Abstract：
Mounting evidence recognizes structural variations (SVs) and repetitive DNA sequences as crucial players in shaping the existing grape phenotypic diversity at intra- and inter-species levels. To deepen our understanding on the abundance, diversity, and distribution of SVs and repetitive DNAs, including transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), we re-sequenced the genomes of the ancient grapes Aglianico and Falanghina. The analysis of large copy number variants (CNVs) detected candidate polymorphic genes that are involved in the enological features of these varieties. In a comparative analysis of Aglianico and Falanghina sequences with 21 publicly available genomes of cultivated grapes, we provided a genome-wide annotation of grape TEs at the lineage level. We disclosed that at least two main clusters of grape cultivars could be identified based on the TEs content. Multiple TEs families appeared either significantly enriched or depleted. In addition, in silico and cytological analyses provided evidence for a diverse chromosomal distribution of several satellite repeats between Aglianico, Falanghina, and other grapes. Overall, our data further improved our understanding of the intricate grape diversity held by two Italian traditional varieties, unveiling a pool of unique candidate genes never so far exploited in breeding for improved fruit quality.
摘要：
越来越多的证据认为结构变异（SV）和重复DNA序列是在种内和种间水平上塑造现有葡萄表型多样性的关键因素。为了加深我们对丰富的理解，多样性,以及SV和重复DNA的分布，包括转座因子（TE）和串联重复的卫星DNA（satDNA），我们重新测序了古葡萄Aglianico和Falanghina的基因组。大拷贝数变体（CNV）的分析检测到了与这些品种的环境特征有关的候选多态性基因。在对Aglianico和Falanghina序列与21种公开可用的栽培葡萄基因组的比较分析中，我们在谱系水平上提供了葡萄TEs的全基因组注释。我们公开了至少两个主要的葡萄品种集群可以根据TE含量来鉴定。多个TE家族似乎显着富集或耗尽。此外,计算机模拟和细胞学分析为Aglianico之间几个卫星重复序列的不同染色体分布提供了证据，Falanghina,和其他葡萄。总的来说,我们的数据进一步改善了我们对两种意大利传统品种复杂的葡萄多样性的理解，揭示了迄今为止从未在育种中利用过的独特候选基因库，以提高水果质量。
