The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell
Open accessAbstract
The handheld Oxford Nanopore MinION sequencer generates ultra-long reads with minimal cost and time requirements, which makes sequencing genomes at the bench feasible. Here, we sequence the gold standard Arabidopsis thaliana genome (KBS-Mac-74 accession) on the bench with the MinION sequencer, and assemble the genome using typical consumer computing hardware (4 Cores, 16 Gb RAM) into chromosome arms (62 contigs with an N50 length of 12.3 Mb). We validate the contiguity and quality of the assembly with two independent single-molecule technologies, Bionano optical genome maps and Pacific Biosciences Sequel sequencing. The new A. thaliana KBS-Mac-74 genome enables resolution of a quantitative trait locus that had previously been recalcitrant to a Sanger-based BAC sequencing approach. In summary, we demonstrate that even when the purpose is to understand complex structural variation at a single region of the genome, complete genome assembly is becoming the simplest way to achieve this goal.
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QUAST: quality assessment tool for genome assemblies
Gurevich, A., Saveliev, V., Vyahhi, N., & Tesler, G. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt086 · Cited by 11,172
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
Initiative, T. A. G. (2000) · Nature · doi:10.1038/35048692 · Cited by 9,301
Versatile and open software for comparing large genomes
Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L. (2004) · Genome Biology · doi:10.1186/gb-2004-5-2-r12 · Cited by 5,254
Cited by
The Third Revolution in Sequencing Technology
van Dijk, E. L., Jaszczyszyn, Y., Naquin, D., & Thermes, C. (2018) · Trends in Genetics · doi:10.1016/j.tig.2018.05.008 · Cited by 1,057
Efficient assembly of nanopore reads via highly accurate and intact error correction
Chen, Y., Nie, F., Xie, S.-Q., Zheng, Y.-F., Dai, Q., Bray, T., Wang, Y.-X., Xing, J.-F., Huang, Z.-J., Wang, D.-P., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20236-7 · Cited by 446
Evolutionary genomics can improve prediction of species’ responses to climate change
Waldvogel, A.-M., Feldmeyer, B., Rolshausen, G., Exposito-Alonso, M., Rellstab, C., Kofler, R., Mock, T., Schmid, K., Schmitt, I., Bataillon, T., et al. (2020) · Evolution Letters · doi:10.1002/evl3.154 · Cited by 348
Current status of structural variation studies in plants
Yuan, Y., Bayer, P. E., Batley, J., & Edwards, D. (2021) · Plant Biotechnology Journal · doi:10.1111/pbi.13646 · Cited by 163
Olanrewaju, O. S., Oyatomi, O., Babalola, O. O., & Abberton, M. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2021.798993 · Cited by 55
Metadata
- Authors
- Michael, T. P., Jupe, F., Bemm, F., Motley, S. T., Sandoval, J. P., Lanz, C., Loudet, O., Weigel, D., & Ecker, J. R.
- Venue
- Nature Communications
- Published
- 2018-02-07
- Volume
- 9
- Issue
- 1
- Pages
- 541-541
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W2949978892
- Cited by
- 286
- References
- 3
- FWCI
- 12.56
- Type
- journal article
- Language
- en
- Open access
- gold
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- Michael, T. P., Jupe, F., Bemm, F., Motley, S. T., Sandoval, J. P., Lanz, C., Loudet, O., Weigel, D., & Ecker, J. R. (2018). High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell. Nature Communications. https://doi.org/10.1038/s41467-018-03016-2
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