The DOI matches its Crossref record; 55 of the 55 references it cites were found in a registry or an index.
Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus
Open accessAbstract
Summary: Homoeologous exchanges (HE s) have been shown to generate novel gene combinations and phenotypes in a range of polyploid species. Gene presence/absence variation (PAV) is also a major contributor to genetic diversity. In this study, we show that there is an association between these two events, particularly in recent Brassica napus synthetic accessions, and that these represent a novel source of genetic diversity, which can be captured for the improvement of this important crop species. By assembling the pangenome of B. napus, we show that 38% of the genes display PAV behaviour, with some of these variable genes predicted to be involved in important agronomic traits including flowering time, disease resistance, acyl lipid metabolism and glucosinolate metabolism. This study is a first and provides a detailed characterization of the association between HE s and PAV s in B. napus at the pangenome level.
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R: A Language and Environment for Statistical Computing
R Core Team (2025) · doi:10.32614/r.manuals · Cited by 352,181
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
BLAST+: architecture and applications
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., & Zdobnov, E. M. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv351 · Cited by 13,344
Conesa, A., Götz, S., García-Gómez, J. M., Terol, J., Talón, M., & Robles, M. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti610 · Cited by 11,495
Jalview Version 2—a multiple sequence alignment editor and analysis workbench
Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M., & Barton, G. J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp033 · Cited by 10,235
InterProScan 5: genome-scale protein function classification
Jones, P., Binns, D., Chang, H.-Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G., et al. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu031 · Cited by 9,301
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Metadata
- Authors
- Hurgobin, B., Golicz, A. A., Bayer, P. E., Chan, C. K., Tirnaz, S., Dolatabadian, A., Schiessl, S. V., Samans, B., Montenegro, J. D., Parkin, I. A. P., Pires, J. C., Chalhoub, B., King, G. J., Snowdon, R., Batley, J., & Edwards, D.
- Venue
- Plant Biotechnology Journal
- Publisher
- Wiley
- Published
- 2018-01-10
- Volume
- 16
- Issue
- 7
- Pages
- 1265-1274
- ISSN
- 1467-7644 (ISSN-L)
- 1467-7652
- OpenAlex
- W2771519711
- Cited by
- 287
- References
- 55
- FWCI
- 17.27
- Type
- journal article
- Language
- en
- Open access
- gold
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- Hurgobin, B., Golicz, A. A., Bayer, P. E., Chan, C. K., Tirnaz, S., Dolatabadian, A., Schiessl, S. V., Samans, B., Montenegro, J. D., Parkin, I. A. P., Pires, J. C., Chalhoub, B., King, G. J., Snowdon, R., Batley, J., & Edwards, D. (2018). Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus. Plant Biotechnology Journal. https://doi.org/10.1111/pbi.12867
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