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Published (Version of record)CC BY-NC-ND V4.0, Open Access
Published (Version of record)CC BY-NC-ND V4.0, Open
Journal article
Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids
Plant Biotechnology Journal (Online), Vol.19(12), pp.2488-2500
12/2021
PMCID: PMC8633514
PMID: 34310022
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Source: InCites
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.
Details
- Title
- Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids
- Creators
- Philipp E Bayer - University of Western AustraliaArmin Scheben - University of Western AustraliaAgnieszka A Golicz - University of MelbourneYuxuan Yuan - University of Western AustraliaSebastien Faure - Innolea SASHuey Tyng Lee - University of GiessenHarmeet Singh Chawla - University of GiessenRobyn Anderson - University of Western AustraliaIan Bancroft - University of YorkHarsh Raman - NSW Department of Primary IndustriesYong Pyo Lim - Chungnam National UniversitySteven Robbens - BASF Innovation CenterLixi Jiang - Zhejiang UniversityShengyi Liu - Chinese Academy of Agricultural SciencesMichael S Barker - University of ArizonaM. Eric Schranz - Wageningen University & ResearchXiaowu Wang - Institute of Vegetables and FlowersGraham King - Southern Cross UniversityJ Chris Pires - University of MissouriBoulos Chalhoub - Zhejiang UniversityRod J Snowdon - University of GiessenJacqueline Batley - University of Western AustraliaDavid Edwards - University of Western Australia
- Publication Details
- Plant Biotechnology Journal (Online), Vol.19(12), pp.2488-2500
- Publisher
- Wiley-Blackwell Publishing Ltd.
- Number of pages
- 13
- Grant note
- Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, and Forestry. Grant Number: 213006-05-4-SB110 ARC. Grant Numbers: DP1601004497, LP130100925, LP140100537
- Identifiers
- 991012961498902368
- Copyright
- © 2021 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.
- Academic Unit
- Science; Faculty of Science and Engineering; Southern Cross Plant Science
- Language
- English
- Resource Type
- Journal article