Biology subjects

Golicz, A.

Publications and source records attributed to Golicz, A..

4 recordsLinked to original sources

bioRxiv2026

Integrating Orthology and Cross-Species Transcriptomics to Unravel Root Drought Responses in Faba Bean and Maize

During soil drying, roots in upper and deeper soil layers experience different hydraulic environments, yet the molecular programs that accompany and potentially drive depth-specific changes in root water uptake capacity remain poorly understood. Here, we address this gap by coupling depth-resolved RNA-seq with previously measured hydraulic uptake profiles in pot-grown faba bean (Vicia faba) and maize (Zea mays), two crop species with contrasting root architecture, sampled from upper (drying) and lower (comparatively wet) root zones at the onset and after four days of soil drying. Differential expression analysis revealed strongly top-region of the roots dominated transcriptional responses in both species, consistent with the steeper hydraulic challenge in drying upper layers. Maize displayed a TIP- and dehydrin-dominated drought response, whereas faba bean induced NIP-like aquaporins and a broader LEA repertoire, suggesting divergent strategies for root water and cellular stress protection. To compare transcriptome responses across these distally related species, we grouped orthologous genes across 26 species using OrthoFinder. With this approach, we identified 905 drought-responsive orthogroups, of which only 17% were shared between species despite broadly convergent gene onthology (GO) enrichment profiles. Phylogenetic tracing showed that 95.7% of faba bean-specific and 90.3% of maize-specific drought-responsive orthogroups are conserved across monocot and dicot lineages, indicating that species-specific drought transcriptomes arise primarily through differential recruitment of ancestral gene families rather than lineage-specific innovation. These findings define a molecular framework linking root hydraulic architecture to gene regulation under drought and identify conserved transcriptional regulatory hubs as targets for broad-spectrum abiotic stress improvement in both faba bean and maize.

plant biology↗

bioRxiv2026

NOHIC: A PIPELINE FOR PLANT CONTIG SCAFFOLDING USING PERSONALIZED REFERENCES FROM PANGENOME GRAPHS

Hi-C data is commonly used for reference-free de novo scaffolding. However, with the rapid increase in high-quality reference genomes, reference-guided workflows are now more practical for assembling large numbers of target genomes without relying on costly and labor-intensive Hi-C sequencing. Recently, a pangenome graph-based haplotype sampling algorithm was introduced to generate personalized graphs for target genomes. Such graphs have strong potential as references for reference-guided contig scaffolding. Here, we present noHiC, a reference-guided scaffolding pipeline supporting key steps of plant contig scaffolding. A distinctive feature of noHiC is the nohic-refpick script, generating a best-fit synthetic reference (synref) from a pangenome graph that is genetically close to the target contigs. This enables the integration of genetic information from many references (up to 48 in our tests) without using them separately during scaffolding. Synrefs showed advantages over highly contiguous conventional references in reducing false contig breaking during reference-based correction. Additionally, nohic-refpick can be combined with fast scaffolders (ntJoin) to rapidly produce highly contiguous assemblies using synrefs derived from pangenome graphs. The noHiC pipeline, used alone or in combination with ntJoin, can generally produce assemblies that are structurally consistent with public Hi-C-based or manually curated genomes. The pipeline is publicly available at https://github.com/andyngh/noHiC. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/712436v1_ufig1.gif" ALT="Figure 1"> View larger version (9K): org.highwire.dtl.DTLVardef@40bd8forg.highwire.dtl.DTLVardef@5d2bbborg.highwire.dtl.DTLVardef@e214a3org.highwire.dtl.DTLVardef@b90b06_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

VC2 regulates baseline vicine content in faba bean

Faba bean (Vicia faba) is a valuable legume crop desired globally for its high nutritional composition. However, the seed vicine and convicine (v-c) content reduces the nutritional quality of faba bean protein and can induce favism in individuals with glucose-6-phosphate dehydrogenase deficiency. Recently, VC1 gene, encoding a bi-functional riboflavin protein, was reported to be responsible for initiating the biosynthetic pathway in V. faba. In low v-c cultivars, a 2 bp insertion in this gene results in a loss of function, but the mutation only partially eliminates v-c biosynthesis, indicating the involvement of other genes. Here, we demonstrate that a novel V. faba riboflavin gene, VC2, is responsible for the residual v-c contents in faba bean. VC2 shares nearly identical functional domains with VC1 and has GTP cyclohydrolase II activity, catalyzing the conversion of GTP into an intermediate molecule in the biosynthetic pathway. Gene expression analysis reveals that VC2 contributes a minor effect to the trait, accounting for approximately 5-10% of total riboflavin gene transcripts which significantly correlates with the baseline contents in low v-c cultivars. Our results illustrate that cultivars carrying the 2 bp inactivating insertion in VC1 still have residual v-c levels due to VC2 activity. Furthermore, we find that VC1 has multiple alleles and exhibits copy number variations, complicating molecular marker development. Conversely, single nucleotide polymorphisms within VC2 provide a reliable alternative for marker-assisted selection in faba bean breeding. In conclusion, our study elucidates the complex genetic regulation of v-c biosynthesis and provides valuable insights to facilitate its elimination in faba bean.

genetics↗

bioRxiv2023

Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts

Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry continues to face a wide variety of production challenges (e.g. disease pressures) as well as a demand for higher-yielding cultivars with improved fruit quality characteristics. Unfortunately, molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops. Here, we describe the construction and analysis of the first pangenome for both blueberry and cranberry. Our analysis of these pangenomes revealed both crops exhibit great genetic diversity, including the presence-absence variation of 48.4% genes in highbush blueberry and 47.0% genes in cranberry. Auxiliary genes, those not shared by all cultivars, are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites, including compounds previously associated with improving fruit quality traits. The discovery of thousands of genes, not present in the previous reference genomes for blueberry and cranberry, will serve as the basis of future research and as potential targets for future breeding efforts. The pangenome, as a multiple-sequence alignment, as well as individual annotated genomes, are publicly available for analysis on the Genome Database for Vaccinium - a curated and integrated web-based relational database. Lastly, the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.

genomics↗