Comparison of CNVs in Buffalo with Other Species

Using a read-depth (RD) and a hybrid read-pair, split-read (RAPTR-SV) CNV detection method, we identified over 1425 unique CNVs in 14 Water Buffalo individual compared to the cattle genome sequence. Total variable sequence of the CNV regions (CNVR) from the RD method approached 59 megabases (~ 2% of the genome) which was nearly equivalent to the 55.6 megabases of variable sequence found in recent CNV survey of the cattle genome. Genes impacted by CNVs were heavily enriched in immunological and sensory pathways. We further performed experiments of CGH arrays, FISH and qPCR to validate selected CNVs. One CNV impacted gene family, PI3, encodes for the trappin/elafin anti-microbial/immune system modulator protein. The Water Buffalo copy number of the PI3 gene (Average CN: 12) is higher than has been identified in Bos taurus (Average CN: 5) and may result in an increased spectrum of resistance to fungal and bacterial skin and mucus membrane pathogens in Buffalo. Notable gene deletions include the Bos taurus bitter taste receptor (T2R65A) and the neuropeptide FF-amid peptide precursor (NPFF) genes; the latter of which is involved in somatostatin secretion from the pancreas and morphine-induced analgesia. Other cross species comparisons promise to reveal more lineage specific gene family expansions and contractions in Buffalo which will in turn lend more insight into the unique biology of this genus.