Meeting Abstract
We aim to address the genomic consequences of adaptive radiation as well as the rapid and repeated speciation in a lineage resulting in extensive ecological diversity. African cichlids present an exciting radiation exhibiting morphological and behavioral diversity. Prior work in the Renn lab employed array-based comparative heterologous genomic hybridization (aCGH) to reveal a large amount of inter- and intra-specific copy number variation events (CNVEs). While next-generation sequencing allows for the sequencing and comparison of a large number of species, the popular short-read sequencing technologies are prone to collapsing reads in repetitive genomic regions, resulting in artificially low CNVE counts. Using the recently published PacBio genome assemblies derived from long-read sequence data for two African cichlid species, Oreochromis niloticus and Metriaclima zebra, we demonstrate that the CNVEs detected by our low-cost aCGH, are better retained by long-read assemblies and more accurately represent true copy number variation. We used BLAST to align our microarray probes to both the Illumina and PacBio genome assemblies for both species and calculated the degree to which the Illumina genome assemblies collapse CNVEs detected using aCGH hybridization ratios. These results support aCGH as a relatively cheap approach to quantify and localize copy number variation.
