The hidden duplication past of the plant pathogen Phytophthora and its consequences for infection

Abstract

Background: Oomycetes of the genus Phytophthora are pathogens that infect a wide range of plant species. For dicot hosts such as tomato, potato and soybean, Phytophthora is even the most important pathogen. Previous analyses of Phytophthora genomes uncovered many genes, large gene families and large genome sizes that can partially be explained by significant repeat expansion patterns.

Results: Analysis of the complete genomes of three different Phytophthora species, using a newly developed approach, unveiled a large number of small duplicated blocks, mainly consisting of two or three consecutive genes. Further analysis of these duplicated genes and comparison with the known gene and genome duplication history of ten other eukaryotes including parasites, algae, plants, fungi, vertebrates and invertebrates, suggests that the ancestor of P. infestans, P. sojae and P. ramorum most likely underwent a whole genome duplication (WGD). Genes that have survived in duplicate are mainly genes that are known to be preferentially retained following WGDs, but also genes important for pathogenicity and infection of the different hosts seem to have been retained in excess. As a result, the WGD might have contributed to the evolutionary and pathogenic success of Phytophthora.

Conclusions: The fact that we find many small blocks of duplicated genes indicates that the genomes of Phytophthora species have been heavily rearranged following the WGD. Most likely, the high repeat content in these genomes have played an important role in this rearrangement process. As a consequence, the paucity of retained larger duplicated blocks has greatly complicated previous attempts to detect remnants of a large-scale duplication event in Phytophthora. However, as we show here, our newly developed strategy to identify very small duplicated blocks might be a useful approach to uncover ancient polyploidy events, in particular for heavily rearranged genomes.

Figure 1

Detection of small duplicated genomic segments. (A) Detection of 2HOM blocks in real and random genomes. In red, a duplicated block of two homologous genes AB is shown. (B) Detection of 3HOM blocks in real and random genomes. In red, a duplicated block of three homologous genes ABC is shown. In this example, also two 2HOM blocks are identified, namely AB (dark green) and BC (light green). (C) All possible situations where the gene orientation in a 2HOM block is conserved and not inverted. (D) Possible situations where the gene orientation in a 2HOM block is conserved but where one segment is inverted.

Figure 2

Duplicated blocks and orientation analysis in Phytophthora and random genomes. The number of (A) 2HOM blocks and (B) 3HOM blocks in P. infestans, P. sojae, and P. ramorum (pink triangles) versus the number of 2HOM, resp. 3HOM blocks in random genomes, i.e. the expected number of blocks based on 1000 simulations (blue distribution). (C) Orientation conservation in the 2HOM and 3HOM blocks in real versus random data.

Figure 3

Number (A) and percentage (B) of 2HOM blocks in the Phytophthora species and reference genomes. The results for real genomes are represented by triangles, the results for the corresponding randomized genomes are represented by the distributions in the same color as the triangle data points. The left Y-axis applies to the random data, the right Y-axis applies to the real data.

Figure 4

K_S dating of the Phytophthora duplication and speciation events. K_S distribution for paralogous and orthologous genes in the (A) P. infestans, (B) P. sojae and (C) P. ramorum genome. The K_S distribution for the P. sojae (Pso) and P. ramorum (Pra) orthologs (left Y-axis), representing the P. sojae-P. ramorum speciation, is indicated by a full grey line. The K_S distribution for the P. sojae (or P. ramorum) and P. infestans (Pin) orthologs (left Y-axis), representing the P. infestans-P. sojae/P. ramorum speciation, is indicated by a grey dotted line. The K_S distribution of the whole paranome (right Y-axis) is shown in light blue shading; the K_S distribution of the paralogs located in duplicated blocks (right Y-axis) is indicated in dark blue shading.

Figure 5

Quality of the genome assembly for the Phytophthora species and for the diatom Phaeodactylum tricornutum. The histograms represent the percentage of genes (left Y-axis) lying on a scaffold of a certain size, measured by the number of genes on a scaffold. The corresponding lines represent the cumulative percentage of genes (right Y-axis).