Hybrid Genome Assembly of Parabacteroides distasonis

Bacterial genomic DNA was extracted from 10 ml overnight cultures of P. distasonis APCS2/PD using phenol/chloroform with precipitation in 3 M sodium acetate and cold absolute ethanol for the generation of long- and short-read sequences for hybrid assembly. DNA was quantified using Qubit BR DNA Assay Kit. Short-read shotgun sequencing of the extracted DNA was carried out using the Accel-NGS 1S Plus DNA Library Kit (Swift Biosciences, MI, USA) and Illumina HiSeq 4000 technology following manufacturer’s instructions. Long-read Oxford Nanopore library preparation was performed according to the manufacturer protocol for Rapid Barcoding Sequencing Kit (SQK-RPK004; Oxford Nanopore Technologies, UK) with the adaptions described by Guerin et al., (2021).^{23 (link)} Pooled samples were loaded into SpotON Flow Cell (Oxford Nanopore Technologies, UK) and MinION sequenced for 48 hours (Oxford Nanopore Technologies,UK). Hybrid assembly of quality-filtered and trimmed Illumina and raw Nanopore reads was conducted by hybridSPAdes (v1.13.1).^{91 (link)} Nine scaffolds greater than 1 kb were generated and were manually curated, joined, and circularized using CLC Sequence Viewer. The assembled and circularized genome and associated plasmid were then submitted to NCBI Prokaryotic Genome Annotation Pipeline. The GenBank file for the genome and associated plasmid was visualized using Proksee.^{72 (link)}