Emblem of Western Australia - the black swan

The black swan (Cygnus atratus) is a large waterbird, a species of swan, native to Western Australia. The black swan's role in Australian heraldry and culture extends to the first founding of the colonies in the eighteenth century. It has often been equated with antipodean identity, the contrast to the white swan of the northern hemisphere indicating 'Australianness'. The black swan is featured on the flag, and is both the state bird and state emblem of Western Australia; it also appears in the Coat of Arms and other iconography of the state's institutions including our University of Western Australia.

The Australian black swan (Cygnus atratus) Photo Credits & acknowledgements – Parwinder Kaur, [CC BY 2.0]

The Noongar People of the South-West of Australia call the black swan Kooldjak along the West and South-West coast, Gooldjak in the South East and it is sometimes referred to as maali in language schools. The black swan is widely referenced in Australian culture, although the character of that importance historically diverges between the prosaic in the East and the symbolic in the West. The black swan is also of spiritual significance in the traditional histories of many Australian Aboriginal peoples across southern Australia.

Within Australia, the black swan is nomadic, with erratic migration patterns dependent upon climatic conditions. It is a large bird with mostly black plumage and a red bill. The black swan was introduced to various countries as an ornamental bird in the 1800s, but has managed to form stable populations. Black swans can be found singly, or in loose companies numbering into the hundreds or even thousands. It is a popular bird in zoological gardens and bird collections, and escapees are sometimes seen outside their natural range. The black swan is fully protected in all states and territories of Australia and must not be shot.

The black swan is almost exclusively herbivorous, and while there is some regional and seasonal variation, the diet is generally dominated by aquatic and marshland plants. Like other swans, the black swan is largely monogamous, pairing for life with about 6% divorce rate [1].

DNA Zoo has been working in collaboration with Prof Dave Burt, Dr Kirsty Short and Anjana Karawita at the University of Queensland, Australia to map the genome of the black swan at chromosome-length in an effort to understand immune responses to the deadly ‘bird flu’ virus and better protect public health. Here, we use in situ Hi-C to complete a chromosome-length assembly of the black swan.

The chromosome-length assembly we share today is based on the primary assembly by the University of Queensland team, led by Dr Kirsty Short and PhD candidate Anjana Karawita shared on NCBI. This draft assembly was scaffolded with 98,929,251 PE 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 Hi-C work 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 with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government, the Government of Western Australia and Dr. Short’s ARC DECRA grant (DE180100512).

The genome of a black swan will hopefully help us understand why these birds are extremely susceptible to the bird flu virus [2]. Right now, our UQ based research collaborators (Dr. Kirsty Short’s lab) are working on annotating the immune genes in the black swan genome assembly and comparing them to genes in the closely related mute swan genome and other avian species less susceptible to bird flu to build a better understanding their immune responses to the highly pathogenic avian influenza (HPAI) aka the bird flu.

Given the virus can occasionally spill over into humans with devastating consequences. Since 2003, this virus has only infected approximately 800 people worldwide, however, more than 50% of infected individuals have not survived the disease. It is important we know more about disease with zoonotic potential early - a key lesson from the current pandemic!

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

Blog by: Parwinder Kaur, Anjana Karawita, Dave Burt and Kirsty Short

Get a sneak peek at the chromosome-length contact map for the black swan below, and don't forget to visit the assembly page https://www.dnazoo.org/assemblies/Cygnus_atratus for more details and statistics!

Citations

Kraaijeveld, Ken; Gregurke, John; Hall, Carol; Komdeur, Jan & Mulder, Raoul A. (May 2004). "Mutual ornamentation, sexual selection, and social dominance in the black swan". Behavioral Ecology. 15 (3): 380–389. doi:10.1093/beheco/arh023

Short KR, Veldhuis Kroeze EJ, Reperant LA, Richard M, Kuiken T. (Dec 2014). Influenza virus and endothelial cells: a species-specific relationship. Front Microbiol. 2014;5:653. doi:10.3389/fmicb.2014.00653

The Model Legume - Medicago truncatula R108

Medicago truncatula aka barrelclover is an annual legume native to the Mediterranean region. It is a low-growing, clover-like plant 10–60 centimetres (3.9–23.6 in) tall with trifoliate leaves. Each leaflet is rounded, 1–2 centimetres (0.39–0.79 in) long, often with a dark spot in the center. The flowers are yellow, produced singly or in a small inflorescence of two to five together; the fruit is a small, spiny pod.

Medicago truncatula flower1 Denman, photo by Harry Rose [CC BY 2.0], via flickr.com.

This species is studied as a model organism for legumes, a plant family that includes soybeans, peanuts, peas and alfalfa, because it has a small diploid genome, is self-fertile, has a rapid generation time and prolific seed production. As such, extensive genomic studies of the species have been undertaken, and a genome assembly for the species has been available to the community thanks to the efforts of the Medicago truncatula Consortium (see Young et al., 2017; Tang et al., 2014).

