To generate a reference genome sequence of the Asian vine snake, muscle tissue from a male green snake (ID: CIB119038) from Xishuangbanna, Yunnan Province, China, was collected. High molecular weight genomic DNA was prepared using the CTAB method, followed by purification using a QIAGEN® Genomic kit (QIAGEN, Valencia, CA, USA) for sequencing according to the standard procedures provided by the manufacturer.
For genome sequencing, DNA was extracted using the SDS method. DNA degradation and extracted DNA contamination were monitored using 1% agarose gels. DNA purity was then detected using a NanoDrop™ One UV-Vis Spectrophotometer (Thermo Fisher Scientific, USA), with OD 260/280 ranging from 1.8 to 2.0 and OD 260/230 ranging from 2.0 to 2.2. Lastly, the DNA concentration was further measured using a Qubit® 4.0 Fluorometer (Invitrogen, USA). In total, 3–4 μg of DNA per sample was used as input material for the ONT library preparations. After the sample was qualified, size selection of long DNA fragments was performed using the PippinHT system (Sage Science, USA). The DNA fragments ends were then repaired, and A-ligation reaction was conducted using a NEBNext Ultra II End Repair/dA-tailing Kit (Cat# E7546). The adapter in SQK-LSK109 (Oxford Nanopore Technologies, UK) was used for further ligation reactions and the DNA library was measured using a Qubit® 4.0 Fluorometer (Invitrogen, USA). A DNA library (700 ng) was constructed and long-read sequencing was performed on a Nanopore PromethION sequencer (Oxford Nanopore Technologies, UK).
For short-read sequencing, a paired-end library was conducted with an insert size of 300 bp and 100 bp paired-end reads, then sequenced using the MGISEQ-2000 platform following the manufacturer’s standard protocols.
For Hi-C sequencing, muscle cells from the Asian vine snake were fixed with formaldehyde, followed by restriction enzyme digestion. Nuclei were extracted by lysing the cross-linked tissue. The cohesive ends were filled in by adding biotinylated nucleotides, and the free blunt ends were ligated. The cross-linking was reversed, and DNA was purified to remove proteins. The purified DNA was then sheared to a length of ∼400 bp and point ligation junctions were pulled down. The Hi-C libraries were sequenced using the Illumina HiSeq platform with PE150 short reads.
For genome sequencing, DNA was extracted using the SDS method. DNA degradation and extracted DNA contamination were monitored using 1% agarose gels. DNA purity was then detected using a NanoDrop™ One UV-Vis Spectrophotometer (Thermo Fisher Scientific, USA), with OD 260/280 ranging from 1.8 to 2.0 and OD 260/230 ranging from 2.0 to 2.2. Lastly, the DNA concentration was further measured using a Qubit® 4.0 Fluorometer (Invitrogen, USA). In total, 3–4 μg of DNA per sample was used as input material for the ONT library preparations. After the sample was qualified, size selection of long DNA fragments was performed using the PippinHT system (Sage Science, USA). The DNA fragments ends were then repaired, and A-ligation reaction was conducted using a NEBNext Ultra II End Repair/dA-tailing Kit (Cat# E7546). The adapter in SQK-LSK109 (Oxford Nanopore Technologies, UK) was used for further ligation reactions and the DNA library was measured using a Qubit® 4.0 Fluorometer (Invitrogen, USA). A DNA library (700 ng) was constructed and long-read sequencing was performed on a Nanopore PromethION sequencer (Oxford Nanopore Technologies, UK).
For short-read sequencing, a paired-end library was conducted with an insert size of 300 bp and 100 bp paired-end reads, then sequenced using the MGISEQ-2000 platform following the manufacturer’s standard protocols.
For Hi-C sequencing, muscle cells from the Asian vine snake were fixed with formaldehyde, followed by restriction enzyme digestion. Nuclei were extracted by lysing the cross-linked tissue. The cohesive ends were filled in by adding biotinylated nucleotides, and the free blunt ends were ligated. The cross-linking was reversed, and DNA was purified to remove proteins. The purified DNA was then sheared to a length of ∼400 bp and point ligation junctions were pulled down. The Hi-C libraries were sequenced using the Illumina HiSeq platform with PE150 short reads.
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