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PubMed2026

Strain Diversity and Resistance to Cucumber Green Mottle Mosaic Virus (CGMMV) in Cucumber.

Cucumber green mottle mosaic virus (CGMMV) is a tobamovirus that causes disease in cucumber crops worldwide, leading to significant economic losses. To study the variability of CGMMV in southeastern Spain, partial genome sequences were obtained from isolates collected in 2017 and 2020 from cucumber crops. Phylogenetic analyses revealed that isolates clustered into two major groups, Asian (AS)-like and European (EU)-like CGMMV isolates. These two groups coexisted in the same area, crops, and even individual plants, although the AS type predominated. The accumulation and symptom expression of molecularly cloned isolates from these two groups were assessed in two cucumber cultivars (resistant and susceptible) under both summer and winter conditions. An in planta antagonistic interaction was detected between the AS and EU isolates, in which the accumulation of CGMMV-EU was suppressed during mixed infections. A multivariate analysis did not identify statistically significant differences because of variations in environmental conditions. Unlike CGMMV-EU, CGMMV-AS did not show significant differences in accumulation based on the plant genotype. To further investigate this, the response to CGMMV-AS infection was analyzed in additional susceptible and resistant cultivars. All cultivars appeared to be similarly susceptible to CGMMV-AS, in contrast to CGMMV-EU, which accumulated to a much lower extent in resistant compared with susceptible plants. These results reinforce the need to continue epidemiological surveillance, identify new sources of resistance, and implement strict control of infected seed trade, given the growing threat that CGMMV-AS isolates pose to cucumber cultivation.

agroinfectious clone↗
PubMed2026

Deciphering differential mRNA and lncRNA expression profiles in response to PEG simulated drought stress in cucumber (Cucumis sativus L.).

Cucumber (Cucumis sativus L.), a vital fruit vegetable of the Cucurbitaceae family, originated in India ∼ 3000 years ago. It is widely used in the culinary, therapeutic, and cosmetic sectors. Cucumber cultivation is significantly impacted by drought stress, especially in arid and semi-arid regions. This study investigates the molecular response to drought using two contrasting cucumber lines: WBC-23-2 (drought-tolerant) and DGPC-59 (drought-sensitive). Drought was simulated using polyethylene glycol (PEG), and effects on physiological and biochemical traits were evaluated. The tolerant line exhibited reduced leaf wilting and higher relative water content (RWC). Based on these physiological markers, transcriptomic profiling was employed to identify the underlying regulatory networks. Analysis identified 4,736 DEGs, suggesting that the tolerant line's superior resilience is driven by preferential activation of genes involved in photosynthesis and glutathione metabolism. Conversely, the sensitive genotype showed enrichment in organonitrogen compound catabolism and water deprivation response. This divergence is further reflected in the regulation of 155 transcription factors (TFs) across various families, indicating distinct regulatory architectures between the two lines. Additionally, 774 drought-responsive long non-coding RNAs (lncRNAs) were identified, acting via cis, trans, and competing endogenous RNA (ceRNA) mechanisms to modulate gene expression. Key candidate genes associated with drought tolerance included WAT1-related protein At5g64700, thaumatin-like protein, berberine bridge enzyme-like 18, probable WRKY transcription factor, and pathogenesis-related protein 1. This study reveals a complex regulatory network of mRNAs, lncRNAs, and TFs underlying drought response and provides a valuable foundation for breeding drought-resilient cucumber cultivars. A web-based genomic resource, CsDTDb, has been developed and made publicly available to facilitate future functional genomics studies related to drought tolerance in cucumber.

DEGs↗
PubMed2025

Expression regulation network in papillae of sea cucumbers: Whole-transcriptome and DNA methylation datasets.

