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PubMed2026

Genome-Wide Identification of SSR and InDel Markers and Experimental Validation of SSR Markers for Distinguishing Cold-Tolerant and Cold-Sensitive Lily Cultivars.

In this study, whole-genome resequencing was performed on the cold-tolerant variety ND-6 and the cold-sensitive variety 'Sorbonne'. After evaluation, the Lilium davidii var. unicolor reference genome was selected to analyze SSR distribution characteristics. Whole-genome InDel identification and comparative analysis were conducted for the two varieties, yielding 34,812,909 and 24,497,857 InDels, respectively. Short InDels were predominant, with deletions slightly outnumbering insertions, mostly located in intergenic regions. Twenty pairs of SSR primers were screened and synthesized. Among them, 10 pairs amplified clearly, with a polymorphism rate of 82.6%, effectively distinguishing the two cultivars examined in this study. This study provides systematic data and a reliable marker resource for the analysis of lily genomic variation, laying a foundation for the identification of cold-tolerant germplasm; validation across additional cultivars and individuals will be required to extend their utility to broader germplasm.

cold resistant lilies↗

PubMed2025

Integrated 16 S rRNA and transcriptome analysis reveal molecular and microbial mechanisms of cold-tolerant germination in hulless barley.

BACKGROUND: Elucidating the mechanisms underlying cold-tolerant germination is crucial for enhancing crop resilience to low temperatures. Hulless barley (Hordeum vulgare var. coeleste L.), with remarkable natural cold adaptation, serves as an ideal model to study cold stress tolerance mechanisms in gramineous crops. In this study, cold-tolerant variety 37 and cold-sensitive variety 44 were screened and used to investigate the molecular mechanisms of cold-tolerant germination, via seed germination assays, combined with phytohormone determination, transcriptome sequencing and 16 S rRNA amplicon sequencing. RESULTS: Low temperature significantly inhibited hulless barley seed germination: the germination rate of cold-sensitive variety 44 decreased by 69%, while that of cold-tolerant variety 37 only decreased by 2%. Transcriptome analysis identified 2,647 and 2,392 differentially expressed genes (DEGs) in variety 37 and 44, respectively. Weighted gene co-expression network analysis (WGCNA) revealed a green module significantly positively correlated with gibberellic acid (GA) content, containing 10 core genes such as late embryogenesis abundant protein (LEA) and Homeobox genes. 16 S rRNA sequencing showed that the cold-tolerant variety 37 had enriched abundances of dominant endophytes including Sphingomonas and Pelomonas, with correlation coefficients of 0.70 and 0.87 with GA content, respectively. Additionally, exogenous GA treatment significantly increased germination rates under cold stress by 176.67% in cold-sensitive variety 44. CONCLUSIONS: This study confirms that the enhanced cold tolerance of hulless barley during seed germination originates from the synergistic interaction between beneficial endophytes (Sphingomonas, Pelomonas), GA, and core genes (e.g., LEA, Homeobox). Exogenous GA application can significantly restore the germination ability of cold-sensitive varieties. These findings provide a critical theoretical basis for improving cold tolerance in hulless barley germplasm.

Hordeum↗

PubMed2026

DNA hypermethylation of abscisic-acid-related genes helps enhance the cold tolerance of tetraploid rice.

Polyploid plants exhibit enhanced stress resistance and superior adaptability to extreme environments, but the underlying molecular mechanisms remain incompletely understood. Here we confirm that tetraploid rice exhibits stronger cold tolerance than diploid rice. This improved tolerance is mediated by reduced malondialdehyde accumulation, elevated antioxidant enzyme activity, and epigenetic regulation of genes involved in abscisic acid (ABA) biosynthesis and signaling. Under cold stress, tetraploid rice induces stress-responsive genes (especially in the ABA pathway) more rapidly and to higher levels than diploid rice. This enhanced gene expression coincides with increased endogenous ABA accumulation. Furthermore, polyploidization and cold stress synergistically induce high methylation at CG, CHG, and CHH sites in genes and transposons (TEs). Notably, the methylation level of class II TEs in tetraploid rice is significantly higher than in diploid rice under low temperatures. To suppress TE activation in gene promoter regions under cold stress, tetraploid rice enhances the methylation level of ABA pathway-related gene promoters, thereby silencing TEs and maintaining genome stability. Collectively, these results enrich the theoretical understanding of the strong stress tolerance in polyploid plants and provide theoretical support for breeding cold-tolerant polyploid rice varieties.

