Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi

Area of Science:

• Plant Pathology
• Fungal Genomics
• Agricultural Science

Background:

• Rust fungi, with over 7000 species, significantly impact agriculture, horticulture, forestry, and ecosystems.
• Phakopsora pachyrhizi, the cause of Asian soybean rust, is a major agricultural pathogen.
• Previous genome assembly efforts for P. pachyrhizi were hindered by its large and complex genome.

Purpose of the Study:

• To generate an accurate genome assembly for Phakopsora pachyrhizi.
• To investigate the role of transposable elements (TEs) in the P. pachyrhizi genome.
• To understand how TEs influence the fungus's adaptation and pathogenicity.

Main Methods:

• Sequencing of three independent P. pachyrhizi genomes.
• Analysis of genome size, haplotype structure, and transposable element content.
• Investigation of TE impact on fungal adaptation and genetic plasticity.

Main Results:

• A genome assembly up to 1.25 Gb was generated, comprising two distinct haplotypes.
• Transposable elements constitute approximately 93% of the P. pachyrhizi genome.
• TEs significantly influence host range adaptation, stress responses, and genetic plasticity.

Conclusions:

• The P. pachyrhizi genome is exceptionally large and heavily influenced by TEs.
• TEs play a crucial role in the evolutionary dynamics and pathogenicity of this significant agricultural rust fungus.
• Understanding the TE-rich genome is key to managing Asian soybean rust disease.