Biology subjects

Patzak, J.

Publications and source records attributed to Patzak, J..

4 recordsLinked to original sources

bioRxiv2025

Contrasting patterns of subtelomeric satellite superfamily in the Cannabaceae family

Satellite DNA (satDNA) is a rapidly evolving component of plant genomes, often found in centromeric, telomeric, and heterochromatic regions. Due to their variability and species- or population-specific distribution, satDNA serves as valuable cytogenetic markers for studying chromosomal rearrangements and karyotype evolution in closely related species. In dioecious species Cannabis sativa, Humulus lupulus, and Humulus japonicus, previous studies have identified species-specific subtelomeric repeats CS-1, HSR1, and HJSR. While these satellites have been used to differentiate sex chromosomes from autosomes, their evolutionary origins, sequence variation and pattern of conservation among related species remain largely unexplored. In this study, we combine bioinformatics analysis with molecular cloning to analyze sequence similarity among these shared satellites and determine their inter-specific chromosomal localization using fluorescence in situ hybridization (FISH). Our results reveal that HSR1 and HJSR satellites are shared among all studied species suggested oaring from a common ancestor. In contrast, CS-1 satellite exhibit higher sequence divergence. Although all satellites are predominantly localized in subtelomeric regions, CS-1 in H. lupulus and HSR in C. sativa are localized in pericentromeric regions. These findings provide new insight into the evolutionary dynamics of satDNA in Cannabaceae family and its role in genome organization.

plant biology↗

bioRxiv2024

Fingerprinting and chemotyping approaches reveal a wide genetic and metabolic diversity among wild hops (Humulus lupulus L.)

Hop (Humulus lupulus L.) is an emblematic industrial crop in the French North East region that developed at the same time as the brewing activity. Presently, this sector, especially microbreweries, are interested in endemic wild hops, which give beer production a local signature. In this study, we investigated the genetic and metabolic diversity of thirty-six wild hops sampled in various ecological environments. These wild accessions were propagated aeroponically and cultivated under uniform conditions (the same soil and the same environmental factors). Our phytochemical approach based on UHPLC-ESI-MS/MS analysis led to the identification of three metabolic clusters based on leaf content and characterized by variations in the contents of twelve specialized metabolites that were identified (including xanthohumol, bitter acids, and their oxidized derivatives). Furthermore, molecular characterization was carried out using sixteen EST-SSR microsatellites, allowing a genetic affiliation of our wild hops with hop varieties cultivated worldwide and wild hops genotyped to date using this method. Genetic proximity was observed for both European wild and hop varieties, especially for Strisselspalt, the historical variety of our region. Finally, our findings collectively assessed the impact of the hop genotype on the chemical phenotype through multivariate regression tree (MRT) analysis. Our results highlighted the WRKY 224 allele as a key discriminator between high- and low-metabolite producers. Moreover, the model based on genetic information explained 40% of the variance in the metabolic data. However, despite this strong association, the model lacked predictive power, suggesting that its applicability may be confined to the datasets analyzed.

plant biology↗

bioRxiv2024

Evolution and functioning of an X-A balance sex determination system in hops

Chromosomal sex determining systems with male heterogamety include actively male-determining-Y and X-A balance systems, both of which are found in animals and plants. The sex-determining genes have been identified in several active-Y plant systems, but the evolution and functioning of X-A balance systems remains mysterious. To study this, we sequenced and compared the genomes of two hop species. The evolution of the hop X-A balance system involved an ancient recombination suppression event across a large X chromosome region shared by both species. In one species, an autosome fused to this ancestral sex chromosome, and recombination was subsequently suppressed again. The two evolutionary strata created in this neo-X have degenerated to different degrees, and evolved correspondingly different dosage compensation levels that correlate with histone modification patterns. Finally, we identified an X-specific ETR1-like ethylene receptor in the ancestral X region. Its dosage may affect sex determination, as part of the counting mechanism of this X-A balance system. One sentence summaryBased on whole genome sequences of the cultivated hop, Humulus lupulus, and its wild relative H. japonicus, we describe the evolution of sex chromosomal regions, three of which that evolved region-specific dosage compensation, and identify a candidate gene involved in their X-A balance sex determining system.

evolutionary biology↗

bioRxiv2024

Centromeric repeat diversity underlies non-Mendelian segregation pattern in hop (Humulus lupulus)

Aberrant meiosis in plants often leads to aneuploidy, genetic instability, and sterility. This can occur due to several factors, including chromosome misalignment, defective synapsis or environmental factors that may result in unusual genetic combinations in the offsprings. Unusual chromosome behavior during male meiosis in Humulus lupulus is linked to irregular chromosome segregation and genome instability. However, the origin of meiotic instability remains unclear. We analyzed the centromeric landscape of H. lupulus to determine its role in aberrant chromosomal segregation during cell division. Using a combination of bioinformatic, molecular and cytogenetic approaches, we identified new centromeric repeats and revealed two types of centromeric organizations. Cytogenetic localization on metaphase chromosomes confirmed the genomic distribution of major repeat arrays and revealed unique features that contribute to aberrant segregation. Two centromeric types are composed of the major repeats SaazCEN and SaazCRM1 which are further accompanied by chromosome-specific centromeric satellites, Saaz40, Saaz293, Saaz85, and HuluTR120. Chromosome 2 displays unbalanced segregation during the cell division, implicating an important role for its centromere structure in segregation patterns. Moreover, Saaz293 is a new marker for studying aneuploidy in hop. Our findings provide new insights on chromosome segregation in hop and highlight the diversity and complexity of the centromere organization in H. lupulus.

plant biology↗