The golden perch (Macquaria ambigua) is one of the most widespread and abundant large native fishes in the lowlands of the Murray-Darling Basin of Eastern Australia and represents an important recreational and commercial fisheries species (1).
This native fish covers approximately 2,250,000 km2 and its distribution exposes the species to a wide variety of climatic and habitat conditions, ranging from isolated groundwater-fed waterholes to broad lowland river channels and streams (2). Distribution and abundance have been affected by environmental changes such as those caused by dams and weirs which have affected stream flows and water temperature regimes and acted as barriers to extensive migrations of adult fish.
Golden perch are medium-bodied and long-lived fish, reaching around 550mm total length and 27 years of age in river habitats. The golden perch is also considered a periodic species. Although they may be strongly site attached for long periods, the golden perch can undertake migrations of tens to thousands of kilometres across a range of river conditions at certain times. They are also highly fecund, with females producing more than half a million eggs (3). The golden perch is reported to spawn between October and April when water temperatures are above 23 degrees Celsius or when warm temperatures coincide with a rise in water level (1).
It is a species member of the threatened "Lowland Riverine Fish Community of the Southern Murray Darling Basin" which is listed under the Flora and Fauna Guarantee Act (1988) as its natural range and abundance has declined since European settlement. It is also listed as part of the endangered Lower Murray River ecological community (NSW Fisheries Management Act, 1994) (4).
To support ongoing management and conservation efforts, DNA Zoo has been working with James O’Dwyer, Dr Nick Murphy and Dr Katherine Harrisson at La Trobe University, Melbourne, to obtain a chromosome-length assembly genome of the golden perch. In 2020 we also produced a chromosome-length assembly of the golden perch’s sister species the Macquarie perch.
The chromosome-length assembly we share today is based on the draft assembly available on NCBI generated by Han Ming Gan, Deakin Genomics Centre. The draft genome assembly of the Murray Darling Basin golden perch lineage was created using MaSuRCA v. 3.2.6 (Zimin et al. 2013), using Oxford Nanopore MinION reads polished with short-insert size Illumina NovaSeq reads.
The above draft was scaffolded to 24 chromosomes with 100,680,198M Hi-C reads generated by DNA Zoo labs using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). See our Methods page for more details.
The sample for Hi-C was kindly provided by Matthew McLellan and Dr Meaghan Duncan from the Narrandera Fisheries Centre (NSW Department of Primary Industries). The Hi-C work was supported by resources provided by DNA Zoo Australia, The University of Western Australia (UWA), La Trobe University team with funding from Australian Research Council-funded project DE190100636. We gratefully acknowledge the computational support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.
The following people contributed to the Hi-C chromosome-length upgrade of the project: Erez Aiden, Olga Dudchenko, Ashling Charles & Parwinder Kaur.
Blog by: Ashling Charles, Katherine Harrisson, James O’Dawyer and Parwinder Kaur.
Citations
1. Ebner, B. C., O. Scholz, and B. Gawne. "Golden perch Macquaria ambigua are flexible spawners in the Darling River, Australia." (2009): 571-578.
2. Faulks, Leanne K., Dean M. Gilligan, and Luciano B. Beheregaray. "Clarifying an ambiguous evolutionary history: range‐wide phylogeography of an Australian freshwater fish, the golden perch (Macquaria ambigua)." Journal of Biogeography 37.7 (2010): 1329-1340.
3. Wright, Daniel W., et al. "Size, growth and mortality of riverine golden perch (Macquaria ambigua) across a latitudinal gradient." Marine and Freshwater Research 71.12 (2020): 1651-1661.
4. O'connor, J. P., D. J. O'mahony, and J. M. O'mahony. "Movements of Macquaria ambigua, in the Murray River, south‐eastern Australia." Journal of Fish Biology 66.2 (2005): 392-403.