• Ragini Mahajan

The Malayan sun bear (Helarctos malayanus) is natively found in parts of Asia, stretching from the Himalayas and the Szechuan region of China to the Malayan peninsula. Their habitats are typically dense with trees, and these bears are famous for being agile and fast tree-climbers! [1]

Belonging to the Ursidae family, they are the smallest bears of their family and are usually under 1.5m tall. To conceal this small size, the normally black colored bears sometimes have a ‘U’ shaped, white patch on their chest that gives the appearance of larger size to predators and attackers. The Malayan sun bear’s walk is often described as unique, as their four legs turn in while walking, obscuring their fairly big paws. [2]

Sun Bear (Helarctos malayanus) by David Lochlin, [CC BY 2.0], via Flickr.com

While the exact population of these bears is not currently known, their numbers are declining as a result of increase deforestation, especially for collection of coffee and rubber plantations. Because of this, The Malayan sun bear is currently designated as ‘Vulnerable’ by the IUCN Red List and there are calls to learn more about these bears and develop conservation efforts. [3]

Today we release the genome assembly for the Malayan sun bear. This is a $1K genome assembly that has a contig n50 = 74 KB and a scaffold n50 = 60 MB (see Dudchenko et al., 2018 for procedure details). We thank the San Antonio Zoo for providing the sample used for this assembly!

This is the 4th member of the Ursidae family we've released on the DNAZoo blog! Check out these assembly pages for the American black bear, grizzly bear, and the polar bear.

Southern right whales are cherished members of the right whales (Eubalaena) genus of baleen whales which comprises only three species.They call Australian waters home, and we owe it to them to ensure they never come so close to extinction and exploitation as they once did.

Southern right whales underwent a dramatic and prolonged demographic bottleneck due to whaling, with the counts dropping from a healthy population of ~100,000 whales in the Southern Hemisphere in the late 1700’s to under 400 whales in 1920’s (1). Because of their enormous blubber reserves, curious nature and preferred calving grounds close to the southern Australian coastlines they were extremely popular as a whaling target, to the extent that whalers would often refer to them as the “right whale to hunt” (1). The nickname has stayed with the animals.

Eubalaena australis (Southern right whale) by Dr. Emma Louise Carroll, University of Auckland, Taken under Department of Conservation permit.

Thanks to international protection from whaling, the species has recovered in some parts of its former range (2). Currently, sightings vary from large aggregations, seen in key winter calving/nursery areas (South Africa, Australia, Argentina, Brazil, sub-Antarctic New Zealand), to regular sightings of small numbers of SRWs in other parts of the historical range (e.g., southeast Australia, mainland New Zealand) (3).

The whales weigh up to 80,000 kilograms and measure 16-18 meters in length (4). They can live up to 80 years, and start reproducing at 7-9 years of age, based on repeated sightings of photo-identified individuals. Females mate with multiple males, and will have only one calf every 3-5 years.

The whales have a form of 'migratory culture' whereby they learn their mothers' preferred migratory destinations in their first year of life. They stay relatively true to these migratory traditions, and it's a factor that shapes their genetic population structure (5, 6).

The location of the offshore foraging grounds of southern right whales are not well understood, and much effort is currently being invested to characterise where the whales are feeding using technology such as satellite tracking (e.g., some tracked New Zealand southern right whales are currently feed just off Western Australia). A place of interest in this respect is the subantarctic island of South Georgia. It is a biodiversity hotspot and an accessible foraging ground for southern right whales. Recent work by the British Antarctic Survey has focused on the recovery of whales from whaling in this ecosystem.

Eubalaena australis (Southern right whale) by Dr. Emma Louise Carroll, University of Auckland, Taken under Department of Conservation permit.

To support ongoing conservation efforts DNA Zoo has been working with Dr. Emma Carroll, School of Biological Sciences, University of Auckland, and Dr. Jennifer Jackson at the British Antarctic Survey to get a chromosome-length genome assembly for the species. For the purpose, a southern right whale sample was collected from South Georgia using funding from EU BEST, DARWIN PLUS, South Georgia Heritage Trust, Friends of South Georgia Island, WWF and logistical support from the Government of South Georgia and the South Sandwich Islands (permit RAP 2017-017). Samples were collected as part of the Ecosystems component of the British Antarctic Survey Polar Science for Planet Earth Programme, funded by The Natural Environment Research Council. Additional acknowledgement to researchers Amy Kennedy, Matt Leslie, Artur Andriolo, Susie Calderan, Russell Leaper and Emilie Stepien, and the Song of the Whale crew and Marine Conservation Research International for vessel charter support.

