Chimp Chromosome 2B - Errors in older assemblies??

[Miller, Ken]

Dear Friends,

   I am attempting to do synteny comparisons  between human chromosome 2 and chimpanzee chromosomes 2A and 2B.  In so doing, I have run across a puzzling aspect of the data. The size of chimpanzee chromosome 2B has been cut in half in the most recent assemblies on the UCSC site.  Specifically:

Version                               Size in bp.                Date     

CGSC 2.1.3/panTro3         247,518,478          Oct. 2010

CSAC 2.1.4/panTro4         247,518,478          Feb 2011

Pan_tro 3.0/panTro5         133,216,015          May 2016

   Is there a reason why the older (2010 and 2011) builds greatly exaggerated the size of chromosome 2B? To add to my confusion, a map of RefSeq genes shows no genes at all on bases 1-100,000,000 of the 2010 and 2011 builds.  By contrast, RefSeq genes are found on the entire length of the 2016 build.

   Does this mean that the 2010 and 2011 builds wrongly included more than 100 million non-existent bases, and that this problem was corrected in the 2016 build?

    Thank you very much for your help!

        Appreciatively,

        Ken Miller

Kenneth R. Miller

Professor of Biology

Brown University

Providence, RI 02912

office: 401-863-3410

https://vivo.brown.edu/display/kemiller

[Jairo Navarro Gonzalez]

Hello Kenneth,

Thank you for using the UCSC Genome Browser and your question about the size of chromosome 2B in chimpanzee.

The reason that there are no RefSeq annotations on bases 1-100,000,000 in panTro4 is due to a large gap at the beginning of the 2B chromosome. Clicking into the annotation on the gap track, we can see that this gap is due to a telomere, which is difficult to assemble since they are made up of repeated segments of DNA. This region was later resolved in panTro5. You can learn more about the panTro5 assembly from the NCBI assembly information page:

https://www.ncbi.nlm.nih.gov/assembly/GCF_000001515.7/

I should note that we do not make the assemblies ourselves, we only display the assembly provided to us by RefSeq. If you have issues with a particular assembly, you will need to take it up with the providers of the assembly. You can find information about who provides each assembly on the Gateway page for the organism:

http://genome.ucsc.edu/cgi-bin/hgGateway?db=panTro4
http://genome.ucsc.edu/cgi-bin/hgGateway?db=panTro5

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro 
UCSC Genomics Institute

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