To elucidate the expression regulation network of papilla size of sea cucumbers (Apostichopus japonicus), the whole-transcriptome and DNA methylome datasets of different sizes of papillae in sea cucumbers were generated. Average clean bases of whole-transcriptome (16.35 G) and DNA methylome (28.92 G) were obtained using RNA sequencing and whole-genome bisulfite sequencing techniques. A total of 3,188 ceRNA networks were also identified including 3,081 long non-coding RNAs (lncRNA)/microRNAs (miRNA)/mRNA networks and 107 circular RNA (circRNA)/miRNA/mRNA networks. Methylome data indicate that there were 3,307 and 3,776 differentially methylated regions (DMRs) with high-level methylation as well as 3,125 and 3,016 DMRs with low-level methylation in big papillae compared to small papillae. The identified DMRs were mainly distributed in introns, promotors, or exons. The whole-transcriptome and DNA methylome datasets generated from this study not only established a robust theoretical foundation (especially from the epigenetic aspect) for elucidating expression regulation network determining papilla size in sea cucumbers but also can be a valuable resource of biomarker mining for papilla appearance-based selective breeding in sea cucumbers.

DNA Methylation↗
PubMed2026

Host genetic regulation of xylem-resident Pseudomonas enhances cucumber growth.

BACKGROUND: Although endophytic microorganisms play a critical role in plant growth and stress resilience, the genetic basis underlying host selection of beneficial microbiota-particularly within the xylem-remains poorly understood. Cucumber (Cucumis sativus), as a crop model with a well-developed system for studying vascular biology, offers a valuable system to investigate the host genetic determinants of xylem microbiome assembly. RESULTS: By conducting population-level microbiome profiling across 109 cucumber accessions, we identified a conserved xylem microbiota dominated by Proteobacteria. Within this community, 20 core amplicon sequence variants (ASVs) were consistently present in xylem sap. Genome-wide association mapping identified a host genetic locus, CsXPR1, which encodes a tetratricopeptide repeat protein that regulates the abundance of the dominant xylem-colonized Pseudomonas ASV_4. Colonization patterns of ASV_4 varied across host genotypes and were correlated with CsXPR1 expression levels, suggesting a precision genetic regulation of bacterial entry into vascular tissues. Pseudomonas fulva strain 220, with 97% 16S rRNA gene identity with ASV_4, could colonize in cucumber xylem by inoculation of either roots or leaves. Genome analysis and plate assays revealed the biosynthesis of indole-3-acetic acid (IAA), solubilization of phosphate, and a range of plant beneficial traits in strain 220. Inoculation with strain 220 significantly enhanced growth in cucumber, but only in CsXPR1 haplotype that exhibited high gene expression and higher recruitment capacity of the strain. These benefits included notable increases in plant height (38%), stem diameter (36%), leaf area (61%), fresh and dry weight (51% and 85%, respectively), and a 4.57-fold increase in 4-methyleneglutamine content within the xylem sap. CONCLUSION: Our findings reveal a complete "gene-to-function" pathway where the host gene CsXPR1 mediates a genotype-dependent growth promotion. It achieves this by regulating the xylem colonization of a beneficial bacterium, Pseudomonas fulva, which in turn enhances plant growth by enriching the xylem sap with the key metabolite 4-methyleneglutamine. Video Abstract.

Cucumis sativus↗
PubMed2026

The CsTBH-CsROP2 Module Regulates Waterlogging Tolerance via Auxin-Mediated Adventitious Root Formation in Cucumber.

Cucumber (Cucumis sativus L.) requires frequent irrigation due to its shallow root system and high transpiration rate of the aboveground parts. However, it is also prone to waterlogging damage. Therefore, understanding its response to waterlogging is crucial for breeding waterlogging-tolerant varieties. Although Rho of Plants GTPases play well-established roles in regulating development and stress signalling, their functions in plant adaptation to waterlogging stress has yet to be fully elucidated. Here, we identified nine CsROP genes in the cucumber genome, which exhibit evolutionary diversification but retain conserved functional domains. Functional analysis revealed that CsROP2 acts as a negative regulator of adventitious root formation. It modulates auxin accumulation in hypocotyl vascular bundles, thereby suppressing adventitious root development and enhancing waterlogging sensitivity. The HD-Zip I transcription factor CsTBH directly binds the CsROP2 promoter and activates its expression. Our study uncovers a CsTBH-CsROP2 module that governs adventitious rooting and waterlogging tolerance by modulating auxin homeostasis. These findings provide new insights into the crosstalk between developmental programmes and stress signalling pathways and offer potential genetic targets for improving stress resilience in cucumber and other crops.

