Biology subjects

Comino, C.

Publications and source records attributed to Comino, C..

7 recordsLinked to original sources

bioRxiv2026

Genotype-dependent transcriptional trajectories during prolonged heat stress in Capsicum annuum L.

Heat stress is one of the most damaging abiotic constraints on crop productivity, and its consequences are expected to intensify as extreme temperature events become more frequent and severe. Pepper (Capsicum annuum L.) is particularly vulnerable to sustained high temperatures, which can disrupt photosynthetic performance, cellular homeostasis, and redox regulation. However, the physiological and transcriptional dynamics underlying genotype-dependent responses to prolonged heat exposure remain insufficiently understood. We combined repeated physiological measurements with time-course RNA sequencing to compare GPC003240, previously identified as a candidate heat-tolerant accession, with two non-elite accessions, GPC010350 and GPC014930, which are phenotypically divergent from each other, under 40/30 {degrees}C Day/night temperatures for up to six days. GPC010350 maintained comparatively stable photosystem II performance and higher stomatal conductance, whereas GPC014930 showed progressive photochemical impairment and lower conductance; GPC003240 displayed a distinct, moderately responsive profile. Transcriptomic responses showed partial functional convergence during the early phase of stress exposure but diverged markedly after six days. When gene expression at day 6 was compared with the pre-treatment baseline separately within each genotype, 4,436 differentially expressed genes were detected in GPC010350, compared with 680 in GPC003240 and only 78 in GPC014930. The late response of GPC010350 was associated with enrichment of RNA- and ribosome-related, biosynthetic, DNA-repair, and genome-maintenance functions. By contrast, GPC014930 showed negative enrichment of photosynthesis, plastid organization, redox homeostasis, and translation-related processes. Global co-expression analysis identified a time-decreasing photosynthesis-associated module (ME5) and two time-increasing modules, ME12 and ME19, that were enriched in genes contributing to the late GPC010350 response. Integration of differential expressions, module membership, and functional annotation highlighted a heat shock transcription factor (Caz03g27980), HSP101 (Caz03g07770), and a dual-specificity phosphatase (Caz05g20970) as candidates for further investigation. Overall, the results suggest that genotype-dependent responses to prolonged heat exposure were associated not only with the magnitude of early transcriptional change, but also with differences in the temporal organization of stress-response, maintenance, and metabolic processes. The contrasting responses of the non-elite accessions GPC010350 and GPC014930 further highlight the value of phenotypically diverse germplasm for uncovering mechanisms relevant to future heat-tolerance breeding.

plant biology↗

bioRxiv2026

A first pangenomic framework for globe artichoke supports SNP-based varietal fingerprinting

Globe artichoke (Cynara cardunculus var. scolymus L.) comprises a broad range of local ecotypes and varietal groups whose genetic diversity has been investigated through different molecular markers. However, recent advances in next-generation sequencing and pangenomics approaches provide new opportunities to capture genome-wide variation at higher resolution and to develop practical tools for varietal discrimination, traceability, and germplasm conservation. In this study, we developed the first pangenomic framework for cultivated artichoke and evaluated pangenome-informed SNP markers for varietal fingerprinting. Whole-genome resequencing data from the Italian local ecotype Asti Sori were integrated with publicly available genomic data from representative globe artichoke and cultivated cardoon accessions to construct and annotate a pangenome. Genome-wide SNP and presence/absence variation (PAV) analyses were combined with pangenome-anchored genotyping-by-sequencing (GBS) data from 45 accessions representing the main cultivated varietal groups. The pangenome revealed a largely conserved core gene repertoire alongside a smaller accessory component, with gene accumulation curves suggesting a tendency toward saturation within the sampled cultivated germplasm. SNP- and PAV-based analyses provided complementary views of accession relationships and consistently resolved the principal cultivated groups. Across the broader germplasm panel, pangenome-anchored GBS-derived SNPs identified well-supported phylogenetic clusters corresponding to recognized varietal types. A reduced panel of 50 SNPs, selected through iterative random subsampling, retained at least 90% of the genetic diversity captured by the full dataset and reproduced its main population structure. This compact pangenome-anchored marker set provides a practical foundation for varietal fingerprinting, DUS-oriented applications, traceability, and conservation of traditional globe artichoke germplasm. Validation across independent collections will be required before routine deployment.

