Genome-scale phylogenetic analysis finds extensive gene transfer among Fungi

TL;DR

This study compares genome evolution in Cyanobacteria and Fungi, revealing that lateral gene transfer significantly influences fungal evolution, contrary to previous assumptions about eukaryotes.

Contribution

It introduces and compares gene transfer inference methods, demonstrating extensive gene transfer in fungi using genome-scale phylogenetic analysis.

Findings

Gene transfer is significant in fungal evolution.

Gene transfer inference methods differ in their assessments.

Taxonomic sampling impacts transfer detection accuracy.

Abstract

Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis we compare the dynamics of genome evolution in two groups of organisms: Cyanobacteria and Fungi. Ancestral genomes are inferred in both clades using two types of methods. First, Count, a gene tree unaware method that models gene duplications, gains and losses to explain the observed numbers of genes present in a genome. Second, ALE, a more recent gene tree-aware method that reconciles gene trees with a species tree using a model of gene duplication, loss, and transfer. We compare their merits and their ability to quantify the role of transfers, and assess the impact of taxonomic sampling on their inferences. We present what we believe is compelling evidence that gene transfer plays a significant role in the evolution of Fungi.