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Protocol publication

[…] whole genomes were compared using Gegenees software version 2.0 along with other piscine S. agalactiae strains that had complete genome sequences, 138spar (ST-261) and GD201008-001 (ST-7) (GenBank access numbers CP007565 and CP003810, respectively), to obtain a percentage identity matrix. This matrix was then used to build a similarity heatmap. The parameters set in Genenees were a Fragment size = 200 bp, Step size = 100 bp and a threshold in heat settings of 0%., The complete genome sequences of the 39 presented strains together with 138spar and GD201008-001, in addition to the draft genome sequence of ST-491 S. agalactiae strain STIR-CD-14 (GenBank access number ANEJ01), were submitted to Bacterial Isolate Genome Sequence Database (BIGSdb). All loci were compared one by one between isolates using a gene-by-gene approach on a GenomeComparator plugin. All loci scheme was previously generated using all genes cluster from a cd-hit-est software v4.6, with a multi-fasta file containing all predicted genes from all strains (n = 42) and the default parameters. A distance matrix with the relative genomic divergence between all isolates was obtained and used to construct a phylogenomic NeighborNet network using SplitsTree 4.0., The 39 strains from this study, along with the S. agalactiae genomes available on GenBank that were at least at the scaffold stage with a number of scaffolds >=30 (n = 103), were used to perform the substitution rate and Bayesian analyses. Using a highly stringent nucleotide-Blast search with an e-value of 1e-20, the CDS of SA20 were aligned against all other strains. All CDSs that met the following requirements were retained: minimal percentage of identity of 98%, difference of length between query and subject <=5 bp, lacking paralogous sequences, and present in all genomes (n = 382 genes) were extracted and concatenated to form the core genome of the species. The cor […]

Pipeline specifications

Software tools BIGSdb, CD-HIT, SplitsTree