Starship giant transposable elements cluster by host taxonomy using k-mer-based phylogenetics

Area of Science:

• Mycology and Genomics
• Transposable Elements
• Phylogenetics

Background:

• Starships are large transposable elements in fungi (Pezizomycotina), up to 700 kbp, carrying numerous accessory genes.
• Current classification relies on the tyrosine recombinase gene (captain), which may not fully represent element relatedness.
• The high variability in Starship length and cargo content poses challenges for comprehensive analysis.

Purpose of the Study:

• To develop and apply a novel k-mer-based phylogenetic method for analyzing Starship element relatedness.
• To compare Starship relationships inferred from whole elements versus solely from captain genes.
• To investigate the influence of host taxonomy and cargo gene content on Starship evolution and transfer.

Main Methods:

• Utilized an alignment-free k-mer-based phylogenetic tree-building approach to analyze entire Starship elements.
• Compared k-mer-derived Starship phylogenies with those based on captain genes.
• Examined Starships from Gaeumannomyces species to correlate phylogenetic relationships with cargo gene similarity.

Main Results:

• K-mer-based phylogenies revealed Starship relationships distinct from those inferred from captain genes alone.
• Element relatedness patterns identified using k-mers corresponded with fungal host taxonomy.
• In Gaeumannomyces, k-mer relationships aligned with the similarity of cargo gene content, indicating its importance.

Conclusions:

• K-mer-based phylogenetics offers a robust method to analyze highly variable Starship elements comprehensively.
• This approach highlights the significance of cargo genes and host phylogeny in shaping Starship evolution.
• Findings provide insights into the dynamics of Starship-mediated horizontal gene transfer events in fungi.