Computational protocol: Complete Genome Sequences of Three Fish-Associated Streptococcus agalactiae Isolates

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Protocol publication

[…] Streptococcus agalactiae is a major cause of streptococcosis in farmed tilapia and has been associated with significant levels of mortality in diseased fish (, ). We have selected three group B Streptococcus (GBS) (S. agalactiae) serotype Ib isolates obtained from the brains of diseased tilapia for complete genome sequencing. The isolates we analyzed belong to clonal complex 552 (CC552) and sequence types 260 (isolates 14-98 and 14-104) and 261 (isolate 14-110) and were typed using molecular serotyping and multilocus sequence typing (MLST), as we previously described for serotype Ia (). Serotype Ib isolates belonging to CC552 have a significantly reduced genome size compared to that of other S. agalactiae genomes () and are predominantly associated with fish and other poikilothermic species ().Sequencing of the isolates was performed using a MiSeq system (Illumina, San Diego, CA) with 250-bp paired-end reads. Libraries with an average 550-bp insert were prepared using a TruSeq Nano DNA library preparation kit (Illumina). De novo assembly of the reads was performed with the SPAdes version 3.5.0 software () and the quality of the assembly assessed with the QUAST software (). The contigs (>200 nucleotides [nt]) were annotated using the NCBI Prokaryotic Genome Annotation Pipeline to predict protein-coding genes and other functional genome units, including structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons, and other mobile elements.The genomes of S. agalactiae Ib isolates 14-98, 14-104, and 14-110 were 1,842,528, 1,815,466, and 1,803,751 bp distributed in 99, 51, and 30 contigs and with average de novo assembly coverages of 193×, 227×, and 154×, respectively. The G+C genome content for each of the three isolates was 35.3%. The genome of isolate 14-98 was composed of a total of 1,980 genes, including 1,761 coding genes, 56 RNA genes (50 tRNA), and 163 pseudogenes, while the genome of isolate 14-104 contained 1,910 genes, of which 1,703 are coding genes, 48 are RNA genes (42 tRNAs), and 159 are pseudogenes. The genome of strain 14-110 was composed of a total of 1,883 genes, with 1,647 coding genes, 59 RNA genes containing 52 tRNAs, and 177 pseudogenes. […]

Pipeline specifications

Software tools SPAdes, QUAST, PGAP
Application De novo sequencing analysis
Organisms Danio rerio, Streptococcus agalactiae, Oreochromis niloticus, Escherichia coli
Diseases Guillain-Barre Syndrome