CsROP2↗
PubMed2026

Natural variants of CsSHN1 orchestrate a temporal regulatory cascade driving fruit skin netting in cucumber.

Fruit skin netting (russeting, Rs) forms when epidermal microcracks are sealed by a suberized periderm, reducing marketability. We previously identified the Rs locus (CsSHN1), which encodes an AP2/ERF transcription factor, as a major determinant of cucumber skin netting, but how fruit growth is temporally coupled to periderm formation remains unclear. Here, we integrated population genomics, time-series multiomics, DNA affinity purification sequencing (DAP-seq), and transgenic assays to decode the CsSHN1-mediated regulatory network. Six functionally relevant CsSHN1 variants were identified across 325 cucumber accessions. Allele distribution and selective sweep analyses revealed breeding-driven selection for smooth fruit skin. Overexpression of a netted allele in a smooth background induced epidermal fissures, altered cell geometry, and increased fruit size, demonstrating a dosage-sensitive effect. Time-series transcriptomics and metabolomics of near-isogenic lines (NILs) defined 3 developmental phases of netting: early suppression of lignin and trehalose genes preceding cracks, growth-driven fissuring accompanied by cell-wall remodeling and defense activation, and maturation-stage cell-wall degradation with strong induction of ligno-suberin biosynthesis. Across the cucumber genome, DAP-seq identified approximately 8,000 in vitro CsSHN1 binding sites. These binding sites were significantly enriched for the GCC-box motif and included genes involved in cutin and suberin biosynthesis. Together, these results show that CsSHN1 orchestrates fruit skin netting through a growth-coupled temporal regulatory cascade, providing a mechanistic framework for manipulating fruit epidermal properties.

Cucumis sativus↗
PubMed2026

Evolutionary conservation and adaptability of cholecystokinin neuropeptide signaling in the sea cucumber Apostichopus japonicus.

BACKGROUND: Food ingestion is fundamental for animal survival and growth, with the cessation of feeding upon nutrient fulfillment being tightly regulated by a variety of satiety factors. Notably, sulfakinin/cholecystokinin (SK/CCK)-type neuropeptide signaling has been identified as an inhibitory regulator of food intake across the animal kingdom. However, its regulatory mechanism in feeding in deuterostome invertebrates remains unclear. Here, we characterized SK/CCK-type signaling in a deuterostome invertebrate, the sea cucumber Apostichopus japonicus (phylum Echinodermata). RESULTS: A single SK/CCK-type precursor in A. japonicus generates two mature peptides (AjSK/CCK1, AjSK/CCK2) that activate a shared receptor (AjSK/CCKR), triggering Ca2+ mobilization via the Gαq-dependent pathway and extracellular signal regulated kinase 1/2 (ERK1/2) phosphorylation. Both peptides induce dose-dependent contraction of longitudinal muscles, while AjSK/CCK2 additionally elicits sustained contraction of the posterior intestine, an effect absent in other gut regions. Long-term injection of both peptides reduces food intake and significantly downregulates orexin-type neuropeptide genes (AjOrexin1P, AjOrexin2P) in the circumoral nerve ring (CNR) and intestine. CONCLUSIONS: Unlike mammals, where CCK inhibits feeding by contracting the pyloric sphincter to delay gastric emptying, SK/CCK-type peptides in sea cucumbers exert their anorexic effect in part by selectively contracting the posterior intestine, thereby inhibiting intestinal emptying. This divergence in action sites highlights the evolutionary adaptability of SK/CCK-type signaling as a conserved inhibitory regulator of feeding across bilaterian animals. Elucidating these mechanisms in the economically important A. japonicus may inform development of appetite-promoting agents for sustainable aquaculture.

