Accurate reconstruction of bacterial pan- and core genomes with PEPPAN

Abstract

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BlastFrost: fast querying of 100,000s of bacterial genomes in Bifrost graphs

“…We used the whole-genome MLST (wgMLST) scheme for the genus Salmonella in EnteroBase [ 3 , 20 ] to test the accuracy of BlastFrost for detecting sequence variants of a large number of query sequences in a large number of related genomes. That wgMLST scheme consists of 21,065 single copy orthologs which had been derived from a pan-genome of 537 representative genomes of Salmonella with PEPPAN [ 20 , 21 ]. EnteroBase identifies diverse sequence variants of those loci in each assembled genome by combining BLASTN [ 8 ] nucleotide and UBLAST [ 22 ] amino acid queries, and also scores the absence of significant hits for each genome.…”

“…All MLST schemes are inherently limited, because they are based on a fixed selection of genes that were present in an initial, representative set of genomes. However, many bacterial genera are associated with open pan-genomes [ 33 ], whose content continues to increase with each additional genome that is sequenced [ 21 ], and such novel sequences are not routinely appended to the MLST schemes. Therefore, it is important to emphasize that BlastFrost and Bifrost are not dependent on MLST or on genomic annotations, but can handle any collection of closely related genomic assemblies.…”

Insights on the Evolutionary Genomics of the Blautia Genus: Potential New Species and Genetic Content Among Lineages

“…Given the myriad of software pipelines for pangenome reconstruction available (over 40) ( Vernikos, 2020 ), we assessed three different pipelines to define the pangenome of the Blautia dataset: Roary ( Page et al, 2015 ), panX ( Ding et al, 2018 ) and PEPPAN ( Zhou et al, 2020 ). Roary and panX, well-established packages based on their number of citations and publication dates, define clusters of homologous proteins in a broadly similar way.…”

“…The pangenome reconstruction of the blautia dataset was performed with Roary ( Page et al, 2015 ), panX ( Ding et al, 2018 ) and PEPPAN ( Zhou et al, 2020 ). For all the programs, input files were generated by prokka (default settings, –kingdom Bacteria ) ( Seemann, 2014 ).…”

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“…The pangenome reconstruction of the blautia dataset was performed with Roary (Page et al, 2015), panX (Ding et al, 2018) and PEPPAN (Zhou et al, 2020). For all the programs, input files were generated by prokka (default settings, -kingdom Bacteria) (Seemann, 2014).…”