The Role of Horizontal Gene Transfer in the Evolution of the Oomycetes

1. Jain R, Rivera MC, Moore JE, Lake JA (2003) Horizontal gene transfer accelerates genome innovation and evolution. Mol Biol Evol 20: 1598–1602. 12777514

2. Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299–304. 10830951

3. Hirt RP, Alsmark C, Embley TM (2015) Lateral gene transfers and the origins of the eukaryote proteome: a view from microbial parasites. Current Opinion in Microbiology 23: 155–162. doi: 10.1016/j.mib.2014.11.018 25483352

4. Soanes D, Richards TA (2014) Horizontal gene transfer in eukaryotic plant pathogens. Annual Review of Phytopathology 52: 583–614. doi: 10.1146/annurev-phyto-102313-050127 25090479

5. Richards TA, Talbot NJ (2013) Horizontal gene transfer in osmotrophs: playing with public goods. Nat Rev Microbiol 11: 720–727. doi: 10.1038/nrmicro3108 24018383

6. Cavalier-Smith T, Chao EE (2006) Phylogeny and megasystematics of phagotrophic heterokonts (kingdom Chromista). J Mol Evol 62: 388–420. 16557340

7. Beakes G, Glockling S, Sekimoto S (2012) The evolutionary phylogeny of the oomycete “fungi”. Protoplasma 249: 3–19. doi: 10.1007/s00709-011-0269-2 21424613

8. Tyler BM (2001) Genetics and genomics of the oomycete–host interface. Trends in Genetics 17: 611–614. 11672843

9. Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, et al. (2006) Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 313: 1261–1266. 16946064

10. Baxter L, Tripathy S, Ishaque N, Boot N, Cabral A, et al. (2010) Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome. Science 330: 1549–1551. doi: 10.1126/science.1195203 21148394

11. Misner I, Blouin N, Leonard G, Richards TA, Lane CE (2014) The secreted proteins of Achlya hypogyna and Thraustotheca clavata identify the ancestral oomycete secretome and reveal gene acquisitions by horizontal gene transfer. Genome Biology and Evolution 7: 120–135. doi: 10.1093/gbe/evu276 25527045

12. Belbahri L, Calmin G, Mauch F, Andersson JO (2008) Evolution of the cutinase gene family: evidence for lateral gene transfer of a candidate Phytophthora virulence factor. Gene 408: 1–8. 18024004

13. Richards TA, Soanes DM, Jones MD, Vasieva O, Leonard G, et al. (2011) Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes. Proc Natl Acad Sci USA 108: 15258–15263. doi: 10.1073/pnas.1105100108 21878562

14. Kemen E, Jones JDG (2012) Obligate biotroph parasitism: can we link genomes to lifestyles? Trends in Plant Science 17: 448–457. doi: 10.1016/j.tplants.2012.04.005 22613788

15. Lind PA, Tobin C, Berg OG, Kurland CG, Andersson DI (2010) Compensatory gene amplification restores fitness after inter-species gene replacements. Molecular Microbiology 75: 1078–1089. doi: 10.1111/j.1365-2958.2009.07030.x 20088865

16. Kamoun S (2009) The secretome of plant-associated fungi and oomycetes. In: Deising H, editor. Plant Relationships: Springer Berlin Heidelberg. pp. 173–180.

17. Raffaele S, Win J, Cano L, Kamoun S (2010) Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans. BMC Genomics 11: 637. doi: 10.1186/1471-2164-11-637 21080964

18. Levesque CA, Brouwer H, Cano L, Hamilton J, Holt C, et al. (2010) Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biology 11: R73. doi: 10.1186/gb-2010-11-7-r73 20626842

19. Money NP, Davis CM, Ravishanker JP (2004) Biomechanical evidence for convergent evolution of invasive growth process among fungi and oomycete water molds. Fungal Genetics and Biology 41: 872–876. 15288023

20. Latijnhouwers M, de Wit PJGM, Govers F (2003) Oomycetes and fungi: similar weaponry to attack plants. Trends Microbiol 11: 462–469. 14557029