Plant Biology↗

bioRxiv2026

Progressive drought transcriptomics and co-expression framework in eggplant (Solanum melongena L.)

Drought is a major constraint for eggplant productivity in Mediterranean and semi-arid environments, yet stage-specific molecular features that distinguish tolerant and sensitive genotypes under progressive water deficit remain limited. Here, we profiled drought responses in two contrasting eggplant (Solanum melongena L.) genotypes from the G2P-SOL core collection, integrating physiology and transcriptomics to resolve genotype-dependent programs at moderate and severe stress. Physiological measurements confirmed divergent drought performance, with the tolerant genotype Berenjena de rabo largo (GPE020510) maintaining water status and stomatal function longer than the sensitive genotype Qianzi (GPE008940). RNA-seq revealed strong transcriptional reprogramming in both genotypes, but with distinct timing and functional priorities across stress transitions. At moderate stress, tolerance was associated with early ABA-centred regulatory control and dehydration protection (including ABI5, TAS14 and LEA/dehydrin-related loci), coupled to transport and redox homeostasis and repression of growth-associated outputs. In contrast, the sensitive genotype showed prominent early regulatory and RNA/protein-turnover signatures alongside weaker representation of cuticle/barrier and chloroplast/light-management functions. Under severe stress, the sensitive genotype shifted toward a broad high-maintenance state enriched in remodeling, detoxification and transporter activity, whereas the tolerant genotype displayed a more targeted adjustment featuring plastid photoprotection, proteostasis and selective metabolic reconfiguration. Co-expression network analysis supported this stage-resolved model by identifying modules and hub genes with contrasting temporal trajectories between genotypes, linking earlier coordinated regulatory/membrane-trafficking and plastid/redox tuning to drought tolerance. Overall, these results indicate that eggplant drought resilience is associated with genotype-specific coordination and timing of protective programs superimposed on a shared basal stress response, and they provide prioritized candidate pathways and genes for functional validation and breeding.

plant biology↗

bioRxiv2026

Long-term salinity reveals genotype-specific transcriptional reprogramming in eggplant

Salinity severely limits eggplant productivity, yet the transcriptional bases of tolerance to prolonged salt exposure remain incompletely understood. Here, we analyzed long-term salinity responses in two contrasting eggplant (Solanum melongena L.) genotypes from the G2P-SOL core collection, focusing on genotype-dependent transcriptional regulation under chronic stress. Plants were exposed to 200 mM NaCl for 23 days at the reproductive stage, and transcriptome profiling was performed at the end of the stress period. Physiological assessment and high-throughput phenotyping confirmed a strong divergence in water status and plant architecture between genotypes under salinity, providing a reference framework for transcriptomic interpretation. RNA-seq analysis revealed marked genotype-specific differences in transcriptional responses. While both genotypes activated a conserved salt-stress program involving redox homeostasis, proteostasis and growth repression, the tolerant genotype displayed a substantially broader and more coordinated transcriptional reprogramming. This response involved large-scale modulation of pathways related to translation and RNA metabolism, hormone signaling crosstalk, membrane transport, cell wall remodeling and oxidative stress management, together with the selective repression of growth- and signaling-related functions. In contrast, the sensitive genotype showed a more limited response dominated by defense- and damage-associated transcripts. Overall, these results indicate that long-term salt tolerance in eggplant is associated with genotype-specific transcriptional reprogramming superimposed on a shared basal stress response. This work highlights regulatory pathways and candidate genes potentially relevant for breeding strategies targeting salt resilience.