ABA↗

PubMed2026

Exogenous ABA enhances cold tolerance of Rhododendron yedoense var. poukhanense under subzero temperature: integrating physiology, transcriptome, and proteome.

Low temperature limits the growth and ornamental value of evergreen shrubs. Rhododendron yedoense var. poukhanense, an important ornamental shrub from Northeast China, frequently suffers freezing damage during winter. While exogenous abscisic acid (ABA) enhances cold tolerance in many plants, its molecular mechanisms at subzero temperatures remain poorly understood in non-model species lacking chromosome-level reference genomes. This study investigated the effects of exogenous ABA on freezing tolerance in R. yedoense var. poukhanense at -4 °C using an integrated physiological, transcriptomic, and proteomic approach. Cutting seedlings were subjected to four treatments: CK (22°C control), A (22°C + ABA), LT (-4°C), and ALT (-4°C + ABA). Photosynthetic pigments, osmotic regulation substances, antioxidant enzyme activities, and malondialdehyde (MDA) content were measured. Transcriptome sequencing and quantitative proteomics were performed, and transcriptome data were validated by quantitative real-time PCR (qRT-PCR) of 15 selected genes. ABA pretreatment reduced visible cold injury severity, partially preserved photosynthetic pigments, decreased MDA content by 28.7%, and promoted recovery of catalase (+43.6%), superoxide dismutase (+31.1%), and peroxidase (+20.0%) activities under freezing stress. Transcriptome analysis revealed 8, 444 differentially expressed genes (DEGs) in LT versus CK and 6, 481 DEGs in ALT versus CK, representing a 23% reduction in transcriptional reprogramming scope attributable to ABA priming. The ALT versus LT comparison identified only 1, 690 additional DEGs, indicating that most cold-responsive genes were pre-activated during the ABA priming phase. Proteome analysis identified 1, 461 differentially expressed proteins (DEPs) in ALT versus CK. Integrated analysis revealed extensive post-transcriptional regulation, with transcript-protein concordance of only 1.0-4.1%, and co-enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in both omics layers. qRT-PCR validation confirmed high reliability of the transcriptome data (R2 = 0.8500). These findings demonstrate that exogenous ABA enhances freezing tolerance through multi-layered molecular regulation encompassing transcriptional buffering, translational reprogramming, and functional reallocation from photosynthesis to stress protection. This study provides the first integrated physiology-transcriptome-proteome framework for ABA-mediated freezing tolerance in an evergreen ornamental shrub and offers theoretical support for ABA-based winter protection strategies.

Rhododendron yedoense var. Poukhanense↗

PubMed2026

Engineering cold stress resilience in capsicum annuum through functional genomics and precision breeding.

This review synthesizes the molecular mechanisms of cold tolerance in pepper, integrating multi-omics data,genome editing, and precision breeding strategies to accelerate the development of cold-resilient cultivars. Cold stress is a significant environmental factor that affects the growth, productivity, and fruit quality of Capsicum annuum by impairing membrane integrity photosynthesis and cellular redox homeostasis. Although pepper has several endogenous cold-responsive regulators such as CaNAC035 and CabHLH035, along with antioxidant defense systems, its cold tolerance remains limited due to low transcriptional activation of key regulators, functional redundancy among cold-responsive genes, and the polygenicity of cold tolerance. These complexities, combined with low genetic diversity and linkage drag, have hindered the improvement of cold-resistant cultivars through conventional breeding. This review brings together the recent progress in understanding the molecular mechanisms of cold stress perception, signal transduction, transcriptional regulation, metabolic reprogramming, and phytohormone interactions in pepper. Precision Breeding 2.0 is a new innovation that combines the integration of multi-omics-based target identification with next-generation genome-editing techniques, allowing precise and multiplex engineering of complex and interconnected regulatory networks instead of single genes. We cover new approaches such as engineering the DREB/CBF pathway, allele-specific editing and targeted disruption of negative regulators to enhance the pathway(s) involved in cold response. Moreover, we propose a roadmap for integration of transcriptomics, proteomics, metabolomics, high-throughput phenomics, and speed breeding to accelerate the identification, validation, and deployment of superior alleles to boost cold tolerance. This review provides a foundation for developing climate-resilient pepper cultivars by connecting functional genomics with precision genome engineering approaches to maintain productivity under variable environmental conditions.

