beta globin locus in rheMac8 assembly

[Humbert, Olivier M]

Greetings,
I have been analyzing the beta globin locus from the newest genome assembly of rhesus macaque rheMac8.
As compared to the older genome assembly rheMac2 or rheMac3, I detected a deletion of about 5kbp in the region following the gamma globin 2 gene (HbG2), which should normally comprise the gene gamma globin gene 1 (HbG1).
Since HbG2 and HbG1 are highly conserved, I was wondering if this deletion came up from a mistake made in the genome assembly or whether it has any biological relevance.

Any feedback on this would be appreciated!

Best,
Olivier Humbert

--
Olivier Humbert, PhD
Fred Hutchinson Cancer Research Center
Clinical Research Division - Kiem Lab
1100 Fairview Ave N, Seattle, WA 98109
Mailstop: D1-100
P: 206-667-6053
ohum...@fhcrc.org

[Matthew Speir]

Hi Olivier,

Thank you for your question about the Rhesus (rheMac8) assembly in the
UCSC Genome Browser.

The UCSC Genome Browser displays genomic assemblies produced by outside
contributors. Here is the GenBank page for the rheMac8/BCM Mmul_8.0.1
assembly: https://www.ncbi.nlm.nih.gov/assembly/2715158. For questions
about the construction of the assembly itself, you should contact the
assembly providers, the Baylor College of Medicine Genome Sequencing
Center:
https://www.hgsc.bcm.edu/non-human-primates/rhesus-monkey-genome-project.

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.

Matthew Speir
UCSC Genome Bioinformatics Group