Beyond genomic variation--comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage.
Beyond genomic variation--comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage.
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DOI：
10.1186/1471-2164-15-250
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发表时间：
2014-03-31
期刊：
影响因子：
4.4
通讯作者：
Bonnema G
中科院分区：
文献类型：
--
作者：
Lin K;Zhang N;Severing EI;Nijveen H;Cheng F;Visser RG;Wang X;de Ridder D;Bonnema G
芜菁甘蓝是一种重要的经济作物品种。在其漫长的育种历史中，产生了大量的形态型，包括大白菜、小白菜等叶类蔬菜、萝卜块茎作物和油料作物。为了研究这种形态变异背后的遗传变异，我们对两种白菜亚种、萝卜作物（萝卜）和快速循环的基因组进行了重新测序、组装和注释。然后，我们分析了所得的两个基因组以及大白菜 Chiifu 参考基因组，以获得白菜泛基因组的印象。三种基因型之间蛋白质编码变化的基因数量低于拟南芥不同种质之间的数量，这可以通过白菜驯化导致的有效种群规模较小来解释。根据许多非芸苔属物种的直系学，我们估计三种白菜形态型之间的分化日期约为 250,000 年，远早于芸苔属驯化（5,000-10,000 年）。通过分析萝卜特有的基因，我们发现了过氧化物酶拷贝数差异的证据，指出苯丙素生物合成途径在形态变异产生中的作用。三种白菜形态型之间的估计分化日期表明，在驯化之前，白菜基因型之间已经存在相当大的分化。因此，我们的研究提供了两个新的白菜参考基因组，提供了一套计算机工具来分析所得的泛基因组，并利用这些工具来揭示白菜中发现的丰富形态变异背后的遗传驱动因素。本文的在线版本 (doi:10.1186/1471-2164-15-250) 包含补充材料，可供授权用户使用。
Brassica rapa is an economically important crop species. During its long breeding history, a large number of morphotypes have been generated, including leafy vegetables such as Chinese cabbage and pakchoi, turnip tuber crops and oil crops. To investigate the genetic variation underlying this morphological variation, we re-sequenced, assembled and annotated the genomes of two B. rapa subspecies, turnip crops (turnip) and a rapid cycling. We then analysed the two resulting genomes together with the Chinese cabbage Chiifu reference genome to obtain an impression of the B. rapa pan-genome. The number of genes with protein-coding changes between the three genotypes was lower than that among different accessions of Arabidopsis thaliana, which can be explained by the smaller effective population size of B. rapa due to its domestication. Based on orthology to a number of non-brassica species, we estimated the date of divergence among the three B. rapa morphotypes at approximately 250,000 YA, far predating Brassica domestication (5,000-10,000 YA). By analysing genes unique to turnip we found evidence for copy number differences in peroxidases, pointing to a role for the phenylpropanoid biosynthesis pathway in the generation of morphological variation. The estimated date of divergence among three B. rapa morphotypes implies that prior to domestication there was already considerably divergence among B. rapa genotypes. Our study thus provides two new B. rapa reference genomes, delivers a set of computer tools to analyse the resulting pan-genome and uses these to shed light on genetic drivers behind the rich morphological variation found in B. rapa. The online version of this article (doi:10.1186/1471-2164-15-250) contains supplementary material, which is available to authorized users.
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