UH Hilo genetics research team releases unprecedented genome assembly for endangered Hawaiian crow

Led by biologist Jolene Sutton, assistant professor at UH Hilo, the research team created a genome assembly that provides critical insights into inbreeding and disease susceptibility of the ‘alalā.

By Susan Enright.

‘Alalā (Hawaiian crow) on perch in large enclosure.
‘Alalā (Hawaiian crow). Photo credit San Diego Zoo Institute for Conservation Research.
Jolene Sutton
Jolene Sutton

The extraordinary findings of a genetic research team at the University of Hawai‘i at Hilo studying the ‘alalā (Hawaiian crow), one of the world’s most endangered bird species, are published in the current issue of the journal Genes.

Biologist Jolene Sutton, an assistant professor at the University of Hawai‘i at Hilo who specializes in evolutionary genetics, led the team of UH Hilo colleagues Martin Helmkampf, a research scientist with the tropical conservation biology and environmental science program, and Renee Bellinger of the Conservation Genomics Research Group, along with collaborators from the Hawai‘i Endangered Bird Conservation Program, San Diego Zoo Global, and Pacific Biosciences, a Silicon Valley company that provides sophisticated genomic analysis systems.

Martin Helmkampf
Martin Helmkampf

The article, “A high-quality, long-read de novogenome assembly to aid conservation of Hawaii’s last remaining crow species,” describes the high-quality reference genome that was generated to assist recovery efforts for the ‘alalā.

“The quality of this assembly places it among the very best avian genomes assembled to date, comparable to intensively studied model systems,” according to a post on the UH Hilo Biology Department News website.

Renee Bellinger
Renee Bellinger

Researchers and conservationists are currently using this resource to better understand genetic diversity in the ‘alalā, and to develop tools that will help inform strategic pairings as part of the conservation-breeding program. This genome assembly is now publicly available.

The paper is the cover story of the August 2018 issue of Genes, a special issue on conservation genetics and genomics.

PacBio reports:

Led by Jolene Sutton, assistant professor at the University of Hawaii, Hilo, the team created an assembly which has provided critical insights into inbreeding and disease susceptibility. They found that the ‘alalā genome is substantially more homozygous compared with more outbred species, and created annotations for a subset of immunity genes that are likely to be important for conservation applications.

As reported in the latest issue of Genes — and featured on its cover — the quality of the assembly places it amongst the very best avian genomes assembled to date, comparable to intensively studied model systems.

“Such genome-level data offer unprecedented precision to examine the causes and genetic consequences of population declines, and to apply these results to conservation management,” the authors state. “Although pair selection and managed breeding using the pedigree has kept the inbreeding level of the ‘alalā population at a relatively low level over the past 20 years, the intensive and ongoing conservation management of the species requires a more detailed approach.”


Story by Susan Enright, public information specialist for the Office of the Chancellor and editor of UH Hilo Stories. She received her bachelor of arts in English and certificate in women’s studies from UH Hilo.

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