Eastern yellow robin (Eopsaltria australis)

Eastern yellow robins belong to the genus Eopsaltria which translates as "dawn-harper". Appropriately, they are among the first birds to be heard at dawn. Read more about eastern yellow robins on the Australian Museum website.

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Eastern Yellow Robin (Eopsaltria australis). Photo credits and acknowledgements - Geoff Park [CC].

Chromosome-length genome assembly

Download the VIC030_NPI.genome.scf.masked_HiC.fasta.gz file containing the chromosome-length assembly of the eastern yellow robin genome. All modifications with respect to the draft (see below) are annotated in the VIC030_NPI.genome.scf.masked_HiC.assembly file. Some basic stats associated with the new reference, VIC030_NPI.genome.scf.masked_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
1,199,530,515
12,953
1,482,134
12,787,735
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
1,201,888,030
8,987
111,210,322
149,447,496
Draft

The chromosome-length genome assembly is based on the draft assembly VIC030_NPI.genome.scf.masked, credited below.

The draft was generated by Han Ming Gan and others at the Deakin Genomics Centre, with assembly by Gabriel Low. The draft was created using MaSuRCA v3.2.8 (Zimin et al. 2013), using Oxford Nanopore MinION and PacBio reads polished with short-insert size Illumina NovaSeq reads. The work was enabled by wildlife authorities including the Victorian Department of Environment, Land, Water and Planning, Parks Victoria, and the Australian Bird and Bat Banding Scheme. The research has been funded by the Holsworth Wildlife Endowment Fund, Australian Research Council grant DP180102359, and Monash University.

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 donated by a female individual, and obtained from Alexandra Pavlova (Monash University, Melbourne).

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 draft was generated by Han Ming Gan and others at the Deakin Genomics Centre, with assembly by Gabriel Low. The draft was created using MaSuRCA v3.2.8 (Zimin et al. 2013), using Oxford Nanopore MinION and PacBio reads polished with short-insert size Illumina NovaSeq reads. The work was enabled by wildlife authorities including the Victorian Department of Environment, Land, Water and Planning, Parks Victoria, and the Australian Bird and Bat Banding Scheme. The research has been funded by the Holsworth Wildlife Endowment Fund, Australian Research Council grant DP180102359, and Monash University.

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.