Complete Genome Sequence of Streptomyces albus Strain G153

ABSTRACT

The genus Streptomyces is a promising source of biologically active secondary metabolites. Here, we report the complete genome sequence of Streptomyces albus strain G153. The assembled genome comprised a single linear chromosome of 6.9 Mbp with a G+C content of 73.3%.

ANNOUNCEMENT

Several Streptomyces albus and closely related strains are used as heterologous hosts for diverse secondary metabolite production (1, 2). Among them, Streptomyces albidoflavus J1074 (formerly known as Streptomyces albus J1074) is one of the most popular host strains, for which the genome sequence is available (3). However, the genome sequence of S. albus G153 has not yet been determined and a difference between them still remains elusive. Here we report a complete genome sequence for S. albus G153.

S. albus G153 was obtained from Tomohisa Kuzuyama cultured under aerobic conditions at 30°C for 3 days (100 mL of TSB medium [Oxoid] containing 50 mg/L of nalidixic acid [Nacalai] in a 300-mL baffled flask). Approximately 1.0 × 10^9 cells were collected and the genomic DNA was purified using Genomic-tips 20/G (Qiagen). Long read sequencing libraries were prepared and multiplexed using the Rapid Barcoding Kit (SQK-RBK004; Oxford Nanopore Technologies). Libraries were sequenced in a FLO-MIN106 flowcell, basecalled (guppy version 5.0.12, Super-Accurate Mode), demultiplexed and adapter-trimmed on the GridION X5 device (GridION software release 21.05.25, Oxford Nanopore Technologies). Long reads were quality checked using Nanoplot version 1.20.0 (4), which totaled 495,782,602 bp consisting of 125,903 reads of N50 length 8,787 bp. Reads longer than 5 kb (approximately x50 coverage) were used for assembly using Canu version 2.2 (5). The resulting single contig was manually confirmed to be full-length linear chromosome like other Streptomyces genomes by comparing it with the J1074 genome. A library for Illumina sequencing for error correction was prepared using a KAPA HyperPlus kit (Kapa Biosystems), and the library was sequenced on a NextSeq 500 sequencer (Illumina) using the 75-cycle high-output mode as single ends. Unfiltered 25,694,300 (1.9 Gbp) Illumina short reads were used for error correction with one round of Pilon version 1.2.4 (6). The assembly quality was assessed using Benchmarking Universal Single-Copy Orthologs (BUSCO) v.1 on the gVolante server (7), and the completeness score reached 100%. The genome was annotated using the DDBJ Fast Annotation and Submission Tool (DFAST) version 1.4.0 (8). All software was used with default settings unless otherwise specified.

The annotated linear genome of S. albus G153 is 6,850,711 bp with a G+C content of 73.3%, containing 6,072 putative coding sequences (CDSs), 21 rRNA genes, 77 tRNA genes, and five CRISPR loci were predicted. D-GENIES (9) comparison with S. albus J1074 revealed only 0.04% mismatched regions, and the Mauve version 2.4.0 (10) alignment revealed an 11,997-bp long insertion sequence (3,292,629 to 3,304,629 bp) in the G153 genome, in which a total of six CDSs were coded, including those annotated as LuxR family transcriptional regulators. LuxR family proteins are often involved in the quorum sensing mechanisms (11) and activate biosynthetic gene clusters in Streptomyces strains (12).

Data availability.

The genome sequences reported here were deposited in DDBJ under accession numbers AP025687, and the raw reads were deposited in the Sequence Read Archive (SRA) under BioProject accession number PRJNA820546 as SRR18498194 and SRR18498195 runs.