Biology subjects

Gagalova, K. K.

Publications and source records attributed to Gagalova, K. K..

4 recordsLinked to original sources

bioRxiv2026

Pedigree-reconciled pan-genomics reveals megabase-scale hitchhiking after a century of canola breeding

Canola breeding has been shaped by strong selection for oil quality, yet the origins of the known oil quality alleles and genomic consequences of their selection are not fully resolved. By integrating pedigree reconstruction with graph pan-genomics we trace inheritance of ancestral genomic regions across historical and contemporary germplasm. Surrounding the low erucic acid allele in BnA08.FAE1, we identify a 17.23 Mb haplotype that approached fixation in Australian canola in the early 2000s. Contradicting the prevailing model, this haplotype predates modern breeding and was likely widespread in ancestral B. napus in the early 1900s. Genomic analyses implicate centromeric recombination suppression and structural variation in its long-term persistence, which has led to megabase-scale diversity loss through hitchhiking of neighbouring alleles. The haplotype contains extensive structural variation and multiple alleles associated with polygenic disease resistance. Together, these findings reveal the long-term consequences of repeated selection on standing variation during crop improvement.

plant biology↗

bioRxiv2026

Transcriptomic analysis reveals SnTox8-mediated reprogramming of wheat defence signalling

Parastagonospora nodorum (Berk.) Quaedvlieg, Verkley & Crousis, a necrotrophic fungal pathogen, is the causal agent for septoria nodorum blotch, a major constraint on global wheat production. Pathogen-produced necrotrophic effectors (NEs) that interact with host-sensitivity genes in an inverse gene-for-gene manner, collectively leading to effector-triggered susceptibility (ETS). Here, we investigated the transcriptional responses of two Triticum aestivum L. genotypes, Mace and Lancer, following infiltration with a novel NE, SnTox8. A total of 12,679 unique differentially expressed genes in Mace and 149 in Lancer were detected from transcriptomic analysis. In the SnTox8-sensitive cultivar, Mace, numerous defence-related genes were induced, including protein phosphorylation cascades, reactive oxygen species bursts, calcium signalling, phytohormone modulation, and suppression of photosynthesis, consistent with findings from other ETS models, in which necrotrophic fungal pathogens hijack host defence systems to proliferate. The interaction also activated genes involved in signal transduction, metabolism, membrane modification, and molecular transport, reflecting a coordinated host reprogramming that promotes cellular dysfunction and cell death, thereby facilitating necrotrophic pathogenesis. In contrast, Lancer, an SnTox8-insensitive cultivar, exhibited minimal transcriptional changes with no evidence of effector recognition or downstream defence-related activities. Overall, this study exhibited that SnTox8 manipulates kinase-mediated immune signalling and metabolic reprogramming to convert defence activation into host cell death, revealing a mechanistic basis for ETS in wheat. The identified SnTox8-Snn8-triggered processes were confirmed through additional transcriptome analysis of Mace mutants. Outcomes from this study establish a foundation for identifying, functionally characterising and validating the corresponding host susceptibility gene Snn8.

molecular biology↗

bioRxiv2025

Benchmarking methods for genome annotation using Nanopore direct RNA in a non-model crop plant

High-quality genome annotations are essential for transcriptomic analyses investigating plant responses to environmental stress. While Nanopore long-read direct RNA (dRNA) sequencing offers a powerful approach for improving genome annotations, studies benchmarking optimal tools for this process have primarily focused on animal models. In this study, we benchmarked five annotation tools: StringTie2, IsoQuant, Bambu, FLAIR, and FLAMES, using dRNA data from barley infected with Net Form Net Blotch disease. We observed substantial variation across tools in isoform detection, structural completeness, splicing classification, and handling of 5' read truncation. Several tools successfully identified novel transcripts, with the top-performing reference-guided approach detecting 994 previously unannotated transcripts, including candidates with predicted roles in disease response. Our results highlight the importance of plant-specific benchmarking of bioinformatic tools and demonstrate the utility of dRNA sequencing for improving genome annotations, supporting ongoing efforts to enhance reference resources for non-model plant species.

bioinformatics↗

bioRxiv2022

Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2

Long-read sequencing technologies have improved significantly since their emergence. Their read lengths, potentially spanning entire transcripts, is advantageous for reconstructing transcriptomes. Existing long-read transcriptome assembly methods are primarily reference-based and to date, there is little focus on reference-free transcriptome assembly. We introduce RNA-Bloom2, a reference-free assembly method for long-read transcriptome sequencing data. Using simulated datasets and spike-in control data, we show that the transcriptome assembly quality of RNA-Bloom2 is competitive to those of reference-based methods. Furthermore, RNA-Bloom2 requires 27.0 to 80.6% of the peak memory and 3.6 to 10.8% of the total wall-clock runtime of a competing reference-free method. Finally, we showcase RNA-Bloom2 in assembling a transcriptome sample of Picea sitchensis (Sitka spruce). Since our method does not rely on a reference, it sets up the groundwork for large-scale comparative transcriptomics where high-quality draft genome assemblies are not readily available.

bioinformatics↗