Key Laboratory of Horticulture Crops Germplasm Resources Utilization, Research Institute of Pomology, Chinese Academy of Agricultural Sciences (CAAS), Ministry of Agriculture and Rural Affairs of the People's Republic of China, Xingcheng 125100, China.
Genes (Basel). 2022 Apr 18;13(4):712. doi: 10.3390/genes13040712.
Circular RNAs (circRNAs) are covalently closed non-coding RNAs that play pivotal roles in various biological processes. However, circRNAs' roles in different tissues of apple are currently unknown. A total of 6495 unique circRNAs were identified from roots, phloem, leaves, flowers and fruits; 65.99% of them were intergenic circRNAs. Similar to other plants, tissue-specific expression was also observed for apple circRNAs; only 175 (2.69%) circRNAs were prevalently expressed in all five different tissues, while 1256, 1064, 912, 904 and 1080 circRNAs were expressed only in roots, phloem, leaves, flowers and fruit, respectively. The hosting-genes of circRNAs showed significant differences enriched in COG, GO terms or KEGG pathways in five tissues, suggesting the special functions of circRNAs in different tissues. Potential binding interactions between circRNAs and miRNAs were investigated using TargetFinder; 2989 interactions between 647 circRNAs and 192 miRNA were predicated in the present study. It also predicted that Chr00:18744403|18744580-mdm-miR160 might play an important role in the formation of flowers or in regulating the coloration of flowers, Chr10:6857496|6858910-mdm-miR168 might be involved in response to drought stress in roots, and Chr03:1226434|1277176 may absorb mdm-miR482a-3p and play a major role in disease resistance. Two circRNAs were experimentally analyzed by qRT-PCR with divergent primers, the expression levels were consistent with RNA-seq, which indicates that the RNA-seq datasets were reliable.
环状 RNA（circRNAs）是共价闭合的非编码 RNA，在各种生物过程中发挥关键作用。然而，circRNAs 在苹果不同组织中的作用目前尚不清楚。从根、韧皮部、叶、花和果实中鉴定出了 6495 个独特的 circRNAs；其中 65.99%为基因间 circRNAs。与其他植物一样，苹果 circRNAs 也表现出组织特异性表达；只有 175（2.69%）个 circRNAs在所有五个不同组织中普遍表达，而 1256、1064、912、904 和 1080 个 circRNAs分别仅在根、韧皮部、叶、花和果实中表达。circRNAs 的宿主基因在五个组织中富集的 COG、GO 术语或 KEGG 途径中存在显著差异，表明 circRNAs 在不同组织中的特殊功能。使用 TargetFinder 研究了 circRNAs 与 miRNAs 之间的潜在结合相互作用；在本研究中预测了 647 个 circRNAs 和 192 个 miRNA 之间的 2989 个相互作用。它还预测 Chr00:18744403|18744580-mdm-miR160 可能在花的形成或花色调控中发挥重要作用，Chr10:6857496|6858910-mdm-miR168 可能参与根对干旱胁迫的响应，Chr03:1226434|1226434 可能吸收 mdm-miR482a-3p 并在抗病性中发挥主要作用。用差异引物通过 qRT-PCR 对两个 circRNAs 进行了实验分析，表达水平与 RNA-seq 一致，表明 RNA-seq 数据集是可靠的。
