pangenome openness

Edge evidence

• horizontal gene transfer causes pangenome openness biolink:causes

  HGT continually adds new accessory genes, keeping the pangenome open.

  • DOI:10.1073/pnas.0506758102 Tettelin et al. introduce the pan-genome concept distinguishing open vs closed pangenomes.
• pangenome openness associated with accessory gene pool biolink:associated_with

  Open pangenomes accumulate large accessory gene pools across strains.

  • DOI:10.1038/nmicrobiol.2017.40 McInerney et al. review the ecological and population drivers of pangenome openness.
• plasmid enables horizontal gene transfer RO:0002327

  Plasmids are mobile vehicles for accessory genes, increasing opportunity for gene acquisition.

  • DOI:10.1099/mgen.0.001021 Gene gain and loss mediated by mobile genetic elements including plasmids.
• prophage promotes pangenome openness RO:0002213

  Prophage-associated gene flux contributes to recent gain/loss and accessory genome expansion.

  • DOI:10.3390/microorganisms12050986 Prophages, integrases, and transfer/mobile elements identified as main drivers of pangenome openness.
• gene gain and loss dynamics shapes pangenome openness

  Open/closed behavior reflects balance of ongoing gene gain versus loss across sampled lineages.

  • DOI:10.1101/2022.04.23.489244 HGT and resultant gene gain and loss dynamics are central drivers of pangenome composition.
• core gene fraction negatively associated with pangenome openness

  A larger conserved core leaves less flexible accessory fraction; empirically anticorrelated with openness.

  • DOI:10.3390/microorganisms12050986 Strong inverse correlation between core gene percentage and openness coefficient (corr = -0.910).
• rare gene fraction positively associated with pangenome openness

  A higher proportion of rare genes indicates continued acquisition and non-saturation of the pangenome.

  • DOI:10.3390/microorganisms12050986 Positive correlation between rare gene percentage and openness coefficient (corr = 0.742).
• sampling bias biases estimate of apparent pangenome openness

  Apparent openness can reflect which genomes were sampled rather than true HGT dynamics.

  • DOI:10.1101/2022.04.23.489244 Gene accumulation curves can be misleading because they may reflect sampling temporal/diversity bias.
• annotation error biases estimate of apparent pangenome openness

  Misannotation inflates or deflates presence/absence calls and can misclassify open/closed status.

  • DOI:10.1101/2022.04.23.489244 Higher rates of annotation error can lead to incorrect estimates of whether a pangenome is open or closed.