Modern sugarcane cultivars are highly polyploid and derived from the hybridization of Saccharum officinarum and S. spontaneum , thus leading to singularly complex genomes . The complex genome has hindered the study of genomic structures. Here, we adopted a computational strategy to isolate highly repetitive and abundant sequences in either S. officinarum or S. spontaneum and isolated four S. spontaneum -enriched retrotransposons. Fluorescence in situ hybridization (FISH) assays with these repetitive DNA sequences generated whole-genome painting signals for S. spontaneum but not for S. officinarum . We demonstrated that these repetitive sequence-based probes distinguish the parental S. spontaneum genome in hybrids derived from crosses between it and S. officinarum . A cytological analysis of 14 modern sugarcane cultivars revealed that the percentages of chromosomes with introgressive S. spontaneum fragments ranged from 11.9 to 40.9% and substantially exceeded those determined for previously investigated cultivars (5–13%). The comparatively higher percentages of introgressive S. spontaneum fragments detected in the aforementioned cultivars indicate frequent recombination between parental genomes. Here, we present the application of our strategy to isolate species-specific cytological markers. This information may help to elucidate complex plant genomic structures and trace their evolutionary histories.

中文翻译：

---

物种特异性丰富的逆转录转座子阐明了现代甘蔗品种的基因组组成

现代甘蔗栽培品种是高度多倍体的，由 Saccharum officinarum 和 S. spontaneum 杂交衍生而来，从而导致基因组异常复杂。复杂的基因组阻碍了基因组结构的研究。在这里，我们采用了一种计算策略来分离 S. officinarum 或 S. spontaneum 中的高度重复和丰富的序列，并分离出四个富含 S. spontaneum 的逆转录转座子。使用这些重复 DNA 序列进行的荧光原位杂交 (FISH) 分析为 S. spontaneum 生成了全基因组着色信号，但对于 S. officinarum 则没有。我们证明了这些基于重复序列的探针区分了亲本 S. spontaneum 基因组中的亲本 S. spontaneum 基因组，该基因组源自它与 S. officinarum 之间的杂交。对 14 个现代甘蔗品种的细胞学分析显示，具有渐渗性 S.spontaneum 片段的染色体百分比范围为 11.9% 至 40.9%，大大超过了先前研究的栽培品种所确定的百分比 (5–13%)。在上述栽培品种中检测到的渐渗性自发性链球菌片段的百分比相对较高表明亲本基因组之间频繁重组。在这里，我们介绍了我们的策略在分离物种特异性细胞学标记方面的应用。这些信息可能有助于阐明复杂的植物基因组结构并追踪它们的进化历史。在上述栽培品种中检测到的渐渗性自发性链球菌片段的百分比相对较高表明亲本基因组之间频繁重组。在这里，我们介绍了我们的策略在分离物种特异性细胞学标记方面的应用。这些信息可能有助于阐明复杂的植物基因组结构并追踪它们的进化历史。在上述栽培品种中检测到的渐渗性自发性链球菌片段的百分比相对较高表明亲本基因组之间频繁重组。在这里，我们介绍了我们的策略在分离物种特异性细胞学标记方面的应用。这些信息可能有助于阐明复杂的植物基因组结构并追踪它们的进化历史。