Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids.
Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids.
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DOI：
10.1111/pbi.13674
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发表时间：
2021-12
影响因子：
13.8
通讯作者：
Edwards D
中科院分区：
文献类型：
--
作者：
Bayer PE;Scheben A;Golicz AA;Yuan Y;Faure S;Lee H;Chawla HS;Anderson R;Bancroft I;Raman H;Lim YP;Robbens S;Jiang L;Liu S;Barker MS;Schranz ME;Wang X;King GJ;Pires JC;Chalhoub B;Snowdon RJ;Batley J;Edwards D
植物基因组在一个物种内表现出显着的存在/不存在变异（PAV）;然而，导致这种变异的因素尚未在芸苔属二倍体和多倍体中进行系统研究。在这里，我们开发了多倍体甘蓝型油菜及其两个二倍体祖先基因组B. rapa和B. oleracea的泛基因组，以推断PAV在二倍体和多倍体之间可能有何不同。对基因丢失的模拟表明，在二倍体中丢失倾向主要与转座因子相关，而在B. napus中，基因丢失倾向与同源重组相关。我们利用这些结果来深入了解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来理解基因存在/缺失的潜在生物和物理原因铺平道路。
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.
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影响因子：
12.3
作者：
Buels R;Yao E;Diesh CM;Hayes RD;Munoz-Torres M;Helt G;Goodstein DM;Elsik CG;Lewis SE;Stein L;Holmes IH
通讯作者：
Holmes IH
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Golicz, Agnieszka A.;Bayer, Philipp E.;Barker, Guy C.;Edger, Patrick P.;Kim, HyeRan;Martinez, Paula A.;Chan, Chon Kit Kenneth;Severn-Ellis, Anita;McCombie, W. Richard;Parkin, Isobel A. P.;Paterson, Andrew H.;Pires, J. Chris;Sharpe, Andrew G.;Tang, Haibao;Teakle, Graham R.;Town, Christopher D.;Batley, Jacqueline;Edwards, David
通讯作者：
Edwards, David
影响因子：
12.3
作者：
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Wortman, Jennifer R.
影响因子：
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作者：
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