgrass management and germplasm conservation.

PMID:42450033 | DOI:10.3390/ijms27135760

Microbiol Resour Announc. 2026 Jul 10:e0033426. doi: 10.1128/mra.00334-26. Online ahead of print.

ABSTRACT

We sequenced the genomes of 77 bacterial strains, tentatively identified as Enterobacter. Of these, 71 were identified as Enterobacter based on genomic analysis. These strains span 11 species of diverse ecological and geographical origin.

PMID:42429961 | DOI:10.1128/mra.00334-26

Nat Commun. 2026 Jul 9. doi: 10.1038/s41467-026-75205-3. Online ahead of print.

ABSTRACT

Wild perennial plants can be domesticated to make agriculture more diverse and resilient, but many have large genomes that have been recalcitrant to analysis. Here, we report phased genome assemblies for Silphium integrifolium Michx. and S. perfoliatum L., two species native to North America under domestication, and demonstrate the utility of trio-binning for genome assembly using an interspecific hybrid. These genomes have chromosomes reaching 1.8 Gb and a helical structure preserved during interphase with a loop circumference of 43 Mb. A genome-informed low coverage and target sequencing strategy enables the refinement of the genus phylogeny, reveals the spatial distribution and structure of natural populations, and identifies 81 loci associated with environmental and domestication traits. Variants in a MATE transporter, α/β hydrolase, and ortholog of Arabidopsis ACT Domain Repeat (ACR4) protein explain significant variance in floral architecture. These advances in genome assembly and genotyping could expand the range of candidates for de novo crop domestication.

PMID:42426026 | DOI:10.1038/s41467-026-75205-3

G3 (Bethesda). 2026 Jul 8:jkag175. doi: 10.1093/g3journal/jkag175. Online ahead of print.

ABSTRACT

The Runner-type peanut (Arachis hypogaea L.) cultivar ‘Tifguard’ carries an introgressed chromosomal segment on chromosome A09 from A. cardenasii that confers resistance to root-knot nematode (RKN). Despite this, a proportion of ‘Tifguard’ plants show RKN symptoms, which could plausibly be attributed to seed mixture or outcrossing. However, recent work has shown that cultivated peanut exhibits surprisingly frequent large-scale chromosomal instability (1-5%), raising the possibility that resistance loss could arise from spontaneous structural genomic change. To test these possibilities, we grew foundation seed in an RKN-infested field and collected symptomatic and asymptomatic plants. Lineages derived by single-seed descent were genotyped using the Axiom Arachis 48K SNP array v2 and whole-genome sequencing. Symptomatic lineages lacked the A. cardenasii introgression on chromosome A09 and instead carried the complete endogenous A. hypogaea A09 region at the expected dosage. There was no evidence of large-scale homoeologous exchange, deletion, or other genomic instability affecting this chromosome. Most susceptible plants were closely related to resistant ‘Tifguard’ but lacked the A09 introgression, with a smaller proportion assignable to known nematode-susceptible cultivars, implicating seed mixture with a possible contribution from cross-pollination rather than genomic instability. Because resistance depends on a single major-effect segment, rare events have disproportionate phenotypic impact, placing high demands on genetic purity. For important traits conferred by major loci, marker-based testing across seed-increase stages could verify trait retention directly, and is increasingly practical as marker costs decline.

PMID:42417136 | DOI:10.1093/g3journal/jkag175

G3 (Bethesda). 2026 Jul 7:jkag165. doi: 10.1093/g3journal/jkag165. Online ahead of print.

ABSTRACT

Polyploidy has repeatedly shaped grass evolution, yet direct observations of how polyploid-derived chromosomes behave when returned to diploidy remain rare. Interspecific crosses between diploid Sorghum bicolor and tetraploid hybrids derived from S. halepense generate mixed-ploidy progeny, providing an opportunity to examine chromosome transmission during the early stages of diploidization. Using genome-wide SNP markers, we characterized chromosomal inheritance patterns in two diploid and two tetraploid families derived from these crosses. Genotype-dosage profiles alone distinguished diploids from tetraploids with complete accuracy, reflecting strong ploidy-dependent differences in dosage-class distributions. Although diploid progeny retained much of the halepense-derived genomic background, several genomic intervals exhibited extended, non-random runs of S. bicolor homozygosity that remained polymorphic in corresponding tetraploid populations. These patterns, together with recurrent segregation distortion across independent families, suggest that the transition from tetraploidy to diploidy can expose allelic combinations that differ in transmission or viability. Analyses of flowering time further indicated that diploid and tetraploid derivatives possess distinct genomic architectures, with major association peaks occurring in different chromosomal regions across ploidy levels. Collectively, these results indicate that early diploidization involves non-random retention and loss of parental haplotypes shaped by both selective and structural constraints. The diploid extractions characterized here provide a rare empirical system for investigating the early stages of diploidization and a practical framework for studying and eventually mobilizing polyploid-derived variation into sorghum germplasm development. However, broader integration into elite breeding programs will require additional evaluation of cross-fertility, meiotic behavior, and chromosomal stability across diverse breeding backgrounds.

