Objective: To sequence the S. salivarius JH genome and catalog its genetic complement. S. salivarius JH harbors the largest streptococcal megaplasmid characterized to date, produces three bacteriocin types and, uncommonly for this species, is beta-hemolytic.
Methods: Genomic fragments of S. salivarius JH were sequenced using the high-throughput Roche Genome Sequencer FLX (GS-FLX) system and assembled into contiguous sequences (contigs) using GS Assembler. Annotation (gene assignment) was achieved using a combination of BLAST algorithms and gene prediction software (GeneMark or fgenesb).
Results: The GS-FLX system generated 113,973 DNA sequence reads totaling 27.9 million bp that were subsequently assembled into 282 contigs. These contigs were then categorized putatively as either chromosomal, megaplasmid-related or as repetitive DNA regions. In this project, over 660 genes were annotated. The chromosome of S. salivarius JH appears very similar in organization to that of its closest genetic relative, the dairy species Streptococcus thermophilus, including the presence of six ribosomal RNA (rrn) operons. Preliminary inter-contig gap closure procedures (flanking the rrn loci) were conducted and some differences, compared to S. thermophilus, were noted. Sequence analysis of the non-chromosomal contigs revealed loci encoding three known bacteriocins (salivaricin A, streptococcin A-FF22 and streptin), tetracycline resistance (Tn916) and different transposase types.
Conclusions: To date, approximately one-third of the total genetic complement of S. salivarius strain JH has been catalogued. Future closure of all remaining inter-contig gaps will ensure the completion of the S. salivarius JH genome sequence. This research was supported by the Otago Medical Research Foundation.