Eastern yellow robin, inland lineage (Eopsaltria australis)

Research indicates that the Eastern Yellow Robin may be on its way to becoming two differently adapted lineages: Eastern Yellow Robins inland of the Great Dividing Range are genetically very different to those on the coastal side in ways that are likely to be ecologically important, and they do not interbreed freely and successfully. Read more about eastern yellow robin, inland lineages on Eastern Yellow Robin Project website.

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Photo Description: Eastern Yellow Robin (Eopsaltria australis) - Inland lineage. Photo Credits and acknowledgements - Geoff Park

Chromosome-length genome assembly

Download the eyr_v1_HiC.fasta.gz file containing the chromosome-length assembly of the eastern yellow robin, inland lineage genome. All modifications with respect to the draft (see below) are annotated in the eyr_v1_HiC.assembly file. Some basic stats associated with the new reference, eyr_v1_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
1,226,241,395
30,380
479,343
4,736,821
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
1,230,412,632
20,980
110,315,225
150,933,131
Draft

The chromosome-length genome assembly is based on the draft assembly eyr_v1 (GCA_003426825.1), credited below.

Gan, H.M., Falk, S., Morales, H.E., Austin, C.M., Sunnucks, P., Pavlova, A., 2019. Genomic evidence of neo-sex chromosomes in the eastern yellow robin. GigaScience, 8(9), giz111. https://doi.org/10.1093/gigascience/giz111.

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 heart 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.

Gan, H.M., Falk, S., Morales, H.E., Austin, C.M., Sunnucks, P., Pavlova, A., 2019. Genomic evidence of neo-sex chromosomes in the eastern yellow robin. GigaScience, 8(9), giz111. https://doi.org/10.1093/gigascience/giz111.

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.