Animals↗
PubMed2026

Genome-wide identification of the HSP70 superfamily in tropical sea cucumber Stichopus monotuberculatus and their expression analysis under low-salinity stress.

Heat shock proteins (HSPs) are a group of evolutionarily conserved molecular chaperones that serve as indispensable core regulators in preserving cellular homeostasis and orchestrating organismal stress responses. The tropical sea cucumber Stichopus monotuberculatus, a high-value aquaculture species, is sensitive to fluctuations in environmental salinity-a challenge that has emerged as a critical bottleneck limiting its large-scale commercial cultivation. However, no systematic investigation has been conducted to characterize the HSP70 superfamily in S. monotuberculatus and elucidate its functional roles in salinity adaptation. In the present study, we performed a comprehensive genome-wide scan and identified 19 HSP70 superfamily genes in the S. monotuberculatus genome, with the HSP70IV subfamily showing remarkable gene expansion, containing 8 distinct copies. Phylogenetic analysis, conserved motif identification, and gene structure characterization demonstrated high evolutionary conservation within each HSP subfamily. These genes were unevenly distributed across the chromosomes of S. monotuberculatus, and prediction of cis-acting elements revealed that their upstream regulatory regions were enriched with numerous functional elements associated with stress response and immune regulation. Salinity stress experiments revealed that under severe low-salinity conditions (18‰), the expression levels of SmHSPA14L and multiple HSP70IV subfamily members were significantly elevated, while SmHYOU1D was significantly downregulated; in contrast, only subtle changes were detected in the expression of most HSP70 genes under moderate low-salinity stress (24‰). These findings strongly suggest that HSP70 genes, particularly the expanded HSP70IV subfamily, may act as key modulators in the low-salinity stress response. This work provides valuable insight into the molecular mechanisms underlying salinity adaptation in tropical sea cucumbers.

Animals↗
PubMed2026

Development of a highly efficient prime editing platform for cucurbits enables breeding of multi-disease-resistant cucumber.

The prime editing (PE) system is a precise genome editing technology that works efficiently in monocots; however, its application is limited by low editing efficiency in dicots, particularly Cucurbitaceae and Solanaceae plants. Here, we first significantly improved the transformation efficiency by introducing spectinomycin in cucurbits, then used the tomato elongation factor 1-alpha (SlEF1α) promoter to enhance PE protein expression, and incorporated the Csy4 ribonuclease to process pegRNAs, collectively addressing multiple constraints limiting PE efficiency in cucurbits. The optimized PE systems, particularly Csy4-PE6d, achieved an average desired editing frequency of 80.83% at targeted loci in cucumber via stable genetic transformation, with frequencies reaching up to 100% at certain sites. Moreover, Csy4-PE6d generated homozygous edits in 36.43% of transgenic lines and demonstrated robust editing activity in melon, pumpkin, and potato. Using the Csy4-PE6d tool, we generated heritable edited cucumber lines with dual resistance to bacterial angular leaf spot and downy mildew by targeting the CsSGR gene. Collectively, this optimized system substantially enhances PE efficiency in Cucurbit crops, providing an effective solution to common challenges such as low editing efficiency and limited heritability in these species.

Disease Resistance↗
PubMed2026

Genome-Wide Identification and Characterization of the TBL Gene Family and Temporal Expression Dynamics During Powdery Mildew Infection in Cucumber (Cucumis sativus).

