Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids

背景+问题：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. 

主要研究：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. 

结果：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. 

结论：We use these results to gain insights into the different causes of gene loss, both in diploids and following polyploidisation, and pave the way for the application of machine learning methods to understanding the underlying biological and physical causes of gene presence/absence.

 摘 要 

植物基因组在同一物种内存在广泛的存在/缺失变异（PAV），但是导致这种变异产生的影响因子还不清楚，尤其是在芸苔属（Brassica）二倍体和多倍体之间的差异。本文中，作者对多倍体欧洲油菜（B. napus）及其两个二倍体祖先种芜菁（B. rapa）和花椰菜（B. oleracea）进行了泛基因组分析，推断二倍体和多倍体之间的PAV差异。通过对基因丢失的建模分析显示，二倍体中丢失倾向与主要与转座元件相关；而在欧洲油菜中，基因丢失倾向主要与同源重组相关。本文的研究结果，揭示了二倍体和多倍体化后基因丢失的不同原因，并为应用机器学习方法探究基因存在/缺失的潜在生物学和物理原因铺平道路。