First nuclear genome assembly of an extinct moa species, the little bush moa (Anomalopteryx didiformis)

High throughput sequencing (HTS) has revolutionized the field of ancient DNA (aDNA) by facilitating recovery of nuclear DNA for greater inference of evolutionary processes in extinct species than is possible from mitochondrial DNA alone. We used HTS to obtain ancient DNA from the little bush moa (Anomalopteryx didiformis), one of the iconic species of large, flightless birds that became extinct following human settlement of New Zealand in the 13th century. In addition to a complete mitochondrial genome at 273.5X depth of coverage, we recover almost 900 Mb of the moa nuclear genome by mapping reads to a high quality reference genome for the emu (Dromaius novaehollandiae). This first nuclear genome assembly for moa covers approximately 75% of the 1.2 Gbp emu reference with sequence contiguity sufficient to identify 87% of bird universal single-copy orthologs. From this assembly, we isolate 40 polymorphic microsatellites to serve as a community resource for future population-level studies in moa. We also compile data for a suite of candidate genes associated with vertebrate limb development. We find that the wingless moa phenotype is likely not attributable to gene loss or pseudogenization among this candidate set, and identify potential function-altering moa coding sequence variants for future experimental assays.