Abstract
Plant genomes demonstrate significant presence/absence variation (PAV) within a species; however, the factors that lead to this variation have not been studied systematically in Brassica across diploids and polyploids. Here, we developed pangenomes of polyploid Brassica napus and its two diploid progenitor genomes B. rapa and B. oleracea to infer how PAV may differ between diploids and polyploids. Modelling of gene loss suggests that loss propensity is primarily associated with transposable elements in the diploids while in B. napus, gene loss propensity is associated with homoeologous recombination. We use these results to gain insights into the different causes of gene loss, both in diploids and following polyploidization, and pave the way for the application of machine learning methods to understanding the underlying biological and physical causes of gene presence/absence.
Original language | English |
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Pages (from-to) | 2488-2500 |
Number of pages | 13 |
Journal | Plant Biotechnology Journal |
Volume | 19 |
Issue number | 12 |
Early online date | 26 Jul 2021 |
DOIs | |
Publication status | Published - Dec 2021 |
Keywords
- Brassica
- gene loss propensity
- machine learning
- pangenome
- transposable elements
- XGBoost
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Dive into the research topics of 'Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids'. Together they form a unique fingerprint.Datasets
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Sequencing reads for Brassica napus Darmor-bzh resequencing along with additional cultivars
Bayer, P. (Creator), Scheben, A. P. (Creator), Golicz, A. (Creator), Yuan, A. (Creator), Faure, S. (Creator), Lee, J. (Creator), Chawla, H. S. (Creator), Bancroft, I. (Creator), Raman, H. (Creator), Lim, Y. P. (Creator), Robbens, S. (Creator), Jiang, L. (Creator), Liu, S. (Creator), Barker, M. S. (Creator), Schranz, E. (Creator), Wang, X. (Creator), King, G. J. (Creator), Pires, C. (Creator), Chalhoub, B. (Creator), Snowdon, R. J. (Creator), Batley, J. (Creator) & Edwards, D. (Creator), The University of Western Australia, 25 Mar 2020
https://www.ebi.ac.uk/ena/browser/view/PRJNA613532
Dataset
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Brassica oleracea, rapa, napus pangenome data
Bayer, P. (Creator), Scheben, A. P. (Creator), Golicz, A. (Creator), Yuan, A. (Creator), Faure, S. (Creator), Lee, J. (Creator), Chawla, H. S. (Creator), Bancroft, I. (Creator), Raman, H. (Creator), Lim, Y. P. (Creator), Robbens, S. (Creator), Jiang, L. (Creator), Liu, S. (Creator), Barker, M. S. (Creator), Schranz, E. (Creator), Wang, X. (Creator), King, G. J. (Creator), Pires, C. (Creator), Chalhoub, B. (Creator), Snowdon, R. J. (Creator), Batley, J. (Creator) & Edwards, D. (Creator), The University of Western Australia, 22 Jul 2020
Dataset