Capsicum↗

PubMed2026

Genome-wide identification and evolutionary analysis of the ERF-VII gene family in the tea plant (Camellia sinensis) and functional characterization of CsRAP2.2 in response to cold stress.

The ERF-VII gene family, a critical branch of the AP2/ERF superfamily, is central to plant stress adaptation. However, its evolutionary history and function in tea plant (Camellia sinensis) remain unclear. Here, we performed integrated evolutionary, genomic, and functional analyses of ERF-VII genes across 14 plant lineages and 20 tea plant cultivars. The phylogenetic analysis revealed that ERF-VII proteins originated after vascular plant divergence, coinciding with the emergence of the N-terminal MCGGA/I motif linked to the oxygen-dependent N-degron pathway. Gymnosperms retained few conserved members, whereas angiosperms exhibited lineage-specific expansion-extensive in monocots via whole-genome duplication, moderate in eudicots with functional diversification. Pan-genome analysis across 20 tea plant cultivars further revealed varietal differences in ERF-VII gene distribution. Transcriptome profiling via the Tea Plant Information Archive identified CsRAP2.2 as a cold-inducible ERF-VII member with sustained expression under low-temperature stress. Functional assays demonstrated that silencing CsRAP2.2 reduced cold tolerance, while overexpression in tea leaves and heterologous expression in Arabidopsis thaliana enhanced cold tolerance by maintaining photosystem II efficiency, reducing membrane lipid peroxidation, and improving antioxidant capacity. Weighted gene co-expression network analysis positioned CsRAP2.2 as a regulatory hub integrating cold, hormone, and oxygen-sensing pathways. These results clarify the evolutionary trajectory of ERF-VII genes and establish CsRAP2.2 as a core cold-tolerance regulator in tea plant. These findings may inform future breeding of cold-resilient tea cultivars.

Camellia sinensis↗

PubMed2025

Bidirectional shifts in Pm20d1 expression impact thermogenesis and metabolism.

BACKGROUND: Peptidase M20 domain containing 1 (PM20D1) is a secreted N-fatty acyl amino synthase and hydrolase that controls tissue and blood levels of N-fatty acyl amino acids. In brown adipocytes, N-fatty acyl amino acids bind to mitochondria and act as uncouplers of mitochondria, independent of UCP1. Interventions aimed at increasing or inhibiting PM20D1 expression considerably impact energy balance and metabolism; however, little is known about naturally occurring variants of the PM20D1/Pm20d1 gene and their impact on phenotype. METHODS: In vivo, gene expression of Pm20d1 in BALB/c, C57BL/6, and Ucp1 KO in brown adipose tissue and other metabolic tissues was measured. In vitro, transcriptional activity of Pm20d1 and brown adipocytes' oxygen consumption in primary culture were assessed. Human PM20D1 circulating levels were quantified. In silico analysis of the Pm20d1 gene sequencing and human polymorphisms associated with PM20D1 was performed. RESULTS: Here, we identified a gain-of-function variant in the Pm20d1 promoter region present in BALB/c mice and absent in C57BL/6 mice. The presence of this variant is accompanied by increased expression of Pm20d1 in brown and white adipose tissues, muscle, liver, and hypothalamus; moreover, it leads to increased cold tolerance and UCP1-independent brown adipose tissue mitochondrial respiration. Inhibition of Pm20d1 in brown adipose tissue results in defective cold tolerance in BALB/c, whereas the brown adipose tissue overexpression of Pm20d1 results in increased cold tolerance in C57BL/6 mice. In humans, variants of the PM20D1 gene are associated with changes in body mass index, whereas at least one variant in the promoter region is associated with increased body mass index and metabolic syndrome. CONCLUSION: Thus, PM20D1 plays a bidirectional role in regulating thermogenesis and body mass, and, at least in part, variants in the promoter region can partially explain the differences in PM20D1 expression and its impact on the metabolic phenotype.

