When can you called a genome closed/no longer draft?
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3.8 years ago

What defines a closed genome?

I suppose we never know if we have everything (we don't know, what we don't know) - so when can we say a genome is complete/finished/closed?

Is it when we have a single sequence for each DNA molecule?

It's a very basic question, but I cannot seem to find a hard defintion/explanation anywhere.

assembly gen • 873 views
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3.8 years ago

we have a single sequence for each DNA molecule?

We would typically say "one continuous string of DNA sequence without gaps", i.e. 1 contig per chromosome.

It is easier to imagine this for bacteria with very small genomes, maybe this article (especially its supplement!) will help you to get a better understanding of this. I assume you've read Shannon Begley's account (or other's) about why complete sequencing of mammalian genomes hasn't happened yet

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thank you very much, that's super helpful!

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and just because seeing it reminded me of your post, here is a super recent manuscript announcing the first complete sequencing of the human chromosome 8: see on Biorxiv

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3.8 years ago
GenoMax 143k

There was an effort to (re)define these standards at the start of next generation sequencing.

For higher Eukaryotic genomes we may not have "finished" genomes for a long while. Partly because current sequencing technologies are still not able to reliably sequence repeat/difficult regions (complete sequence of human X chromosome was just published, almost 2 decades after human genome was "done").

Like many software projects, a genome reaches v.1.0 status and then keeps evolving via major genome builds over time.

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and then keeps evolving

I see what you did there. :D

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thank you! Very helpful

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