Chromatin Biology Impacts Adaptive Evolution of Filamentous Plant Pathogens

PLoS Pathogens

Volumn 12, Issue 11, 2016, Pages

  Seidl, Michael F ^a   Cook, David E ^a   Thomma, Bart P H J ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMOSOME; DYNAMICS; EVOLUTION; FILAMENTOUS FUNGUS; GENE EXPRESSION; GENETIC VARIABILITY; NONHUMAN; PROTEIN EXPRESSION; REVIEW; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTION INITIATION; ADAPTATION; CHROMATIN; FUNGUS; GENETICS; MICROBIOLOGY; OOMYCETES; PLANT; PLANT DISEASE;

ADAPTATION, PHYSIOLOGICAL; BIOLOGICAL EVOLUTION; CHROMATIN; FUNGI; OOMYCETES; PLANT DISEASES; PLANTS;

EID: 85002158020     PISSN: 15537366     EISSN: 15537374     Source Type: Journal    
DOI: 10.1371/journal.ppat.1005920     Document Type: Review

References (29)

1. Seidl MF, Thomma BPHJ, Sex or no sex: evolutionary adaptation occurs regardless. Bioessays. 2014;36: 335–345doi: 10.1002/bies.20130015524531982
2. Cook DE, Mesarich CH, Thomma BPHJ, Understanding plant immunity as a surveillance system to detect invasion. Annu Rev Phytopathol. 2015;53: 541–563doi: 10.1146/annurev-phyto-080614-12011426047564
3. Rovenich H, Boshoven JC, Thomma BPHJ, Filamentous pathogen effector functions: of pathogens, hosts and microbiomes. Curr Opin Plant Biol. 2014;20C: 96–103
4. Raffaele S, Kamoun S, Genome evolution in filamentous plant pathogens: why bigger can be better. Nat Rev Microbiol. 2012;10: 417–430doi: 10.1038/nrmicro279022565130
5. Dong S, Raffaele S, Kamoun S, The two-speed genomes of filamentous pathogens: waltz with plants. Curr Opin Genet Dev. 2015;35: 57–65doi: 10.1016/j.gde.2015.09.00126451981
6. Galazka JM, Freitag M, Variability of chromosome structure in pathogenic fungi-of “ends and odds.” Curr Opin Microbiol. 2014;20C: 19–26
7. Faino L, Seidl MF, Shi-Kunne X, Pauper M, van den Berg GCM, Wittenberg AHJ, et al. Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen. Genome Res. 2016;26: 1091–1100doi: 10.1101/gr.204974.11627325116
8. de Jonge R, Bolton MD, Kombrink A, van den Berg GCM, Yadeta KA, Thomma BPHJ, Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen. Genome Res. 2013;23: 1271–1282doi: 10.1101/gr.152660.11223685541
9. Friedman N, Rando OJ, Epigenomics and the structure of the living genome. Genome Res. 2015;25: 1482–1490doi: 10.1101/gr.190165.11526430158
10. Grewal SIS, Jia S, Heterochromatin revisited. Nat Rev Genet. 2007;8: 35–46doi: 10.1038/nrg200817173056
11. Raffaele S, Farrer RA, Cano LM, Studholme DJ, MacLean D, Thines M, et al. Genome evolution following host jumps in the Irish potato famine pathogen lineage. Science. 2010;330: 1540–1543doi: 10.1126/science.119307021148391
12. Berthelot C, Muffato M, Abecassis J, Roest Crollius H, The 3D organization of chromatin explains evolutionary fragile genomic regions. Cell Rep. 2015;10: 1913–1924doi: 10.1016/j.celrep.2015.02.04625801028
13. Schotanus K, Soyer JL, Connolly LR, Grandaubert J, Happel P, Smith KM, et al. Histone modifications rather than the novel regional centromeres of Zymoseptoria tritici distinguish core and accessory chromosomes. Epigenetics Chromatin. 2015;8: 41doi: 10.1186/s13072-015-0033-526430472
14. Carvalho CMB, Lupski JR, Mechanisms underlying structural variant formation in genomic disorders. Nat Rev Genet. 2016;17: 224–238doi: 10.1038/nrg.2015.2526924765
