Don’t desert us!

The addax (Addax nasomaculatus) is considered the most desert adapted antelope on the planet but is also among the most endangered, with less than 100 individuals left in the wild. Although the species was once found across the Sahelo-Saharan region of North Africa, they are now only present in a small area of Niger. Addax are able to live in extreme conditions and can face temperatures between -5 and 60 °C. They have large, flat hooves that allow them to walk across the desert without sinking into the sand and they rarely need to drink, since they obtain most of their liquids from the plants they eat, including wild melons. The primary threats faced by addax are hunting and changes in habitat use and their survival in the wild now relies on a series of large-scale reintroductions.

Addax (Addax nasomaculatus) by Josh more, [CC BY-NC-ND 2.0], via flickr.com

Fortunately, since the 1920s, addax have successfully been managed in captive populations across the globe. These insurance populations have proved invaluable for reintroductions and translocations into Tunisia, Morocco and Chad and will continue to represent a crucial component of addax management going forward. As part of this, researchers and conservationists are integrating genetic information into planning and decision making (Dicks et al. 2023). The availability of high quality genetic and genomic resources can therefore directly support addax conservation.

Today, we share a chromosome-length assembly for addax created using a combination of PacBio HiFi and Illumina Hi-C sequencing. PacBio HiFi sequencing was carried out at the University of Louisville Sequencing Technology Center from a male addax fibroblast cell line donated by the San Diego Frozen Zoo and contigged using HiFiasm (Cheng et al., 2021). The HiFi sequencing was made possible thanks to support from the Environment Agency – Abu Dhabi to the University of Edinburgh and the Royal Zoological Society of Scotland. Hi-C sequencing was carried out by the DNA Zoo using a blood sample donated by a female individual from SeaWorld.

Previously we shared an addax genome assembly using a draft generated by Hempel et al., 2021. The new genome assembly dramatically improves the contiguity of the assembly, boosting contig N50 from 10kb to 65.7Mb. We hope that this improved chromosome-level assembly will serve as an important backbone for future studies investigating this beautiful species of antelope on the brink of extinction.

Check out the chromosome-length contact map of the new addax reference below, and follow the assembly link for more details and info!

Nosy knowtrias

Also known as the nutria, the coypu (Myocastor coypus [Molina, 1782]), is a large amphibious rodent from about 5 to 7 kg (Woods et al. 1992). Native to South America, its range includes Argentina, Chile, Paraguay, Uruguay, as well as the southern parts of Bolivia and Brazil. It is associated with aquatic habitats and primarily feeds on vegetation along the river banks (Woods et al. 1992). Coypu shares some ecological adaptations with another amphibious species, the beaver (e.g., it can remain submerged for about 10 min!). The two species however are phylogenetically distant. The main external morphological difference between the beavers and the coypu is probably the tail that is flat in the formers.

Underwater picture of a wild coypu (Myocastor coypus) taken with an underwater camera trap. Photo by Quentin Martinez and Cécile Molinier.

In the late 19th and early 20th centuries, coypus have been exported for fur production to Europe, North America, Asia, and Africa. Due to accidental escapes and voluntary releases, the species is now considered as one of 100 of the world's worst invasive alien species (GISD 2021). At high densities, their burrows present along the river banks may impact the overall wetland ecosystems. The expansion of the coypu seems to be limited by the extreme temperature of cold winters. However with the overall global warming, some models predict a massive worldwide expansion of the species (Jarnevich et al. 2017).

We are still discovering new things about this species. As an example, recent evidence shows that the coypu may have reduced olfactory capabilities in comparison to its close terrestrial relatives (Martinez et al. 2020). Indeed, it was found that the relative size of their olfactory organs is reduced, including the loss of two olfactory turbinals, a nasal structure involved in olfaction. In order to investigate the olfactory question from a genomics perspective and test if there is a relation between the morphology and the genome (Martinez et al. 2023), today we release the chromosome-length assembly for the coypu Myocastor coypus.

The new genome assembly via Hi-C upgrade of a draft generated by combining Nanopore long reads with Illumina short reads, made by Marie-Ka Tilak, Quentin Martinez, Rémi Allio, Pierre-Henri Fabre and team from Institut des Sciences de l'Évolution de Montpellier (ISEM) and Université de Montpellier (UM).