Unfortunately, the reference genotype (Jemalong A17) originally selected for the chromosome-length genome sequencing and assembly proved to be recalcitrant to transformation. M. truncatula R108 accession is more attractive for genetic studies due to its high transformation efficiency and functional genomic resources, but has been lacking a chromosome-length genome assembly.

To address this we performed in situ Hi-C (~30×) to anchor, order, orient scaffolds, and correct misjoins in contigs from a draft genome assembly for the R108 barrelclover from (Moll et al., 2017) resulting in a chromosome-length genome assembly. The new assembly allowed us to accurately annotate the chromosome 4/8 translocation between the R105 and A17 accessions as well as map the Tnt1 retrotransposon insertions creating a resource for downstream insertional mutagenesis studies. Read more about this in our research article “Delineating the Tnt1 Insertion Landscape of the Model Legume Medicago truncatula cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly” now available open access in IJMS, Special Issue - Functional Genomics for Plant Breeding 2.0.

We gratefully acknowledge the frozen leaf sample provided by Scott Schaeffer at the Nakata Lab (USDA, ARS). The Hi-C work was enabled 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.

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

Blog by: Parwinder Kaur

17 beeutiful genome assemblies

Sweat bees (Hymenoptera: Halictidae) encompass a wide range of social behaviors, from solitary individuals that live and reproduce independently to eusocial colonies with overlapping generations and a non-reproductive worker caste. Some species are capable of producing both social and solitary nests, often depending on environmental context.

Within the sweat bees, there have been two independent gains and a dozen losses of eusociality. These replicated gains and losses of social behavior enable a comparative approach to identify the core factors that shape the emergence and breakdown of eusociality and provide insights into the most costly aspects of social life. We performed this exact comparative analysis in our latest preprint "Convergent selection on juvenile hormone signaling is associated with the evolution of eusociality in bees".

For these genomic comparisons we needed, you guessed it, genome assemblies. Today, together with the Kocher Lab at Princeton University we share 17 chromosome-length sweat bee genome assemblies that span solitary, eusocial and polymorphic species to accompany the preprint.

17 sweat bees with shiny new chromosome-length genome assemblies. Photo attributions can be found on individual assembly pages.

The assembled species include:

1. Bicolored striped sweat bee (Agapostemon virescens): www.dnazoo.org/assemblies/Agapostemon_virescens

2. Pure green sweat bee (Augochlora pura): www.dnazoo.org/assemblies/Augochlora_pura

3. Golden green sweat bee (Augochlorella aurata): www.dnazoo.org/assemblies/Augochlorella_aurata

4. Ligated furrow bee (Halictus ligatus): www.dnazoo.org/assemblies/Halictus_ligatus

5. Giant furrow bee (Halictus quadricinctus): www.dnazoo.org/assemblies/Halictus_quadricinctus

6. Orange-legged furrow bee (Halictus rubicundus): www.dnazoo.org/assemblies/Halictus_rubicundus

7. White-legged sweat bee (Lasioglossum albipes): www.dnazoo.org/assemblies/Lasioglossum_albipes

8. Common furrow bee (Lasioglossum calceatum): www.dnazoo.org/assemblies/Lasioglossum_calceatum

9. Figueres' sweat bee (Lasioglossum figueresi): www.dnazoo.org/assemblies/Lasioglossum_figueresi

10. White-banded sweat bee (Lasioglossum leucozonium): www.dnazoo.org/assemblies/Lasioglossum_leucozonium

11. Sharp-collared sweat bee (Lasioglossum malachurum): www.dnazoo.org/assemblies/Lasioglossum_malachurum

12. Margined sweat bee (Lasioglossum marginatum): www.dnazoo.org/assemblies/Lasioglossum_marginatum

13. Evening primrose sweat bee (Lasioglossum oenotherae): www.dnazoo.org/assemblies/Lasioglossum_oenotherae

14. Lobe-spurred sweat bee (Lasioglossum pauxillum): www.dnazoo.org/assemblies/Lasioglossum_pauxillum

15. Viereck's sweat bee (Lasioglossum vierecki): www.dnazoo.org/assemblies/Lasioglossum_vierecki

16. Zephyr sweat bee (Lasioglossum zephyrum): www.dnazoo.org/assemblies/Lasioglossum_zephyrum

17. Alkali bee (Nomia melanderi): www.dnazoo.org/assemblies/Nomia_melanderi

The same genome assemblies and gene annotations are also available through the Princeton Halictid Genome Browser.

We searched the chromosome-length genome assemblies for genes that both experienced positive selection when eusociality arose and relaxed selection when eusociality was secondarily lost in the sweat bees. Strikingly, the analysis highlighted proteins that bind and transport juvenile hormone – a key regulator of insect development and reproduction. Read more about this in the preprint, and see also the Kocher lab twittorial!

To give you some taste of the data, see a collage of chromosome-length contact maps below, and visit the individual assembly pages for more information!

A collage of chromosome-length contact maps for the 17 sweat bee species. For individual contact maps visit https://tinyurl.com/yfy6agsx or follow the species-specific links above.

Fun fact: these genome assemblies constitute our 200-216th assembled species. Can you beelieve it?!