Assembly and comparison of two closely related Brassica napus genomes.
Assembly and comparison of two closely related Brassica napus genomes.
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DOI：
10.1111/pbi.12742
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发表时间：
2017-12
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;Hurgobin B;Golicz AA;Chan CK;Yuan Y;Lee H;Renton M;Meng J;Li R;Long Y;Zou J;Bancroft I;Chalhoub B;King GJ;Batley J;Edwards D
随着越来越多的植物基因组序列变得可用，很明显，基因含量在个体之间是不同的，并且预测物种的基因含量的挑战也随之而来。然而，基因组比较经常被组装和注释中的变化所混淆。区分真正的基因缺失和组装或注释中的变异对于准确鉴定物种中保守和可变基因是必不可少的。在这里，我们呈现了B. napus栽培品种Tapidor的从头组装，并与甘蓝型油菜栽培品种Darmor-bzh的改进组装进行了比较。两个品种使用相同的方法进行注释，以允许比较基因含量。我们确定了每个品种独特的基因，并将其与由于组装和注释变化而产生的人工制品区分开来。我们证明，使用一个共同的注释管道可以导致不同的基因预测，即使是密切相关的品种，和重复区域，在组装过程中崩溃的影响全基因组比较。在解释了组装和注释的差异后，我们证明了Darmor-bzh的基因组比Tapidor的基因组包含更多的基因。我们的研究结果是比较B. napus基因组之间真正差异的第一步，并突出了未来生产B. napus泛基因组的潜在错误来源。
As an increasing number of plant genome sequences become available, it is clear that gene content varies between individuals, and the challenge arises to predict the gene content of a species. However, genome comparison is often confounded by variation in assembly and annotation. Differentiating between true gene absence and variation in assembly or annotation is essential for the accurate identification of conserved and variable genes in a species. Here, we present the de novo assembly of the B. napus cultivar Tapidor and comparison with an improved assembly of the Brassica napus cultivar Darmor‐bzh. Both cultivars were annotated using the same method to allow comparison of gene content. We identified genes unique to each cultivar and differentiate these from artefacts due to variation in the assembly and annotation. We demonstrate that using a common annotation pipeline can result in different gene predictions, even for closely related cultivars, and repeat regions which collapse during assembly impact whole genome comparison. After accounting for differences in assembly and annotation, we demonstrate that the genome of Darmor‐bzh contains a greater number of genes than the genome of Tapidor. Our results are the first step towards comparison of the true differences between B. napus genomes and highlight the potential sources of error in future production of a B. napus pangenome.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
16.6
作者：
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：
14.9
作者：
Agarwala, Richa;Barrett, Tanya;Zbicz, Kerry
通讯作者：
Zbicz, Kerry
影响因子：
7
作者：
Cantarel, Brandi L.;Korf, Ian;Yandell, Mark
通讯作者：
Yandell, Mark
影响因子：
12.3
作者：
Langmead B;Trapnell C;Pop M;Salzberg SL
通讯作者：
Salzberg SL