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.).

  • Ruqayya Khan

The South American tapir, Tapirus terrestris, is the largest surviving native terrestrial mammal in the Amazon. Although tapirs are physically similar to pigs, they are actually an odd-toed ungulate that's more closely related to horses and rhinoceroses [1]. South American tapirs primarily forage and consume vegetation native to the Amazon, including fruits like the mombin and the huito [2].

As in other tapir species, the South American tapir's nose and upper lip combine into a flexible snout like an elephant's trunk. The elongated nose is not just for show! The tapir makes up for their relatively poor eyesight with their strong sense of smell, helping them to locate food and potential mates. Their trunks are also prehensile, meaning they're able to grip tree branches to clear off fruit and leaves.

The ICUN categorizes the South American tapir as vulnerable with its population in declining trend. The biggest threats to the South American tapir are similar to many Amazonian species: habitat loss to logging and poaching their meat and hides [3]. Natural predators of the tapir are jaguars and crocodiles. In a threatening situation, tapirs may emit a high pitched squealing noise. Additionally, tapirs are great swimmers and may escape from predators by swimming away while using their magnificent snouts as snorkels [4].

South American Tapir (Tapirus terrestris) by Allan Hopkins, [CC BY-NC-ND 2.0], via flickr.com

Today we share the chromosome-length assembly for the South American tapir. This is a $1K genome assembly with contig N50 = 46 Kb and scaffold N50 = 47 Mb (see Dudchenko et al., 2018 for procedure details). The genome was generated using a sample from the T.C. Hsu Cryo-Zoo at the University of Texas MD Anderson Cancer Center stored all the way back in 1977! We thank Drs. Asha Multani, Sen Pathak, Richard Behringer, Liesl Nel-Themaat and Arisa Furuta in the Department of Genetics at the MD Anderson Cancer Center for their help with this sample.

This is the second tapir species in our collection of genome assemblies (out of four recognized extant species of tapir). Check out this blog post and assembly page for the Malayan tapir, the only Old-World species of tapir. Interestingly, the species are hugely different in terms of karyotype: the Malayan tapir has a karyotype of 2n=52 whereas the South American Tapir has a karyotype of 2n=80! Check out the whole genome alignment plot below to find all the chromosomal breaks between the two.

Whole-genome alignment plot between Tapirus_terrestris_HiC and Tapirus_indicus_HiC

The dingo is the Australian canine, which is thought to be introduced to Australia by seafarers from Asia around 5000 year ago (1). Since then the dingo has become Australia’s apex predator on land and has integrated into local ecosystem. By controlling populations of native and introduced herbivores including introduced mesopredators such as red foxes and cats, dingoes are fundamental for maintaining balance in the ecosystem. Additionally, by controlling populations of herbivores, dingoes benefit plant communities and other smaller native prey such as small marsupials and rodents (2).

Cooinda the Alpine dingo; Photo: Bargo Dingo Sanctuary.

The dingo is a medium-sized canine, with males being slightly larger than females. The dingo breeds once a year and usually produces a litter of four to six pups. The dingo may have multiple coat colours: ginger with white feet, darker tan to black, white, and golden yellow. Interestingly, like wolves, dingoes howl to communicate. The extensive hybridisation with domestic dogs has raised concerns over the persistence of pure dingoes in the wild.

Morphological and genetic studies have indicated a subgrouping in dingoes – Desert, Alpine and Tropical, primarily based on their geographical distribution. Skull shape differ between dingoes from different climatic zones, where the skulls of dingoes from the southeastern alpine regions of Australia are wider than the skulls of dingoes from the northwestern desert parts of Australia (3). Genetic studies however have supported the presence of only two lineages: Desert and Alpine (4). Alpine dingoes are found in the high elevation Australian alps and grow a thicker fur during late autumn. Alpine dingoes are typically larger than desert dingoes (5).

Here we release a chromosome-length genome assembly of the Alpine dingo - Cooinda. Cooinda is a pure dingo and was raised in the Bargo dingo sanctuary. Unfortunately, she has now passed, but it is expected she will go on display at the Australia Museum, Sydney as the type representative of the Alpine dingo. This assembly has a contig N50 = 23,108,747bp and scaffold N50 = 64,752,584bp. See Dudchenko et al., 2018 for details on the procedure. Thank you to Bargo Dingo Sanctuary for providing the sample for this assembly.

The assembly is now available on NCBI as UNSW_AlpineDingo_1.0:


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