Biology subjects

Bazakos, C.

Publications and source records attributed to Bazakos, C..

5 recordsLinked to original sources

bioRxiv2024

A plant-specific clade of serine/arginine-rich proteins regulates RNA splicing homeostasis and thermotolerance in tomato

High temperatures cause heat stress (HS), which has negative effects on plant growth and development and affects many cellular processes including pre-mRNA splicing. In tomato plants the splicing profile of many of genes is altered under HS, including that of HSFA2, a central transcriptional regulator of thermotolerance. To identify the core splicing regulators of HS-sensitive alternative splicing, we used HSFA2 as bait and identified two plant-specific members of the serine/arginine-rich family of splicing factors, namely RS2Z35 and RS2Z36, that inhibit HSFA2 intron splicing. Single and double CRISPR mutants of these proteins show dysregulated splicing of many genes and exhibit lower basal and acquired thermotolerance. Individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) of tomato leaves revealed that the majority of HS-sensitive alternatively spliced RNAs are bound by RS2Z35 and RS2Z36 and this interaction occurs at purine-rich RNA motifs. Phenotypic and transcriptome analyses revealed that RS2Z35 and RS2Z36 are important players in the stress response and thermotolerance in plants that mitigate the negative effects of HS on RNA splicing homeostasis.

plant biology↗

bioRxiv2024

Decoding strawberry volatile cultivar diversity through comparative transcriptome analysis

This study presents a comparative transcriptomic analysis of three commercial strawberry cultivars: Rociera, Calderon, and Victory, aimed at uncovering the molecular basis of their distinct flavor and aroma profiles. Through RNA sequencing, we analyzed the transcriptomic landscape of these varieties, uncovering a notable array of differentially expressed genes (DEGs) between them. Specifically, Rociera showed a higher count of DEGs compared to Victory, suggesting significant differences in gene expression related to flavor and aroma between those cultivars. Our further investigations revealed pivotal metabolic pathways-- such as those involving furanones, amino acids, fatty acids, and terpenoids--participating in generating volatile organic compounds in strawberries. These pathways exhibited variety-specific expression patterns, underlining the genetic determinants of each varietys unique sensory characteristics. Gene Ontology (GO) enrichment analysis underscored important pathways like phototropism, sugar-mediated signaling, and terpenoid biosynthesis, highlighting the genetic intricacy that influences strawberry flavor and aroma. Additionally, our study identified 31,677 single nucleotide polymorphisms (SNPs) with a significant impact on genes associated with volatile compound biosynthesis. Notably, SNPs linked to key enzymes such as lipoxygenase 6, omega-6 fatty acid desaturase (FaFAD1), and phenylalanine ammonia-lyase 1 (PAL) were discovered, shedding light on the genetic variations that underlie flavor differences. Therefore, this research advances our comprehension of the genetic elements that impact strawberry fruit flavor and aroma, offering invaluable insights for molecular breeding endeavors focused on enhancing strawberry flavor.

plant biology↗

bioRxiv2023

Genome sequencing, assembly and annotation of the carob tree, Ceratonia siliqua (Eudicots:Fabaceae)

The carob tree, Ceratonia siliqua, is an evergreen tree that belongs to the family of Fabaceae. It has been cultivated for thousands of years in Mediterranean countries and thus, has a considerable impact on the nutrition of humans as well as other animals of this region. Despite its importance, genomic resources are still scarce for this plant species. To fill this gap, we undertook the sequencing, assembly and annotation of the carob tree genome, which resulted in the first, nearly chromosome-level assembly for this plant species. The total assembly size is 492 Mbp which is close to the previously estimated genome size. The assembly N50 is 34.99 Mbp, thus showing a high contiguity, which is also evident from the fact that >98% of the assembly is contained in as few as 17 very large contigs. Moreover, both the genome sequence as well as the predicted gene set contain more than 96% of conserved, full-length BUSCOs. Finally, a comparative orthology analysis with 10 other plant species showed that the vast majority of the predicted carob tree genes have orthologs in the other plants and only a small fraction of them appears to be species-specific. Additional analyses are in progress for a more detailed study of the agronomic traits of this important legume.

genomics↗

bioRxiv2022

A wide foodomics approach coupled with metagenomics elucidates the environmental signature of Protected Geographical Indication potatoes

The term "terroir" has been widely employed to link differential geographic phenotypes with sensorial signatures of agricultural food products, influenced by agricultural practices, soil type and climate. Nowadays, the Geographical Indications labeling has been developed to safeguard the quality of plant-derived food that is linked to a certain terroir and is generally considered as an indication of superior organoleptic properties and phytochemical profile. As the dynamics of agroecosystems are highly intricate, consisting of tangled networks of interactions between plants, microorganisms, and the surrounding environment, the recognition of the key molecular components of terroir fingerprinting remains a great challenge to protect both the origin and the safety of food commodities. Furthermore, the contribution of microbiome as a potential driver of the terroir signature has been underestimated until recently. Herein, we present a first comprehensive view of the multi-omic landscape related to transcriptome, proteome, epigenome, and metagenome of the popular Protected Geographical Indication potatoes of Naxos.

plant biology↗

bioRxiv2018

The complex genetic architecture of shoot growth natural variation in Arabidopsis thaliana

One of the main outcome of quantitative genetics approaches to natural variation is to reveal the genetic architecture underlying the phenotypic space. Complex genetic architectures are described as including numerous loci (or alleles) with small-effect and/or low-frequency in the populations, interactions with the genetic background, environment or age... Linkage or association mapping strategies will be more or less sensitive to this complexity, so that we still have an unclear picture of its extent. By combining high-throughput phenotyping under two environmental conditions with classical QTL mapping approaches in multiple Arabidopsis thaliana segregating populations as well as advanced near isogenic lines construction and survey, we have attempted to push back the limits of our understanding of quantitative phenotypic variation. Integrative traits such as those related to vegetative growth used in this work (highlighting either cumulative growth, growth rate or morphology) all showed complex and dynamic genetic architecture with respect to the segregating population and condition. The more resolutive our mapping approach, the more complexity we uncover, with several instances of QTLs visible in near isogenic lines but not detected with the initial QTL mapping, indicating that our phenotyping resolution was less limiting than the mapping resolution with respect to the underlying genetic architecture. In an ultimate approach to resolve this complexity, we intensified our phenotyping effort to target specifically a 3Mb-region known to segregate for a major quantitative trait gene, using a series of selected lines recombined every 100kb. We discovered that at least 3 other independent QTLs had remained hidden in this region, some with trait- or condition-specific effects, or opposite allelic effects. If we were to extrapolate the figures obtained on this specific region in this particular cross to the genome- and species-scale, we would predict hundreds of causative loci of detectable phenotypic effect controlling these growth-related phenotypes.

genetics↗