Argentine black and white tegu (Salvator merianae)
Salvator merianae has recently been shown to be one of the few partially warm-blooded lizards, having a temperature up to 10 C (18 F) higher than the ambient temperature at night time during their reproductive season! Read more about Argentine black and white tegu on Wikipedia.
Close-up view of the head of an Argentine black and white tegu by Christoph Anton Mitterer [CC BY-SA 2.0], from flickr.com
Chromosome-length genome assembly
Download the HLtupMer6_HiC.fasta.gz file containing the chromosome-length (2n=38) assembly of the Argentine black and white tegu genome. All modifications with respect to the draft (see below) are annotated in the HLtupMer6_HiC.assembly file. Some basic stats associated with the new reference, HLtupMer6_HiC, are listed below. The full data release can be explored here. Note that chromosome-length genome assembly based on another draft is available for this species, here.
Contig length (bp) | Number of contigs | Contig N50 (bp) | Longest contig (bp) |
|---|---|---|---|
2,033,833,041 | 23,183 | 370,220 | 3,748,346 |
Scaffold length (bp) | Number of scaffolds | Scaffold N50 (bp) | Longest scaffold (bp) |
|---|---|---|---|
2,067,734,641 | 4,375 | 314,194,259 | 414,523,068 |
Draft
The chromosome-length genome assembly is based on the draft assembly HLtupMer6 (GCA_003586115.2), credited below.
Roscito, Juliana G., Katrin Sameith, Martin Pippel, Kees-Jan Francoijs, Sylke Winkler, Andreas Dahl, Georg Papoutsoglou, Gene Myers, and Michael Hiller. 2018. "The Genome of the Tegu Lizard Salvator Merianae: Combining Illumina, PacBio, and Optical Mapping Data to Generate a Highly Contiguous Assembly." GigaScience 7 (12). https://doi.org/10.1093/gigascience/giy141.
Method
3D Assembly was performed using 3D-DNA pipeline (Dudchenko et al., Science, 2017). The genome was reviewed using Juicebox Assembly Tools (Dudchenko et al., bioRxiv, 2018). See Methods for more information.
Hi-C sample
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. We thank Texas State Aquarium and Houston Zoo for additional Argentine black and white tegu samples.
Hi-C Contact maps
Hi-C data was aligned to the draft reference using Juicer (Durand, Shamim et al., Cell Systems, 2016), and contact maps visualizing the alignments with respect to the draft and the new reference were built using 3D-DNA (Dudchenko et al., Science, 2017). The contact maps can be explored below via Juicebox.js interactive tool (Robinson et al., Cell Systems, 2018). To explore the assembly in greater detail, please download the .hic and .assembly files from the data release folder and use Juicebox Assembly Tools (Dudchenko et al., bioRxiv, 2018).
References
If you use this genome assembly in your research, please check that the conditions of use associated with the draft permit it, and acknowledge the following work.
Roscito, Juliana G., Katrin Sameith, Martin Pippel, Kees-Jan Francoijs, Sylke Winkler, Andreas Dahl, Georg Papoutsoglou, Gene Myers, and Michael Hiller. 2018. "The Genome of the Tegu Lizard Salvator Merianae: Combining Illumina, PacBio, and Optical Mapping Data to Generate a Highly Contiguous Assembly." GigaScience 7 (12). https://doi.org/10.1093/gigascience/giy141.
Dudchenko, O., Batra, S.S., Omer, A.D., Nyquist, S.K., Hoeger, M., Durand, N.C., Shamim, M.S., Machol, I., Lander, E.S., Aiden, A.P., Aiden, E.L., 2017. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92–95. https://doi.org/10.1126/science.aal3327.
Dudchenko, O., Shamim, M.S., Batra, S., Durand, N.C., Musial, N.T., Mostofa, R., Pham, M., Hilaire, B.G.S., Yao, W., Stamenova, E., Hoeger, M., Nyquist, S.K., Korchina, V., Pletch, K., Flanagan, J.P., Tomaszewicz, A., McAloose, D., Estrada, C.P., Novak, B.J., Omer, A.D., Aiden, E.L., 2018. The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. bioRxiv 254797. https://doi.org/10.1101/254797.
Disclaimer
This is a work in progress. If you notice any discrepancies in the map or have data that confirms or contradicts the suggested reference, please email us at thednazoo@gmail.com or leave a comment on the Forum.