SRX4284757 HiC_Bm-sync-fieldStrain-rep1 SRP151138 bp0 Cell cultures were crosslinked for 25 minutes at 37C in 1.25% formaldehyde in a total volume between 1 and 10 ml, depending on the number of parasites harvested. The reaction was quenched for 15 min at 37C, followed by extensive washes to remove cellular debris. To map the inter- and intrachromosomal contact counts, crosslinked parasites were subjected to the in situ Hi-C prodecure, using MboI for restriction digests. Libraries were generated using NEBNext Multiplex Oligos for Illumina and Kapa HiFi Hotstart ReadyMix (Kapa Biosystems) and amplified for a total of 12 PCR cycles (15s at 98C, 30s at 55C, 30s at 62C) and were subsequently sequenced using the Illumina HiSeq2500 platform, generating 50 bp paired-end reads. SRS3448914 HiC_Bm-sync-fieldStrain-rep1 HiC_Bm-sync-fieldStrain-rep1 Hi-C GENOMIC Restriction Digest Illumina HiSeq 2500 SRX4284758 HiC_Bm-async-labStrain-rep1 SRP151138 bp0 Cell cultures were crosslinked for 25 minutes at 37C in 1.25% formaldehyde in a total volume between 1 and 10 ml, depending on the number of parasites harvested. The reaction was quenched for 15 min at 37C, followed by extensive washes to remove cellular debris. To map the inter- and intrachromosomal contact counts, crosslinked parasites were subjected to the in situ Hi-C prodecure, using MboI for restriction digests. Libraries were generated using NEBNext Multiplex Oligos for Illumina and Kapa HiFi Hotstart ReadyMix (Kapa Biosystems) and amplified for a total of 12 PCR cycles (15s at 98C, 30s at 55C, 30s at 62C) and were subsequently sequenced using the Illumina HiSeq2500 platform, generating 50 bp paired-end reads. SRS3448915 HiC_Bm-async-labStrain-rep1 HiC_Bm-async-labStrain-rep1 Hi-C GENOMIC Restriction Digest Illumina HiSeq 2500 SRX4284759 HiC_Tg-Brady-WT-rep1 SRP151138 bp0 Cell cultures were crosslinked for 25 minutes at 37C in 1.25% formaldehyde in a total volume between 1 and 10 ml, depending on the number of parasites harvested. The reaction was quenched for 15 min at 37C, followed by extensive washes to remove cellular debris. To map the inter- and intrachromosomal contact counts, crosslinked parasites were subjected to the in situ Hi-C prodecure, using MboI for restriction digests. Libraries were generated using NEBNext Multiplex Oligos for Illumina and Kapa HiFi Hotstart ReadyMix (Kapa Biosystems) and amplified for a total of 12 PCR cycles (15s at 98C, 30s at 55C, 30s at 62C) and were subsequently sequenced using the Illumina HiSeq2500 platform, generating 50 bp paired-end reads. SRS3448916 HiC_Tg-Brady-WT-rep1 HiC_Tg-Brady-WT-rep1 Hi-C GENOMIC Restriction Digest Illumina HiSeq 2500 SRX4284760 HiC_Tg-Tachy-WT-rep1 SRP151138 bp0 Cell cultures were crosslinked for 25 minutes at 37C in 1.25% formaldehyde in a total volume between 1 and 10 ml, depending on the number of parasites harvested. The reaction was quenched for 15 min at 37C, followed by extensive washes to remove cellular debris. To map the inter- and intrachromosomal contact counts, crosslinked parasites were subjected to the in situ Hi-C prodecure, using MboI for restriction digests. Libraries were generated using NEBNext Multiplex Oligos for Illumina and Kapa HiFi Hotstart ReadyMix (Kapa Biosystems) and amplified for a total of 12 PCR cycles (15s at 98C, 30s at 55C, 30s at 62C) and were subsequently sequenced using the Illumina HiSeq2500 platform, generating 50 bp paired-end reads. SRS3448922 HiC_Tg-Tachy-WT-rep1 HiC_Tg-Tachy-WT-rep1 Hi-C GENOMIC Restriction Digest Illumina HiSeq 2500 SRX4284761 HiC_Pk-Troph-WT-rep1 SRP151138 bp0 Cell cultures were crosslinked for 25 minutes at 37C in 1.25% formaldehyde in a total volume between 1 and 10 ml, depending on the number of parasites harvested. The reaction was quenched for 15 min at 37C, followed by extensive washes to remove cellular