A Multi-Platform Draft de novo Genome Assembly and Comparative Analysis for the Scarlet Macaw (Ara macao)

Strong biological interest in traits such as the acquisition and utilization of speech, cognitive abilities, and longevity catalyzed the utilization of two next-generation sequencing platforms to provide the first draft de novo genome assembly for the large, new world parrot Ara macao (Scarlet Macaw).  Despite the challenges associated with genome assembly for an outbred avian species, including 951,507 high quality putative single nucleotide polymorphisms, the final genome assembly (> 1.035 Gb) includes more than 997 Mb of unambiguous sequence data (excluding N’s). Cytogenetic analyses including ZooFISH revealed complex rearrangements associated with two scarlet macaw macrochromosomes (AMA6, AMA7), which supports the hypothesis that translocations, fusions, and intragenomic rearrangements are key factors associated with karyotype evolution among parrots.  In silico annotation of the scarlet macaw genome provided robust evidence for 15,305 nuclear gene models, their predicted transcripts and proteins, and a complete mitochondrial genome.  Comparative analyses involving the scarlet macaw (A. macao), chicken (Gallus gallus), and zebra finch (Taeniopygia guttata) genomes revealed high levels of nucleotide-based conservation as well as evidence for overall genome stability among the three highly divergent species.