Biology subjects

Walkowiak, S.

Publications and source records attributed to Walkowiak, S..

7 recordsLinked to original sources

bioRxiv2026

GENOME ASSEMBLIES FOR 28 PHAEOSPHAERIACEAE ISOLATES FROM CANADA

Glume blotch and Septoria Tritici Blotch (STB) are destructive crop diseases caused by fungal pathogens formerly classified under the genus Septoria. Recent taxonomical revisions have led to the reclassification and renaming of these fungi, some of which are now under the genus Parastagonospora, family Phaeosphaeriaceae, order Pleosporales, and class Dothideomycetes. In this study, we performed whole genome sequencing and assembly for 28 Phaeosphaeriaceae isolates from Canada. Sequencing was performed using a combination of Oxford Nanopore Technologies (ONT) long-read and Illumina short-read sequencing platforms. Most of the genomes were very complete, BUSCO >99%, with the genomes assemblies derived from ONT sequencing having very few contigs that likely encompass entire chromosomes or chromosome arms. To determine the relationship between these isolates and similar fungi that have been previously characterized, we performed whole genome alignments to 2,668 other Dothidiomycete genomes obtained from NCBI using NUCmer. Comparative genomic analysis revealed that 27 of the isolates clustered discretely with either Parastagonospora nodorum, or Parastagonospora pseudonodorum (Parastagonospora avenae f. sp. tritici), with one genome having no other similar genome in NCBI which we hypothesize to be the first genome assembly of Phaeosphaeria pontiformis. Both P. nodorum and P. pseudonodorum species were isolated from wheat and barley and only the latter was isolated from durum, while the P. pontiformis was isolated from wheat. In summary, we sequenced and assembled the genomes of 28 isolates of Phaeosphaeriaceae spp. from Canada and the genomes add to our foundational knowledge of these plant pathogens and efforts to better understand their diversity.

microbiology↗

bioRxiv2026

Near telomere-to-telomere Linum genomes reveal a lineage-specific DNA transposon associated with chromosome architecture remodeling

Chromosome number variation and structural reorganization are key drivers of plant evolution, yet their genomic basis remains unclear due to incomplete representation of repetitive regions in existing assemblies. The Linum genus exhibits exceptional karyotypic diversity (n = 7-43), providing a powerful system to investigate chromosome evolution. Here, we generated near telomere-to-telomere (T2T) genome assemblies for four species, including cultivated flax (L. usitatissimum cv. CDC Bethune; n = 15), its wild progenitor (L. bienne; n = 15), and two related species (L. decumbens and L. grandiflorum; n = 8). Together with published genomes of L. lewisii (n = 9) and L. tenue (n = 10), these enabled reconstruction of chromosome evolution across six lineages. Phylogenomic analyses revealed a shared ancestral whole-genome duplication (WGD) associated with the n = 9 karyotype, followed by lineage-specific WGDs and divergent diploidization. The transition from n = 8 to the derived n = 15 flax lineage not only occurred without chromosome length expansion, but also with genome size reduction, indicating extensive internal restructuring. Comparative analyses showed that this restructuring was associated with lineage-specific expansion of a single DNA transposon family (TE_00003234; hAT), which is highly enriched in expansive pericentromeric regions that are characterized by low gene density and nucleotide diversity, suppressed recombination, segregation distortion, and extensive synteny disruption, unlike the LTR retrotransposon-rich pericentromeres typical of most plant genomes. These findings support a model in which lineage-specific DNA transposon expansion is associated with remodeling of pericentromeric architecture and large-scale chromosome restructuring following polyploidization.

genomics↗

bioRxiv2025

Wheat and barley stripe rust pan-genome facilitates discovery of the predominant North American lineage's origin in somatic hybridization

Wheat and barley stripe rust, caused by Puccinia striiformis formae speciales tritici (Pst) and hordei (Psh) respectively is a perennial and endemic threat to those crops worldwide. Outside the Himalayan region the fungus has not been observed reproducing sexually, despite being characterised extensively over the past 100 years by researchers in many countries. Scientific literature divides P. striiformis into lineages termed PstS0, PstS1, up to PstS18. Here we describe the first North American P. striiformis pan-genome, comprising 24 Pst and 3 Psh genomes from North America including five phased assemblies using chromosome conformation capture to separate two haploid genomes. We identify the origin of the predominant North American Pst lineage; PstS18, as a somatic hybridization event between PstS1 and another unknown lineage. As well as identifying gene families which distinguish haplotypes on a trans-lineage and trans-species level, we also show ongoing gene family loss and expansion in clonal lineages after their emergence.

microbiology↗

bioRxiv2023

From overconfidence to task dropout in a spatial navigation test: evidence for the Dunning-Kruger effect across 46 countries

