Horizontal Gene Transfer in Eukaryotes: Fungi-to-Plant and Plant-to-Plant Transfers of Organellar DNA

Abstract

This review focuses on horizontal gene transfer (HGT) involving bacteria, fungi, and plants (Viridiplantae). It highlights in particular the persistent challenge of recognizing HGT, which requires a combination of methods from bioinformatics, phylogenetics, and molecular biology. Non-phylogenetic methods rely on compositional structure, such as G/C content, dinucleotide frequencies, codon usage biases, or co-conversion tracts, while phylogenetic methods rely on incongruence among gene trees, one of which is taken to represent the true organismal phylogeny. All methods are handicapped by short sequence lengths with limited or highly uneven substitution signal; the statistical problems of working with taxon-rich alignments of such sequences include low support for inferred relationships, and difficult orthology assessment. Plant-to-plant HGT is known from two dozen mitochondrial genes and species of phylogenetically and geographically widely separated ferns, gymnosperms, and angiosperms, with seven cases involving parasitic plants. Only one nuclear HGT has come to light, and extremely few fungi-to-plant transfers. Plant mitochondrial genomes, especially in tracheophytes, are prone to take up foreign DNA, but evolutionary consequences of this are still unclear.