We gratefully acknowledge the collaboration, samples from Argentina and the draft assembly provided by Mark Yandell's lab at University of Utah with contributions from Michael S. Campbell, Brian Dalley, Edgar J. Hernandez, Barry Moore, Andrea Chirife, Matias Di Martino, Mariano Sironi, Luciano O. Valenzuela, Marcela Uhart, Victoria J. Rowntree, Guy D. Eroh, Sancy A. Leachman and Jon Seger. Construction of the SRW draft assembly was funded and supported by the Illumina Corporation, by the H.A. and Edna Benning Fund, and by the US National Science Foundation.

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

Today we share the resulting genome assembly. Check out the 21 chromosomes below!

The assembly will facilitate ongoing conservation efforts. In particular we hope it will help with the development of a genotyping panel to help understand the kin relationships of the whales, which in turn, will tell us about their abundance and recovery. This is the work that Dr. Emma Carroll and team of collaborators are doing on New Zealand southern right whales at the University of Auckland.

Once the pandemic is over, come meet these beautiful whales at their nursery grounds located in Augusta in Western Australia during mid-July to late August!

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

1. Jackson, J. A., Patenaude, N. J., Carroll, E. L. & Baker, C. S. How few whales were there after whaling? Inference from contemporary mtDNA diversity. Mol. Ecol. 17, 236–251 (2008).
2. Bannister, J. L. Population trend in right whales off southern Australia 1993–2010. Unpubl. Rep. Present. to Int. Whal. Comm. Work. South. right whales, 13–16 Sept. 2011, Buenos Aires, Argentina (2011). Available at: https://iwc.int/home

3. Carroll, E. L. et al. Population structure and individual movement of southern right whales around New Zealand and Australia. Mar. Ecol. Prog. Ser. 432, 257–268 (2011).

4. Vashchenko YV, Clapham PJ. "Pushed to the Edge: Soviet Catches of Right Whales in the Eastern North Pacific". Alaska Fisheries Science Center Quarterly Research Reports (2011).

5. Carroll, E. L. et al. Cultural traditions across a migratory network shape the genetic structure of southern right whales around Australia and New Zealand. Nature Scientific Reports. 5, 16182 (2015).

6. Valenzuela LO, Sironi M, Rowntree VJ, Seger J. Isotopic and genetic evidence for culturally inherited site fidelity to feeding grounds in southern right whales (Eubalaena australis). Mol. Ecol. 18,782-791 (2009).

7. Carroll, E.L. et al. Genetic diversity and connectivity of southern right whales (Eubalaena australis) found in the Brazil and Chile-Peru wintering grounds and the South Georgia (Islas Georgias del Sur) feeding ground. Journal of Heredity. 111, 263-276 (2020).

Raspberries are small red berries with a rich red colour and a sweet juicy taste. They are a good source of vitamins, minerals, and antioxidants and thus are healthy as well as delicious. Red raspberry (R. idaeus subsp. idaeus L.) is an economically-important member of the genus Rubus, part of the Rosaceae family. Although red raspberries are closely related to other important crops such as strawberry, apple and rose, the method by which the fruits develop as aggregates of individual drupes in the genus Rubus, rather than as true fruits, is unique in the Rosaceae family.

'Anitra' Red raspberry, Graminor Ltd.

The red raspberry industry has grown enormously over the past 20 years and currently over 800,000 tonnes of raspberries are produced globally per annum, with a production price in excess of US $3.5 billion. As such, there is a significant breeding effort worldwide, which is hampered by the out-crossing, highly heterozygous nature of the genome, and severe inbreeding depression in the species. Breeding new varieties of red raspberry follows processes that have remained largely unchanged for decades, and the adoption of molecular markers in red raspberry breeding has been slower than for related species such as strawberry.

Selection for traits such as summer and autumn fruiting, thornlessness and fruit flavour will benefit significantly from the development of molecular markers, and enhanced knowledge of the genome of red raspberry will hasten their development. Comparative genome analysis to other sequenced Rosaceous species will facilitate the study of the complex evolution of fleshy fruits in the Rosaceae.

'Anitra' Red raspberry, Graminor Ltd.

Today, we share the chromosome-length genome assembly for the Red raspberry (R. idaeus subsp. idaeus L.), generated using plants from Graminor Ltd. in Norway. Check the contact map for the new Red raspberry genome assembly below:

This is the third cane berry we've released on the DNAZoo, check out these blog posts on blackberry ‘Hillquist’ (R. argutus) and blackberry ‘Burbank Thornless’ (R. ulmifolius), by Margaret Worthington.

Key people involved in the project are Jahn Davik (NIBIO), Daniel James Sargent (NIAB-EMR), Dag Røen (Graminor Ltd.), and Muath Alsheikh (Graminor Ltd.).


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