PMID:42413025 | DOI:10.1093/g3journal/jkag165

Proc Natl Acad Sci U S A. 2026 Jul 14;123(28):e2532666123. doi: 10.1073/pnas.2532666123. Epub 2026 Jul 7.

ABSTRACT

The main axis of the plant body is established in early embryogenesis. Polar growth and asymmetric division of the Arabidopsis zygote require the Mitogen-Activated Protein (MAP) kinase kinase kinase YODA and the MAP kinases MPK3/MPK6, but regulation of this signaling cascade is not well understood. Here, we show that three BSU1-LIKE phosphatases (BSL1-3) are essential positive regulators: A combined loss causes closely similar defects to loss of the YODA MAP kinase cascade, resulting in nonpolar embryos; transcriptional profiling and cell-fate markers confirm that BSL phosphatases and the MAP kinase cascade regulate the same process. Unexpectedly, the founding member of the family, BSU1, appears dispensable. These results cast doubt on the view of BSU1-family phosphatases as core components of brassinosteroid hormone signaling. MPK3 activity shows striking sensitivity to BSL dosage, and genetic interactions with activated MPK3 suggest that BSL phosphatases function downstream of YODA and either in conjunction with or downstream of MPK3/MPK6, implying a novel mechanism of MPK regulation.

PMID:42412928 | DOI:10.1073/pnas.2532666123

Plant Dis. 2026 Jul 6. doi: 10.1094/PDIS-02-26-0339-RE. Online ahead of print.

ABSTRACT

Tomato spotted wilt virus (TSWV) and late leaf spot (LLS) are among the major constraints to peanut production. Cultivated peanut has narrow genetic bases and lacks strong sources of resistance. Wild species, on the other hand, harbor diverse and strong resistances to multiple pathogens. In this study, we evaluated advanced breeding lines carrying introgressions from multiple wild Arachis species (A. stenosperma, A. batizocoi, A. valida, and A. cardenasii) across three contrasting field environments and experimental designs in Georgia, USA using complementary incidence- and severity-based phenotyping. Genotype effects were highly significant for both diseases. Several wild-derived lines -particularly those from A. stenosperma ancestry- showed strong and stable TSWV resistance across environments. Interestingly, some lines lacking detectable wild segments also showed high resistance to TSWV, suggesting cryptic or undetected introgressions. LLS resistance was primarily associated with the characteristic A. cardenasii segments on A02 and A03, and lines stacking these introgressions consistently outperformed both cultivated parents and Georgia-06G, the most popular cultivar in the USA. Correlations between TSWV and LLS responses were weak, confirming genetic independence and emphasizing the need to screen both traits. A small subset of lines combined resistance to both diseases, and many also retained resistance loci to root-knot nematode (RKN), expanding their value as multi-trait donors. These findings demonstrate the power of wild introgression breeding for enhancing disease resistance and provide a foundation for deploying stacked alleles through marker-assisted and multi-environment selection.

PMID:42410685 | DOI:10.1094/PDIS-02-26-0339-RE

bioRxiv [Preprint]. 2026 Jun 16:2026.06.12.731976. doi: 10.64898/2026.06.12.731976.

ABSTRACT

Polycomb Repressive Complex 2 (PRC2) is a conserved epigenetic regulator that represses gene expression through methylation of histone H3 lysine 27 (H3K27me3). In animals, plants, and some fungi, PRC2-directed facultative heterochromatin plays essential roles in development and cellular differentiation. Here, we show that the replication-dependent histone chaperone Chromatin Assembly Factor 1 (CAF-1) is required for proper structure and function of facultative heterochromatin in the model fungus Neurospora crassa. Loss of CAF-1 causes widespread transcriptional misregulation, particularly within PRC2-repressed regions, and leads to redistribution of H3K27me3, reduced ASH1-dependent H3K36 methylation, and accumulation of chromatin marks associated with active transcription. CAF-1 was not required for repressive histone methylation within constitutive heterochromatin. A double mutant lacking both CAF-1 and PRC2 components displayed a synergistic silencing defect, suggesting these complexes make distinct contributions to facultative heterochromatin. Together, our findings indicate that CAF-1 works in concert with PRC2 to silence transcription within N. crassa facultative heterochromatin domains.

