Eastern water dragon (Intellagama lesueurii lesueurii)
The eastern water dragon is Autralia's largest dragon lizard. It is more often heard than seen as it dives into the water when disturbed. It can remain submerged for around one hour! Read more about eastern water dragons on the Australian Museum website.
Photo Description - The Eastern Water Dragon (Intellagama lesueurii). Photo credits: Celine Frere, University of the Sunshine Coast [CC].
Chromosome-length genome assembly
Download the EWD_hifiasm_HiC.fasta.gz file containing the chromosome-length assembly of the Eastern water dragon genome. All modifications with respect to the draft (see below) are annotated in the EWD_hifiasm_HiC.assembly file. Some basic stats associated with the new reference, EWD_hifiasm_HiC, are listed below. The full data release can be explored here.
Contig length (bp) | Number of contigs | Contig N50 (bp) | Longest contig (bp) |
|---|---|---|---|
1,816,116,528 | 1,457 | 11,213,063 | 55,971,000 |
Scaffold length (bp) | Number of scaffolds | Scaffold N50 (bp) | Longest scaffold (bp) |
|---|---|---|---|
1,816,535,528 | 619 | 268,945,440 | 353,375,234 |
Draft
The chromosome-length genome assembly is based on the draft assembly EWD_hifiasm, credited below.
This genome assembly was created in collaboration with Associate Prof. Celine Frere, Drs. Dan Powell and Nicola Kent at The University of Sunshine Coast, Australia. The draft genome assembly effort was supported by The Australian Amphibian and Reptile Genomics Initiative (AusARG), a collaborative at Bioplatforms Australia framework initiative building genomic resources for thorough understanding of evolution and conservation of Australia's unique native Amphibians and Reptiles that are now under threat, through climate, disease or habitat modification. The draft genome assembly was created using high-fidelity long reads from Pacific Biosciences technology (circular consensus sequencing). The reads were assembled using the long-read assembler Hifiasm (Cheng et al., 2021).
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 liver sample for in situ Hi-C preparation was obtained from Celine Frere (University of the Sunshine Coast).
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.
This genome assembly was created in collaboration with Associate Prof. Celine Frere, Drs. Dan Powell and Nicola Kent at The University of Sunshine Coast, Australia. The draft genome assembly effort was supported by The Australian Amphibian and Reptile Genomics Initiative (AusARG), a collaborative at Bioplatforms Australia framework initiative building genomic resources for thorough understanding of evolution and conservation of Australia's unique native Amphibians and Reptiles that are now under threat, through climate, disease or habitat modification. The draft genome assembly was created using high-fidelity long reads from Pacific Biosciences technology (circular consensus sequencing). The reads were assembled using the long-read assembler Hifiasm (Cheng et al., 2021).
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.