Rampant Interkingdom Horizontal Gene Transfer in Pezizomycotina? An Updated Inspection of Anomalous Phylogenies

Horizontal gene transfer (HGT) is a significant source of diversity in prokaryotes and a key factor in their genome evolution. Although similar processes have been postulated for eukaryotes, the validity of HGT's impact remains contested, particularly between long-distance-related organisms like those from different kingdoms. Among eukaryotes, the fungal subphylum Pezizomycotina has been frequently cited in the literature for experiencing HGT events, with over 600 publications on the subject. The proteomes of 421 Pezizomycotina species were meticulously examined to identify potential instances of interkingdom HGT. Furthermore, the phylogenies of over 275 HGT candidates previously reported were revisited. Manual scrutiny of 521 anomalous phylogenies revealed that only 1.5% display patterns indicative of interkingdom HGT. Moreover, novel interkingdom HGT searches within Pezizomycotina yielded few new contenders, casting doubt on the prevalence of such events within this subphylum. Although the detailed examination of phylogenies suggested interkingdom HGT, the evidence for lateral gene transfer is not conclusive. The findings suggest that expanding the number of homologous sequences could uncover vertical inheritance patterns that have been misclassified as HGT. Consequently, this research supports the notion that interkingdom HGT may be an extraordinary occurrence rather than a significant evolutionary driver in eukaryotic genomes.