Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids
| Autor: | HueyTyng Lee, Michael S. Barker, Steven Robbens, Philipp E. Bayer, Armin Scheben, Ian Bancroft, Yuxuan Yuan, Agnieszka A. Golicz, J. Chris Pires, Sébastien Faure, M. Eric Schranz, Robyn Anderson, Lixi Jiang, Xiaowu Wang, Yong Pyo Lim, Harmeet Singh Chawla, David Edwards, Jacqueline Batley, Graham J.W. King, Rod J. Snowdon, Harsh Raman, Boulos Chalhoub, Shengyi Liu |
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| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Transposable element
pangenome Brassica Plant Science Biology Genome Polyploidy Polyploid Gene Research Articles Genetics Brassica napus fungi food and beverages biology.organism_classification Plant genomes Diploidy Biosystematiek gene loss propensity machine learning Biosystematics Ploidy EPS transposable elements Agronomy and Crop Science Recombination Genome Plant Biotechnology Research Article XGBoost |
| Zdroj: | Plant Biotechnology Journal, 19(12), 2488-2500 Plant Biotechnology Journal Plant Biotechnology Journal 19 (2021) 12 |
| ISSN: | 1467-7644 1435-8603 |
| Popis: | Summary 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. |
| Databáze: | OpenAIRE |
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