Inquiry about the coding density equation about bakta

[oschwengers]

Hi Ahmed,
Of course, short/long read sequencing indeed can have a strong impact on assembly lengths. Especially short read draft assemblies can suffer from too many contig edges which make it very difficult to detect all CDS proximate or even spanning contig edges. The coding density is only summing up all bases that are part of an annotated genome feature divided by the genome length.
I hope this helps. Otherwise, can you elaborate a bit more?

[AhmedElsherbini]

Thank you Oliver for your response.

Summing up all the bases of the annotated genome is (~the sum of the whole length of CDS) / the sum of the total contigs length, right?
if we focus on long read assemble genomes and NO statistical difference between the two species's CDS number, nor total length,
so my guess now for the difference in coding density, could be longer CDS in the more species with high density, or pseudogenes, / transposons (they are short in lenght anyway) in the less dense species. does it make sense now?

Best,
Ahmed

[oschwengers]

Hi, the coding density is not limited to CDS but comprises all genomic features, e.g. non-coding RNA genes, regulatory elements, DNA motifs, etc.

Regarding your question, I guess in theory yes, that could be, but I'd be rather reluctant to use these kind of statistics. I'd rather directly compare certain genes presence/absence, etc.

[AhmedElsherbini]

Absolutely, you are right.

I followed this with tools like Panaroo and PPanGGolin for gene presence/absence comparison. Mobilome ( insertion elements ) is the main thing being enriched in the sister species with lower coding density.

Just, I wanted to investigate the causality of this coding density, as I get a lot of questions regarding this 2 % difference.