Laboratory of Genetics, Wageningen University & Research (WUR), Droevendaalsesteeg, PB Wageningen, The Netherlands.
Laboratorio de Evolución y Domesticación de las Plantas, Facultad de Agronomía, Universidad de la República, Garzón, Montevideo, Uruguay.
Ann Bot. 2019 Feb 15;123(3):521-532. doi: 10.1093/aob/mcy186.
The genus Solanum includes important vegetable crops and their wild relatives. Introgression of their useful traits into elite cultivars requires effective recombination between hom(e)ologues, which is partially determined by genome sequence differentiation. In this study we compared the repetitive genome fractions of wild and cultivated species of the potato and tomato clades in a phylogenetic context.
Genome skimming followed by a clustering approach was used as implemented in the RepeatExplorer pipeline. Repeat classes were annotated and the sequences of their main domains were compared.
Repeat abundance and genome size were correlated and the larger genomes of species in the tomato clade were found to contain a higher proportion of unclassified elements. Families and lineages of repetitive elements were largely conserved between the clades, but their relative proportions differed. The most abundant repeats were Ty3/Gypsy elements. Striking differences in abundance were found in the highly dynamic Ty3/Gypsy Chromoviruses and Ty1/Copia Tork elements. Within the potato clade, early branching Solanum cardiophyllum showed a divergent repeat profile. There were also contrasts between cultivated and wild potatoes, mostly due to satellite amplification in the cultivated species. Interspersed repeat profiles were very similar among potatoes. The repeat profile of Solanum etuberosum was more similar to that of the potato clade.
The repeat profiles in Solanum seem to be very similar despite genome differentiation at the level of collinearity. Removal of transposable elements by unequal recombination may have been responsible for structural rearrangements across the tomato clade. Sequence variability in the tomato clade is congruent with clade-specific amplification of repeats after its divergence from S. etuberosum and potatoes. The low differentiation among potato and its wild relatives at the level of interspersed repeats may explain the difficulty in discriminating their genomes by genomic in situ hybridization techniques.
茄属植物包括重要的蔬菜作物及其野生近缘种。将其有用性状导入优良品种需要同源（e）基因之间的有效重组，而这部分取决于基因组序列的分化。在本研究中，我们在系统发育背景下比较了马铃薯和番茄分支野生种和栽培种的重复基因组部分。
采用基因组刮擦法结合聚类方法，如 RepeatExplorer 管道中实现的方法。对重复类进行注释，并比较其主要结构域的序列。
重复丰度和基因组大小呈正相关，番茄分支物种的较大基因组中发现含有较高比例的未分类元件。分支间的重复元件家族和谱系基本保守，但相对比例不同。最丰富的重复是 Ty3/Gypsy 元件。在高度动态的 Ty3/Gypsy Chromoviruses 和 Ty1/Copia Tork 元件中，丰度差异显著。在马铃薯分支中，早期分支的 Solanum cardiophyllum 表现出不同的重复特征。栽培种和野生马铃薯之间也存在差异，主要是由于卫星扩增。马铃薯之间的散布重复特征非常相似。Solanum etuberosum 的重复特征与马铃薯分支更为相似。
尽管在共线性水平上存在基因组分化，但茄属植物的重复特征似乎非常相似。通过不等交换去除转座元件可能导致了番茄分支的结构重排。番茄分支的序列变异与该分支与 Solanum etuberosum 和马铃薯分化后的重复特化扩增一致。在散布重复水平上，马铃薯与其野生近缘种之间的低分化可能解释了为什么用基因组原位杂交技术难以区分它们的基因组。
