Author: slquinlan

Plant J. 2025 Nov;124(4):e70554. doi: 10.1111/tpj.70554.

ABSTRACT

Climate uncertainty is intensifying the need for greater plasticity in carbohydrate reserve utilization to support winter survival and spring growth in woody perennials. In poplar, the single-copy SUT4, which encodes a tonoplast-localized sucrose transporter, and the SUT5/SUT6 genome duplicates, which encode plasma membrane-localized transporters, are expressed year-round, with SUT4 showing the highest expression during cool seasons. Given its role in vacuolar sucrose efflux and winter-predominant expression, SUT4 may play a key role in modulating seasonal carbohydrate dynamics. While SUT4-knockdown and knockout effects have been studied under greenhouse conditions, their impact under field conditions remains unexplored. Here, we report a field-based study comparing CRISPR knockout mutants of winter-expressed SUT4 and SUT5/SUT6 in Populus tremula × alba. We show that sut4, but not sut5/6, mutants exhibited earlier autumn leaf senescence, delayed spring bud flush, reduced stem growth, and altered sugar partitioning in winter xylem and bark relative to controls. After 2 years in the field, all genotypes flowered before leaf flush in early spring; however, sut4 mutants produced sterile ovules despite developing normal-looking catkins. Metabolic profiling revealed disrupted sucrose and raffinose dynamics in elongating sut4 catkins. This was accompanied by transcriptomic signatures of elevated stress and downregulation of proanthocyanidin biosynthesis and circadian clock genes. These findings highlight the critical role of SUT4 in coordinating sugar allocation, stress responses, and seasonal development in poplar.

PMID:41241958 | DOI:10.1111/tpj.70554

Plants (Basel). 2025 Oct 31;14(21):3337. doi: 10.3390/plants14213337.

ABSTRACT

Climate change is shifting where suitable habitats occur for many species across the planet. Sarracenia purpurea L., the most widely distributed pitcher plant species in North America, already faces significant threats from land use change. While S. purpurea is well studied at physiological and local scales, threat assessments for this species at biogeographic scales are absent. Here, we remedy this by using Habitat Suitability Models to predict current suitable habitats and estimate climate-based shifts in the suitable habitat for S. purpurea in the near (2040) and long term (2100). The models predicted large areas of habitat loss in the southeastern United States and the western portion of the Great Lakes region by 2040. While the models also predict significant gains in suitable habitats north of the current S. purpurea range, the limited dispersal ability of this species precludes the possibility of natural migration to newly suitable habitats. Our results suggest that the degradation of considerable portions of current suitable habitats is already occurring and will continue in the future. Particularly threatened are the southern subspecies (e.g., Sarracenia purpurea subsp. venosa) of S. purpurea. We therefore urge land managers to make conservation efforts targeting threatened subspecies and encourage further the biogeographic investigation of less widely distributed congenerics of S. purpurea.

PMID:41225887 | PMC:PMC12608460 | DOI:10.3390/plants14213337

New Phytol. 2025 Nov 9. doi: 10.1111/nph.70712. Online ahead of print.

ABSTRACT

Monoterpene indole alkaloids (MIA) are a diverse class of plant natural products produced by a subset of lineages within the Asterid clade of eudicots. The diversity of MIAs provides a unique opportunity to study not only the evolution of biosynthetic genes but also their regulation. In this study, we investigate the cell type specificity of biosynthetic genes and coexpressed transcription factors (TFs) in two MIA-producing Asterid species, Catharanthus roseus, a well-studied MIA-producing species, and Camptotheca acuminata, which belongs to an early-diverging lineage of the Asterid clade. We generated single-cell RNA-seq data from the C. acuminata stem, the primary site of camptothecin biosynthesis. We found that MIA biosynthetic genes in C. acuminata are specific to exceptionally rare cell populations. We discovered MYB and bHLH TFs coexpressed in the same cell types as MIA biosynthetic genes in the C. acuminata stem. Interestingly, the C. roseus orthologs of these TFs are idioblast-specific and activate MIA biosynthetic genes in C. roseus upon overexpression. We constructed an extended gene regulatory network for the idioblast metabolic regulon in C. roseus, which contains both feedback and feedforward activation loops. This study demonstrates co-option of the same clades of TFs for regulation of cell-type-specific MIA biosynthesis across two Asterid species separated by c. 115 million years of evolution. Investigating cell-type-specific TFs that are coexpressed with biosynthetic genes across multiple species is a powerful strategy to increase the power for the discovery of plant metabolic regulators.

PMID:41208325 | DOI:10.1111/nph.70712

Plant Biotechnol J. 2025 Nov 7. doi: 10.1111/pbi.70454. Online ahead of print.

