Dear all,

I found this an interesting read:

Cooley, N.P., Wright, E.S. Many purported pseudogenes in bacterial genomes are bona fide genes. BMC Genomics 25, 365 (2024). https://doi.org/10.1186/s12864-024-10137-0
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-10137-0

It's actually more about assembly quality (and its factors) than about pseudogenes as such. I like their idea that pseudogene count could be used as an indicator of genome quality. Makes sense if you consider that it is biologically improbable to find a pseudogene where the closest reference has a functional gene.

Marco