Scientists from CSIRO, Australia’s national science agency, have sequenced the first ever full genome of the rare and elusive Spotted Handfish (Brachionichthys hirsutus) – a critically endangered marine fish endemic to Tasmania.
Once plentiful around Tasmania’s south-east coast the species’ numbers have dwindled. In 1996, it became the first marine fish listed as critically endangered.
Scientists now estimate fewer than 2,000 individuals remain in the wild.
The rapid decline of the Spotted Handfish is attributed to historic fishing practices, coastal development, climate change and the arrival of invasive species.
The genome is a critical tool needed to help conserve the species and took a coordinated effort, led by CSIRO’s Applied Genomics Initiative (AGI).
CSIRO Senior Research Scientist, Dr Gunjan Pandey, said the genome sequence will help ongoing efforts to boost population numbers and monitor genetic diversity.
“The genome helps us understand how an organism functions,” Dr Pandey said.
“It provides a foundation for understanding gene expression in daily life and offers insights into its evolutionary history.
“With the genome, we can assist with species detection, monitor populations, and even estimate the fish's lifespan.”
Principal Investigator, Carlie Devine, who specialises in the conservation and management of the Spotted Handfish, said this rich genetic information will help inform conservation strategy over the long term.
“Conservation measures are expanding to include genetics,” Ms Devine said.
"Recognising a multidisciplinary approach alongside ecology research is essential for effective conservation of threatened species.”
Dr Pandey said the opportunity to sequence the genome of the elusive animal arose when a Spotted Handfish passed away of natural causes in captivity.
“Marine species like the Spotted Handfish are notoriously difficult to work with,” Dr Pandey said.
“The DNA degrades rapidly and becomes contaminated with microorganisms.
“This makes assembling a pure genome extremely challenging.”
The team was able to sequence the complete genome from a small amount of poor-quality DNA, using what’s called a low-input protocol. This was done in collaboration with the Biomolecular Resource Facility at Australian National University.
“We are one of only three teams globally using this protocol,” Dr Pandey said.
“We customised the entire process - from the set-up of the lab to the bioinformatics software - to sequence a high-quality genome from poor-quality DNA.
“What used to take six to twelve months, we can now accomplish in days. This technology holds huge promise for our understanding and conservation of endangered species across Australia and around the world.”
CSIRO scientists have been monitoring the Spotted Handfish since 1997, keeping an eye on nine localised populations within the Derwent Estuary.
CSIRO's multi-pronged approach to conserving the Spotted Handfish includes a captive breeding program, as well as innovative approaches to habitat restoration.
Access the Spotted Handfish genome.