PMID:42367878 | PMC:PMC13307951 | DOI:10.64898/2026.06.12.731976

Plant Biotechnol J. 2026 Jul 4. doi: 10.1111/pbi.70714. Online ahead of print.

ABSTRACT

Sesame (Sesamum indicum L., 2n = 26) is one of the oldest oilseed crops and is often called the ‘queen of oilseeds’ due to its high content of unsaturated fatty acids and natural antioxidants. Despite its long history, the origin and global spread of cultivated sesame remain unresolved. We assembled a telomere-to-telomere (T2T), high-quality reference genome of sesame (cv. Yuzhi11) to investigate sequence differences between genomes and its origin and the local adaptation evolution of flowering time (DF). We generated a 305 Mb T2T sesame reference genome (cv. Yuzhi11) with > 99.99% base-level accuracy, identifying 31 063 protein-coding genes. Repetitive elements accounted for 52.03% of the genome. Population genomic analysis of 927 accessions from 14 regions identified four major groups. Integrative analyses of linkage disequilibrium decay (LD), nucleotide diversity (π), and fixation index (F_ST) support East Africa as the center of origin, with subsequent migration through the Middle East, to South Asia, South-East Asia, East Asia and ultimately to other parts of the world. Genome-wide association studies (GWAS) and selection scans identified 30 genes associated with flowering time. SiUBP16 is a candidate associated with 7.6% of DF variation. Early-flowering accessions carried up to 225 favourable alleles. A flowering time prediction model for high-latitude regions achieved 96% accuracy. We present a high-quality T2T reference genome for cultivated sesame, shedding light on its origin, evolutionary history, and regional flowering time adaptation. This genome insights valuable tools for breeding programs aimed at improving yield and environmental adaptation in sesame and related crops.

PMID:42400294 | DOI:10.1111/pbi.70714

Microbiol Spectr. 2026 Jun 22:e0412425. doi: 10.1128/spectrum.04124-25. Online ahead of print.

ABSTRACT

Pattern-triggered immunity (PTI) provides broad-spectrum protection in plants by activating defense responses upon perception of conserved microbial signatures such as bacterial flagellin. In vitro transcriptome profiling revealed that the Pseudomonas syringae pv. tomato DC3000 two-component regulator CvsR mirrors some of the broader regulatory patterns observed under the exposure to PTI in planta. Our analyses indicated that during infection in planta, CvsR primarily governs a small core regulon centered on carbonic anhydrase and its associated transporter. Comparative RNA-seq analyses between the ΔcvsR and wild-type strain further confirm this narrow regulatory scope. Moreover, the majority of bacterial transcriptional shifts appear to reflect indirect consequences of response to the host immune environment rather than direct CvsR-dependent regulation, including responses associated with sulfate starvation. Together, these findings suggest that PTI-driven bacterial transcriptional reprogramming is shaped predominantly by host immune status, with CvsR exerting modest, targeted control restricted to a limited set of genes.

IMPORTANCE: Pattern-triggered immunity (PTI) provides broad-spectrum disease resistance in plants by recognizing conserved microbial patterns such as bacterial flagellin. Activation of PTI alters the environment that pathogens encounter during infection, yet how bacteria respond to these immune-imposed conditions at the molecular level remains poorly understood. In this study, we profile the bacterial transcriptome directly in planta during infection with RNA-seq, providing a detailed view of pathogen responses under immune pressure. We focus on the previously identified two-component regulator CvsR and show that, despite widespread transcriptional changes induced by PTI, CvsR directly controls only a small core set of genes in planta. Instead, most bacterial transcriptional shifts reflect indirect responses to the immune-modified host environment. By capturing pathogen gene expression during infection, this work clarifies how plant immunity constrains bacterial physiology and provides insight that can inform sustainable strategies for crop protection.

PMID:42390087 | DOI:10.1128/spectrum.04124-25