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

Genome Biology and Evolution

Volumn 6, Issue 5, 2014, Pages 1079-1085

  Van Hooff, Jolien J E ^a,d   Snel, Berend ^a,b   Seidl, Michael F ^a,b,c  

^a UTRECHT UNIVERSITY   (Netherlands)

^b CENTRE FOR BIOSYSTEMS GENOMICS   (Netherlands)

^c WAGENINGEN UNIVERSITY   (Netherlands)

^d UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

Author keywords

Genome expansion; Oomycetes; Paleopolyploidy; Segmental duplication

Indexed keywords

EVOLUTION; GENE DUPLICATION; GENETICS; GENOME; PATHOGENICITY; PHYTOPHTHORA;

BIOLOGICAL EVOLUTION; GENE DUPLICATION; GENOME; PHYTOPHTHORA;

EID: 84902957015     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evu081     Document Type: Article

References (40)

1. Adhikari BN, et al. 2013. Comparative genomics reveals insight into virulence strategies of plant pathogenic oomycetes. PLoS One 8: e75072.
2. Altschul SF, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
3. Amborella Genome Project. 2013. The amborella genome and the evolution of flowering plants. Science 342: 1241089.
4. Aury JM, et al. 2006. Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 444: 171-178.
5. Baxter L, et al. 2010. Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome. Science 330(6010): 1549-1551.
6. Bertier L, Leus L, D'hondt L, de Cock AW, HöfteM. 2013. Host adaptation and speciation through hybridization and polyploidy in Phytophthora. PLoS One 8: e85385.
7. Blair JE, Coffey MD, Park S, Geiser DM, Kang S. 2008. A multi-locus phylogeny for Phytophthora utilizing markers derived from complete genome sequences. Fungal Genet Biol. 45: 266-277.
8. Blanc G, Wolfe KH. 2004. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16: 1667-1678.
9. Chen K, Durand D, Farach-Colton M. 2000. NOTUNG: a program for dating gene duplications and optimizing gene family trees. J Comput Biol. 7: 429-447.
10. Christoffels A, et al. 2004. Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. Mol Biol Evol. 21: 1146-1151.
11. Dehal P, Boore JL. 2005. Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol. 3: e314.
12. Enright AJ, Van Dongen S, Ouzounis CA. 2002. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30: 1575-1584.
13. Gijzen M. 2009. Runaway repeats force expansion of the Phytophthora infestans genome. Genome Biol. 10: 241.
14. Govers F, Gijzen M. 2006. Phytophthora genomics: the plant destroyers' genome decoded. Mol Plant Microbe Interact. 19: 1295-1301.
15. Haas BJ, et al. 2009. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature 461: 393-398.
16. Jiang N, Bao Z, Zhang X, Eddy SR, Wessler SR. 2004. Pack-MULE transposable elements mediate gene evolution in plants. Nature 431: 569-573.
17. Jiang RH, Govers F. 2006. Nonneutral GC3 and retroelement codon mimicry in phytophthora. J Mol Evol. 63: 458-472.
18. Jiang RH, Tyler BM. 2012. Mechanisms and evolution of virulence in oomycetes. Annu Rev Phytopathol. 50: 295-318.
19. Jiang RHY, et al. 2013. Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica. PLoS Genet. 9(6): e1003272.
20. Jurka J, et al. 2005. Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 110: 462-467.
21. Kroon LPNM, Brouwer H, De Cock AWAM, Govers F. 2012. The genus Phytophthora anno 2012. Phytopathology 102: 348-364.
22. Lamour KH, et al. 2012. Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici. Mol Plant Microbe Interact. 25: 1350-1360.
23. Lévesque CA, et al. 2010. Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biol. 11(7): R73.
24. Lynch M, Conery JS. 2000. The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
25. Martens C, Van de Peer Y. 2010. The hidden duplication past of the plant pathogen Phytophthora and its consequences for infection. BMC Genomics 11: 353.
26. Rebollo R, Horard B, Hubert B, Vieira C. 2010. Jumping genes and epigenetics: towards new species. Gene 454: 1-7.
27. Sansome E. 1977. Polyploidy and induced gametangial formation in British isolates of Phytophthora infestans. J Gen Microbiol. 99: 311-316.
28. Scannell DR, Byrne KP, Gordon JL, Wong S, Wolfe KH. 2006. Multiple rounds of speciation associated with reciprocal gene loss in polyploidy yeasts. Nature 440: 341-345.
29. Seidl MF, Van den Ackerveken G, Govers F, Snel B. 2011. A domain-centric analysis of oomycete plant pathogen genomes reveals unique protein organization. Plant Physiol. 155: 628-644.
30. Seidl MF, Van den Ackerveken G, Govers F, Snel B. 2012. Reconstruction of oomycete genome evolution identifies differences in evolutionary trajectories leading to present-day large gene families. Genome Biol Evol. 4: 199-211.
31. Sémon M, Wolfe KH. 2007. Consequences of genome duplication. Curr Opin Genet Dev. 17: 505-512.
32. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
33. Tripathy S, Tyler BM. 2006. The repertoire of transfer RNA genes is tuned to codon usage bias in the genomes of phytophthora sojae and phytophthora ramorum. Mol Plant-Microbe Interact. 19: 1322-1328.
34. Tyler BM, et al. 2006. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 313: 1261-1266.
35. Van De Peer Y. 2004. Computational approaches to unveiling ancient genome duplications. Nat Rev Genet. 5: 752-763.
36. Vilella AJ, et al. 2009. Ensembl Compara Gene Trees: complete, duplication- aware phylogenetic trees in vertebrates. Genome Res. 19: 327-335.
37. Wang Y, et al. 2011. Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms. PLoS One 6: e28150.
38. Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24: 1586-1591.
39. Yang Z, Nielsen R. 1998. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J Mol Evol. 46: 409-418.
40. Young ND, et al. 2011. The medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480: 520-524.