Thermogenesis↗

PubMed2026

Establishment of a cBSA-mediated miRNA delivery system in Camellia sinensis and functional validation of the Cs-miR163/CsSK1 module in cold stress response.

Cold stress severely limits tea (Camellia sinensis) yield and quality. MicroRNAs (miRNAs) are key post-transcriptional regulators of plant cold responses; however, in vivo functional validation in tea plants is hindered by the lack of efficient genetic transformation and nucleic acid delivery systems. In this study, a cationized bovine serum albumin (cBSA)-mediated miRNA delivery system was established in tea plants. The cold-responsive miRNA Cs-miR163 and its target gene CsSK1 (a negative regulator of cold tolerance) were used as a model. Direct cleavage of CsSK1 mRNA by Cs-miR163 was confirmed by 5' RLM-RACE and GUS transient expression assays, and enhanced cold tolerance was demonstrated in Arabidopsis overexpression lines. The cBSA preparation protocol was optimized, yielding stable cBSA/miRNA complexes with high protective capacity across temperatures of 15-35 °C and pH 4.5-7.2. Delivery parameters were systematically evaluated; optimal conditions were determined as 2 mg/mL cBSA with 10 nM miRNA and solution uptake into 3-cm cuttings for 5 days, enhancing miRNA delivery efficiency by approximately 48-fold. Transmission electron microscopy provided direct ultrastructural evidence that cBSA/miRNA nanocomplexes are internalized into tea plant cells via adsorptive-mediated endocytosis involving electrostatic membrane adsorption, membrane invagination, and cytoplasmic release. Under optimized conditions, cBSA-mediated delivery of Cs-miR163 silenced CsSK1 expression by approximately 72%, reduced relative electrolyte leakage and ROS accumulation, and markedly enhanced cold tolerance. The regulatory role of the Cs-miR163/CsSK1 module was clarified, and the established system provides a promising strategy for functional genomics in woody plants that warrants further testing in additional species and tissues.

Camellia sinensis↗

PubMed2026

Transcriptome analysis of brown adipose tissue in Brandt's vole treated with tannic acid under cold exposure.

BACKGROUND: Tannic acid (TA) is a hydrolysable plant secondary metabolite known to influence multiple physiological processes in animals; however, its role in regulating brown adipose tissue (BAT) thermogenesis remains poorly understood. Notably, the overwinter food caches of Brandt's voles predominantly consist of Artemisia species, which are rich in TA. This study aimed to determine whether TA contributes to cold tolerance in Brandt's voles by activating BAT thermogenesis. Adult male voles were administered TA, after which the masses of BAT and inguinal white adipose tissue (iWAT) were measured, and temperature changes in BAT, the body surface, and the rectum were recorded following exposure to - 20 °C. In addition, transcriptomic analyses of BAT were performed, and the expression and protein levels of key thermogenic markers were assessed. RESULTS: The results showed that TA reduced iWAT mass while exerting minimal effects on BAT mass. TA-treated voles exhibited significantly elevated temperatures in BAT, the body surface, and the rectum after cold exposure. Histological analyses revealed that TA treatment reduced adipocyte area in iWAT while increasing the number of nuclei in brown adipocytes in BAT. In BAT, differentially expressed genes (DEGs) in voles receiving a low TA dose were significantly enriched in pathways related to fat digestion and absorption and peroxisome proliferator-activated receptor (PPAR) signaling. In contrast, DEGs in voles administered a high TA dose were predominantly associated with brown adipocyte differentiation and the upregulation of cold-induced thermogenesis. Moreover, TA administration increased the expression of FFAR4 and UCP1, as well as the protein levels of PGC-1α, PPARγ, and UCP1 following cold exposure. CONCLUSIONS: Collectively, these findings demonstrate that TA enhances cold tolerance in Brandt's voles by promoting thermogenic gene expression and stimulating brown adipocyte differentiation in BAT, providing novel insights into the role of plant secondary metabolites in mammalian cold adaptation and herbivore-plant interactions.