Cell-wall polysaccharide O-acetylation contributes to cell-wall assembly, organ development, and plant-pathogen interactions, but the cucumber TBL gene family remains poorly characterized. Here, 37 CsTBL genes were identified genome-wide and analyzed using phylogenetic, syntenic, conserved-motif, gene-structure, promoter, protein-structure, Gene Ontology, and transcriptome approaches, followed by RT-qPCR analysis after powdery mildew inoculation. All CsTBL proteins contained the conserved GDS and DxxH motifs, whereas accessory motifs and predicted structural features varied among clades. Intraspecific analysis identified dispersed, WGD/segmental, and tandem duplication categories, and cross-species synteny was more extensive with melon than with Arabidopsis. Homology-derived annotations associated CsTBL genes with cell-wall polysaccharide metabolism, Golgi/endomembrane compartments, and O-acetyltransferase activity, including six genes assigned to xylan O-acetyltransferase-related annotations. Expression profiling revealed tissue- and developmental-stage-dependent patterns, whereas the publicly available powdery mildew RNA-seq dataset provided descriptive temporal expression profiles in Podosphaera xanthii-inoculated samples. Independent RT-qPCR analysis using time-matched mock controls revealed distinct post-inoculation responses among six selected genes. Relative to the corresponding mock controls, CsTBL2 was consistently repressed; CsTBL15 showed transient induction at 1 dpi followed by repression; CsTBL24 exhibited a biphasic response; CsTBL25 was induced at all sampled post-inoculation time points; CsTBL26 showed progressive induction; and CsTBL30 reached its highest observed expression level at 3 dpi. Integrated functional annotation and expression evidence highlighted CsTBL26 as a priority candidate for further functional characterization, while CsTBL24 and CsTBL25 represented fruit-associated candidates with distinct powdery mildew responses; CsTBL30 remained an additional strongly infection-responsive candidate. These findings provide an evolutionary and expression-based framework for the functional characterization of the cucumber TBL gene family.

O-acetylation↗
PubMed2026

Ossicle occurrence characteristics and related molecular mechanisms in the sea cucumber Apostichopus japonicus.

To investigate the morphogenetic pattern and molecular mechanism of ossicle formation in the sea cucumber Apostichopus japonicus, this study systematically examined the morphological development and temporal sequence of spicules using the NaClO maceration method, in-situ squash preparation and microscopic observation. Comparative transcriptome sequencing was performed between doliolaria and pentactula larvae to screen differentially expressed genes (DEGs) related to ossicles formation, followed by pathway enrichment analysis. The function of the candidate key gene papilin-like was verified using siRNA-mediated gene silencing. The results were as follows: 1) Ossicles of A. japonicus first appeared at the late auricularia stage, initiating as X-shaped ossicles at the base of the oral tentacles. The number of X-shaped ossicles increased dramatically during the doliolaria stage. X-shaped ossicles were gradually replaced by table-shaped and rosette-shaped ossicles at the pentactula stage, suggesting that X-shaped ossicles may differentiate into these two ossicle types. The morphology of table-shaped ossicles showed a "simple-complex-simple" pattern with development. 2) Key genes related to ossicles formation, including CA1, COL1A2, and papilin-like, were identified by transcriptome analysis. After papilin-like knockdown, abnormal morphologies were observed in table-shaped ossicles of 1-year-old A. japonicus, such as spine-like protrusions on the outer margin of the disc and loss of table legs, confirming its crucial roles in maintaining ossicle morphology. This study clarified the morphological development pattern of ossicles in A. japonicus and identified a key regulatory gene (papilin-like) involved in ossicle morphogenesis, providing preliminary insights into the underlying molecular regulatory mechanism. These findings enrich our understanding on ossicles formation in echinoderms, and provide important morphological and molecular biological information for further studies on the developmental mechanism of ossicles in A. japonicus.

Animals↗
PubMed2026

Signaling mechanisms of vasopressin/oxytocin-type neuropeptide-induced muscle contraction in the sea cucumber Apostichopus japonicus.

