Plant Genome. 2019 Jun;12(2). doi: 10.3835/plantgenome2018.12.0094.
Mulberry ( C. K. Schneid) leaves have been used as the food for the domesticated silkworm, , for more than 5000 yr, and the mulberry-silkworm relationship is one of the best-known and oldest models of plant defense-insect adaptation. The availability of a genome assembly of mulberry provides us with an opportunity to mine the characteristics and distribution of transposable elements (TEs) in this species and to examine their relationship to genes and gene expression. In this study, a significantly correlated inverse relationship between the percentage coverage of genes and TEs was observed. The TE-rich regions appeared to have a lower percentage of putatively expressed genes. Distribution patterns between different TE superfamilies were detected in the mulberry genome. The elements (the TE making up the greatest proportion of the mulberry genome) were significantly overrepresented within genes in the mulberry genome, and they may have a dominant influence on evolution of the mulberry genome. Approximately 96.93% (330/344) of the TE-containing genes assigned to pathways were assigned to metabolism-related pathways. The TE-related alternative splicing events accounted for 7.58% (402/5,302) of all alternative splicing types in the mulberry genome, suggesting that TEs are one of the driving forces in the formation of the alternatively spliced genes. The results will be valuable in improving our understanding of the important roles of TEs in mulberry genome evolution.
桑树（C. K. Schneid）叶子被用作家蚕的食物已有 5000 多年的历史，桑树与家蚕的关系是植物防御与昆虫适应的最佳模式之一。桑树基因组组装的出现为我们提供了一个机会，以便挖掘该物种中转座元件（TEs）的特征和分布，并研究它们与基因和基因表达的关系。在这项研究中，观察到基因和 TEs 的覆盖率之间呈显著负相关的关系。富含 TEs 的区域似乎有较低比例的假定表达基因。在桑树基因组中检测到不同 TE 超家族之间的分布模式。在桑树基因组中，元素（构成桑树基因组最大比例的 TE）在基因中显著过表达，它们可能对桑树基因组的进化具有主导影响。大约 96.93%（330/344）分配到途径的含有 TE 的基因被分配到代谢相关途径。TE 相关的选择性剪接事件占桑树基因组中所有选择性剪接类型的 7.58%（402/5,302），表明 TEs 是形成选择性剪接基因的驱动力之一。这些结果将有助于我们更好地理解 TEs 在桑树基因组进化中的重要作用。
