High‐Quality Genome Assembly of <i>Diplocarpon coronariae</i> Unveils <scp>LTR</scp> Retrotransposon‐Driven Structural Dynamics in Fungi Evolution

Long terminal repeat retrotransposons (LTR-RTs) are recognised as a significant evolutionary force capable of shaping the structure and function of the genomes in eukaryotes, including animals, plants, and fungi. However, much remains largely unknown about how LTR-RTs influence the evolution of fungi at the chromosomal level. Here, we assembled the genome of an important plant pathogenic fungus, Diplocarpon coronariae (strain XN1), at the chromosomal level and obtained high-precision, full-length transcriptome annotations through transcriptome evidence and manual curation. Using high-quality genomes and gene annotations, we identified the two-speed genome and constructed a pan-genome graph of D. coronariae. Through comparative genomics, we discovered that LTR-RTs contributed to sequence and structural evolution among different strains of D. coronariae. Based on gene families constructed from the genomes of multiple species within Leotiomycetes, LTR-RTs were found to be involved in the formation of species-specific gene families as well as the expansion of gene families. Furthermore, through interspecies comparative genomics analysis, we identified a young chromosome, Chr15, specifically present in D. coronariae XN1. Chr15 likely originated from conserved topologically associating domains (TADs) and gradually expanded with the burst insertion of LTR-RTs, forming a completely new chromosome. This study provides new insights into the complexity and formation mechanisms of LTR retrotransposon-driven chromosomal and genomic structural evolution in fungi.