15. Sasaki T, Lynch KL, Mueller CV, Friedman S, Freitag M, Lewis ZA, Heterochromatin controls γH2A localization in Neurospora crassa. Eukaryotic Cell. 2014;13: 990–1000doi: 10.1128/EC.00117-1424879124
16. Galazka JM, Klocko AD, Uesake M, Honda S, Selker EU, Freitag M, Neurospora chromosomes are organized by blocs of importin alpha-dependent heterochromatin that are largely independent of H3K9me3. Genome Res. 2016; gr.203182.115
17. Connolly LR, Smith KM, Freitag M, The Fusarium graminearum histone H3 K27 methyltransferase KMT6 regulates development and expression of secondary metabolite gene clusters. PLoS Genet. 2013;9: e1003916doi: 10.1371/journal.pgen.100391624204317
18. Soyer JL, Ghalid El M, Glaser N, Ollivier B, Linglin J, Grandaubert J, et al. Epigenetic control of effector gene expression in the plant pathogenic fungus Leptosphaeria maculans. PLoS Genet. 2014;10: e1004227. doi: 10.1371/journal.pgen.100422724603691
19. Pham KTM, Inoue Y, Vu BV, Nguyen HH, Nakayashiki T, Ikeda K-I, et al. MoSET1 (Histone H3K4 Methyltransferase in Magnaporthe oryzae) regulates global gene expression during infection-related morphogenesis. PLoS Genet. 2015;11: e1005385. doi: 10.1371/journal.pgen.100538526230995
20. Luco RF, Pan Q, Tominaga K, Blencowe BJ, Pereira-Smith OM, Misteli T, Regulation of alternative splicing by histone modifications. Science. 2010;327: 996–1000doi: 10.1126/science.118420820133523
21. Li F, Mao G, Tong D, Huang J, Gu L, Yang W, et al. The histone mark H3K36me3 regulates human DNA mismatch repair through its interaction with MutSα. Cell. 2013;153: 590–600doi: 10.1016/j.cell.2013.03.02523622243
22. Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, Lee KK, et al. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell. 2005;123: 581–592doi: 10.1016/j.cell.2005.10.02316286007
23. Waszak SM, Delaneau O, Gschwind AR, Kilpinen H, Raghav SK, Witwicki RM, et al. Population variation and genetic control of modular chromatin architecture in humans. Cell. 2015;162: 1039–1050doi: 10.1016/j.cell.2015.08.00126300124
24. Skinner MK, Environmental epigenetics and a unified theory of the molecular aspects of evolution: A Neo-Lamarckian concept that facilitates Neo-Darwinian evolution. Genome Biol Evol. 2015;7: 1296–1302doi: 10.1093/gbe/evv07325917417
25. Depotter JR, Seidl MF, Wood TA, Thomma BPHJ, Interspecific hybridization impacts host range and pathogenicity of filamentous microbes. Curr Opin Microbiol. 2016;32: 7–13doi: 10.1016/j.mib.2016.04.00527116367
26. Qutob D, Chapman BP, Gijzen M, Transgenerational gene silencing causes gain of virulence in a plant pathogen. Nat Commun. 2013;4: 1349doi: 10.1038/ncomms235423322037
27. Chujo T, Scott B, Histone H3K9 and H3K27 methylation regulates fungal alkaloid biosynthesis in a fungal endophyte-plant symbiosis. Mol Microbiol. 2014;92: 413–434doi: 10.1111/mmi.1256724571357
28. Song Q, Smith AD, Identifying dispersed epigenomic domains from ChIP-Seq data. Bioinformatics. 2011;27: 870–871doi: 10.1093/bioinformatics/btr03021325299
29. Croll D, Zala M, McDonald BA, Breakage-fusion-bridge cycles and large insertions contribute to the rapid evolution of accessory chromosomes in a fungal pathogen. PLoS Genet. 2013;9: e1003567doi: 10.1371/journal.pgen.100356723785303