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!

Genome assembly on the fly

Today we share two genome assemblies for the moth fly Clogmia albipunctata.

The first assembly was done in collaboration with Johannes (“Yogi”) Jaeger, Eva Jimenez Guri, Luca Cozzuto, Toni Hermoso Pulido, Julia Ponomarenko and Karl Wotton at the at EMBL/CRG Research Unit in Systems Biology, Barcelona (Spain) who generated and assembled the DNA-Seq data, as well as Urs Schmidt-Ott from the University of Chicago who provided the material for Hi-C. We used Hi-C to anchor, order and orient sequences into 6 chromosome-length scaffolds, as well as to remove contaminants. Funding for the Hi-C analysis was provided by the University of Chicago to Urs Schmidt-Ott.

We also share another assembly for this species, based on a draft genome assembly from Vicoso, Bachtrog, PLoS Biol. 2015, for comparison. The assemblies are largely independent, except that some of the same Hi-C data was used for both.

In Dudchenko, Science 2017, we observed that the contents of chromosome arm 2L of Drosophila melanogaster tend to be located on the same chromosome arm throughout Dipterans. As you can see below, this effect is seen in the moth fly as well!

Hi-C map of the new genome assembly for the moth fly. The 1D tracks show the the distribution of alignments of sequences from 2L chromosome arm of Drosophila melanogaster genome assembly (release 6 by The FlyBase Consortium/Berkeley Drosophila Genome Project/Celera Genomics), in dark blue, and the coverage track, in light blue. The majority of 2L alignments fall onto a single chromosome.