Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus.

ABSTRACT: Phased telomere-to-telomere (T2T) genome assemblies are revolutionizing our understanding of long-hidden genome biology "dark matter" such as centromeres, rDNA repeats, inter-haplotype variation, and allele-specific expression (ASE), yet insights into dikaryotic fungi that separate their haploid genomes into distinct nuclei are limited. Here, we explore the impact of dikaryotism on the genome biology of a long-term asexual clone of the wheat pathogenic fungus Puccinia striiformis f. sp. tritici We use Oxford Nanopore Technologies (ONT) duplex sequencing combined with Hi-C to generate a T2T nuclear-phased assembly with >99.999% consensus accuracy. We show that this fungus has large regional centromeres enriched in LTR retrotransposons, with a single centromeric dip in methylat

SUBMITTER: Tam R 

PROVIDER: S-EPMC12129025 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature