Whole Genome Analysis of 132 Clinical Saccharomyces cerevisiae Strains Reveals Extensive Ploidy Variation

Abstract

Budding yeast has undergone several independent transitions from commercial to clinical lifestyles. The frequency of such transitions suggests that clinical yeast strains are derived from environmentally available yeast populations, including commercial sources. However, despite their important role in adaptive evolution, the prevalence of polyploidy and aneuploidy has not been extensively analyzed in clinical strains. In this study, we have looked for patterns governing the transition to clinical invasion in the largest screen of clinical yeast isolates to date. In particular, we have focused on the hypothesis that ploidy changes have influenced adaptive processes. We sequenced 144 yeast strains, 132 of which are clinical isolates. We found pervasive large-scale genomic variation in both overall ploidy (34% of strains identified as 3n/4n) and individual chromosomal copy numbers (36% of strains identified as aneuploid). We also found evidence for the highly dynamic nature of yeast genomes, with 35 strains showing partial chromosomal copy number changes and eight strains showing multiple independent chromosomal events. Intriguingly, a lineage identified to be baker’s/commercial derived with a unique damaging mutation in NDC80 was particularly prone to polyploidy, with 83% of its members being triploid or tetraploid. Polyploidy was in turn associated with a >2× increase in aneuploidy rates as compared to other lineages. This dataset provides a rich source of information on the genomics of clinical yeast strains and highlights the potential importance of large-scale genomic copy variation in yeast adaptation.

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References 102

1. 1.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

2. 2.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

3. 3.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

4. 4.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

5. 5.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

6. 6.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

7. 7.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

8. 8.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

9. 9.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

10. 10.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

11. 11.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

12. 12.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

13. 13.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

14. 14.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

15. 15.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

16. 16.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

17. 17.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

18. 18.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

19. 19.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

20. 20.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

21. 21.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

22. 22.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

23. 23.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

24. 24.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

25. 25.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

26. 26.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

27. 27.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

28. 28.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

29. 29.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

30. 30.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

31. 31.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

32. 32.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

33. 33.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

34. 34.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

35. 35.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

36. 36.
    The Complete Spectrum of Yeast Chromosome Instability Genes Identifies Candidate CIN Cancer Genes and Functional Roles for ASTRA Complex Components · 2011

    No notice
37. 37.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

38. 38.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

39. 39.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

40. 40.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

41. 41.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

42. 42.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

43. 43.
    Karyotypic Determinants of Chromosome Instability in Aneuploid Budding Yeast · 2012

    No notice
44. 44.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

45. 45.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

46. 46.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

47. 47.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

48. 48.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

49. 49.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

50. 50.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

51. 51.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

52. 52.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

53. 53.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

54. 54.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

55. 55.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

56. 56.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

57. 57.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

58. 58.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

59. 59.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

60. 60.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

61. 61.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

62. 62.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

63. 63.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

64. 64.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

65. 65.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

66. 66.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

67. 67.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

68. 68.
    Inference of population structure using multilocus genotype data: dominant markers and null alleles · 2007

    No notice
69. 69.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

70. 70.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

71. 71.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

72. 72.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

73. 73.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

74. 74.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

75. 75.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

76. 76.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

77. 77.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

78. 78.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

79. 79.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

80. 80.
    The fascinating and secret wild life of the budding yeast S. cerevisiae · 2015

    No notice
81. 81.
    Dosage compensation can buffer copy-number variation in wild yeast · 2015

    Corrected
82. 82.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

83. 83.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

84. 84.
    Saccharomyces cerevisiae: a nomadic yeast with no niche? · 2015

    No notice
85. 85.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

86. 86.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

87. 87.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

88. 88.
    Acquisition of Aneuploidy Provides Increased Fitness during the Evolution of Antifungal Drug Resistance · 2009

    No notice
89. 89.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

90. 90.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

91. 91.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

92. 92.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

93. 93.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

94. 94.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

95. 95.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

96. 96.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

97. 97.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

98. 98.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

99. 99.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

100. 100.

     This reference’s wording can’t be shown under the paper’s licence.

     Not in our library

101. 101.

     This reference’s wording can’t be shown under the paper’s licence.

     Not in our library

102. 102.

     This reference’s wording can’t be shown under the paper’s licence.

     Not in our library

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• nQuire: a statistical framework for ploidy estimation using next generation sequencing · 2018
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• Genome evolution across 1,011 Saccharomyces cerevisiae isolates · 2018
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• Extremely Rare Polymorphisms in Saccharomyces cerevisiae Allow Inference of the Mutational Spectrum. · 2017
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• Loss of Heterozygosity Drives Adaptation in Hybrid Yeast · 2017
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