Purpose: The genome sequence of the yogurt isolate S. thermophilus ACA-DC 2 was analyzed in order to shed light on its technological potential. Comparative genomics analysis among the existing complete genome sequences of S. thermophilus was also performed.
Methods: The genome of S. thermophilus ACA-DC 2 was sequenced with a combined approach of Illumina HiSeq and PacBio sequencing technologies. The Illumina FASTQ sequences were assembled into contigs (ABySS 1.5.1). The latter were linked and placed into scaffolds based on the alignment of the PacBio continuous long read data. Finally, gap closure within the scaffolds was performed (GapFiller 1.10). The genome sequence was annotated using the RAST pipeline. Full chromosome alignments were calculated with Progressive Mauve, providing information for the pangenome, the core genome and the singletons of the examined sequences. The GIs, CRISPRs and the antimicrobial peptides were predicted with IslandViewer, CRISPRcompar and BAGEL3, respectively.
Results: The genome analysis of S. thermophilus ACA-DC 2 revealed the absence of pathogenic features. Full chromosome alignments showed a high degree of synteny among the different strains. The pangenome of the 12 strains sequenced so far comprised about 2,300 genes. Concerning S. thermophilus ACA-DC 2, approximately 110 unique genes involved in various biological processes were identified. Four potential antimicrobial peptides but no CRISPR system were predicted.
Significance: The extensive use of S. thermophilus strains as starter cultures in dairy industry and the demand for qualitative and safe products render the in silico analysis of the genome sequence of S. thermophilus ACA-DC 2 a useful tool for the exploitation of its technological potential.