Copy Number Variation of CCL3-like Genes Affects Rate of Progression to Simian-AIDS in Rhesus Macaques (Macaca mulatta)
(A) Metaphase FISH image of A431 cell line confirming diploid copy number of two CCL3L1 genes (Note: Therefore using our assay we consider the A431 cell line to have a diploid copy number of four genes since it also contains two copies of CCL3). (B) Whole-genome shotgun read depth analysis showing estimation of CCL3L copy number in the rhesus macaque genome donor as 6 copies per diploid genome based on rheMac2 assembly. Green and orange lines denote shotgun reads aligned to CCL3L region of the January 2006 assembly of the rhesus macaque reference genome with orange lines showing those that likely represent regions of duplications based on the read-depth analysis (See Methods). (C) Interphase FISH image of the MMU2 9133 rhesus macaque cell line, which has an estimated diploid copy number of 10 copies of CCL3L. (D) Validation of rtPCR estimates of CCL3L copy number. Black dots represent rtPCR copy number estimates for the A431 human cell line, the rhesus genome donor, and MMU2 9133 rhesus cell line. Red dots represent an independent estimate of copy number for all three samples based on either FISH or WGS analysis. See supplemental material for additional information regarding the copy number estimation methods.