Telomere-to-telomere assemblies of Paracoccidioides genomes

Area of Science:

• Mycology
• Genomics
• Evolutionary Biology

Background:

• Paracoccidioides is a genus of dimorphic fungal pathogens endemic to Latin America.
• Understanding the genomic basis of Paracoccidioides evolution is crucial for public health in endemic regions.

Purpose of the Study:

• To generate high-quality, long-read de novo genome assemblies for key Paracoccidioides species.
• To perform comparative genomic analyses to identify evolutionary events and genetic features contributing to pathogenicity.

Main Methods:

• Utilized long-read sequencing technology for de novo genome assembly of 11 Paracoccidioides isolates.
• Conducted comparative genomic analyses, including identification of chromosomal rearrangements and gene duplications.
• Analyzed mitochondrial genomes and transposable element distribution.

Main Results:

• Generated the first complete telomere-to-telomere assemblies for Paracoccidioides brasiliensis and Paracoccidioides americana.
• Identified chromosomal fusion and fission events distinguishing P. brasiliensis and P. americana.
• Discovered a 90 kb tandem duplication in P. americana containing siderophore biosynthesis genes and putative virulence factors.
• Observed incongruent phylogenetic signals between nuclear and mitochondrial genomes, suggesting introgression.
• Found enrichment of RNA transposable elements near telomeres, correlated with genome size.

Conclusions:

• The generated genome assemblies are valuable resources for Paracoccidioides research.
• Comparative genomics reveals significant evolutionary events shaping Paracoccidioides species.
• Mitochondrial introgression and specific gene duplications may play roles in the adaptation and pathogenicity of these fungi.