A nuclear genome assembly of an extinct flightless bird, the little bush moa

Abstract

We present a draft genome of the little bush moa (Anomalopteryx didiformis) - one of approximately nine species of extinct flightless birds from Aotearoa, New Zealand - using ancient DNA recovered from a fossil bone from the South Island. We recover a complete mitochondrial genome at 249.9X depth of coverage and almost 900 Mb of a male moa nuclear genome at ~4-5X coverage, with sequence contiguity sufficient to identify more than 85% of avian universal single-copy orthologs. We describe a diverse landscape of transposable elements and satellite repeats; estimate a long-term effective population size of ~240,000; identify a diverse suite of olfactory receptor genes and an opsin repertoire with sensitivity in the UV range; show that the wingless moa phenotype is likely not attributable to gene loss or pseudogenization; and identify potential function-altering coding sequence variants in moa that could be synthesized for future functional assays. This genomic resource should support further studies of avian evolution and morphological divergence.