Plant one on me

Today, we share the chromosome-length genome assemblies for two petunia species, the white Petunia axillaris and the red Petunia exserta. These were done in collaboration with Michel Moser and Cris Kuhlemeier at the University of Bern. The P. axillaris assembly is based on a previously published draft from (Bombarely, Moser et al. 2016), and the P. exserta is generated using hitherto unpublished data.

Petunia is genus of 20 species of flowering plants of South American origin. P. axillaris is one of the two species that were used to create the world's most popular bedding plant, the petunia hybrid Petunia x hybrida [1]. P. exserta was only discovered in the Serras de Sudeste of Brazil in 1987 and is already considered to be near extinction in the wild [2].

Learn more about petunias and petunia genetics from (Bombarely, Moser et al. 2016)!

First chromosome-length genome assembly of a snake

Today, we're sharing a chromosome-length genome assembly for the Burmese python, the first chromosome-length assembly (as far as we know) for a snake. The assembly is based on the draft Python_molurus_bivittatus-5.0.2 (GCA_000186305.2) from (Castoe et al., 2013).

Burmese pythons are found throughout Southern and Southeast Asia where their population is decreasing, and the species is classified as vulnerable. Yet in Florida these non-native snakes are flourishing and causing the population of many native species, from birds to mammals, to plummet.

Check out the whole genome alignment to the green anole lizard genome assembly AnoCar2.0, showing nearly perfect conservation of synteny between a lizard and a snake (the species are thought to have diverged roughly 150M years ago). Comparing to the chicken, GRCg6a, allows us to examine conservation of synteny across the Sauria. This is a 250M year old group spanning the birds, non-avian dinosaurs, and non-dinosaur reptiles. The chromosome-scale synteny blocks are a real sight for Sauri(s)!

For more about this, you might want to read "The genome of the green anole lizard and a comparative analysis with birds and mammals," from (Alföldi, Di Palma et al., 2011).

Whole genome alignment between the 18 chromosomes of the Burmese python and 13 chromosomes of the green anole assembly from (Alföldi, Di Palma et al., 2011).

Whole genome alignments between the Burmese python, the green anole and chicken genome assemblies.

Welcome to the DNA Zoo!

Over a quarter of all assessed species are threatened with extinction [1]. The DNA Zoo is a consortium focused on facilitating conservation efforts through the rapid generation and release of high-quality genomics resources. We believe that these efforts can not only aid threatened nonhuman populations, but will greatly facilitate our understanding of our own species - Homo sapiens.

To begin, we are sharing chromosome-length genome assemblies for 50 mammalian species, including 14 endangered or vulnerable species. Most of the shared assemblies were created by upgrading fragmentary genome assemblies shared by other groups at the NCBI Assembly database. We improved these drafts using Hi-C. The rest were assembled from scratch using Hi-C and DNA-Seq. In each case, the resulting genome assemblies have chromosome-length scaffolds.

Check out the Assemblies webpage to see what's available, and the Methods page to find out more about our latest approaches for genome assembly. To make sure the data can have the greatest possible impact, we are sharing the data with minimal restrictions on usage and publication.

Visitors - young and old - may enjoy learning more about our assembled species by reading the Chromognomes comic series, a collaboration between DNA Zoo and Adam Fotos.

Finally, we are extremely grateful to the many zoos and individual partners who have donated samples and otherwise supported this effort. Check out the Collaborators page to learn more.

DNA Zoo is always looking for additional samples. If you have samples from a species we have not yet released, or would like us to upgrade a published draft, feel free to get in touch. Through the generous support of our commercial partners, we are often able to make end-to-end genomes, from relatively low quality material, at no charge.

Follow the project on Twitter @thednazoo or join the mailing list to stay up-to-date.

Welcome to the DNA Zoo!