What is the interpretation of sequence enrichment in whole genome sequencing?

Question

[marongiu.luigi]

While in RNAseq an enrichment of sequences is associated with increased gene expression, what is the interpretation of an enrichment of sequences in whole genome sequences?

In particular, what does it mean if one does not get whole genomes but only a few genes?

It looks to me that there is a fragmentation of genomes. Does this mean that there are more cells or micro-organisms containing these genes (then why there is no the whole genome?) or is it just an artifact?

Thank you

[GenoMax]

Based on what you wrote below (which should have been in the original question)

I am looking at a paper that used long-read sequencing (PacBio) on the virome of fecal human samples.

It may simply mean that certain kind of virii are present in greater numbers than others in the sample. Depending on shared genes. those can be "enriched" in the data.

[lieven.sterck]

back in the days, and I'm thus not sure this is currently still common to do, these 'enrichments' did occur to enrich the genic regions of the genome. This was particularly done for very large genomes which were, given the techniques available at the time, too difficult or impossible to sequence. To bypass this people tended to enrich for the genic regions and mainly sequence those and thus dropped TE rich regions, telomores, centromers ...

Answer 1

[Mensur Dlakic]

There is no such a thing as gene enrichment during the assembly. All cells have all the genes.

There are many reasons why some portions of the genome will not get assembled. Some of it is the randomness of the assembly process. Repetitive sequences will also hamper the assembly. For reasons we do not always understand, there are genomic regions that do not amplify well, and they won't assemble either because of low coverage.

You may want to read the paper below and similar articles:

https://pubmed.ncbi.nlm.nih.gov/32937018/

Answer 2

[young_bioinformatician]

Hi,

I didn't fully understand your explanation, but if you observe duplicate genes, this could indicate contamination or evolutionary processes. If the organism is bacterial and the genes in question are likely to be subject to evolutionary pressures, you might consider the possibility of gene duplication events. Otherwise, the duplicates could be a result of contamination. The fragmentation could be related to sequencing. However, you need to explain your situation better to make sense of it. Which sequencing technology, which organism, which assembly program?

[marongiu.luigi]

I am looking at a paper that used long-read sequencing (PacBio) on the virome of fecal human samples. There is evidence of gene enrichment, but -- as you pointed out -- the viruses will contain all genes since WGS is not RefSeq analysis. Thus, does the statement of gene enrichment make sense or is it an issue of contamination?