PRJNA433423
Ancient DNA sequencing of the extinct little bush moa (Anomalopteryx didiformis)
Researchers from the Royal Ontario Museum and Harvard University have used high-throughput sequencing to recover ancient DNA from the extinct little bush moa to assemble the first reference-based moa nuclear genome assembly. The nine currently recognized moa species are iconic birds of New Zealand that became extinct following human settlement in the 13th century and are best known for the large size of some species and the complete absence of wings in all species. Favorable preservation conditions have allowed moa to be well-studied both morphologically and by PCR-based sequencing of mitochondrial DNA. However, genome-wide nuclear sequences allowed us to rigorously test the phylogenetic relationships within Palaeognathae (the group of birds that contains moa and other flightless ratites such as the ostrich, emu, cassowary, kiwi, rheas, and extinct elephant birds, as well as the volant, or flighted, tinamous), and to investigate patterns of selection for candidate genes with potential roles in limb development associated with losses of flight in birds.  BioProject PRJNA433423 contains the data for the SRA reads, the mitochondrial genome, and the nuclear genome assembly generated using reference-based mapping to a related species (emu, Dromaius novaehollandiae, accession GCA_003342905.1) BioProject PRJNA534317 provides an error-corrected version of the primary genome assembly, where mapDamage2 (Jonsson et al. 2013) was used to recalibrate base quality scores to account for patterns of DNA damage typical of ancient DNA, followed by masking of sites that lacked coverage at minimum BASEQ=20 following recalibration.