Transcriptome-wide identification and functional prediction of novel and flowering-related circular RNAs from trifoliate orange (Poncirus trifoliata L. Raf.)
Transcriptome-wide identification and functional prediction of novel and flowering-related circular RNAs from trifoliate orange (Poncirus trifoliata L. Raf.)
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DOI：
10.1007/s00425-018-2857-2
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发表时间：
2018-02
期刊：
影响因子：
4.3
通讯作者：
Ren-Fang Zeng;Jing-Jing Zhou-Jing;Chun-Gen Hu;Jinzhi Zhang
中科院分区：
文献类型：
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作者：
Ren-Fang Zeng;Jing-Jing Zhou-Jing;Chun-Gen Hu;Jinzhi Zhang
在柑橘中总共鉴定出了 558 个潜在的环状 RNA (circRNA)，并对它们进行了分析和比较。在枳橙的两个基因型中鉴定出 176 个差异表达的 circRNA。环状 RNA (circRNA) 在转录控制和 microRNA (miRNA) 功能中发挥着多种作用。然而，关于柑橘中 circRNA 的信息知之甚少。为了鉴定柑橘 circRNA 并研究其功能作用，对早熟三叶橙（一种早花三叶橙突变体，Poncirus trifoliata L. Raf.）及其野生型进行了高通量测序。通过生物信息学分析共鉴定出558个潜在的circRNA，其中86.02%是正义重叠的circRNA。本研究对它们的序列特征、选择性环化和其他特征进行了研究。与野生型相比，在早熟枳中，有176个circRNA被鉴定为差异表达的circRNA，其中61个显着上调，115个下调，表明它们可能在早期开花过程中发挥重要作用。通过桑格测序和实时聚合酶链式反应验证了一些circRNA的选择性环化和差异表达。通过基因本体论（GO）和京都基因与基因组百科全书（KEGG）分析预测差异表达的circRNA及其宿主基因的功能。我们发现许多差异表达的circRNA具有丰富的miRNA结合位点：发现29个circRNA作为16个miRNA的靶标。总的来说，这些结果将有助于揭示circRNA在柑橘生长发育中的生物学功能。
A total of 558 potential circular RNAs (circRNAs) were identified in citrus, and these were analyzed and compared. One hundred seventy-six differentially expressed circRNAs were identified in two genotypes of trifoliate orange. Circular RNAs (circRNAs) play diverse roles in transcriptional control and microRNA (miRNA) function. However, little information is known about circRNAs in citrus. To identify citrus circRNAs and investigate their functional roles, high-throughput sequencing of precocious trifoliate orange (an early-flowering trifoliate orange mutant, Poncirus trifoliata L. Raf.) and its wild type was performed. A total of 558 potential circRNAs were identified by bioinformatic analysis, and 86.02% of these were sense-overlapping circRNAs. Their sequence features, alternative circularization, and other characteristics were investigated in this study. Compared with the wild type, 176 circRNAs were identified as differentially expressed circRNAs, 61 were significantly up-regulated and 115 were down-regulated in precocious trifoliate orange, indicating that they may play an important role in the early flowering process. Alternative circularization and differential expression of some circRNAs were verified by Sanger sequencing and real-time polymerase chain reaction. The functions of differentially expressed circRNAs and their host genes were predicted by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. We found that many differentially expressed circRNAs had abundant miRNA binding sites: 29 circRNAs were found to act as the 16 miRNA targets. Overall, these results will help to reveal the biological functions of circRNAs in growth and development of citrus.