Abstract
Data deposition to NCBI GenomesThis Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession AMXX00000000 (SMACv1.0, unscaffolded genome assembly). The version described in this paper is the first version (AMXX01000000). The scaffolded assembly (SMACv1.1) has been deposited at DDBJ/EMBL/GenBank under the accession AOUJ00000000, and is also the first version (AOUJ01000000). 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 14,405 nuclear gene annotation models, their predicted transcripts and proteins, and a complete mitochondrial genome. Comparative analyses involving the scarlet macaw, chicken, and zebra finch genomes revealed high levels of nucleotide-based conservation as well as evidence for overall genome stability among the three highly divergent species. Application of a new whole-genome analysis of divergence involving all three species yielded prioritized candidate genes and noncoding regions for parrot traits of interest (i.e., speech, intelligence, longevity) which were independently supported by the results of previous human GWAS studies. We also observed evidence for genes and noncoding loci that displayed extreme conservation across the three avian lineages, thereby reflecting their likely biological and developmental importance among birds.
Highlights
Despite the biological importance of numerous non-model and non-agricultural species worldwide, current research programs for many of these species include minimal genome-wide sequence and polymorphism data, thereby limiting the implementation of genomic approaches for addressing biological questions in these species [1]
When applied to scarlet macaw metaphase spreads, individual chicken chromosome paints hybridized predominantly to a single macrochromosome pair, with the exception of GGA1 and GGA4, which hybridized to three and two scarlet macaw chromosomes, respectively (Figure 2). These results are compatible with Zoo-FISH experiments conducted between chicken and a variety of other avian species where a high degree of conserved synteny has been observed for the macrochromosomes, with the exception that GGA1 and GGA4 each tend to share homology with 2 or 3 chromosomes in other bird species [31]
Perhaps the most interesting results obtained from our Zoo-FISH experiments are the complex rearrangements associated with scarlet macaw macrochromosomes AMA6 and AMA7 (Figure 2), which support the hypothesis that translocations, fusions, and intragenomic rearrangements are major factors associated with karyotype evolution among parrots (Psittaciformes) [35]
Summary
Despite the biological importance of numerous non-model and non-agricultural species worldwide, current research programs for many of these species include minimal genome-wide sequence and polymorphism data, thereby limiting the implementation of genomic approaches for addressing biological questions in these species [1]. The avian order Psittaciformes is but one example of an underserved biological group, with some genomic resources that have recently become available via completion of the Puerto Rican parrot genome (Amazona vittata) [2], and the Budgerigar (Melopsittacus undulatus budgerigar) sequencing initiative (http:// aviangenomes.org/budgerigar-raw-reads/). The conservation status of this family has strongly catalyzed research in many important biological areas including phylogenetics, population genetics, natural history, nutrition, and conservation biology [10,11,12,13,14]
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