Greater prairie chicken (Tympanuchus cupido)
The greater prairie chicken, a member of the genus of grouse found only in North America, is a vulnerable species, with the Attwater's prairie chicken subspecies listed as critically endangered, and among the rarest birds in the world! Read more about greater prairie chickens in Audubon Field Guide.
Gregory "Slobirdr" Smith, Greater Prairie Chicken (Tympanuchus cupido), from flickr.com [CC BY-SA 2.0]
Chromosome-length genome assembly
Download the T_cupido_pinnatus_GPC_3440_v1_HiC.fasta.gz file containing the chromosome-length assembly of the greater prairie chicken genome. All modifications with respect to the draft (see below) are annotated in the T_cupido_pinnatus_GPC_3440_v1_HiC.assembly file. Some basic stats associated with the new reference, T_cupido_pinnatus_GPC_3440_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) |
|---|---|---|---|
979,919,245 | 60,668 | 47,484 | 790,671 |
Scaffold length (bp) | Number of scaffolds | Scaffold N50 (bp) | Longest scaffold (bp) |
|---|---|---|---|
983,924,394 | 11,967 | 68,568,989 | 185,320,317 |
Draft
The chromosome-length genome assembly is based on the draft assembly T_cupido_pinnatus_GPC_3440_v1 (GCA_001870855.1), credited below.
Johnson,J., Novak,B.J., Athrey,G., Shapiro,B. and Phelan,R. Whole genome sequence analysis reveals evolutionary history of extinct Heath Hen. Unpublished. https://www.ncbi.nlm.nih.gov/nuccore/MOXI00000000.1.
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, and provided to us by Houston Zoo.
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.
Johnson,J., Novak,B.J., Athrey,G., Shapiro,B. and Phelan,R. Whole genome sequence analysis reveals evolutionary history of extinct Heath Hen. Unpublished. https://www.ncbi.nlm.nih.gov/nuccore/MOXI00000000.1.
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.