The myoregulatory action of vasopressin/oxytocin (VP/OT)-type neuropeptides is evolutionarily conserved across Bilateria. In vertebrates, the signaling cascades involved have been comprehensively characterized in several muscle types, including uterine and gastrointestinal smooth muscles. VP/OT-type neuropeptide-induced muscle contraction or relaxation has been reported in a variety of invertebrates, but the downstream signaling pathways responsible for these effects have yet to be elucidated. Here, using heterologous cell systems and in vitro pharmacological experiments, we investigated the signaling pathways underlying VP/OT-type neuropeptide (holotocin) induced contraction of the longitudinal muscle of the body wall (LMBW) in the sea cucumber Apostichopus japonicus (phylum Echinodermata), a deuterostome invertebrate. Holotocin-induced contraction of the LMBW comprised two distinct phases: an initial rapid phasic contraction followed by a sustained tonic contraction. Pharmacological experiments revealed that upon binding to its receptor AjHOR, holotocin activates a Gαq-dependent pathway, leading to phospholipase C (PLC) activation and subsequent hydrolysis of phosphatidylinositol 4,5-bisphosphate (PIP2) into inositol 1,4,5-trisphosphate (IP3) and diacylglycerol (DAG). IP3 triggers Ca2+ release from intracellular Ca2+ stores via IP₃ receptors (IP3R), but depletion of intracellular Ca2+ does not activate store-operated Ca2+ entry (SOCE). DAG activates protein kinase C (PKC), which may modulate the activity of ion channels in the plasma membrane, resulting in membrane depolarization, opening of voltage-gated Ca2+ channels (VGCCs), and subsequent influx of extracellular Ca2+. Overall, this study reveals similarities and differences in the signaling pathways mediating smooth muscle contraction in invertebrates and vertebrates, providing new insights into the evolution of these mechanisms across the Bilateria.

Ca(2+)↗
PubMed2026

Molecular adaptation of caspase genes to salinity stress in the tropical sea cucumber Stichopus monotuberculatus: A comparative analysis across echinoderms.

Apoptosis is an essential physiological process that plays a critical role in development and tissue homeostasis. Caspases, as central regulators of apoptosis, are crucial in controlling inflammation and cell death. In this study, we investigated the caspase gene family in Stichopus monotuberculatus to explore their potential roles in salinity stress adaptation. Five caspase genes were identified from the genome of S. monotuberculatus, including Smcaspase3, Smcaspase6, Smcaspase8a, Smcaspase8b, and Smcaspase8c. Phylogenetic analysis revealed that these Smcaspase genes clustered into distinct caspase subfamilies and showed high conservation with homologs from other echinoderms and representative vertebrates. Conserved motif and gene structure analyses showed relatively similar structural patterns within each clade, whereas divergence was observed among different subfamilies. Promoter analysis identified numerous cis-acting elements related to gene regulation, immune response, and growth and development. Expression profiling under salinity stress showed that Smcaspase8a was significantly upregulated, particularly under prolonged stress, whereas the other genes exhibited limited transcriptional responses. Our findings highlight caspase function in salinity stress and provide the foundation of molecular salinity adaptation mechanisms in S. monotuberculatus.

Animals↗
PubMed2025

Large-scale analysis of MYB genes in Cucurbitaceae identifies a novel gene regulating plant height.

The MYB transcription factor (TF) family, which is involved in plant growth and development, is large and diverse. Previous studies on MYB family in Cucurbitaceae were mostly based on a single genome or focused on the R2R3 subfamily. Here, we analyzed 91 genomes of 11 Cucurbitaceae species and identified a total of 15 858 MYB genes. According to phylogenetic relationships, these genes were divided into 27 subgroups. The identified MYB genes were further classified into 121 MYB orthologous gene groups (OGGs), including 25 core, 57 softcore, 19 shell and 20 line-specific/cloud groups. Whole-genome duplication was the most common mechanism of MYB genes expansion. In core group, the higher proportions of MYB genes were found to be in the coexpression network constructed by the RNA-seq data. Through the comprehensive analysis including phylogeny and gene expression profile of cucumber MYB genes, as well as genetic variations in 103 cucumber germplasms, we identified a MYB gene CsRAX5, which may be related to cucumber plant height. We used gene editing technology to knockout and overexpress CsRAX5. In the knockout lines, Csrax5, the height was significantly increased compared with wild type (WT), whereas after overexpression the height of CsRAX5-OE plants was significantly decreased compared with WT. These results indicated that MYB gene CsRAX5 negatively regulated cucumber plant height. The large-scale analysis of MYB genes in Cucurbitaceae in this study provides insights for further investigating the evolution and function of MYB genes in Cucurbitaceae crops.

