Summary
Publication
Lin, Y., Wang, J., Delhomme, N., Schiffthaler, B., Sundström, G., Zuccolo, A., Nystedt, B., Hvidsten, T.R., Torre, A.R., Cossu, R.M., Hoeppner, M.P., Lantz, H., Scofield, D.G., Zamani, N., Johansson, A., Mannapperuma, C., Robinson, K.M., Mähler, N., Leitch, I.J., Pellicer, J., Park, E., Montagu, M.V., Peer, Y.V., Grabherr, M.G., Jansson, S., Ingvarsson, P.K., & Street, N.R. (2018). Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen. Proceedings of the National Academy of Sciences of the United States of America.
Name
Populus tremuloides - Reference Genome
Resource Type
Genome Assembly
Organism
Details
Program, Pipeline, Workflow or Method Name
ABySS
Program Version
1.3.6
Date Performed
Thursday, June 13, 2019 - 12:15
Data Source
Description and Download
P. tremula genome was assembled using a hierarchical assembly approach that comprised separate contig assemblies of the 454 and Illumina data that were merged in a stepwise manner, with the final merged assembly subsequently scaffolded using the MP libraries. Other approaches were tested including: hybrid assemblies using the CLC de novo tool, ABySS, and GS-Assembler, but these approaches performed worse than the hierarchical approach. The P. tremuloides genome was produced using a single assembly of Illumina short-read, PE libraries assembly was performed using only ABySS. Both assemblies contained >100,000 scaffolds and had relatively low contiguity. Source: https://www.pnas.org/content/115/46/E10970

Downloads

Genomic scaffolds
All Gene Models CDS (fasta format)
All Gene Models Protein (fasta format)
All Gene Models GFF (Fasta format)
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