SMRT sequencing the ‘Alalā genome!

Post date: Nov 18, 2015 8:13:49 PM

Our poster abstract for the 2016 Plant and Animal Genome (PAG) conference is now online here, which means I can finally post some details about current and upcoming research!

The ‘Alalā is also known as the Hawaiian crow (Corvus hawaiiensis). It is endemic to Hawai‘i, and is the only surviving lineage of the crow family, Corvidae, in all the Hawaiian Islands. Fossil evidence suggests there were historically 3-6 species or subspecies across the islands (e.g. Culliney et al. 2012), but the ‘Alalā may always have been restricted to Hawai‘i Island (a.k.a. the Big Island). By the 1990s, the species had declined to less than 20 individuals due to a variety of factors, and today it is "extinct in the wild". However, thanks to incredible efforts and collaborations, just under 120 birds now exist in two captive breeding facilities maintained by San Diego Zoo Global. Now, finally, after many years of very hard work by very many people, the ‘Alalā may be ready to go home - back to the wild. A reintroduction experiment is scheduled to begin in 2016!

Which brings me back to our genome project. The goal of our genomic research is to aid recovery efforts for the ‘Alalā, by providing an essential tool to evaluate and manage the genetic variation remaining to this critically small population. In particular, single molecule real-time (SMRT) sequencing by PacBio is expected to generate very long reads for whole genome shotgun sequencing. With read lengths expected to average 10-15 kb, this will allow contiguous draft assemblies of contig N50 up to 5 Mb! Such detailed assemblies will help us focus our population genetic studies on complex genes associated with immunity and behavior, so that we can help to reestablish the ‘Alalā back into the wild.

An ‘Alalā in the wild. Photo from Wikipedia.