Journal Article↗
PubMed2026

A novel phage vB_VhaM_HVS-1 inhibits host cell associated Vibrio harveyi.

INTRODUCTION: Vibrio harveyi is a major pathogen causing skin ulceration syndrome and mass mortality in sea cucumber Apostichopus japonicus aquaculture. METHODS: In this study, a pathogenic strain NB-3 was isolated from diseased A. japonicus and identified as V. harveyi based on morphological, physiological, and genomic analyses. A novel lytic phage vB_VhaM_HVS-1 belonging to the family Straboviridae (class Caudoviricetes) was isolated from A. japonicus breeding pond silt. RESULTS: The phage exhibited a latent period of 50 min and a burst size of approximately 168 PFU/cell, and its genome lacked lysogeny-related genes, suggesting a lytic nature. Phage treatment significantly reduced the number of cell-associated bacteria, decreasing the association rate from 2.3% to nearly 0. Flow cytometry revealed that phage infection protected coelomocytes from V. harveyi-induced damage, increasing the proportion of viable cells from 78.17% to 88.54%. CONCLUSION: These findings demonstrate that phage vB_VhaM_HVS-1 effectively reduces V. harveyi association with coelomocytes and alleviates host cell apoptosis. The phage shows strong potential as an alternative biocontrol agent against V. harveyi infection in sea cucumber aquaculture.

aquaculture disease↗
PubMed2026

Comparative transcriptome analysis provides insights into dorso-ventral color pattern formation of Holothuria edulis.

Animal body color patterns are highly diverse and play critical roles in camouflage, intraspecific communication, and environmental adaptation. Holothuria edulis, an important echinoderm inhabiting tropical waters, exhibits a typical dorsoventral dichromatism. This unique body color difference represents a key phenotypic trait for its habitat adaptation; however, the core differential genes regulating this trait remain to be elucidated. In this study, comparative transcriptome sequencing was performed on the dorsal and ventral body wall tissues of H. edulis, leading to the identification of a number of differentially expressed genes (DEGs), followed by GO functional annotation and KEGG pathway enrichment analysis. GO enrichment analysis indicated that the DEGs were significantly enriched in functional categories such as extracellular region, peptidase inhibitor activity, and tetrapyrrole binding. KEGG pathway analysis further revealed significant enrichment of protein digestion and absorption, the TNF signaling pathway, and cholesterol metabolism. Notably, the pigmentation-related gene FMO2 was highly expressed in the dorsal body wall tissue, whereas cyp1a1, ZIC1, Slc7a11, WNT-1, and ADAMTS20 were highly expressed in the ventral body wall tissue. This study identified DEGs and enriched pathways associated with dorsoventral body color differences in H. edulis, providing new insights into the molecular regulatory mechanisms underlying body color pattern formation. From the perspective of aquaculture applications, body color is one of the important traits affecting the quality and market value of sea cucumber products. Elucidating the molecular mechanisms of body color variation can provide a scientific basis for molecular marker-assisted breeding of superior sea cucumber variety.

Animals↗
PubMed2026

Transcriptomic characterization of the intestine in Stichopus monotuberculatus under gradient temperature stress and HSP gene family-mediated molecular adaptation.