ABSTRACT

Solanum tuberosum L. (potato) is a key food crop, with its tubers serving as an important food source worldwide. Tuber development is a tightly regulated process involving the transition of a hooked stolon (a modified stem) to a tuber following the perception of mobile signals within the stolon tip. While genes like FLOWERING LOCUS T homologue StSP6A and the transcription factors (TF) StPOTH1, StBRC1b and StBEL5 have been implicated in this process, little is known about cell-type-specific gene expression and its regulation during tuber initiation. To further our understanding of tuber initiation and development, we generated single nuclei multi-ome data (gene expression and chromatin accessibility from the same nucleus) from hooked stolons of tetraploid S. tuberosum cv. Atlantic. Nuclei (20079) were assigned to 27 clusters, representing 10 annotated cell types. Differential chromatin and motif enrichment analysis revealed binding sites of TF families known to play a role in cell type development in Arabidopsis that were enriched in analogous cell types in potato stolon tips. By coupling gene co-expression and information from differential chromatin analysis, we identified novel TFs with putative roles in stolon vasculature development. Co-accessibility analysis further uncovered putative regulatory enhancers involved in stolon/tuber development. We identified cells that metabolise starch and used gene co-expression analysis to uncover novel TFs involved in the transition from source to sink. This dataset of cell-type-specific gene expression and accessible chromatin from the same nucleus is a powerful resource for discovering genes and regulatory sequences involved in the earliest stages of tuber development.

PMID:41204754 | DOI:10.1111/pbi.70454

New Phytol. 2025 Nov 2. doi: 10.1111/nph.70700. Online ahead of print.

ABSTRACT

Myrothamnus flabellifolia is a dioecious resurrection plant endemic to southern Africa that has become an important model for understanding desiccation tolerance. Despite its ecological and medicinal significance, genomic and transcriptomic resources for the species are limited. We generated a chromosome-level, haplotype-resolved reference genome assembly and annotation for M. flabellifolia and conducted transcriptomic profiling across a natural dehydration-rehydration time course in the field. Genome architecture and sex determination were characterized, and co-expression network and cis-regulatory element (CRE) enrichment analyses were used to investigate dynamic responses to desiccation. The 1.28-Gb genome exhibits unusually consistent chromatin architecture with unique chromosome organization across highly divergent haplotypes. We identified an XY sexual system with a small sex-determining region on Chromosome 8. Transcriptomic responses varied with dehydration severity, pointing to early suppression of growth, progressive activation of protective mechanisms, and subsequent return to homeostasis upon rehydration. Late embryogenesis abundant and early light-induced protein transcripts were dynamically regulated and showed enrichment of abscisic acid and stress-responsive CREs pointing toward conserved responses. Together, this study provides foundational resources for understanding the genomic architecture and reproductive biology of M. flabellifolia and offers new insights into the mechanisms of desiccation tolerance.

PMID:41178124 | DOI:10.1111/nph.70700

Methods Mol Biol. 2026;2987:231-252. doi: 10.1007/978-1-0716-5001-1_16.

ABSTRACT

Reproduction of apomictic and sexual plants within Cenchrus, previously classified as both Cenchrus and Pennisetum, has been studied since the 1950s. Seventeen of approximately 108-120 Cenchrus species contain apomictic cytotypes. Apomictic cytotypes are polyploids and all are classified as developing via apospory. While most apomictic species in Cenchrus produce viable offspring that are highly maternally clonal, the ability for sexual reproduction has been retained. With advancement in molecular technologies, understanding the genetic composition, physical location, and genes associated with apospory has been forthcoming. Additional gains including whole-genome assembly of Cenchrus species to study the evolutionary mechanisms underlying apomixis are on the horizon.

PMID:41165987 | DOI:10.1007/978-1-0716-5001-1_16

Theor Appl Genet. 2025 Oct 29;138(11):286. doi: 10.1007/s00122-025-05065-w.

ABSTRACT

The RKN resistance locus Rmi1 was fine-mapped to two genes on chromosome 10, a glycosyl hydrolase family 9 β-1,4-endoglucanase gene and a type I pectin methylesterase gene. Root-knot nematodes (Meloidogyne spp.) are a serious threat to soybean production in the southeast USA, with yield losses of more than $165 million in 2023. Development and deployment of resistant soybean cultivars is the most effective strategy for managing these nematode pests; however, the identity of the resistance genes and underlying mechanism of resistance remains obscure. An additive resistance gene, Resistance to M. incognita-1 (Rmi1), to the predominant species, was first identified in soybean cultivar Forrest but never mapped to a genomic region. Multiple mapping studies have identified a major quantitative trait locus (QTL) with additive action on chromosome 10. In this study, a population consisting of 170 F_2:3 families derived from a cross of Bossier (susceptible) × Forrest (resistant) was initially used to confirm that Rmi1 is in the chromosome 10 QTL. Subsequently, 884 F_5:6 recombinant inbred lines (RILs) derived from the same cross were used to fine-map the Rmi1 causal gene(s) to two genes – a β-1,4-endoglucanase (Glyma.10G017000, EG) and a pectin methylesterase/methylesterase inhibitor (Glyma.10G017100, PME1). Both gene candidates have the potential to play a role in the resistance response to M. incognita. Both gene promoters harbor SNPs and indels and the encoded proteins exhibit amino acid polymorphisms, including a premature stop in PME1 of resistant soybeans. Additionally, both genes show a higher expression level in susceptible roots compared to resistant roots in the absence of infection. This suggests that Rmi1 may confer one or more pre-existing differences related to cell wall modification in soybean roots, ultimately leading to a decrease in susceptibility.

