The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens

1. NelsonMIHolmesEC 2007 The evolution of epidemic influenza. Nat Rev Genet 8 196 205 doi:10.1038/nrg2053

2. ShahNSWrightABaiG-HBarreraLBoulahbalF 2007 Worldwide emergence of extensively drug-resistant tuberculosis. Emerg Infect Dis 13 380 387

3. HarrisSRFeilEJHoldenMTGQuailMANickersonEK 2010 Evolution of MRSA during hospital transmission and intercontinental spread. Science 327 469 474 doi:10.1126/science.1182395

4. SinghRPHodsonDPHuerta-EspinoJJinYBhavaniS 2011 The emergence of Ug99 races of the stem rust fungus is a threat to world wheat production. Annu Rev Phytopathol 49 465 481 doi:10.1146/annurev-phyto-072910-095423

5. HuC-CHsuY-HLinN-S 2009 Satellite RNAs and Satellite Viruses of Plants. Viruses 1 1325 1350 doi:10.3390/v1031325

6. RobicsekAJacobyGAHooperDC 2006 The worldwide emergence of plasmid-mediated quinolone resistance. Lancet Infect Dis 6 629 640

7. WilsonEB 1907 The supernumerary chromosomes of Hemiptera. Science 26 870 871

8. WittenbergAHJvan der LeeTAJBen M'barekSWareSBGoodwinSB 2009 Meiosis drives extraordinary genome plasticity in the haploid fungal plant pathogen Mycosphaerella graminicola. PLoS ONE 4 e5863 doi:10.1371/journal.pone.0005863

9. van de WouwAPCozijnsenAJHaneJKBrunnerPCMcDonaldBA 2010 Evolution of linked avirulence effectors in Leptosphaeria maculans is affected by genomic environment and exposure to resistance genes in host plants. PLoS Pathog 6 e1001180 doi:10.1371/journal.ppat.1001180

10. RaffaeleSFarrerRACanoLMStudholmeDJMacLeanD 2010 Genome evolution following host jumps in the Irish potato famine pathogen lineage. Science 330 1540 1543 doi:10.1126/science.1193070

11. ColemanJJRounsleySDRodriguez-CarresMKuoAWasmannCC 2009 The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genet 5 e1000618 doi:10.1371/journal.pgen.1000618

12. MiaoVPWCovertSFVanEttenHD 1991 A fungal gene for antibiotic resistance on a dispensable (“B”) chromosome. Science 254 1773 1776

13. MaL-Jvan der DoesHCBorkovichKAColemanJJDaboussiM-J 2010 Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464 367 373 doi:10.1038/nature08850

14. StukenbrockEHBankeSJavan-NikkhahMMcDonaldBA 2007 Origin and domestication of the fungal wheat pathogen Mycosphaerella graminicola via sympatric speciation. Mol Biol Evol 24 398 411

15. GoodwinSBM'barekSBDhillonBWittenbergAHJCraneCF 2011 Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis. PLoS Genet 7 e1002070 doi:10.1371/journal.pgen.1002070

16. McDonaldBAMartinezJ 1991 Chromosome Length Polymorphisms in a Septoria tritici Population. Curr Genet 19 265 271

17. StukenbrockEHJørgensenFGZalaMHansenTTMcDonaldBA 2010 Whole-genome and chromosome evolution associated with host adaptation and speciation of the wheat pathogen Mycosphaerella graminicola. PLoS Genet 6 e1001189 doi:10.1371/journal.pgen.1001189

18. LengelerKBFoxDSFraserJAAllenAForresterK 2002 Mating-type locus of Cryptococcus neoformans: a step in the evolution of sex chromosomes. Eukaryot Cell 1 704 718

19. EllisonCEStajichJEJacobsonDJNatvigDOLapidusA 2011 Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma. Genetics 189 55 69 doi:10.1534/genetics.111.130690

20. CharlesworthDCharlesworthBMaraisG 2005 Steps in the evolution of heteromorphic sex chromosomes. Heredity 95 118 128 doi:10.1038/sj.hdy.6800697

21. GreenDM 1990 Muller's Ratchet and the evolution of supernumerary chromosomes. Genome 33 818 824

22. JonesR 1991 B-Chromosome Drive. Am Nat 137 430 442

23. AkagiYAkamatsuHOtaniHKodamaM 2009 Horizontal chromosome transfer, a mechanism for the evolution and differentiation of a plant-pathogenic fungus. Eukaryot Cell 8 1732 1738 doi:10.1128/EC.00135-09