Small homologous blocks in phytophthora genomes do not point to an ancient whole-genome duplication

Abstract

Genomes of the plant-pathogenic genus Phytophthora are characterized by small duplicated blocks consisting of two consecutive genes (2HOM blocks) and by an elevated abundance of similarly aged gene duplicates. Both properties, in particular the presence of 2HOM blocks, have been attributed to a whole-genome duplication (WGD) at the last common ancestor of Phytophthora. However, large intraspecies synteny-compelling evidence for a WGD-has not been detected. Here, we revisited the WGD hypothesis by deducing the age of 2HOM blocks. Two independent timing methods reveal that the majority of 2HOM blocks arose after divergence of the Phytophthora lineages. In addition, a large proportion of the 2HOM block copies colocalize on the same scaffold. Therefore, the presence of 2HOM blocks does not support a WGD at the last common ancestor of Phytophthora. Thus, genome evolution of Phytophthora is likely driven by alternative mechanisms, such as bursts of transposon activity.

Keywords: genome expansion; oomycetes; paleopolyploidy; segmental duplication.

Fig. 1.—

Species tree, as previously established by Blair et al. (2008), with gene (and small-scale) duplication frequency indicated. The gene duplication frequency is elevated at the last common ancestor of Phytophthora and in some extant Phytophthora lineages.

Fig. 2.—

Two examples of phylogenetically analyzed 2HOM blocks. For both 2HOM blocks, phylogenetic trees of the genes and an illustration of the positions on the scaffolds are given. Bootstrap supports based on 100 replicates are displayed on the branches. (A) A Phytophthora infestans 2HOM block, likely the result of a species-specific, possibly segmental duplication, is displayed. (B) A 2HOM block of P. infestans (species-specific duplication), P. ramorum, P. sojae, and P. capsici (derived from a shared, possibly segmental duplication) has a more complex duplication history.

Fig. 3.—

K_s distributions of Phytophthora infestans. (A) 2HOM block paralogs and (B) full paranome. Peaks in the distributions of orthologous sets of gene pairs indicate speciation events. Dashed lines indicate examples of distributions following a pattern of exponential decay. Full paranome distributions of the other Phytophthora spp. are available in supplementary figure S1, Supplementary Material online.