Animals↗

PubMed2026

Integrative analysis of transcriptome and chromatin accessibility reveals promoter-proximal regulation and identifies candidate ABC transporters associated with cold stress responses in maize.

BACKGROUND: Low-temperature stress is a formidable environmental constraint that severely limits the growth and productivity of maize (Zea mays L.), particularly during the highly vulnerable early seedling stage. While cold tolerance is a critical agronomic objective, the integrated transcriptional and epigenetic regulatory mechanisms that govern this trait remain largely elusive. Characterizing these coordinated molecular networks is fundamental to the genetic enhancement of cold resilience in maize. METHODS: Using two maize inbred lines contrasting in chilling response (ZHB12 tolerant, B73 sensitive), we performed integrative time‑course RNA‑seq and ATAC‑seq to thoroughly and systematically characterize the precise dynamic interplay between gene expression and chromatin accessibility under cold stress conditions at the seedling stage. RESULTS: Physiological assessments confirmed that ZHB12 possesses superior cold tolerance, manifested by significantly attenuated electrolyte leakage and reduced foliar damage compared to B73. Transcriptomic profiling revealed a massive, time-dependent divergence in gene expression between the two genotypes, with a major regulatory transition identified at 24 h of cold exposure. Functional enrichment analysis demonstrated that ZHB12 preferentially activates a robust defense repertoire, including Photosystem II electron transport, diterpenoid biosynthesis, and ATP biosynthetic pathways. Notably, multiple ATP-binding cassette (ABC) transporter genes were coordinately upregulated under chilling, suggesting their potential involvement in cellular homeostasis. ATAC-seq analysis indicated that cold stress is associated with chromatin remodeling in ZHB12, with increased accessibility observed in proximal promoter regions. Integrative analysis identified a core set of dual-responsive genes, in which increased promoter accessibility coincided with transcriptional upregulation. These genes were predominantly enriched in transporter activity and transcriptional regulation, suggesting potential epigenetic link to the superior stress response of ZHB12. CONCLUSION: Our findings reveal extensive transcriptional and chromatin accessibility changes in ZHB12 under cold stress. The observed associations between promoter accessibility and gene activation, particularly in genes involved in transport processes, highlight candidate regulators potentially contributing to cold tolerance. This study provides a molecular framework and identifies high-value candidate genes that may inform future efforts in breeding cold-tolerant maize, pending functional validation.

Zea mays↗

PubMed2026

Genome-wide identification of WOX transcription factors and functional characterization of WOX4 and WOX13 involved in cold stress response in Malus baccata.

INTRODUCTION: Cold stress is a major abiotic threat to apple production. Malus baccata has exceptional cold hardiness and is widely used as a superior cold-resistant rootstock. The WUSCHEL-related homeobox (WOX) transcription factor family regulates plant growth, development and stress adaptation, whereas the functions of WOX genes in cold tolerance of M. baccata remain elusive. METHODS: In the present work, 19 MbWOX family members were identified and characterized at the genome-wide level. Evolutionary analysis, cis-element prediction, transcriptome profiling and real-time quantitative PCR (RT-qPCR) were performed to screen core cold-responsive genes. Overexpression vectors were constructed and transformed into Arabidopsis seedlings for functional verification. RESULTS: Evolutionary analysis revealed that segmental duplication drove the expansion of the MbWOX family, and these genes contained a variety of stress-responsive cis-elements. Combined transcriptome and RT-qPCR analyses confirmed that MbWOX4 and MbWOX13 were core cold-responsive genes with distinct expression patterns. The two genes participated in cold signal transduction by interacting with different transcription factor networks. Functional tests revealed that MbWOX4 and MbWOX13 isoforms differentially modulated seedling cold tolerance under low-temperature stress.

