PanGBank: a large-scale resource of precomputed microbial pangenomes built with PPanGGOLiN

Key results

1. 01

   ShownThe first release is built from GTDB release 232 and has two collections. GTDB all (GenBank plus RefSeq) covers over 4,600 prokaryotic species. GTDB refseq (RefSeq only, original annotations kept) covers 2,044 species.

   In both collections, most pangenomes contain fewer than 50 genomes. Only about one hundred species have more than 1,000 genomes. 24 species (GTDB refseq) and 27 (GTDB all) went over the 2,000-genome cap and were dereplicated; these are mainly bacteria of public health importance. GTDB all has more regions of genomic plasticity (RGPs), modules and gene families (Table 1). · PanGBank content; Genome dereplication

2. 02

   ShownIncluding metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) gives broader taxonomic coverage. GTDB all spans 55 phyla, and around 40% of those phyla are covered only by environmental genomes. GTDB refseq is almost entirely isolate genomes.

   About 40% of GTDB all genomes are MAGs or SAGs. GTDB all holds about 150 archaeal pangenomes, which the authors attribute largely to the environmental genomes. Bacterial pangenomes make up most of both collections (Fig. 3A to 3C). · PanGBank content

3. 03

   ShownAfter completeness filtering, the GTDB all collection (about 40% MAGs or SAGs) partitions much like the isolate-based GTDB refseq collection. The proportions of persistent, shell and cloud genomes agree strongly between the two collections.

   Some GTDB all pangenomes have slightly lower persistent fractions; the median decrease across matched species is 0.4 percentage points (Supplementary Figs S1, S2). Filters: completeness is the higher of the CheckM v1 and v2 values; genomes below 70% are dropped; species are dropped if their GTDB representative is below 85%; each species needs at least 15 genomes. · PanGBank content; Input filtering and species selection

4. 04

   ShownIn the Acinetobacter baumannii pangenome, antimicrobial resistance (AMR) gene families sit mostly in the variable genome. Three insertion hotspots found in more than 500 genomes (spots 7, 11 and 47) are rich in AMR-carrying RGPs. Spot 47, at the comM insertion site, holds the most diverse AMR repertoire.

   AMRFinderPlus v4.2.7 found 123 AMR-associated gene families across 2,002 genomes: 79 cloud, 39 shell and 5 persistent. Half concern beta-lactam or aminoglycoside resistance. Spots 7, 11 and 47 occur in over 500 genomes, and more than 40% of their RGPs carry AMR genes. Spot 47 holds 33 AMR gene families, including those of AbaR1 from strain AYE. · PanGBank use case

5. 05

   SuggestedIn A. baumannii, PPanGGOLiN's RGP clustering and projection recover known resistance-island structure. Spot 47 splits into 56 RGP clusters. In dog isolate ABO21-A003, the RGP with the most AMR genes maps to spot 31, the AbGRI2 island.

   At max grr 0.8, spot 47 gives 56 RGP clusters, close to the 53 genetic configurations described by Bi et al. ABO21-A003 is not in the pangenome; after projection it had four RGPs with AMR genes. Three fall in spots 7, 11 and 47. The fourth, CP136181.1 RGP 5, falls in spot 31 and matches AbGRI2 (reported by André et al.), with three blaTEM1 and two aphA1 copies. · PanGBank use case