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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%