Identification of transposons near predicted lncRNA and mRNA pools of Prunus mume using an integrative transposable element database constructed from Rosaceae plant genomes
Identification of transposons near predicted lncRNA and mRNA pools of Prunus mume using an integrative transposable element database constructed from Rosaceae plant genomes
复制标题
利用蔷薇科植物基因组构建的综合转座元件数据库鉴定梅花预测 lncRNA 和 mRNA 库附近的转座子
DOI：
10.1007/s00438-018-1449-y
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发表时间：
2018-10-01
影响因子：
3.1
通讯作者：
Wang，Jia
中科院分区：
文献类型：
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作者：
Ma，Kaifeng;Zhang，Qixiang;Wang，Jia
本研究旨在构建蔷薇科植物转座因子数据库及其在转录组学中的应用。TE对基因调控的进化效应已经被探索，TE插入可以是基因结构和功能变化的分子基础。然而，一个特定的蔷薇科植物TE数据库（RPTEdb）是缺乏的。几种蔷薇科植物的基因组已被测序，提供了在全基因组水平上挖掘TE数据的机会。因此，我们构建了RPTEdb，这是一个包含蔷薇科植物基因组中19，596个注释TE的集体和综合数据库，使用先前描述的鉴定和注释方法以及已发表的基因组序列。用户友好的基于网络的数据库提供了通过超链接访问研究工具，包括浏览，TE树，工具，JBrowse和搜索部分，并通过在主网页上输入序列。接下来，我们进行了一个高级应用，在该应用中，我们鉴定了梅花'复盘调质'的白色和红色花瓣组织转录组中预测的长非编码RNA（lncRNA）和mRNA结构域附近的TE，揭示了16个与16个差异表达的lncRNA结构域重叠或接近的TE，以及54个与54个差异表达的mRNA结构域重叠或接近的TE，并讨论了TE的可能功能。我们相信，RPTEdb将有助于了解TE在蔷薇科植物基因组的结构，功能和进化动力学的作用。
This study focused on the construction of a database of transposable elements (TEs) from Rosaceae plants, the third most economically important plant family in temperate regions, and its transcriptomics applications. The evolutionary effects of TEs on gene regulation have been explored, and TE insertions can be the molecular bases of changes in gene structure and function. However, a specific Rosaceae plant TE database (RPTEdb) is lacking. The genomes of several Rosaceae plants have been sequenced, providing the opportunity to mine TE data at a whole-genome level. Therefore, we constructed the RPTEdb, a collective and comprehensive database of 19,596 annotated TEs in the genomes of Rosaceae plants using previously described identification and annotation methods and published genome sequences. The user-friendly web-based database provides access to research tools through hyperlinks, including Browse, TE tree, tools, JBrowse, and search sections, and through the inputting of sequences on the main webpage. Next, we performed one advanced application in which TEs near predicted long non-coding RNA (lncRNA) and mRNA domains within white and red petal-tissue transcriptomes of Prunus mume 'Fuban Tiaozhi' were identified, revealing 16 TEs that overlapped or were near 16 differentially expressed lncRNA domains, and 54 TEs that overlapped or were near 54 differentially expressed mRNA domains, and the TEs' possible functions were also discussed. We believe that the RPTEdb will contribute to the understanding of TE roles in the structural, functional and evolutionary dynamics of Rosaceae plant genomes.