DNA Zoo Blog

This blog aims to shout out the release of new assemblies and sharing of data on this website.

  • Ruqayya Khan

The Risso’s dolphin, Grampus griseus, sets some impressive #travelgoals. Some estimates say that the Risso’s dolphin may spend as much as 77% of their lives traveling [1]! Their geographical range is spread across the world, although they prefer deeper waters over the coast. From temperate to tropical waters, the Risso’s dolphin can be found in pods of 10-30 individuals [2].


Sometimes called the gray dolphin, the coloring of this species changes with age. Risso’s dolphins start their lives as black or dark gray in color and then lighten to a gray/white as they mature. The skin of this species is often marked by many scars, usually caused by teeth raking from other dolphins [3].


Unlike most cetaceans, the Risso’s dolphin lacks any upper teeth but instead can have several rows of peg-like teeth on their lower jaw. These teeth are useful in catching their preferred prey the cephalopods and also may play a role in mating behavior [4].

Risso's Dolphin, Grampus griseus by Robin Agarwal, [CC BY-NC 2.0], via flickr.com.

Today, we share the chromosome-length assembly for the Risso’s dolphin. This is a $1K de novo genome assembly with a contig N50 = 62 Kb and a scaffold N50 = 93 Mb. See Dudchenko et al., 2018 for details on the assembly procedure.


The sample for this genome assembly was provided to us by Barbie Halaska, Necropsy Manager at The Marine Mammal Center in Sausalito, California. As the world’s largest marine mammal hospital, the Center prides itself on gathering and providing open research data that is free to access, reuse, repurpose and redistribute in service to ocean conservation and marine mammal health.


This sample was collected by The Marine Mammal Center under the Marine Mammal Health and Stranding Program (MMHSPR) Permit No. 18786-04 issued by the National Marine Fisheries Service (NMFS) in accordance with the Marine Mammal Protection Act (MMPA) and Endangered Species Act (ESA). The work at DNA Zoo was performed under Marine Mammal Health and Stranding Response Program (MMHSRP) Permit No. 18786-03.


Want to compare this genome against other members of the Delphinidae family? You’re in luck as this is the DNAZoo’s 8th genome assembly of a dolphin species! Check out the assembly pages for the bottlenose dolphin and the Commerson’s dolphin.


We thank Barbie Halaska, Laura Sherr, Giancarlo Rulli and Ben Neely for their help with this genome assembly!


Learn more about the impact of The Marine Mammal Center’s scientific research by visiting the TMMC website at MarineMammalCenter.org.


  • T.Hains & K.-P. Koepfli

Pangolins are some of the most interesting animals on the planet both from the perspective of biology as well as pangolins being the most illegally trafficked mammal in the world. Pangolins are the sole members of the mammalian order Pholidota (which is Greek for “horny scale”), which is split into three genera: the Asian pangolins (genus Manis), the African tree pangolins (genus Phataginus), and the African ground pangolins (genus Smutsia).


Due to the illegal wildlife trade for pangolin scales, which are highly valued in the Asian traditional medicine markets, populations of pangolin species in both Africa and Asia are rapidly decreasing. The Asian species are typically smaller than their African counterparts, with tens of thousands of animals trafficked illegally each year. The eight known pangolin species are listed as either Vulnerable, Endangered, or Critically Endangered according the IUCN Red List of Threatened Species. Many international efforts on both policy and scientific fronts are aiming to prevent the extinction of these species and you can learn more about pangolin conservation efforts by visiting the Save Pangolins website.

Time-calibrated, molecular phylogenetic tree of pangolins, summarizing their distribution and revised classification. Time to most recent common ancestors (in million years) are indicated at the tree nodes. From Gaubert et al. (2017).

Recently, we released a chromosome-length assembly for the African tree pangolin, here. Today, we follow-up with chromosome-length assemblies for two Asian species of pangolins: the Malayan pangolin (Manis javanica) and the Chinese pangolin (Manis pentadactyla). These genome assemblies are upgrades from the drafts published by (Choo, Rayko et al., 2016).

