Greetings
May I kindly know the difference between a genome status of whole genome and of a metagenome, and if a metagenomic sequence can be a whole genome?
Can a metagenome sequence be a complete genome?
A whole genome means that all of its nucleotides are known, and that all chromosomes (usually 1 for prokaryotes) are assembled without interruptions.
A metagenome is usually composed of contigs, which vary in size and number. A small number of large contigs usually means that a metagenome is close to being complete. It is possible, though not very likely, to assemble a whole genome from metagenomic samples. In such a case they would be called whole genomes rather than metagenomes, which means that this designation is related to genome completeness rather than sample origin.
It is possible, though not very likely, to assemble a whole genome from metagenomic samples
I was under the impression that each organism has a genome, and metagenomes are relevant only where a colony of different species co-exists. Am I missing something? I'm unable to understand your statement above.
Sorry about the confusion - I could have been more explicit in my explanation.
I am talking about a metagenome as a super-genome, or a collection of all genomes in a given community. In that sense, collecting a metagenomic sample means having a mix of DNA molecules from various sources, which we sequence in a way that is principally the same as with a single genome. After binning our DNA sequences into groups, we get several metagenome-assembled genomes (MAGs), which I think the OP was referring as metagenome sequences. MAGs assembled from short reads are usually incomplete regardless of coverage depth, as it is too difficult to fully resolve any individual genome from a metagenomic sample. That is what I was trying to state above: from metagenomic samples one doesn't really expect to get even a single complete genome, though it is quite possible to get quite a few near-complete MAGs.
Okay.. thank you so much for the answer. But I thought a whole genome also has contigs because there is where I found that Whole-genome sequence/shotgun: Is a genome composed of more than 1 contigs, that needs to be attached to each other by scaffolding. genome status is a term used in PATRIC to state wether a genome is WGS, complete or partial.
May I kindly know if a sequence of 4000bp qualifies to be a WGS.
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What do you mean by "status"?