Stay golden!

With a plush mane of vibrant orange fur, the resemblance of the golden lion tamarin (Leontopithecus rosalia) to an actual lion stops there. While the golden lion tamarin is the largest of the four tamarins species, adult monkeys are only 15-25 centimeters tall and weigh around 400-800 grams [1]. Native to the coastal forests of Eastern Brazil, the wild population of golden lion tamarins has deceased due to drastic habitat loss. A survey in 2018 found the wild population to be around 3,200 individuals [2]. Thanks to breeding and reintroduction programs at zoos around the world, this number has risen from the previous estimate of 1,400 individuals in 2015.

Golden lion tamarin by Tambako the Jaguar, [CC BY-ND 2.0], via flickr.com

Golden lion tamarins live in troops of 2-8 monkeys, consisting of a breeding pair and their offspring. The commonly give birth to twins, occasionally having triplets and quadruplets [3]. They're very vocal, communicating with each other via chirps, screams, and yelps. In the wild, golden lion tamarins will sleep in new dens in hollow trees every night. This is likely a survival tactic to prevent predators from tracking them [4].

Today, we release the genome assembly of the golden lion tamarin, Leontopithecus rosalia. This is a $1K genome assembly with a scaffold N50 = 121 Mb and a contig N50 = 56 Kb. For assembly procedure details, please see our Methods page. Many thanks Coari from the Houston Zoo for providing the sample for this genome assembly. Read more about Coari and her partner Zuno in this blog post by the Houston Zoo!

Check out below how the chromosomes in the new assembly relate to those of the white-tufted-ear marmoset Callithrix jacchus and human. For comparison with the marmoset we used the recent genome assembly from McDonnell Genome Institute at Washington University, here, and the human genome assembly used is hg38 (GRCh38.p13), by the Genome Reference Consortium.

Whole-genome alignment plots between the golden lion tamarin chromosome-length genome assembly (Leontopithecus_rosalia_HiC) and that of the white-tufted-ear marmoset (Callithrix_jacchus_cj1700_1.1).

Whole-genome alignment plots between the golden lion tamarin chromosome-length genome assembly (Leontopithecus_rosalia_HiC) and the human genome (GRCh38).

This is the 11th primate genome the DNA Zoo has released! Interested in more New World primates? Check out, e.g., the assembly pages for the pygmy marmoset and the Bolivian squirrel monkey.

Perch Perfect

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).

Photo Description - Golden Perch (Macquaria ambigua) Photo Credit - www.petwave.com.au

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.

Pig deal of a turtle

The Pig-nosed turtle (Carettochelys insculpta) is the sole surviving member of its entire family, Carettochelyidae, and sits alone on a branch of the tree of life reaching back around 140 million years. That is more than 70 million years before the extinction of the dinosaurs!

Photo Description: The Pig-nosed turtle (Carettochelys insculpta) Photo credits: Photograph by Wilth licensed under CC BY-NC-SA 2.0 [Source link: https://search.creativecommons.org/photos/22e0f3d2-8a1d-4ca6-bf49-c9cd69553cca]

This strange turtle has a large leathery shell 60-70 cm with no distinct scutes and has a long, fleshy snout with large nostrils, much like that of a pig (hence the common name of the species). This unique freshwater turtle has many unusual morphological, ecological and behavioural characteristics. Unlike other freshwater turtles, the pig-nosed turtle has broad paddle-like flippers, each with two claws, resembling those of a sea turtle more than a freshwater species [1].

The pig-nosed turtle is a relict both evolutionarily and geographically, with its current distribution likely reflecting a previous era when Australia was connected to New Guinea [2]. In Australia, the pig-nosed turtle is an endemic of only a few rivers within the Northern Territory, while it has a much greater distribution across much of southern New Guinea. The increased commercial activity across its range in New Guinea is bringing the species into closer contact with humans. The species is threatened by increased demand for individuals and eggs, for both food and the international pet trade [3]. Livestock, feral animals and agriculture also threaten the habitat of the species in Australia [4].

Today, we share the chromosome-length upgrade to the publicly available draft Carettochelys_insculpta-1.0 (GCA_007922185.1) generated by Brad Shaffer (University of Los Angeles), Patrick Minx (Washington University School of Medicine) and Peter Scott (West Texas A&M University).

The specimen that was used for the upgrade was collected by Matthew Young in collaboration with the Njanjma Rangers, traditional owners of West Arnhem, and was supported by funding from the Holsworth Wildlife Research Endowment Fund under the supervision of Arthur Georges at the University of Canberra, Australia. This effort has been supported by The Australian Amphibian and Reptile Genomics Initiative (AusARG), an initiative of Bioplatforms Australia building genomic resources for thorough understanding of evolution and conservation of Australia’s unique native amphibians and reptiles that are now under threat, through climate, disease or habitat modification.

The Hi-C work for the chromosome-length upgrade was supported by resources provided by DNA Zoo Australia, The University of Western Australia (UWA) and DNA Zoo, Aiden Lab at Baylor College of Medicine (BCM) with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.

Decoding the genetic blueprint of this endangered species with the addition of chromosome conformation scaffolding will assist in many ways with its conservation and management. Wildlife trafficking for the illegal pet trade and traditional medicines is a concerning threat for the persistence of wild populations of pig-nosed turtles. This will also facilitate developing wildlife forensics resources for the assignment of provenance of trafficked individuals to their source populations, to combat the illegal trade and to aid conservation work repatriating seized pig-nosed turtles.

The following people contributed to the Hi-C chromosome-length upgrade of the project: Erez Aiden, Olga Dudchenko, Ashling Charles & Parwinder Kaur.

Citations

1. Cogger, H.G. 2018. Reptiles and Amphibians of Australia. CSIRO Publishing, Canberra Australia.

2. Cogger, H.G. & Heatwole, H. (1981). The Australian reptiles: Origins, biogeography, distribution patterns and island evolution. Monographia Biologicae 41:1331-1373.

3. Shepherd, C.R., Gomez, L. & Nijman, V. (2020). Illegal wildlife trade, seizures and prosecutions: a 7.5-year analysis of trade in pig-nosed turtles Carettochelys insculpta in and from Indonesia. Global Ecology and Conservation. 24, p.e01249.

4. Eisemberg, C., van Dijk, P.P., Georges, A. & Amepou, Y. (2018). Carettochelys insculpta. The IUCN Red List of Threatened Species 2018: e.T3898A2884984. https://dx.doi.org/10.2305/IUCN.UK.2018-2.RLTS.T3898A2884984.en. Downloaded on 08 April 2021.