Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.09.01.748723

Haplotype-resolved genome assembly of barberry reveals structural divergence and allele-specific expression during infection by wheat stripe rust pathogen

Wang, J.·Xu, Y.·Duan, Y.·Kang, Z.·Zhao, J.
View original source ↗Export metadata ↓

Abstract

Barberry is an ecologically and medicinally important perennial shrub and an alternate host of Puccinia striiformis f. sp. tritici (Pst), the causal agent of wheat stripe rust. However, its genome architecture and molecular responses to Pst infection remain poorly understood. Here, we generated a haplotype-resolved, chromosome-level genome assembly of Berberis aggregata using PacBio HiFi and Hi-C sequencing. The two haplotypes, Ba5A and Ba5B, were assembled into 14 pseudochromosomes each, with genome sizes of approximately 1.13 and 1.16 Gb, respectively, and showed high continuity and completeness. Comparative analyses revealed extensive divergence between the haplotypes, including widespread structural variation, substantial hemizygosity, and TE-rich, gene-poor non-alignable regions. Haplotype-specific hemizygous genes also exhibited distinct functional biases, with Ba5A enriched in immune-related processes and Ba5B associated with transport and cell-envelope functions. Dual RNA-seq across infection stages revealed stage-dependent host transcriptional reprogramming, characterized by early pathogen perception followed by stronger defense activation and photosynthesis repression, whereas Pst displayed a coordinated colonization program consistent with its biotrophic lifestyle. Allele-specific expression analysis showed that ~25-28% of genes exhibited significant haplotype-biased expression, and a subset transitioned from unbiased expression at 0 dpi to Ba5A- or Ba5B-biased expression during infection. Integration with differential expression analysis further identified infection-responsive induced-biased genes associated with defense-related processes, including responses to fungal pathogens. These findings show that haplotype divergence and dynamic allele-specific regulation jointly contribute to transcriptional responses during Pst infection, providing new insights into the genomic basis of barberry-rust pathogen interactions.

Explore related subjects

genomicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Wang, J., Xu, Y., Duan, Y., Kang, Z., Zhao, J.. 2026-09-05. Haplotype-resolved genome assembly of barberry reveals structural divergence and allele-specific expression during infection by wheat stripe rust pathogen. https://doi.org/10.64898/2026.09.01.748723

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Integrative Nanopore and Illumina sequencing reveals age-associated tRNA modification and CCA-tail dynamics in yeast

Aging is characterized by a progressive loss of proteostasis. Transfer RNAs (tRNAs) are essential regulators of translation, yet their dynamics during aging remain poorly understood due to challenges in sequencing highly modified RNAs. Here we present a benchmarked Nanopore direct RNA sequencing (RNA004 chemistry) resource that profiles the Saccharomyces cerevisiae tRNAome during replicative aging at single-molecule resolution. Using in vitro transcribed tRNA controls, we establish modification detection thresholds and validate key findings with orthogonal Illumina sequencing. While overall tRNA abundance remains largely stable, our resource reveals age-associated terminal A cleavage at the 3' CCA tail of mature tRNAs, targeted T-loop and anticodon modification changes, and single-molecule evidence of modification co-occurrence. This dataset provides a resource for exploring tRNA regulation, translation fidelity, and longevity.

genomics↗
bioRxiv2026

A hydrogen-producing mitochondrion in an anaerobic eukaryotrophic rhizarian

Diverse eukaryotes thrive under low oxygen conditions, in part through highly modified mitochondrion-related organelles (MROs) that use alternate metabolic pathways to support ATP production and cofactor recycling. Anaerobic lifestyles have evolved repeatedly across the eukaryotic tree of life, each providing an independent opportunity to understand how eukaryotes adapt to life in low oxygen conditions. Here, we use single-cell transcriptomics to reconstruct the MRO metabolism of PCE SSF, a benthic eukaryotrophic flagellate and the first cultivated representative of Novel Clade 12 (NC12; Rhizaria), an independently anaerobic rhizarian lineage. PCE SSF possesses an anaerobic hydrogen-producing mitochondrion capable of hydrogenosome-type substrate-level phosphorylation. It also retains a nearly complete but likely branched tricarboxylic acid pathway that lacks citrate synthase and malate dehydrogenase. The function of citrate synthase may instead be fulfilled by the typically cytosolic ATP citrate lyase, previously reported in this context only in the anaerobic cercozoan, Brevimastigomonas motovehiculus. Unlike B. motovehiculus, however, PCE SSF retains only Complex II and the NuoE/NuoF subunits of the electron transport chain and lacks a mitochondrial genome. Together, these features indicate an atypical and reduced mitochondrial metabolism, highlighting the diversity of evolutionary solutions to anaerobic energy metabolism in eukaryotes.

genomics↗
bioRxiv2026

Targeted CRISPRi screening reveals unexpected resilience across the RNA polymerase III transcriptome

Increased RNA polymerase III (Pol III) activity and tRNA abundance are widely linked to cancer cell growth, yet the functional requirement for individual Pol III genes and core components remains unclear, in part due to the difficulty of achieving gene-specific perturbation of highly conserved loci. Here, we developed an inducible CRISPR interference platform and a custom single-guide RNA (sgRNA) library enabling gene-specific targeting of Pol III-transcribed genes and Pol III machinery. Genome-wide screening identified several Pol III dependencies in diploid fibroblasts and HEK293T cells, including multiple initiator methionine tRNA genes among the strongest fitness dependencies. Unexpectedly, glioblastoma models remained largely insensitive to repression of both individual Pol III genes and core Pol III components, despite efficient target repression. These findings establish a general strategy for gene-specific interrogation of conserved Pol III genes and indicate that glioblastoma models tolerate extensive perturbation of Pol III genes and machinery.

genomics↗