@article{41a0bab891044e8e8c656e9fd8247441,
title = "Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids",
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.",
keywords = "Brassica, XGBoost, gene loss propensity, machine learning, pangenome, transposable elements",
author = "Bayer, {Philipp E.} and Armin Scheben and Golicz, {Agnieszka A.} and Yuxuan Yuan and Sebastien Faure and Lee, {Huey Tyng} and Chawla, {Harmeet Singh} and Robyn Anderson and Ian Bancroft and Harsh Raman and Lim, {Yong Pyo} and Steven Robbens and Lixi Jiang and Shengyi Liu and Barker, {Michael S.} and Schranz, {M. Eric} and Xiaowu Wang and King, {Graham J.} and Pires, {J. Chris} and Boulos Chalhoub and Snowdon, {Rod J.} and Jacqueline Batley and David Edwards",
note = "Funding Information: This work is funded by the Australia Research Council (Projects DP1601004497, LP140100537 and LP130100925), and resources provided by the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia. Dr. Philipp Bayer acknowledges the support of the Forrest Research Foundation. YP Lim was supported by Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, and Forestry (IPET) through Golden Seed Project (213006‐05‐4‐SB110), funded by Ministry of Agriculture, Food and Rural Affairs (MAFRA), Ministry of Oceans and Fisheries (MOF), Rural Development Administration (RDA) and Korea Forest Services (KFS), South Korea. This work was supported by UK Biotechnology and Biological Sciences Research Council BB/L002124/1 and BB/R019819/1 to IB. Publisher Copyright: {\textcopyright} 2021 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.",
year = "2021",
month = dec,
doi = "10.1111/pbi.13674",
language = "English (US)",
volume = "19",
pages = "2488--2500",
journal = "Plant Biotechnology Journal",
issn = "1467-7644",
publisher = "Wiley-Blackwell",
number = "12",
}