debris. To map the inter- and intrachromosomal contact counts, crosslinked parasites were subjected to the in situ Hi-C prodecure, using MboI for restriction digests. Libraries were generated using NEBNext Multiplex Oligos for Illumina and Kapa HiFi Hotstart ReadyMix (Kapa Biosystems) and amplified for a total of 12 PCR cycles (15s at 98C, 30s at 55C, 30s at 62C) and were subsequently sequenced using the Illumina HiSeq2500 platform, generating 50 bp paired-end reads. SRS3448917 HiC_Pk-Troph-WT-rep1 HiC_Pk-Troph-WT-rep1 Hi-C GENOMIC Restriction Digest Illumina HiSeq 2500 SRX4284762 HiC_Py-IDC-PanK1Mut-rep1 SRP151138 bp0 Cell cultures were crosslinked for 25 minutes at 37C in 1.25% formaldehyde in a total volume between 1 and 10 ml, depending on the number of parasites harvested. The reaction was quenched for 15 min at 37C, followed by extensive washes to remove cellular debris. To map the inter- and intrachromosomal contact counts, crosslinked parasites were subjected to the in situ Hi-C prodecure, using MboI for restriction digests. Libraries were generated using NEBNext Multiplex Oligos for Illumina and Kapa HiFi Hotstart ReadyMix (Kapa Biosystems) and amplified for a total of 12 PCR cycles (15s at 98C, 30s at 55C, 30s at 62C) and were subsequently sequenced using the Illumina HiSeq2500 platform, generating 50 bp paired-end reads. SRS3448918 HiC_Py-IDC-PanK1Mut-rep1 HiC_Py-IDC-PanK1Mut-rep1 Hi-C GENOMIC Restriction Digest Illumina HiSeq 2500 SRX4284763 HiC_Pb-Gam-Smc4mut-rep1 SRP151138 bp0 Cell cultures were crosslinked for 25 minutes at 37C in 1.25% formaldehyde in a total volume between 1 and 10 ml, depending on the number of parasites harvested. The reaction was quenched for 15 min at 37C, followed by extensive washes to remove cellular debris. To map the inter- and intrachromosomal contact counts, crosslinked parasites were subjected to the in situ Hi-C prodecure, using MboI for restriction digests. Libraries were generated using NEBNext Multiplex Oligos for Illumina and Kapa HiFi Hotstart ReadyMix (Kapa Biosystems) and amplified for a total of 12 PCR cycles (15s at 98C, 30s at 55C, 30s at 62C) and were subsequently sequenced using the Illumina HiSeq2500 platform, generating 50 bp paired-end reads. SRS3448919 HiC_Pb-Gam-Smc4mut-rep1 HiC_Pb-Gam-Smc4mut-rep1 Hi-C GENOMIC Restriction Digest Illumina HiSeq 2500 SRX4284764 HiC_Pb-Gam-Smc2mut-rep1 SRP151138 bp0 Cell cultures were crosslinked for 25 minutes at 37C in 1.25% formaldehyde in a total volume between 1 and 10 ml, depending on the number of parasites harvested. The reaction was quenched for 15 min at 37C, followed by extensive washes to remove cellular debris. To map the inter- and intrachromosomal contact counts, crosslinked parasites were subjected to the in situ Hi-C prodecure, using MboI for restriction digests. Libraries were generated using NEBNext Multiplex Oligos for Illumina and Kapa HiFi Hotstart ReadyMix (Kapa Biosystems) and amplified for a total of 12 PCR cycles (15s at 98C, 30s at 55C, 30s at 62C) and were subsequently sequenced using the Illumina HiSeq2500 platform, generating 50 bp paired-end reads. SRS3448920 HiC_Pb-Gam-Smc2mut-rep1 HiC_Pb-Gam-Smc2mut-rep1 Hi-C GENOMIC Restriction Digest Illumina HiSeq 2500 SRX4284765 HiC_Bm-async-fieldStrain-rep1 SRP151138 bp0 Cell cultures were crosslinked for 25 minutes at 37C in 1.25% formaldehyde in a total volume between 1 and 10 ml, depending on the number of parasites harvested. The reaction was quenched for 15 min at 37C, followed by extensive washes to remove cellular debris. To map the inter- and intrachromosomal contact counts, crosslinked parasites were subjected to the in situ Hi-C prodecure, using MboI for restriction digests. Libraries were generated using NEBNext Multiplex Oligos for Illumina and Kapa HiFi Hotstart ReadyMix (Kapa Biosystems) and amplified for