title: Illumina sequencing of Fol4287 deletion strain: RFP#11
design: We sequenced ten partial pathogenicity chromosome deletion strains which were obtained from fluorescenceassisted cell sorting (FACS) of a strain in which the two arms of the pathogenicity chromosome were labelled with GFP and RFP respectively (DOI: 10.1111/1462-2920.15095). The original strain used for FACS containing GFP on the long arm (DOI: 10.1111/mpp.12440) and RFP inserted in the ORF of FOXG_14135 on the short arm of the pathogenicity chromosome. Six GFP deletion strains, including GFP#8, GFP#20, GFP#22, GFP#26, GFP#27 and GFP#29, were obtained by selecting spores without green fluorescence, while four RFP deletion strains, including RFP#11, RFP#12, RFP#14 and RFP#16, were obtained by selecting spores without red fluorescence. Partial deletion of ten deletions strains were confirmed by PCR using primers across the pathogenicity chromosome. The karyotypes of some deletion strains, including GFP#8, GFP#26, GFP#29, RFP#11 and RFP#12, were assessed. We sequenced these deletion strains to assess which parts of the pathogenicity chromosome were lost.