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

	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%