Overconfidence and the Dunning-Kruger effect have been reported in many cognitive domains. However, there is little examination in the field of spatial navigation. Here, we examined overconfidence in navigation ability in 376,836 participants from 46 countries. We tested navigation using our virtual wayfinding task in the app-based video game Sea Hero Quest, examined self-ratings of navigation ability and how many game levels participants had played before they dropped out. The main goal of this analysis was to investigate how performance of overconfident participants influenced the dropout rate from our experimental task embedded in a video game. First, we measured and modelled overestimation at baseline game levels. Age was found to be the strongest predictor of overestimation across the entire sample. Higher age was associated with increased overconfidence in all 46 countries and 11 distinct cultural clusters. Female participants were more likely to overestimate their performance across most of the life course (19-59 years old), however older men (60-70 years old) displayed highest overconfidence amongst all age-gender groups. Overconfidence also varied widely across countries. Secondly, we estimated performance on follow-up game levels for those who were previously identified as overconfident and we found that those who were more likely to display the Dunning-Kruger effect (i.e., poor performance while being overconfident) were predominantly female and older participants. Finally, survival analysis methods with time-dependent covariates revealed that poor wayfinding performance, while being overconfident, was one of the strongest predictors of task dropout. This Dunning-Kruger bias on participants dropout existed universally across all countries in our data.

neuroscience↗

bioRxiv2022

Cultural determinants of the gap between self-estimated navigation ability and wayfinding performance: evidence from 46 countries.

Cognitive abilities can vary widely. Some people excel in certain skills, others struggle. However, not all those who describe themselves as gifted are. One possible influence on self-estimates is the surrounding culture. Some cultures may amplify self-assurance and others cultivate humility. Past research has shown that people in different countries can be grouped into a set of consistent cultural clusters with similar values and tendencies, such as attitudes to masculinity or individualism. Here we explored whether such cultural dimensions might relate to the extent to which populations in 46 countries overestimate or underestimate their cognitive abilities in the domain of spatial navigation. Using the Sea Hero Quest navigation test and a large sample (N=383,187) we found cultural clusters of countries tend to be similar in how they self-rate ability relative to their actual performance. Across the world population sampled, higher self-ratings were associated with better performance. However, at the national level, higher self-ratings as a nation were not associated with better performance as a nation. Germanic and Near East countries were found to be most overconfident in their abilities and Nordic countries to be most under-confident in their abilities. Gender stereotypes may play a role in mediating this pattern, with larger national positive attitudes to male stereotyped roles (Hofstedes masculinity dimension) associated with a greater overconfidence in performance at the national level. We also replicate, with higher precision than prior studies, evidence that older men tend to overestimate their navigation skill more than other groups. These findings give insight into how culture and demographics may impact self-estimates of our abilities.

neuroscience↗

bioRxiv2022

An autoactive NB-LRR gene causes Rht13 dwarfism in wheat

Semidwarfing genes have greatly increased wheat yields globally, yet the widely used gibberellin (GA) insensitive genes Rht-B1b and Rht-D1b have disadvantages for seedling emergence. Use of the GA sensitive semidwarfing gene Rht13 avoids this pleiotropic effect. Here we show that Rht13 encodes a nucleotide-binding site/leucine-rich repeat (NB-LRR) gene. A point mutation in the semidwarf Rht-B13b allele autoactivates the NB-LRR gene and causes a height reduction comparable to Rht-B1b and Rht-D1b in diverse genetic backgrounds. The autoactive Rht-B13b allele leads to transcriptional upregulation of pathogenesis-related genes including class III peroxidases associated with cell wall remodelling. Rht13 represents a new class of reduced height (Rht) gene, unlike other Rht genes which encode components of the GA signalling or metabolic pathways. This discovery opens new avenues to use autoactive NB-LRR genes as semidwarfing genes in a range of crop species, and to apply Rht13 in wheat breeding programmes using a perfect genetic marker.

plant biology↗

bioRxiv2019

Chromosome-scale genome assembly provides insights into rye biology, evolution, and agronomic potential

We present a chromosome-scale annotated assembly of the rye (Secale cereale L. inbred line Lo7) genome, which we use to explore Triticeae genomic evolution, and ryes superior disease and stress tolerance. The rye genome shares chromosome-level organization with other Triticeae cereals, but exhibits unique retrotransposon dynamics and structural features. Crop improvement in rye, as well as in wheat and triticale, will profit from investigations of rye gene families implicated in pathogen resistance, low temperature tolerance, and fertility control systems for hybrid breeding. We show that rye introgressions in wheat breeding panels can be characterised in high-throughput to predict the yield effects and trade-offs of rye chromatin.

genomics↗