The eagle has landed

This week we are releasing a genome assembly for the golden eagle, Aquila chrysaetos. The golden eagle is North America's largest bird of prey, and a protected species in the United States.

The chromosome-length assembly is based on the draft from (Van Den Bussche et al., 2017), an important resource for population genomic studies in golden eagles. The sample for Hi-C library preparation used for the upgrade was donated by a female named Bonnie at the Texas State Aquarium.

Check out the alignments against the chicken genome assembly to understand how chromosomes of the golden eagle relate to those of other bird species in the DNA Zoo collection. While we've seen a lot of birds (and non-avian reptiles) displaying a highly conservative karyotype (see, for example, our blog post about the prairie chicken and the band-tailed pigeon), the golden eagle genome tells a very different story, with extensive rearrangements.

Whole-genome alignments of the golden eagle chromosomes to those of chicken (genome assembly GRCg6a, NCBI accession: GCF_000002315.5).

A genome for Uncle Fester

The Argentine black and white tegu, also known as the giant tegu, is the largest species of tegu lizards. A rare trait in the overwhelmingly cold-blooded lizard family, they can raise their body temperature by up to 10°C above their surroundings [1]!

Tegus are very affectionate and often kept as pets. Unfortunately, escaped and released tegus pose a serious threat to endangered species in environments like South Florida where it is classified as invasive species [2].

Today, we are releasing two chromosome-length genome assemblies for the giant tegu, both based on work from Michael Hiller's group at the Max Planck Institute of Molecular Cell Biology and Genetics to create the first ever genomics resource for Lacertoidea lizards.

The first assembly is based on the draft from (Roscito, Sameith & Parra et al., Nature Genetics, 2018) generated using the Illumina sequencing technology. The second assembly is generated using the later upgrade of the draft from (Roscito et al., GigaScience, 2018) that uses Pacific Biosciences long reads.

The blood sample for in situ Hi-C preparation was donated by a male individual named Uncle Fester, and provided to us by Shedd Aquarium.

See how the 19 chromosomes of the Argentine black and white tegu relate to those of the anole lizard, genome assembly from (Alföldi, Di Palma et al., Nature, 2011):

Whole genome alignment showing the correspondence between the 19 chromosomes of the Argentine black and white tegu and the assembled chromosomes of the green anole lizard, AnoCar2.0 assembly from (Alföldi, Di Palma et al., 2011).

Also, check out some examples of the intricate chromosome-wide folding patterns of the Argentine tegu genome, below, illustrating the formation of a chromosome-wide 3D clique – a feature rarely seen in mammals.

Thing, you're a handful!

Screenshot from Juicebox Assembly Tools (Dudchenko et al., bioRxiv, 2018), showing a fragment of the Hi-C map featuring two chromosomes, outlined in blue.

Turtle power

Green sea turtles are an endangered species that have undergone an estimated 90 percent population decrease over the past half century [1]. To help with the conservation efforts and to inform studies into the unique turtle body plan, we upgrade a draft genome assembly for Chelonia mydas from Wang, Pascual-Anaya, Zadissa & Li et al., 2013. We are grateful to SeaWorld for the sample used for in situ Hi-C preparation!

The chromosome-length genome assembly, shared here, supports previous hypotheses about close relatedness between turtles and the bird-crocodilian lineage, see whole genome alignment to chicken genome assembly CRCg6a below.

Whole genome alignment of the latest chicken genome assembly GRCg6a to the new chromosome-length assembly for the green sea turtle.

Read more about turtles, their unique anatomical features and their development in Wang, Pascual-Anaya, Zadissa & Li et al., 2013!