The genomic diversification of grapevine clones
The genomic diversification of grapevine clones
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DOI：
10.1186/s12864-019-6211-2
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发表时间：
2019-12-12
期刊：
影响因子：
4.4
通讯作者：
Cantu, Dario
中科院分区：
文献类型：
--
作者：
Vondras, Amanda M.;Minio, Andrea;Cantu, Dario
背景：无性繁殖无性系积累体细胞突变。这项研究的目的是更好地了解克隆多样性，并涉及定义整个基因组的体细胞突变的性质。对15个仙粉黛葡萄克隆的基因组进行了测序，并利用其中一个克隆仙粉黛03产生的高度连续的基因组参考进行了比较。结果：虽然大多数杂合变异是共享的，但体细胞突变在个体和克隆的亚群中积累。总体而言，杂合突变在基因间隔区最常见，内含子比外显子更频繁。重复基因间隔区的CpG、CHG和CHH位点比基因间隔区和非重复基因间隔区的CpG、CHG和CHH位点发生转换突变的百分比要大得多，这可能是因为该区域的甲基化水平较高，而且甲基化的胞嘧啶经常自发脱氨。在少数发生在外显子的突变中，较大比例的突变发生在相对较少的克隆中时，可能是有害的。结论：这些数据支持三个主要结论。首先，重复的基因间空间是克隆基因组多样化的主要驱动力。其次，克隆积累了可能有害的突变。第三，这些数据表明，针对编码区的有害变异进行了选择，或者通过某种机制，编码中的突变频率低于基因组的非编码区。
Background: Vegetatively propagated clones accumulate somatic mutations. The purpose of this study was to better appreciate clone diversity and involved defining the nature of somatic mutations throughout the genome. Fifteen Zinfandel winegrape clone genomes were sequenced and compared to one another using a highly contiguous genome reference produced from one of the clones, Zinfandel 03.Results: Though most heterozygous variants were shared, somatic mutations accumulated in individual and subsets of clones. Overall, heterozygous mutations were most frequent in intergenic space and more frequent in introns than exons. A significantly larger percentage of CpG, CHG, and CHH sites in repetitive intergenic space experienced transition mutations than in genic and non-repetitive intergenic spaces, likely because of higher levels of methylation in the region and because methylated cytosines often spontaneously deaminate. Of the minority of mutations that occurred in exons, larger proportions of these were putatively deleterious when they occurred in relatively few clones.Conclusions: These data support three major conclusions. First, repetitive intergenic space is a major driver of clone genome diversification. Second, clones accumulate putatively deleterious mutations. Third, the data suggest selection against deleterious variants in coding regions or some mechanism by which mutations are less frequent in coding than noncoding regions of the genome.