Manis pentadactyla. Photo credit to Ms. Sarita Jnawali of NTNC – Central Zoo [CC BY 2.0], via flickr.com.
Manis javanica, photo by budak [CC BY-NC-ND 2.0], via flickr.com.

The Chinese pangolin can be found in northern India and Southeast Asia as well as southern China, while the Malayan pangolin can be found throughout Southeast Asia.

In contrast to the previously reported tree pangolin (Phataginus tricuspis) genome assembly (https://www.dnazoo.org/assemblies/Phataginus_tricuspis), which possess 57 (!) chromosome pairs making the tree pangolin the mammal with one of the largest chromosome count out there, the Malayan pangolin possesses only 19 chromosome pairs while the Chinese pangolin possess 20 chromosome pairs. See how the chromosomes of the three species relate to each other in the whole-genome alignment plot below.

Whole-genome alignments between the new chromosome-length genome assemblies of the the Malayan (ManJav1.0_HiC), the Chinese (M_pentadactyla-1.1.1_HiC) pangolin and the tree pangolin (Jaziri_pseudohap2_scaffolds_HiC).

According to Gaubert et al. 2018, the genus Manis split from the African genera roughly 38 million years ago and the split between the Malayan and Chinese pangolin is estimated at about 13 million years ago. This makes Pholidota a remarkable group in studying genome rearrangements and the role of chromosome numbers in diversification and speciation.

Lastly, pangolins are susceptible to coronaviruses, and there have been many mentions of pangolins in the media in relation to COVID-19 as a possible intermediate host for the transmission of SARS-CoV-2 to humans. The data does not seem to link pangolins directly to the current outbreak, but a virus related to pangolin coronavirus may have donated a receptor-binding domain to SARS-CoV-2 (Xiao et al., 2020). More generally, pangolin coronaviruses could represent a future threat to public health if wildlife trade is not effectively controlled.

If you happen to have samples for the African ground pangolins, please reach out. We’d love to work together to fill in the gaps in the pangolin phylogeny!

The Helmeted Honeyeater Lichenostomus melanops cassidix, named for its ‘helmet’ of head feathers, is a critically endangered subspecies of the yellow-tufted honeyeater (L. melanops) that is widespread in south-eastern Australia.

Photo Description - Helmeted Honeyeater (Lichenostomus melanops cassidix) Photo Credits and acknowledgements - Image: Bruce Lyon.

As do most related honeyeaters, it uses its long, brush-tipped tongue to collect nectar, which comprises a quarter of its diet [1]. It also consumes invertebrates, honeydew from bugs, manna (sugary exudate from damaged foliage), lerp (the sugary coating on scale insects) and sap exuding from scars on branches caused by gliding possums [2]. Each breeding pair vigorously defends its territory where it feeds, and helps neighboring pairs to drive out the intruders [3]. Females usually lay two eggs per clutch and attempt three or four clutches per season.


The Helmeted Honeyeater belongs to family Meliphagidae, an iconic Australo-Papuan group that evolved around 20 million years ago. Genus Lichenostomus, as currently recognized, split from other honeyeaters about 8 million years ago [4].

The State of Victoria, Australia, made the beautiful Helmeted honeyeater Victoria’s bird emblem in 1971 [5]. Of the four subspecies of Yellow-tufted honeyeater, the Helmeted Honeyeater is the largest and most colourful [6]. It is also most threatened (critically endangered under IUCN criteria [7]) with only about 250 individuals remaining in the single wild population despite decades of intensive management and supplementation from a captive breeding program at Healesville Sanctuary [8]. It is one of the most intensively monitored bird populations in Australia. Recent results have revealed that the population lost much of its genetic diversity over recent decades [9], with the most-inbred birds producing only one-tenth as many young over their lifetimes compared to the least-inbred birds [8].

To reverse population decline, genetic rescue was recommended. That is, genes from a closely related subspecies, L. m. gippslandicus diverged from the common ancestor up to 50,000 years ago [10], were proposed to be introduced into the Helmeted Honeyeater population. Because the two subspecies historically exchanged genes, this management action would reinstate historical gene flow. Inter-subspecies crosses were successful in captivity and the hybrid young produced from such pairings released into the wild in 2019 [11].

