Conservation genomics of a critically endangered Hawaiian bird: A high quality genome assembly of the ‘alala will assist in population management and reintroduction

The ‘alalā, a species of crow endemic to the Hawaiian islands, is critically endangered and extinct in the wild. Its former role in Hawaiian forest ecosystems and significance in native Hawaiian culture elevate interest in preventing its extinction and restoring sustainable wild populations. Following years of intensive management and captive propagation, a reintroduction experiment is now scheduled for September 2016.

Using PacBio SMRT® sequencing, we were able to assemble a 1.09 GB genome assembly in 1,026 contigs with an N50 of 11 Mb using a single 30 kb insert library size selected with a 20 kb cut-off. Ninety-eight percent (98%) of CEGMA genes with chicken orthologs had alignment to the ‘alala assembly, of which 91.1% are fully intact.  The data were collected using P6-C4 chemistry and 6 hour movies yielding a readlength N50 of 18.2 kb.

Our immediate plans for the assembly include conducting studies on MHC and other functional loci, to elucidate the molecular basis of traits associated with inbreeding depression, and for assessing variation at a suite of candidate genes associated with traits that will be potentially important for successful reintroduction.

The availability of a high-quality reference genome, tools for evaluating structural variation and traits associated with fitness, as well as neutral loci, will allow evaluation of conservation breeding and reintroduction efforts from a genome-wide perspective. To date, this is feasible for a small number of species, but efforts for the ‘alalā and other species with significant genomic resources will issue a new era in conservation management.