Malus baccata↗

PubMed2026

Identification of aquaporin (AQP) genes in the noble scallop Chlamys nobilis and characterization of their expression under low-temperature stress.

Aquaporins (AQPs) are transmembrane channel proteins essential for water homeostasis and cellular stress responses. In marine bivalves, their roles in cold tolerance remain poorly understood despite frequent winter mortality events in aquaculture. Here, we identified nine AQP genes in the genome of the economically important noble scallop Chlamys nobilis. Phylogenetic analysis revealed strong conservation with other bivalve AQPs, and structural features, including conserved NPA motifs and ar/R selectivity filters, support their canonical water/glycerol transport functions. Tissue-specific expression profiling showed predominant enrichment in osmoregulatory tissues (gills, intestine) and gonads. Under both chronic and acute low-temperature stress from 23 °C to 9 °C, most CnAQP genes exhibited transient upregulation followed by suppression. Notably, CnAQP4 displayed sustained upregulation, implicating it as a key mediator of long-term cold adaptation. Promoter analysis further revealed abundant cis-elements linked to growth and development as well as immune regulation. Our findings provide the first comprehensive characterization of the AQP family in C. nobilis, highlighting its critical role in maintaining cellular integrity during cold stress and offering molecular targets for selective breeding of cold-tolerant scallop strains.

Animals↗

PubMed2025

Cytogenetics and genomics analysis of cold-hardy perennial wheatgrass: insights into agronomic performance, chromosome composition, and gene expression.

Intermedium wheatgrass (Thinopyrum intermedium), a perennial species with extensive root systems and high tolerance to cold, drought, and salinity, is a valuable genetic resource for the development of perennial crops. Over a decade-long selection process, two cold-hardy perennial wheatgrass lines were developed by crossing wheat-Thinopyrum partial amphiploids with Th. intermedium. These lines inherited key traits from Th. intermedium, including plant stature, spike morphology, and postharvest regrowth. Transcriptome-based single-nucleotide polymorphism tracing and sequential multicolor genomic in situ hybridization analyses revealed variations in the chromosome compositions of the perennial wheatgrass lines. The introgression of wheat chromosomes enhanced grain weight and size, while preserving the cold-hardy, perennial characteristics of the wheatgrass lines compared to Th. intermedium. Genome-wide gene expression was generally suppressed in the wheatgrass lines relative to Th. intermedium, particularly in conserved genes. This suppression was especially pronounced in genes involved in cell division and DNA repair pathways. In contrast, genes associated with cold tolerance and the water stress response were upregulated. We identified eight cold-tolerance genes in the Th. intermedium chromosomes and validated three of them, Thint.J05G452200, Thint.J05G452300, and Thint.V05G408900, using qRT-PCR. These genes encode proteins associated with cold tolerance and are potential candidates for further functional validation. Additionally, three chromosomes from homoeologous group 6 were introgressed, carrying six genes potentially associated with superior grain traits. Among them, TraesCS6D02G287800, which encodes a specific protein, exhibited high expression levels in both wheatgrass lines, suggesting its critical role in enhancing grain traits. Our results indicate that the suppression of grass gene expression, likely due to the introgression of wheat chromosomes and the upregulation of pathways related to cold tolerance and overwintering ability, contributes to the adaptive features of the wheatgrass lines. This study provides a genomic foundation for understanding gene expression regulation in distant hybrid progeny and offers valuable insights for designing new breeding strategies for perennial wheat or wheatgrass.

Chromosomes, Plant↗

PubMed2026

Distinct molecular responses to acute cold exposure revealed by comparative transcriptomic and metabolomic profiling in the bay scallop Argopecten irradians.

