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Table 5 Genomic origins of Pgt sRNAs. The Pgt sRNAs map in similar proportions to the two haplotypes. More than half of sRNAs are conserved and have a homologous counterpart. Late wave sRNAs preferentially originate from repetitive regions and the centromeres

From: The stem rust fungus Puccinia graminis f. sp. tritici induces centromeric small RNAs during late infection that are associated with genome-wide DNA methylation

 

Early wave sRNAs

Late wave sRNAs

No differential expression

Up-regulated in germinated spores

Up-regulated during early infection

Up-regulated during late infection

 

# of sRNAs

2663

530

4005

639

Centromeric sRNAs

1.1%

1.9%

23.9%

3.3%

On chromosomes A

50.4%

50.4%

49.6%

49.3%

On chromosomes B

49.6%

49.6%

50.4%

50.8%

sRNAs with homologous counterpart

68.1%

67.5%

54.8%

44.6%

Homologous counterpart is on alternate haplotype chromosome

82.6%

85%

18.2%

36.8%

Mapping to repeats

24.9%

30.9%

88.3%

62.1%

Mapping to genes

77.1%

68.3%

16%

48.4%

Overlap with methylated CG sites (late infection)

10.9%

22.8%

94%

49.8%

Overlap with methylated CG sites (germinated spores)

11.6%

22.5%

95.5%

51.6%

Classification of repeats with mapped sRNAs

 Class I (retrotransposons)

58.7%

58.6%

56.4%

61.8%

  Gypsy LTR

29.6%

16.2%

29.8%

28.7%

  Copia LTR

9.9%

19.9%

14.2%

13.3%

 Class II (DNA transposons)

38.4%

37.2%

42.2%

37.2%

  Tc1-Mariner

5.5%

5.2%

2.9%

4.1%

  MuDR

5.6%

3.1%

6.9%

7.8%