bacteria
De novo assembly was performed to generate sequences of UTNGt2 sample using Illumina HiSeq X Ten platform as previously described (custom service, Macrogen Inc., Seoul, Korea) (Tenea et al., 2020b). In brief, the sequencing library was prepared by random fragmentation of the DNA or cDNA sample, followed by 5 and 3 adapter ligation according to the protocol provided by the manufacturer (Macrogen Inc., Seoul, Korea). Sequencing data were converted into raw data for analysis. The overall quality of reads generated by FastQC (v0.11.5, http://www.bioinformatics.babraham.ac.uk/projects/fastqc), total bases, total reads, GC content, and basic statistics were calculated. To reduce biases in the analysis, adapter trimming and quality filtering were performed. Trimmomatic v0.36 (http://www.usadellab.org/cms/?page=trimmomatic) was used to remove adapter sequences. The quality of filtered reads, total bases, total reads, GC content, and basic statistics were calculated. De novo assembly was performed by various k-mer using SPAdes 3.15.1 (http://cab.spbu.ru/software/spades/). K-mer analysis was performed to provide information about coverage, heterozygosity, and estimated genome size (Jellyfish v2.2.10, http://www.genome.umd.edu/jellyfish.html). Using filtered reads, de novo assembly was performed using a De Bruijn graph assembler (http://qb.cshl.edu/genomescope/). The reads were split into multiple K-mers (Oligonucleotides with length K, K equal integer), which were further aligned with each other, and the sequences were extended one base at a time based on the overlap information of K-mers. The best k-mer was selected based on various statistics from assembly results (number of contigs, total base of contigs, N50, etc.) and the best-assembled sequence set was determined. The assembled genome was validated using mapping strategy and BUSCO analysis (https://busco.ezlab.org/, BUSCO version 3.0) (Seppey et al., 2019). The filtered reads were aligned to the assembled genome, and their insert size was estimated for validation. To assess the completeness of the genome assembly, BUSCO analysis was performed based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. By default, bacteria DB was used for analysis. After the complete genome or draft genome was assembled, BLAST analysis was carried out to identify to which species each scaffold showed similarity.