Genome Sequencing and Phylogenetic Analysis of Bacterial Strain K1

Genomic DNA of K1 was extracted using a bacterial genomic DNA isolation kit (Biotech Corporation, Beijing, China). The harvested DNA was detected via the agarose gel electrophoresis, and it was quantified using a Qubit^® 2.0 Fluorometer (Thermo Scientific, USA). 16S rRNA was amplified using the universal primers 27F and 1492R as previously described (Gao et al., 2017 (link)). The 16S rRNA sequence was blasted at NCBI (https://www.ncbi.nlm.nih.gov), and sequences of related strains were downloaded. A phylogenetic tree was then built according to the neighbor-joining method using Mega-X software (Kumar et al., 2018 (link)). The neighbor-joining tree was constructed based on bootstrap values with 1,000 replications. To further distinguish the K1 strain, the whole genome of K1 was sequenced using the Nanopore PromethION platform and Illumina NovaSeq PE150 at the Beijing Novogene Bioinformatics Technology Co., Ltd.
A total of 5,378,358,199-bp paired end reads were generated. These reads were assembled using Unicycler v0.4.7 (https://github.com/rrwick/Unicycler, Wick et al., 2017 (link)). K1 genome sequences were uploaded to the Type Strain Genome Server (TYGS) for genome-based taxonomic classification (Meier-kolthoff and Göker, 2019 (link)). The genome sequences of strain K1 were submitted to NCBI and assigned an accession number (CP093546).