plant biology↗

bioRxiv2023

New insights on the role of SlDMR6-1 in drought avoidance in tomato

The DOWNY MILDEW RESISTANCE 6 (DMR6) protein is a 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase, involved in salicylic acid (SA) metabolism, and its inactivation in tomato was found to increase SA levels and to confer disease-resistance against several pathogens. SA is also recognized as an abiotic stress-tolerance enhancer, and we tested the resistance to drought stress in Sldmr6-1 tomato mutants generated by the CRISPR/Cas9 technique. Wild-type (WT) tomato cultivar San Marzano and its Sldmr6-1 mutants were subjected to water deprivation for 7 days. At the end of the period, while WT plants exhibited severe wilting, the T2 Sldmr6-1 mutant plants showed turgid leaves and maintained higher Soil Relative Water Content (SRWC). Sldmr6-1 mutants adopted a water saving behaviour reducing transpiration rate (E) by decreasing stomatal conductance (Gs). Assimilation rate (A) decreased in parallel to E under drought stress, resulting in no alteration of the CO2 concentration in the sub-stomatal chamber (Ci) and increasing the Water Use Efficiency (WUE, A/E). Defence mechanisms of the photosynthetic machinery triggered in Sldmr6-1 mutants, that under drought stress showed up-regulation of the genes SlAPX and SlGST (anti-oxidant related) as well as down-regulation of SlCYP707A2 gene, which is involved in ABA catabolism. Our results suggest that the disabling of SlDMR6-1 in tomato plants leads to a drought-avoidance strategy through tight control of stomatal closure controlling water loss. In addition, it was highlighted, for the first time in tomato, that Sldmr6-1 mutants showed reduced susceptibility to Phytophthora infestans, the causal agent of Late Blight.

plant biology↗

bioRxiv2019

Epigenetic bases of grafting-induced vigour in eggplant

In horticulture, grafting is a popular technique used to combine positive traits from two different plants. This is achieved by joining the plant top part (scion) onto a rootstock which contains the stem and roots. Despite its wide use, the biological mechanisms driving rootstock-induced alterations of the scion phenotype remain largely unknown. Given that epigenetics plays a crucial role during distance signalling in plants, we studied the genome-wide changes induced by DNA methylation in eggplant (Solanum melongena) plants grafted onto two interspecific rootstocks used to increase scion vigour. As a control, we compared any epigenetic effect found in such grafts to patterns detected in self-grafted plants. We found that vigour was associated with a specific change in scion gene expression and a genome-wide hypomethylation in CHH context. Interestingly, this hypomethylation correlated with the down-regulation of younger and potentially more active LTR retrotransposons (LTR-TEs), suggesting that graft-induced epigenetic modifications are associated to both physiological and molecular phenotypes in grafted plants. We propose that rootstocks can promote vigour by reducing DNA methylation in the scion genome, following similar principles found in some heterotic hybrids.

plant biology↗

bioRxiv2019

Methylation content sensitive enzyme ddRAD (MCSeEd): a reference-free, whole genome profiling system to address cytosine/ adenine methylation changes

Methods for investigating DNA methylation nowadays either require a reference genome and high coverage, or investigate only CG methylation. Moreover, no large-scale analysis can be performed for N6-methyladenosine (6mA). Here we describe the methylation content sensitive enzyme double-digest restriction-site-associated DNA (ddRAD) technique (MCSeEd), a reduced-representation, reference-free, cost-effective approach for characterizing whole genome methylation patterns across different methylation contexts (e.g., CG, CHG, CHH, 6mA). MCSeEd can also detect genetic variations among hundreds of samples. MCSeEd is based on parallel restrictions carried out by combinations of methylation insensitive and sensitive endonucleases, followed by next-generation sequencing. Moreover, we present a robust bioinformatic pipeline (available at https://bitbucket.org/capemaster/mcseed/src/master/) for differential methylation analysis combined with single nucleotide polymorphism calling without or with a reference genome.

genomics↗