'Hillquist' blackberry (Rubus argutus)
'Hillquist' was originally discovered in Ashland, VA by L.G. Hillquist, who noticed that some of the wild blackberries growing in his backyard possessed an unusual fruiting habit known as primocane fruiting. Read more about 'Hillquist' blackberries on USDA National Agricultural Library website.
'Hillquist' blackberry at the University of Arkansas, photo by Margaret Worthington
Chromosome-length genome assembly
Download the Hillquist_genome_v1_purged_primary_contigs_HiC.fasta.gz file containing the chromosome-length (2n=14) assembly of the 'Hillquist' blackberry genome. All modifications with respect to the draft (see below) are annotated in the Hillquist_genome_v1_purged_primary_contigs_HiC.assembly file. Some basic stats associated with the new reference, Hillquist_genome_v1_purged_primary_contigs_HiC, are listed below. The full data release can be explored here.
Contig length (bp) | Number of contigs | Contig N50 (bp) | Longest contig (bp) |
|---|---|---|---|
297,859,595 | 1,105 | 557,470 | 5,512,874 |
Scaffold length (bp) | Number of scaffolds | Scaffold N50 (bp) | Longest scaffold (bp) |
|---|---|---|---|
298,237,095 | 350 | 38,624,057 | 45,459,684 |
Draft
The chromosome-length genome assembly is based on the draft assembly Hillquist_genome_v1_purged_primary_contigs, credited below.
This genome assembly was generated as part of a collaborative effort between the University of Arkansas, USDA-ARS, North Carolina State University, DNA Zoo, NIAB-EMR, Pairwise Plants, and the Wellcome Sanger Institute.
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 leaves sample for in situ Hi-C preparation was obtained from Nahla V. Bassil, USDA-ARS National Clonal Germplasm Repository.
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 generated as part of a collaborative effort between the University of Arkansas, USDA-ARS, North Carolina State University, DNA Zoo, NIAB-EMR, Pairwise Plants, and the Wellcome Sanger Institute.
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.