Meeting Abstract
118.6 Monday, Jan. 7 ANALYSIS OF COPY NUMBER VARIATION ACROSS AFRICAN CICHLID GENOMES BEZAULT, E*; RENN, S; Reed College, Portland (OR); Reed College, Portland (OR) ebezault@reed.edu
Structural variation has been shown to be a major source of evolutionary novelty. The African cichlids, known as one of the most explosive example of adaptive radiations, offer an excellent model to study the genetics of adaptation and diversification in Vertebrates. The sequencing of the genome of 5 species and their annotation (Cichlid Genome Consortium & Broad Institute) provide key genomic resources to study their evolution. The interest of array-based Comparative Genomic Hybridization (aCGH) to study Copy Number Variation (CNV) is widely accepted, yet challenging when conducted across distantly related taxa. To analyze CNV at the whole genome level across African cichlids lineages, we have developed a high-density multi-species microarray platform (12plex 135K NimbleGen array). To ensure high hybridization efficiency at a wide phylogenetic level among African cichlids, the probes have been selected based on the consensus sequence from the multiple genome alignment of the 5 cichlid species sequenced. Furthermore this exon-focus array includes 70K probes targeted on the EnsEMBL tilapia genome annotation, specifically representing ~24K predicted-genes. At the overall genome level, this array presents an average probe interval of 6Kb, which could expectedly allow the detection of structural variation of 30-60Kb. We first used this array to analyze CNV among the 5 species previously sequenced, representing 3 major evolutionary lineages of African Cichlids: Oreochromines, Neolamprologines and Haplochromines, with representatives of 2 different lake radiations and 1 non-radiating riverine species. We therefore compared the results obtained from aCGH with the ones derived from genome sequencing. The aCGH approach will be extended at population level as well as broader phylogenetic scale within African cichlids, to identify CNV associated with adaptation and diversification.