PMID:41160124 | DOI:10.1007/s00122-025-05065-w

Biotechnol Biofuels Bioprod. 2025 Oct 27;18(1):109. doi: 10.1186/s13068-025-02703-9.

ABSTRACT

BACKGROUND: Liquid fuels from lignocellulosic feedstocks are required for transition to a sustainable bioeconomy. However, the recalcitrance of carbon-containing feedstock cell walls to deconstruction poses a barrier to cost effective biological conversion of plant biomass to biofuels. One-step consolidated bioprocessing (CBP) in which anaerobic thermophilic bacteria convert lignocellulosic biomass into liquid fuels is a platform for overcoming the recalcitrance of plant biomass.

RESULTS: The amounts of hemicellulosic and pectic polysaccharides, two complex cell wall glycans that contribute to plant biomass recalcitrance and that are partially solubilized during CBP of switchgrass aerial biomass by Clostridium thermocellum were evaluated in the liquor, solid residues and residue washate recovered during a 120-h CBP process. After 120 h, 24% of milled switchgrass was solubilized in the C. thermocellum CBP platform. Higher concentrations of arabinose, xylose, galactose, and glucose accumulated in the CBP-fermentation liquor and washate compared to fermentation controls without C. thermocellum, indicating that C. thermocellum solubilized hemicelluloses, but did not fully metabolize them. After five days of fermentation, the relative amount of rhamnose in the solid residues increased by 16% compared to controls, and CBP solid residues had more than 23% increased reactivity against RG-I reactive monoclonal antibodies, indicating that the pectic polymer rhamnogalacturonan I (RG-I) was not effectively solubilized from switchgrass biomass by C. thermocellum CBP. Similarly, the amount of mannose (Man) in the CBP solid residues increased by 7% and reactivity against galactomannan reactive antibodies increased by greater than 14%, indicating that the hemicellulosic polymer galactomannan was also resistant to degradation by C. thermocellum during CBP fermentation.

CONCLUSIONS: These findings show that C. thermocellum is unable to effectively degrade RG-I pectic and galactomannan hemicellulosic components in switchgrass biomass. Targeting these polymers for improved solubilization could enhance the efficiency of conversion of grass biomass to biofuels.

PMID:41146239 | DOI:10.1186/s13068-025-02703-9

Commun Mater. 2025;6(1):34. doi: 10.1038/s43246-025-00749-8. Epub 2025 Feb 22.

ABSTRACT

Because proteins do not efficiently pass through the plasma membrane, protein therapeutics are limited to target ligands located at the cell surface or in serum. Lipid nanoparticles can facilitate delivery of polar molecules across a membrane. We hypothesized that because most proteins are amphoteric ionizable polycations, proteins would associate with anionic lipids, enabling microfluidic chip assembly of stable EP-LNPs (Encapsulated Proteins in Lipid NanoParticles). Here, by employing anionic lipids we were able to efficiently load proteins into EP-LNPs at protein:lipid w:w ratios of 1:20. Several proteins with diverse molecular weights and isoelectric points were encapsulated at efficiencies of 70 75%-90% and remained packaged for several months. Proteins packaged in EP-LNPs efficiently entered mammalian cells and fungal cells with cell walls. The proteins delivered intracellularly were functional. EP-LNPs technology should improve cellular delivery of medicinal antibodies, enzymes, peptide antimetabolites, and dominant negative proteins, opening new fields of protein therapeutics.

PMID:41146908 | PMC:PMC12553553 | DOI:10.1038/s43246-025-00749-8

J Exp Bot. 2025 Oct 28:eraf471. doi: 10.1093/jxb/eraf471. Online ahead of print.

ABSTRACT

Climate change is rapidly modifying environmental conditions for plant-microbe interactions. Extreme climate conditions and altered climate patterns have increased the frequency and severity of plant disease outbreaks worldwide, posing a major threat to global food security. Climate-related stress affects host-microbe interactions by modulating plant immunity and pathogen virulence. Understanding how plants perceive and respond to thermal stresses, and how this intersects with disease resistance mechanisms, is essential for mitigating future crop losses. This review synthesizes current knowledge on the molecular and cellular basis of temperature sensing, its effects on immune signaling and cell biology in model plant Arabidopsis. Advancing our understanding of these interactions is critical for developing climate resilient crops capable of withstanding the complex stresses.

PMID:41147144 | DOI:10.1093/jxb/eraf471