a total of 12 PCR cycles (15s at 98C, 30s at 55C, 30s at 62C) and were subsequently sequenced using the Illumina HiSeq2500 platform, generating 50 bp paired-end reads. SRS3448921 HiC_Bm-async-fieldStrain-rep1 HiC_Bm-async-fieldStrain-rep1 Hi-C GENOMIC Restriction Digest Illumina HiSeq 2500 SRX4284766 HiC_Pb-Gam-WT-rep1 SRP151138 bp0 Cell cultures were crosslinked for 25 minutes at 37C in 1.25% formaldehyde in a total volume between 1 and 10 ml, depending on the number of parasites harvested. The reaction was quenched for 15 min at 37C, followed by extensive washes to remove cellular debris. To map the inter- and intrachromosomal contact counts, crosslinked parasites were subjected to the in situ Hi-C prodecure, using MboI for restriction digests. Libraries were generated using NEBNext Multiplex Oligos for Illumina and Kapa HiFi Hotstart ReadyMix (Kapa Biosystems) and amplified for a total of 12 PCR cycles (15s at 98C, 30s at 55C, 30s at 62C) and were subsequently sequenced using the Illumina HiSeq2500 platform, generating 50 bp paired-end reads. SRS3448926 HiC_Pb-Gam-WT-rep1 HiC_Pb-Gam-WT-rep1 Hi-C GENOMIC Restriction Digest Illumina HiSeq 2500 SRX4284767 HiC_Bm-sync-fieldStrain-rep2 SRP151138 bp0 Cell cultures were crosslinked for 25 minutes at 37C in 1.25% formaldehyde in a total volume between 1 and 10 ml, depending on the number of parasites harvested. The reaction was quenched for 15 min at 37C, followed by extensive washes to remove cellular debris. To map the inter- and intrachromosomal contact counts, crosslinked parasites were subjected to the in situ Hi-C prodecure, using MboI for restriction digests. Libraries were generated using NEBNext Multiplex Oligos for Illumina and Kapa HiFi Hotstart ReadyMix (Kapa Biosystems) and amplified for a total of 12 PCR cycles (15s at 98C, 30s at 55C, 30s at 62C) and were subsequently sequenced using the Illumina HiSeq2500 platform, generating 50 bp paired-end reads. SRS3448923 HiC_Bm-sync-fieldStrain-rep2 HiC_Bm-sync-fieldStrain-rep2 Hi-C GENOMIC Restriction Digest Illumina HiSeq 2500 SRX4284768 HiC_Bm-sync-labStrain-rep1 SRP151138 bp0 Cell cultures were crosslinked for 25 minutes at 37C in 1.25% formaldehyde in a total volume between 1 and 10 ml, depending on the number of parasites harvested. The reaction was quenched for 15 min at 37C, followed by extensive washes to remove cellular debris. To map the inter- and intrachromosomal contact counts, crosslinked parasites were subjected to the in situ Hi-C prodecure, using MboI for restriction digests. Libraries were generated using NEBNext Multiplex Oligos for Illumina and Kapa HiFi Hotstart ReadyMix (Kapa Biosystems) and amplified for a total of 12 PCR cycles (15s at 98C, 30s at 55C, 30s at 62C) and were subsequently sequenced using the Illumina HiSeq2500 platform, generating 50 bp paired-end reads. SRS3448924 HiC_Bm-sync-labStrain-rep1 HiC_Bm-sync-labStrain-rep1 Hi-C GENOMIC Restriction Digest Illumina HiSeq 2500 SRX4284769 HiC_Bm-sync-labStrain-rep2 SRP151138 bp0 Cell cultures were crosslinked for 25 minutes at 37C in 1.25% formaldehyde in a total volume between 1 and 10 ml, depending on the number of parasites harvested. The reaction was quenched for 15 min at 37C, followed by extensive washes to remove cellular debris. To map the inter- and intrachromosomal contact counts, crosslinked parasites were subjected to the in situ Hi-C prodecure, using MboI for restriction digests. Libraries were generated using NEBNext Multiplex Oligos for Illumina and Kapa HiFi Hotstart ReadyMix (Kapa Biosystems) and amplified for a total of 12 PCR cycles (15s at 98C, 30s at 55C, 30s at 62C) and were subsequently sequenced using the Illumina HiSeq2500 platform, generating 50 bp paired-end reads. SRS3448925 HiC_Bm-sync-labStrain-rep2 HiC_Bm-sync-labStrain-rep2 Hi-C GENOMIC Restriction Digest Illumina HiSeq 2500