Table 1. Sequence complexity in control (wild-type developing genome), PGM KD, SPT5m KD and DCL2/3 KD.

Dataset	PGM	SPT5m	DCL2/3	Control
PGM	89.00 Mb	88.64 Mb	88.74 Mb	76.09 Mb
	100.0%	99.6%	99.71%	85.5%
PGM not Control	12.91 Mb	12.66 Mb	12.66 Mb	0.00 Mb
	100.0%	98.05%	98.04%	0.0%

The 91 Mb PGM assembly was used as a proxy for the germline genome, as explained in the text. Samples of Illumina paired-end reads were mapped to the assembly and regions covered by at least 2 RPKM (reads per kilobase per million mapped reads) were scored as explained in ‘Materials and Methods’ section. The stringency of this cutoff explains the value of 89 Mb found for the PGM sample itself. The ‘PGM’ reference contains contigs covered by the PGM dataset. The ‘PGM not Control’ contains contigs covered by the PGM dataset but not by the control (wild-type) dataset, representing the MIC restricted regions. Each column indicates the sum of the lengths of contigs covered by the given dataset.