Large scale application to BGCs from Streptomyces
We used antiSMASH (v8.0.3) to profile 43,182 BGCs across 1,353 Streptomyces chromosomes labeled as complete on NCBI. Afterwards, codoff v1.2.3 was used to assess the Discordance Percentile of BGCs to their genomic contexts. Because research has shown BGCs are enriched on the tails of Streptomyces chromosomes (e.g. Lorenzi et al. 2021, van Bergeijk and Terlouw et al. 2020, and Jørgensen et al. 2024) and these regions can often undergo horizontal transfer (e.g. Thibessard and Leblond 2014., Tidjani et al. 2019, and Lorenzi et al. 2021), we looked at how the distribution of Discordance Percentile for BGCs changed as a factor of genome localization. Specifically, we regarded the center of complete linear Streptomyces chromosomes as their origin of replication (this is a proxy - usually Streptomyces chromosomes are not split in half and symmetrical) and measured the distance of BGCs to the scaffold center.
A 2d-histogram of codoff Discordance Percentile vs distance to center of scaffold across all BGCs revealed that BGCs closer to the conserved center of chromosomes had more concordant codon usage to the genome-wide profile than BGCs further away (in the tails of the chromosomes). Given the findings from past studies referenced above, this result is thus in line with expectations. It also revealed that overall, most BGCs exhibit concordant codon usage profiles to the genomes they were found in - in line with views that BGCs are mostly evolving vertically (e.g. McDonald and Currie 2017 and Chase et al. 2021)
