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.

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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!

The ant hunter

The southern tamandua (Tamandua tetradactyla) is one of the two living species of lesser anteaters. Sometimes also called collared or vested anteaters, southern tamanduas have a very variable fur coloration pattern that can range from a complete or partial black vest to a fully golden or black in some individuals. The southern tamandua is distributed throughout most of tropical South America from the east of the Andes of Colombia and Venezuela to northern Uruguay and northern Argentina. Unlike giant anteaters that are fully terrestrial, southern anteaters are semi-arboreal and occupy a wide variety of habitats, such as open savannas, grasslands, rainforests and mangroves. Mainly nocturnal, their activity pattern also depends on the availability of ants and termites on which they almost exclusively feed, and which they hunt both on the ground and in trees.

Southern tamandua by Instituto Últimos Refúgios, [CC BY-NC], via inaturalist.org

In terms of conservation, the southern anteater is currently classified as Least Concern on the IUCN Red List of Threatened Species. Although there are currently no major threats identified to this anteater species, it is hunted for meat in some portions of its range, sometimes killed by domestic dogs, more and more often sold as a pet species, and is frequently found as roadkill in some countries such as French Guiana. Moreover habitat loss and degradation, wildfires, and land use change represents a threat in some areas.

Today, we share a chromosome-length assembly for the southern anteater. This is a Hi-C upgrade to a draft genome hybrid assembly generated by combining Nanopore long reads with Illumina short reads by Rémi Allio, Frédéric Delsuc and team at Centre National de la Recherche Scientifique (CNRS) and Université de Montpellier as part of the ConvergeAnt project. The original sample used for the initial draft assembly comes from a fresh roadkill individual found near Kourou (French Guiana) in 2018. The corresponding specimen (M3075) is part of the JAGUARS collection curated by Benoit de Thoisy (Institut Pasteur de Cayenne and Kwata NGO, French Guiana). The sample for the Hi-C upgrade was donated by Fiera from the Houston Zoo.

Check out the contact map for the southern anteater's 28 chromosomes below, and find more data and links related to this assembly on the corresponding assembly page!