Small Homologous Blocks in Phytophthora Genomes Do Not Point to an Ancient Whole-genome Duplication

Overview

Journal Genome Biol Evol

Publisher Oxford University Press

Specialties Biology
Genetics
Molecular Biology

Date 2014 Apr 25

PMID 24760277

Citations 4

Authors

Jolien J E van Hooff

Berend Snel

Michael F Seidl

Affiliations

Soon will be listed here.

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.

Citing Articles

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Comparative analysis of genomes reveals oomycete pathogenesis in crops.

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Ali S, Shao J, Lary D, Kronmiller B, Shen D, Strem M Genome Biol Evol. 2017; .

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Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen.

Faino L, Seidl M, Shi-Kunne X, Pauper M, van den Berg G, Wittenberg A Genome Res. 2016; 26(8):1091-100.

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References

Aury J, Jaillon O, Duret L, Noel B, Jubin C, Porcel B . Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature. 2006; 444(7116):171-8. DOI: 10.1038/nature05230. View

Kroon L, Brouwer H, de Cock A, Govers F . The genus Phytophthora anno 2012. Phytopathology. 2011; 102(4):348-64. DOI: 10.1094/PHYTO-01-11-0025. View

Blanc G, Wolfe K . Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell. 2004; 16(7):1667-78. PMC: 514152. DOI: 10.1105/tpc.021345. View

Jiang R, Govers F . Nonneutral GC3 and retroelement codon mimicry in Phytophthora. J Mol Evol. 2006; 63(4):458-72. DOI: 10.1007/s00239-005-0211-3. View

Wang Y, Wang X, Tang H, Tan X, Ficklin S, Feltus F . Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms. PLoS One. 2011; 6(12):e28150. PMC: 3229532. DOI: 10.1371/journal.pone.0028150. View

Rebollo R, Horard B, Hubert B, Vieira C . Jumping genes and epigenetics: Towards new species. Gene. 2010; 454(1-2):1-7. DOI: 10.1016/j.gene.2010.01.003. View

Scannell D, Byrne K, Gordon J, Wong S, Wolfe K . Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature. 2006; 440(7082):341-5. DOI: 10.1038/nature04562. View

Lamour K, Mudge J, Gobena D, Hurtado-Gonzales O, Schmutz J, Kuo A . Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici. Mol Plant Microbe Interact. 2012; 25(10):1350-60. PMC: 3551261. DOI: 10.1094/MPMI-02-12-0028-R. View

. The Amborella genome and the evolution of flowering plants. Science. 2013; 342(6165):1241089. DOI: 10.1126/science.1241089. View

10.

Jiang N, Bao Z, Zhang X, Eddy S, Wessler S . Pack-MULE transposable elements mediate gene evolution in plants. Nature. 2004; 431(7008):569-73. DOI: 10.1038/nature02953. View

11.

Levesque C, Brouwer H, Cano L, Hamilton J, Holt C, Huitema E . Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biol. 2010; 11(7):R73. PMC: 2926784. DOI: 10.1186/gb-2010-11-7-r73. View

12.

Jiang R, Tyler B . Mechanisms and evolution of virulence in oomycetes. Annu Rev Phytopathol. 2012; 50:295-318. DOI: 10.1146/annurev-phyto-081211-172912. View

13.

Seidl M, Van den Ackerveken G, Govers F, Snel B . Reconstruction of oomycete genome evolution identifies differences in evolutionary trajectories leading to present-day large gene families. Genome Biol Evol. 2012; 4(3):199-211. PMC: 3318443. DOI: 10.1093/gbe/evs003. View

14.

Blair J, Coffey M, Park S, Geiser D, Kang S . A multi-locus phylogeny for Phytophthora utilizing markers derived from complete genome sequences. Fungal Genet Biol. 2007; 45(3):266-77. DOI: 10.1016/j.fgb.2007.10.010. View

15.

Young N, Debelle F, Oldroyd G, Geurts R, Cannon S, Udvardi M . The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature. 2011; 480(7378):520-4. PMC: 3272368. DOI: 10.1038/nature10625. View

16.

Semon M, Wolfe K . Consequences of genome duplication. Curr Opin Genet Dev. 2007; 17(6):505-12. DOI: 10.1016/j.gde.2007.09.007. View

17.

Lynch M, Conery J . The evolutionary fate and consequences of duplicate genes. Science. 2000; 290(5494):1151-5. DOI: 10.1126/science.290.5494.1151. View

18.

Baxter L, Tripathy S, Ishaque N, Boot N, Cabral A, Kemen E . Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome. Science. 2010; 330(6010):1549-1551. PMC: 3971456. DOI: 10.1126/science.1195203. View

19.

Yang Z, Nielsen R . Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J Mol Evol. 1998; 46(4):409-18. DOI: 10.1007/pl00006320. View

20.

Seidl M, Van den Ackerveken G, Govers F, Snel B . A domain-centric analysis of oomycete plant pathogen genomes reveals unique protein organization. Plant Physiol. 2010; 155(2):628-44. PMC: 3032455. DOI: 10.1104/pp.110.167841. View