Acute cold stress can elicit distinct molecular responses even when bay scallop populations show similar phenotypic outcomes. We compared a seventh-generation fast-growing bay scallop line (BS) with a commercial control population (CC) during a 72-h acute cold exposure at -1 ± 0.3 °C. RNA-seq was used as the discovery layer, representative BS cold-responsive genes were evaluated by qRT-PCR, and paired LC-MS profiles provided a comparative metabolic layer. At baseline, 138 genes differed between BS and CC; after cold exposure, 134 of these baseline differences disappeared and 61 of 65 cold-state differences newly emerged. BS showed a larger transcriptomic response magnitude than CC, with 1129 cold-responsive genes compared with 28 genes in CC, and this ordering remained robust across multiple sensitivity analyses. Survival after 72 h was identical in BS and CC (83/90, 92.2% in each population). Biochemical responses were time-dependent and marker-specific: CAT, LZM, T-SOD and T-AOC showed population-by-time interactions, whereas GSH-Px and MDA did not, and the 72-h differences were not consistently favourable to BS. Metabolomic cold effects were strongly concordant between populations, and no feature showed a significant population-by-cold interaction. Features putatively assigned to arachidonic acid metabolism were enriched, but this provider-annotated pathway signal remains exploratory because authentic-standard confirmation was not performed. These findings indicate population-specific differences in molecular responsiveness but do not establish superior cold tolerance in BS.

Animals↗

PubMed2025

Genetic and phenotypic diversity of wine-associated Hanseniaspora species.

The genus Hanseniaspora includes apiculate yeasts commonly found in fruit- and fermentation-associated environments. Their genetic diversity and evolutionary adaptations remain largely unexplored despite their ecological and oenological significance. This study investigated the phylogenetic relationships, genome structure, selection patterns, and phenotypic diversity of Hanseniaspora species isolated primarily from Australian wine environments, focusing on Hanseniaspora uvarum, the most abundant non-Saccharomyces yeast in wine fermentation. A total of 151 isolates were sequenced, including long-read genomes for representatives of the main phylogenetic clades. Comparative genomics revealed ancestral chromosomal rearrangements between the slow-evolving lineage (SEL) and fast-evolving lineage (FEL) that could have contributed to their evolutionary split, as well as significant loss of genes associated with mRNA splicing, chromatid segregation and signal recognition particle protein targeting in the FEL. Pangenome analysis within H. uvarum identified extensive copy number variation, particularly in genes related to xenobiotic tolerance and nutrient transport. Investigation into the selective landscape following the FEL/SEL divergence identified diversifying selection in 229 genes in the FEL, with significant enrichment in genes within the lysine biosynthetic pathway. Furthermore, phenotypic screening of 116 isolates revealed substantial intraspecific diversity, with specific species exhibiting enhanced ethanol, osmotic, copper, SO₂, and cold tolerance.

Wine↗

PubMed2026

Genomic signatures of cold adaptation in a Himalayan drosophilid.

Drosophila nepalensis is a cold-adapted drosophilid endemic to the Himalayan region. Its ability to survive in harsh, cold conditions makes it a valuable Drosophila model for investigating how adaptation to thermal extremes may influence species persistence under future climate change. Here, we report the first de novo genome assembly of D. nepalensis, based on a hybrid sequencing strategy that combines Illumina short reads and Oxford Nanopore long reads. Illumina sequencing generated 49.88 million 150 bp paired-end reads (∼14.96 Gbp), while Nanopore sequencing produced 1.35 million long reads totaling ∼0.76 Gbp. The assembled genome spanned ∼178 Mb with an N50 of 83.6 kb and 98% BUSCO completeness, comparable to other well-annotated Drosophila genomes. Annotation identified 10,560 protein-coding genes, including transcription factor-rich and stress-related domains such as zinc fingers, WD40 repeats, and ankyrin motifs. Comparative orthology analysis across 6 Drosophila species identified 14,168 orthologous clusters, of which 9,173 were shared among all 6 species, indicating a conserved core genomic set across the sampled taxa. D. nepalensis showed 83 unique orthogroups and 50 singletons, suggesting some lineage-specific gene expansions associated with cold adaptation and endemicity, including families encoding caspase-family apoptotic regulators, chromatin remodeling proteins (HMGB/protamine-like), and SNARE-domain vesicle trafficking factors. Gene family evolution analysis revealed the highest expansions in the cold-tolerant Himalayan drosophilid, D. nepalensis, including significant expansions in serine protease, chaperone, and neurotransmitter transporter families, alongside dramatic contractions of core histone gene families, suggesting lineage-specific chromatin remodeling and ecological specialization.