To support ongoing conservation efforts led by a multidisciplinary Recovery Team, including the Department of Environment, Land, Water and Planning, The Friends of the Helmeted Honeyeater and Zoos Victoria, DNA Zoo has been working with Paul Sunnucks and Alexandra Pavlova at Monash University to generate a chromosome-length assembly genome for a female Helmeted Honeyeater.

The chromosome-length assembly we share today is based on the draft assembly available on NCBI generated by Han Ming Gan of the Deakin Genomics Centre, and the Monash University team, with funding from Zoos Victoria and Australian Research Council-funded project LP160100482 (Lichenostomus melanops cassidix isolate B80296). The draft genome assembly was created using MaSuRCA v. 3.3.4 (Zimin et al. 2013), using Oxford Nanopore MinION reads polished with short-insert size Illumina NovaSeq reads. The above draft was scaffolded using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). See our Methods page for more details!


The sample used to generate the Hi-C library was kindly provided by Leanne Wicker (Zoos Victoria). The Hi-C work was supported by resources provided by DNA Zoo Australia, Faculty of Science, The University of Western Australia (UWA), DNA Zoo, Zoos Victoria, Holsworth Wildlife Endowment and Monash University, with additional computational resources and 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, David Weisz, Ashling Charles, Ruqayya Khan & Parwinder Kaur.


Blog by: Parwinder Kaur, Alexandra Pavlova and Paul Sunnucks

Citations

1. https://www.helmetedhoneyeater.org.au/fact-files/helmeted-honeyeaters/

2. https://www.encyclopedia.com/environment/encyclopedias-almanacs-transcripts-and-maps/australian-honeyeaters-meliphagidae

3. Smales, I.J. (2004).Population ecology of the Helmeted Honeyeater Lichenostomus melanops cassidix: long-term investigations of a threatened bird. Honours thesis, Melbourne University, Melbourne, Victoria

4. Joseph, L., Toon, A., Nyári, Á.S., Longmore, N.W., Rowe, K., Haryoko, T., Trueman, J., Gardner, J.L., 2014. A new synthesis of the molecular systematics and biogeography of honeyeaters (Passeriformes: Meliphagidae) highlights biogeographical and ecological complexity of a spectacular avian radiation. Zool Scr 43, 235-248.

5. Delacombe, Rohan; Bolte, Henry (10 March 1971). "Faunal Emblems for the State of Victoria" (PDF). Victoria Government Gazette – Online Archive 1836–1997. State Library of Victoria.

6. Wakefield, N., 1958. The Yellow-tufted Honeyeater with a description of a new subspecies. Emu 58, 163–194

7. Garnett, S., Szabo, J., Dutson, G., 2011. Action Plan for Australian Birds 2010. CSIRO Publishing, Melbourne.

8. Harrisson, K.A., Magrath, M.J., Yen, J.D., Pavlova, A., Murray, N., Quin, B., Menkhorst, P., Miller, K.A., Cartwright, K., Sunnucks, P., 2019. Lifetime fitness costs of inbreeding and being inbred in a critically endangered bird. Curr Biol 29, 2711–2717.

9. Harrisson, K.A., Pavlova, A., Gonçalves da Silva, A., Rose, R., Bull, J.J., Lancaster, M., Murray, N., Quin, B., Menkhorst, P., Magrath, M.J.L., Sunnucks, P., 2016. Scope for genetic rescue of an endangered subspecies though re-establishing natural gene flow with another subspecies. Mol Ecol 25, 1242–1258.

10. Pavlova, A., Selwood, P., Harrisson, K.A., Murray, N., Quin, B., Menkhorst, P., Smales, I., Sunnucks, P., 2014. Integrating phylogeography and morphometrics to assess conservation merits and inform conservation strategies for an endangered subspecies of a common bird species. Biol Conserv 174, 136–146.

11. https://www.zoo.org.au/healesville/whats-on/news/helmeted-honeyeater-release/

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