Plant Killers on the Spot Arnab Pain and Christiane Hertz-Fowler

neWs & analysis

genome watch Plant killers on the spot Arnab Pain and Christiane Hertz-Fowler

This month’s Genome Watch discusses and lipases), inhibitors of host defence‑related of candidate effectors was identified and found two related but distinct plant pathogens proteins, and toxins. The RLXR and Crinkler to be expanded in Phytophthora spp. belonging to the oomycetes, a group of (CRN) effectors are mainly encoded in the Key host‑degrading enzymes such as filamentous, fungus-like eukaryotes. repeat‑rich regions and contain a conserved cutinases and endoxylanases are absent in amino‑terminal signal for host targeting and P. ultimum, and there are fewer carbohy‑ The lifestyle of oomycetes varies from sapro‑ a highly diverse carboxy‑terminal effector drate hydrolases than in Phytophthora spp., phytic to pathogenic. Phytophthora infestans domain. The 563 predicted RXLR effector pro‑ reflecting the differences in host specifici‑ is one of the most destructive potato patho‑ teins in P. infestans represent a highly diverse ties and pathogenicity mechanisms between gens, causing losses of US$6.7 billion annually lineage‑specific expansion containing 151 dis‑ the genera. P. ultimum also contains an worldwide. P. infestans str. T30‑4 is the third tinct subfamilies. Expansion of the effector expanded repertoire of subtilisin‑like proteases. Phytophthora species to be sequenced, after gene families seems to have been facilitated by Surprisingly, P. ultimum and Phytophthora spp. Phytophthora ramorum and Phytophthora sojae. non‑allelic homologous recombination and genomes encode cell adhesion proteins of the At 240 Mbp, it has the largest genome of the tandem gene duplication, and it is likely that cadherin family, marking the first time that these sequenced chromalveolates1,2. Comparison of their localization in repeat‑rich regions of the proteins have been detected outside metazoa. the 3 Phytophthora spp. genomes with those genome facilitated their rapid evolution. These studies show how multispecies com‑ of 10 other eukaryotes3 revealed numerous The genome of the related oomycete parisons can address questions such as the small duplications of 2–3 consecutive genes Pythium ultimum6, another plant pathogen, evolution of pathogenicity. They also highlight in the 3 Phytophthora spp., possibly indicat‑ has also been sequenced recently, allowing the fact that not all oomycete plant pathogens ing that a whole genome duplication event a further in‑depth analysis of the genomic contain a “similar toolkit for survival and occurred in their common ancestor. changes in the oomycete lineages. Most pathogenesis” (REF. 6). The P. infestans genome contains around Pythium spp. are soil inhabitants that live Arnab Pain is at the Computational Bioscience 18,000 protein‑coding genes, of which half as saprophytes or facultative plant patho‑ Research Center, KAUST, Thuwal 23955‑6900, are shared between the 3 Phytophthora spp. gens. Despite there being many phenotypic Kingdom of Saudi Arabia. genomes. Strikingly, around two‑thirds of features (such as lifestyle, host range and host Christiane Hertz‑Fowler is at the Centre for Genomic the genome contains repetitive DNA that specificity) that differentiate the phytopatho‑ Research, School of Biological Sciences, is non‑randomly distributed, giving rise to genic Pythium spp. from the sequenced P h y t o University of Liverpool, Liverpool L69 3BX, UK. repeat‑rich and repeat‑poor regions. These phthora spp., there is considerable sequence e‑mails: [email protected]; repeats may have mediated the species‑ conservation between the genomes. The gene C.Hertz‑[email protected] specific rearrangements that shape the order is largely the same between the sequenced doi:10.1038/nrmicro2433 Phytophthora spp. genomes. The repeat‑ species, although it is frequently interrupted 1. Haas, B. J. et al. Genome sequence and analysis of the rich regions are mostly composed of by local segmental DNA inversions. Irish potato famine pathogen Phytophthora infestans. Nature 461, 393–398 (2009). expanded families of Gypsy DNA ele‑ The 42.8 Mb P. ultimum DAOM BR144 2. Tyler, B. M. et al. Phytophthora genome sequences ments, which, together with a second genome contains 15,297 protein‑coding genes uncover evolutionary origins and mechanisms of pathogenesis. Science 313, 1261–1266 (2006). element termed ‘Albatross’, account for at but lacks genes encoding RXLR effectors and 3. Martens, C. & Van de Peer, Y. The hidden duplication past least 29% of the genome and are the main has fewer genes encoding CRN effectors. The of the plant pathogen Phytophthora and its consequences for infection. BMC Genomics 11, 353 (2010). cause of the differences in genome conservation of the export signal of CRN 4. Kamoun, S. A catalogue of the effector secretome of plant sizes between Phytophthora spp. proteins and its variable expansion across pathogenic oomycetes. Annu. Rev. Phytopathol. 44, 41–60 (2006). Pathogenicity of Phytophthora spp. is sequenced oomycetes highlights its early evo‑ 5. Whisson, S. C. et al. A translocation signal for delivery of mediated by secreted effector proteins lution in the last common ancestor of Pythium oomycete effector proteins into host plant cells. Nature 450, 115–118 (2007). 4,5 that modulate host physiology . and Phytophthora. In addition, using known 6. Levesque, C. A. et al. Genome sequence of the necrotrophic plant pathogen, Pythium ultimum, reveals Effector proteins include plant properties of effector genes, such as localiza‑ original pathogenicity mechanisms and effector tissue‑degrading hydrolytic tion to gene‑poor regions, the presence of repertoire. Genome Biol. 11, R73 (2010). enzymes (such as long non‑coding regions and inclusion in Competing interests statement proteases the predicted secretome, a new family The author declares no competing financial interests.