Drosophila nepalensis↗

PubMed2026

Identifying the regulatory network of the key lipid metabolism transcription factor peroxisome proliferator-activated receptor in oysters.

Rising seawater temperatures driven by global warming have led to summer mass mortality events that pose significant challenges for the oyster industry. Peroxisome proliferator-activated receptor (PPAR) serves as a key transcriptional regulator of lipid metabolism and plays an essential role in thermal adaptation. However, the upstream regulatory mechanisms of PPAR remain poorly understood in marine organisms. In this study, we identified two PPAR subtypes (PPARα and PPARβ/δ) in oysters and compared transcriptomic data in different tissues and under various environmental stressors, with PPARα exhibiting higher expression levels and responsiveness to environmental stresses. We observed significantly higher PPARα gene expression levels and promoter activity in the relatively cold-tolerant Crassostrea gigas compared to C. angulata. The low expression of the inhibitory transcription factor CTNNB1 in C. gigas may contribute to higher gene expression of PPARα. Additionally, the expression genome-wide association study (eGWAS) identified 9 significant SNPs and 124 candidate regulatory genes associated with PPARα expression, including ubiquitination, phosphorylation, signaling pathways, lipid metabolism, and glucose metabolism. We provided the first experimental validation of the PPARα ubiquitination-degradation pathway in marine organisms via Co-IP, which was mediated by the E3 ligase RFWD3. The protein kinase SNF1 and signaling-related proteins PIKA and KCNK2 indirectly modulated PPARα downstream pathway activation to varying degrees. This study presents the first systematic investigation of PPARα expression regulation in marine organisms. It identifies key molecular regulators and provides novel insights into lipid metabolic regulation and molecular targets for genetic improvement of heat tolerance in oysters under global warming.

Animals↗

PubMed2026

DeepLabCut-based automated system reveals diverse temperature tolerance among medaka strains and related Oryzias species.

Temperature is a critical environmental factor influencing the physiology and behavior of ectothermic animals, yet conventional methods for evaluating thermal tolerance in fish rely on subjective manual observation of loss of equilibrium (LOE), limiting experimental throughput and introducing observer bias. Here, we developed an automated temperature tolerance evaluation system integrating DeepLabCut-based pose estimation with custom image processing algorithms to objectively quantify the timing of LOE during thermal stress tests. Our system incorporated region partitioning and color transformation preprocessing to improve keypoint detection accuracy, followed by a classification model combining ResNet34-based frame features with keypoint coordinates to objectively determine the timing of LOE without manual observation. Validation against manual annotation showed that the automated system achieved an accuracy comparable to the natural variability between trained investigators, and outperformed naive human observers, supporting its validity as an objective and reproducible alternative to manual scoring. Using this system, we characterized cold and heat tolerance across six medaka strains (Oryzias latipes: d-rR/TOKYO, HB11A, OK-Cab, HO5 and HdrR-II1; O. sakaizumii: HNI-II). Cold and heat tolerance assessment revealed inter-strain variation, with HdrR-II1 among the most cold- and heat-tolerant strains and HNI-II the least tolerant of both cold and heat stress. We further evaluated cold tolerance in medaka-related species (O. sinensis, O. cabaranensis, O. curvinotus, O. luzonensis, O. celebensis, and O. javanicus) and zebrafish (Danio rerio), revealing substantial interspecific variation that broadly corresponded with latitudinal distribution. O. latipes, distributed at the highest latitudes among the tested species, exhibited the greatest cold tolerance, whereas O. celebensis, O. javanicus, and other tropical or low-latitude species showed comparatively low cold tolerance. Our automated system provides a robust, high-throughput platform for thermal tolerance evaluation and, combined with the genetic and genomic resources available in medaka, establishes a foundation for elucidating the molecular mechanisms underlying temperature adaptation in fish.

Animals↗