Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes

Abstract

Horizontal gene transfer (HGT) can radically alter the genomes of microorganisms, providing the capacity to adapt to new lifestyles, environments, and hosts. However, the extent of HGT between eukaryotes is unclear. Using whole-genome, gene-by-gene phylogenetic analysis we demonstrate an extensive pattern of cross-kingdom HGT between fungi and oomycetes. Comparative genomics, including the de novo genome sequence of Hyphochytrium catenoides , a free-living sister of the oomycetes, shows that these transfers largely converge within the radiation of oomycetes that colonize plant tissues. The repertoire of HGTs includes a large number of putatively secreted proteins; for example, 7.6% of the secreted proteome of the sudden oak death parasite Phytophthora ramorum has been acquired from fungi by HGT. Transfers include gene products with the capacity to break down plant cell walls and acquire sugars, nucleic acids, nitrogen, and phosphate sources from the environment. Predicted HGTs also include proteins implicated in resisting plant defense mechanisms and effector proteins for attacking plant cells. These data are consistent with the hypothesis that some oomycetes became successful plant parasites by multiple acquisitions of genes from fungi.

A link between host plant adaptation and pesticide resistance in the polyphagous spider mite Tetranychus urticae

“…3C). This is in agreement with Richards et al (70,71) who showed that the closely related species Phytophthora ramorum acquired its extracellular ID-RCDs from filamentous ascomycetes through horizontal gene transfer.…”

Genome-scale comparative analysis of gene fusions, gene fissions, and the fungal tree of life

“…For all candidate gene fusions we calculated a phylogeny for each individual domain component of the gene fusion using a custom-built pipeline (35,36). We followed this pipeline analysis by a series of manual steps: BLAST checks of taxon sampling, multiple sequence alignment, alignment masking (37), amino acid substitution model selection (38), and tree calculation using PHYML with 100 bootstrap replicates (39).…”

“…The remaining 10 genes were selected from a list of genes we favor for phylogenetic analysis (Table S4, gray shading). We then generated an alignment for each individual gene family using a modification of a custom built gene-by-gene phylogeny pipeline (35,36) integrating the trimAL (37) alignment masking tool. The resulting alignments were concatenated together using a custom Perl script.…”

Widespread horizontal transfer of the cerato-ulmin gene between Ophiostoma novo-ulmi and Geosmithia species

“…Formation of transient hyphal or conidial anastomoses, direct uptake of DNA, presence of mobile elements in the vicinity of the transferred sequence and recombination have been proposed (Mehrabi et al 2011;Richards et al 2011;Fitzpatrick 2012). Richards et al (2009) showed that in two gene transfers from a fungus to the bryophyte moss Physcomitrella patens, the HGT was located near to a putative transposable element.…”

“…lycopersici (Akagi et al 2009;Ma et al 2010). Finally, Richards et al (2011) showed how interkingdom gene transfer from filamentous fungi to oomycetes of at least 21 genes with roles in nutrient acquisition, degradation of plant surface components, and suppression of plant defences led to the appearance of plant pathogenic oomycetes.…”