This project was funded by l‘Agence Nationale de la Recherche (Défi des autres savoirs, Grant DS10, ANR-17-CE02-0005 RHINOGRAD 2017 granted to Pierre-Henri Fabre). We thank the other collaborators of this project: Cécile Molinier, Benoit de Thoisy and Vincent Goanec.

In accordance with the local program for pest management and in collaboration with Régis Gibert and Nathalie Vazzoler-Antoine the original sample comes from a wild Myocastor coypus (34130, Lansargues, France). The sample (QM1153) used fot assembly is now part of the ISEM collection. Browse the 20 chromosome-length scaffolds of the new assembly using the interactive map below!

References:

GISD. Of the World's Worst Invasive Alien Species. Global Invasive Species Database. http://www.iucngisd.org/gisd/100_worst.php. 100, (2021).

Jarnevich, C. S., Young, N. E., Sheffels, T. R., Carter, J., Sytsma, M. D., & Talbert, C. (2017). Evaluating simplistic methods to understand current distributions and forecast distribution changes under climate change scenarios: an example with coypu (Myocastor coypus). NeoBiota, 32(1), 107.

Martinez, Q., Clavel, J., Esselstyn, J. A., Achmadi, A. S., Grohé, C., Pirot, N., & Fabre, P. H. (2020). Convergent evolution of olfactory and thermoregulatory capacities in small amphibious mammals. Proceedings of the National Academy of Sciences, 117(16), 8958-8965.

Martinez Q, Courcelle M, Douzery E, Fabre PH. When morphology does not fit the genomes: the case of rodent olfaction. Biol Lett. 2023 Apr;19(4):20230080. doi: 10.1098/rsbl.2023.0080. Epub 2023 Apr 12. PMID: 37042683; PMCID: PMC10092080.

The pest is yet to come

The bluegreen aphid, or blue alfalfa aphid (Acyrthosiphon kondoi), is a species of aphid found in many regions of the world, including all states of Australia. The aphid are most noticeable in the springtime, but they can also be active during winter and autumn. It is mainly a pest of plants in the family Leguminosae, affecting crops such as pea, lupin, medics, lentil and cowpea. Heavy infestation of aphids can cause significant plant damage through their feeding on upper leaves, stems and terminal buds of host plants. This subsequently causes the deformation of leaves and removes critical nutrients from the plant, making it become yellow and wilt as a result.

Photo Description – Bluegreen aphid (Acyrthosiphon kondoi) Photo Credits and acknowledgements - Jesse Rorabaugh CC0 (No rights reserved, public domain)

Bluegreen aphids are very similar in appearance to the closely related pea aphids (Acyrthosiphon pisum) but can be distinguished from other aphids by their long legs, antennae and cornicles and are often found to be more grey-green to blue-green in colour.

Aphids can reproduce both asexually and sexually, however in Australia, the sexual phase is often lost. Bluegreen aphid reproduces asexually whereby females give birth to live young, which are often referred to as clones. Once aphids gain wings, they fly into crops from broad leaf weeds or other crop legumes and medics, and colonies of aphids start to build up.

A study published in 2012 by Humphries et al., found a new biotype of bluegreen aphid in south-eastern Australia (Acyrthosiphon kondoi Shinji) that was able to overcome resistance in a broad range of pasture legumes, causing severe damage and mortality in seedlings in previously resistant pasture legume cultivars. This biotype hasn’t been observed since. The CSIRO estimates that the annual economic impact of invertebrate pests, including bluegreen aphids, ranges between $500 million for loss of production in Australia and upwards of $2 billion dollars in New Zealand.

Here we report the first chromosome-length reference genome assembly for bluegreen aphids, which was assembled using a DNA-Seq data from a single aphid biotype (an asexual clone) of A. kondoi Shinji, collected from narrow-leafed lupin (Lupinus angustifolius L.) near Kelleberrin, Western Australia. Draft genome assembly from a combination of Illumina short reads, Eurofins Long Distance Jumping libraries and PacBio long sequence reads was led by Prof Karam Singh, CSIRO & Dr Lars Kamphuis, Curtin University. Subsequently, in situ Hi-C data was generated by DNA Zoo Australia which was used to generate a chromosome length reference genome for bluegreen aphid.

See the 5 chromosomes of the new genome assembly in the interactive contact map below:

This data provides a much-needed genetic resource to help combat bluegreen aphid infestations, supporting functional and molecular research into the species and efforts toward critical legume crop survival.