Question: Why is the new platypus assembly (11 years 'newer') not chromosome level?
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gravatar for Luis Nassar
3 months ago by
Luis Nassar100
Luis Nassar100 wrote:

I often see this trend on GenBank assemblies where you have older chromosome level assemblies and then newer PacBio/illumina assemblies which are not.

Are these older assemblies actually better, or do we have more stringent requirements on what to call 'chromosome level' now? I would think with the improvement of technology the newer assemblies would be best.

In this case I'm looking at the platypus assemblies. Here is a 2007 Washington University chromosom level assembly: https://www.ncbi.nlm.nih.gov/assembly/GCA_000002275.2/

And here is the latest 2018 BGI scaffold level assembly done with PacBio/illumina: https://www.ncbi.nlm.nih.gov/assembly/GCA_002966995.1/#/def

Another example: African malaria mosquito from 2006: https://www.ncbi.nlm.nih.gov/assembly/GCF_000005575.2 Then contig level from 2016 with PacBio: https://www.ncbi.nlm.nih.gov/assembly/GCA_001542645.1

sequencing assembly genome • 214 views
ADD COMMENTlink written 3 months ago by Luis Nassar100
2

That is a difficult question to answer. Part of the reason could be that there are just not that many people working on that organism to have enough resources available to reconcile new assemblies with an original.

New assemblies are put out by companies as demonstration of their technology and are available for people to use as they please. Companies are not really interested in delving deep into finishing them and they may not be better than originals (in terms of placement).

As technology changes for better over time the resulting assemblies should be of better quality but someone (or a group) needs to spend the time to sit down and go through the necessary comparisons/validation. This can take time and a lot of effort (and would likely not result in a publication). While not quite the same thing, this is similar to $1K genome needing $100K in annotation.

ADD REPLYlink modified 3 months ago • written 3 months ago by genomax67k

Thank you for the answer. I wasn't aware of how much work went into the assembling step past just running the pipeline. But it does make sense that many of these 'older' chromosome level assemblies had groups that were willing to dedicate much more time to the process as it led to publications at that time. Also as they were the first of the species at during that time.

ADD REPLYlink written 3 months ago by Luis Nassar100
2

I think you might be putting to much focus on the "chromosome level" label.

Those assemblies are considered as chromosome NOT because they have the nearly full chromosomes sequenced but because the sequence assembly was taken to a 'next' level by using other types of information that basically assigns sequences to biological chromosomes (typically genetic or fish maps) .

On the sequence level those new assemblies are much more complete than the older ones, they just did not take the additional effort (as also pointed out by genomax ) to construct those (pseudo) chromosome level assembly

ADD REPLYlink written 3 months ago by lieven.sterck4.7k
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