The increasing frequency of extreme temperature events under climate change poses a growing threat to the stability of tropical sea cucumber aquaculture. To characterize the molecular responses of the tropical sea cucumber Stichopus monotuberculatus to acute temperature stress, juveniles were exposed for 96 h to 15 °C, 20 °C, 25 °C, 30 °C, and 35 °C, followed by transcriptomic profiling of the intestine. By transcriptomic analysis, 2258, 634, 1618, and 2980 differentially expressed genes (DEGs) were identified at 15, 20, 30, and 35 °C compared to control, respectively. More DEGs were generally detected at temperatures further from 25 °C, with the 35 °C group showing the largest transcriptional response. Although cold and heat stress both affected metabolism and protein homeostasis, their enrichment profiles differed. At 15 °C, DEGs were mainly enriched in the spliceosome and p53 signaling pathways, highlighting RNA processing and p53 signaling as prominent features of the cold-stress response. At 35 °C, DEGs were mainly enriched in the PI3K-Akt signaling pathway, ubiquitin-mediated proteolysis, and mitophagy, indicating enhanced regulation of cell survival, protein turnover, and mitochondrial quality control. HSP genes also responded differently to cold and heat stress. Most HSP70 and HSP90 family members were downregulated at low temperatures, whereas HSP70 genes and small heat shock proteins were markedly upregulated at high temperatures. Overall, the intestinal transcriptome showed distinct responses to cold and heat stress. These results identify pathways and HSP genes potentially involved in the temperature response of S. monotuberculatus and provide useful information for evaluating temperature tolerance and defining suitable temperatures for its aquaculture.

Heat shock protein↗
PubMed2026

A small viral protein suppresses immune amplification by two distinct mechanisms.

Diverse viral suppressors of RNA interference (RNAi) and RNA silencing (VSRs) interact directly with core protein and/or RNA components of the host RNAi pathway. However, the specific counter-defense function of any VSR biochemical activity is fully validated only when it is shown as essential for viral infection in the wild-type but not mutant hosts defective in antiviral RNAi. Here, we investigated the role of VSR activities for direct binding to small-interfering RNA duplexes (siRNA), long double-stranded RNA (dsRNA), or RNA-dependent RNA polymerase 1 (RDR1) during plant infection by wild-type and mutant cucumber mosaic virus (CMV), a positive-strand RNA virus expressing the 110-residue 2b protein as its VSR. We demonstrate that a C-terminally truncated 2b mutant (2b1-93) active in direct binding to siRNA and dsRNA, but not RDR1, was able to suppress the amplification of virus-derived siRNAs (vsiRNA) and antiviral RNAi mediated by RDR6, but not RDR1. By contrast, an N-terminally truncated 2b mutant (2b18-110) inactive in direct binding to siRNA or dsRNA was able to suppress vsiRNA amplification and antiviral RNAi mediated by RDR1, but not RDR6, and was less effective to promote systemic CMV infection and disease development than 2b1-93. Together, our results show that whereas RDR1 suppression requires direct binding of VSR-2b to RDR1, but not siRNA or dsRNA, RDR6 suppression depends on direct binding to siRNA and dsRNA, but not RDR1. Therefore, CMV, through its VSR-2b, suppresses two parallel vsiRNA amplification pathways by distinct molecular mechanisms, and this unique property may account for the unusually wide host range of CMV.IMPORTANCEHost amplification of antiviral immunity is essential for robust control of viral infections. However, little is known about the mechanisms that viruses have evolved to suppress immune amplification in plants. Here, we characterized whole plant infection by cucumber mosaic virus (CMV) with its viral suppressor of RNA interference (RNAi) mutated to become inactive in direct binding to small-interfering RNA duplexes (siRNA), long double-stranded RNA (dsRNA), or RNA-dependent RNA polymerase 1 (RDR1). We demonstrate maximal suppression of both RDR1- and RDR6-mediated antiviral RNAi amplification by the CMV 2b protein, a viral suppressor of RNAi (VSR). Notably, whereas RDR1 suppression requires direct binding of 2b to RDR1 but not siRNA or dsRNA, RDR6 suppression depends on direct binding to siRNA and dsRNA, but not RDR1. Our findings reveal a novel counter-defense strategy evolved by a wide host range positive-strand RNA virus to suppress two pathways of immune amplification by distinct mechanisms.

Cucumovirus↗