The lion king

The lion is a large cat native to Africa and India. Lions have captured our imagination for centuries, from the paleolithic cave art to modern movies and characters in books, lions are at the top of the food chain. The lions have long been associated with kingship, nobility and commanding power. The Swahili word for lion, simba means "king," "strong," and "aggressive", and the sacred "Lion God" in India is a fierce avatar of the Hindu god Vishnu.

Hubert, the lion from the Oklahoma City Zoo who's genome assembly we are sharing today. Photo credit: Andrea Johnson

Did you know that lions are the only cats that live in large social groups? They are called prides. A pride can have from 3 to 30 lions and is made up of lionesses (mothers, sisters, and cousins) and their cubs, along with a few unrelated adult males. The pride has a close bond and is not likely to accept a stranger. Both males and females scent mark to define their territory.

A lion’s life is filled with sleeping, napping, and resting. Over the course of 24 hours, lions have short bursts of intense activity, followed by long bouts of lying around that total up to 21 hours!

Are lions in trouble? It is estimated that there are between 6,000 and 10,000 African lions in Africa. The Asian lion which used to be found across the Middle East and India is represented by only about 500 to 674 individuals, with more than half living in a reserve that used to be royal hunting grounds in an area of dry teak forest called the Gir Forest, now under national protection by the Indian government. The remainder of this particular subspecies lives in zoos.

Due to many issues such as disease, hunting by humans, and loss of habitat, the conservationists are very concerned about the population of lions in Africa. The International Union for Conservation of Nature (IUCN) classifies lions as Vulnerable, but they note that the vast majority of the population is inferred to have declined at a rate that meets the criteria for Endangered. The Asiatic lion currently exists as a single subpopulation in India, and is thus vulnerable to extinction from unpredictable events, such as an epidemic or large forest fire and is fully protected in India.

Today, we share the chromosome-length assembly for the South African lion (Panthera leo krugeri). The assembly was generated from a sample donated by Hubert, the king of the Oklahoma City Zoo lion pride. Thank you to Jennifer D’Agostino, DVM, DACZM, Candice Rennels, Director of Public Relations, Rebecca Snyder, Director of conservation and science and others at the Oklahoma City Zoo for their help with this sample!

This is a $1K de novo genome assembly. See our Methods page for details on the procedure. We gratefully acknowledge the Pawsey Supercomputing Center for the computational support for this assembly, and the computational assistance from the DNA Zoo Australia team at the University of Western Australia. Check the interactive map of Hubert's chromosomes below, and look for more data and info on the assembly page!

SRA update for 300 genome assemblies

We are excited to report that with our last assembly release we've hit the 300 assemblies mark, which means it's time to do some raw sequencing data upload to NCBI Sequence Read Archive!

The new data have now been uploaded under our usual BioProject accession PRJNA512907 (some more data can be found under collaborative bioproject accessions like PRJNA679437). Overall, as of today the uploaded data cover Hi-C and WGS data spanning 605 experiments and 40,240,196,863,263 bases!

We thank Illumina, Baylor College of Medicine GARP core, Macrogen, Novogen and the Broad Institute for their help with the data production! And thank you to Maya and Judah for the celebratory postcard!

As always, we share the data without restrictions: see our data usage policy here.

Subscribe below or follow us on twitter for more upcoming updates!

Sustainability beleafs

Narrow-leafed lupin (NLL; Lupinus angustifolius) is a key rotational crop for sustainable farming systems, whose grain is high in protein content. It is a gluten-free, non-GM, alternative protein source to soybean and as such has gained an interest as a human food ingredient.

Photo Description –Narrow-leafed lupin (Lupinus angustifolius) cultivar Coyote in a field near Northam in 2021. Photo Credits and acknowledgements – Lars Kamphuis

NLL is a grain legume grown as a break crop in rotation with cereal crops, thereby reducing the need for fertilizers, increasing cereal yields and importantly providing disease breaks. NLL and other lupins thrive on nutrient poor soils due to their symbiosis with beneficial bacteria to fix atmospheric nitrogen and to efficiently mobilize phosphorus from soils.

NLL is a relatively young pulse crop, having only begun the process of domestication in the early 20th Century in Germany, which was concluded by the release of the first fully domesticated cultivar with low alkaloid content, permeable seeds, early flowering and non-shattering pods in the 1960s in Australia. To date four lupin species have been domesticated, including white lupin, yellow lupin, pearl lupin and NLL, with NLL being the predominant lupin grown worldwide (85% of all lupins).

The lupin grain is mainly used for animal and aquaculture feed, but in recent years has gained interest as a human health food and food additive. This is because lupin grain is rich in protein (30-40% of whole seeds), has low amounts of undesired starch compared to other pulses, is high in dietary fibre (25-30%), low in fat and carbohydrates and gluten-free. In human food products, lupin kernel flour is predominantly used as a food additive in bread and pasta and has been shown to reduce insulin resistance. It’s attractiveness as a gluten free, non-GM alternative to soybean has resulted in the production of a series of lupin-based gluten-free foods including pasta and meat replacement products for the vegetarian and vegan markets. Furthermore, specific lupin seed proteins have been demonstrated to reduce glycaemia to comparable levels as achieved with the predominately used hypoglycaemic drug metformin, and have additional nutraceutical properties, for example, that improve inflammatory related diseases, as well as anti-microbial properties.

Here we report a chromosome-length reference genome for NLL which was generated using ~98.5x coverage PacBio long read sequence data, assembled with CANU, and scaffolded using ~ 50x in situ Hi-C sequencing. The interactive contact map of the NLL’s chromosomes is included below.

This data provides a much-needed foundational resource that supports functional and molecular research into the Leguminosae for sustainable agriculture and feeding the future. More details are available in the research article “A pan-genome and chromosome-length reference genome of narrow-leafed lupin (Lupinus angustifolius) reveals genomic diversity and insights into key industry and biological traits”, read now in The Plant Journal, here!