California condor (Gymnogyps californianus)
The California condor is the largest North American land bird. It is also one of the world's longest-living birds, with a lifespan of up to 60 years! Read more about California condors on San Diego Zoo website.
Image by PublicDomainImages from Pixabay [Pixabay License]
Chromosome-length genome assembly
Download the gc_PacBio_HiC.fasta.gz file containing the chromosome-length assembly of the California condor genome. All modifications with respect to the draft (see below) are annotated in the gc_PacBio_HiC.assembly file. Some basic stats associated with the new reference, gc_PacBio_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) |
|---|---|---|---|
1,239,863,868 | 1,174 | 17,075,248 | 77,968,233 |
Scaffold length (bp) | Number of scaffolds | Scaffold N50 (bp) | Longest scaffold (bp) |
|---|---|---|---|
1,240,179,868 | 542 | 85,346,818 | 219,006,665 |
Draft
The chromosome-length genome assembly is based on the draft assembly gc_PacBio, credited below.
The PacBio draft genome assembly was generated by Cynthia Steiner (San Diego Zoo) and Oliver Ryder (San Diego Zoo). We also acknowledge David Mindell (UC Berkeley), Rauri Bowie (UC Berkeley) and Jeff Wall (UCSF), The Peregrine Fund, Chris Parish and Rick Watson for their help with this effort.
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 provided to us by The Peregrine Fund.
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.
The PacBio draft genome assembly was generated by Cynthia Steiner (San Diego Zoo) and Oliver Ryder (San Diego Zoo). We also acknowledge David Mindell (UC Berkeley), Rauri Bowie (UC Berkeley) and Jeff Wall (UCSF), The Peregrine Fund, Chris Parish and Rick Watson for their help with this effort.
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.