Identification and characterization of long non-coding RNAs involved in embryo development of <i>Ginkgo biloba</i>

Long non-coding RNAs (lncRNAs) are important regulatory factors for plant growth and development. Despite this, little is known about the regulatory interactions of lncRNAs with mRNA during embryo development. Here, we used a bioinformatics genome-wide approach to identify lncRNAs involved in embryo development of <i>Ginkgo biloba</i>, based on RNA sequencing datasets from <i>G. biloba</i> embryos during early, middle, late developmental stages. In total, 2326 lncRNAs were identified in the <i>G. biloba</i> embryos, of which 1307 and 1019 could be classified as long intergenic non-coding RNAs and antisense lncRNAs, respectively. Among them, a total of 657 differentially expressed lncRNAs were identified in the different developmental stages of the <i>G. biloba</i> embryos. Based on the functional annotation of potential target genes of lncRNAs, 50, 33, and 76 lncRNAs were predicted to target genes involved in plant hormone signal transduction, plant hormone biosynthesis, and circadian rhythm regulation, respectively. A lncRNA (17)-miRNA (25)-PCgene (52) network was constructed for the <i>G. biloba</i> embryo. Three lncRNAs (lnc000823, lnc002072, lnc000866) were predicted as target mimics of miR159, which targeted two transcription factors with variety of functions, Gb_11536 (<i>MYB33</i>) and Gb_23921 (<i>MYB101</i>). The data generated in this study provide a better understanding of the roles of lncRNAs in embryo development of <i>G. biloba</i> and plants in general.

长链非编码RNA（long non-coding RNAs，lncRNAs）是调控植物生长发育的重要因子。尽管如此，目前对于胚胎发育过程中lncRNAs与mRNA的调控互作仍知之甚少。本研究基于银杏（*Ginkgo biloba*）胚胎发育早期、中期及晚期的RNA测序数据集，采用全基因组生物信息学方法鉴定参与银杏胚胎发育的lncRNAs。本研究共在银杏胚胎中鉴定出2326条lncRNAs，其中1307条可归类为基因间长链非编码RNA（long intergenic non-coding RNAs，lincRNAs），1019条为反义lncRNAs（antisense lncRNAs）。其中，在银杏胚胎不同发育阶段中共鉴定出657个差异表达lncRNAs（differentially expressed lncRNAs）。基于lncRNAs潜在靶基因（potential target genes）的功能注释（functional annotation），本研究预测分别有50、33和76条lncRNAs的靶基因参与植物激素信号转导（plant hormone signal transduction）、植物激素生物合成（plant hormone biosynthesis）以及昼夜节律调控（circadian rhythm regulation）。本研究构建了银杏胚胎的lncRNA(17)-miRNA(25)-蛋白编码基因（protein-coding gene，PCgene）(52)调控网络。研究预测3条lncRNAs（lnc000823、lnc002072、lnc000866）可作为miR159的靶模拟物（target mimics），而miR159的靶基因为两个具有多种功能的转录因子（transcription factors）Gb_11536（*MYB33*）和Gb_23921（*MYB101*）。本研究产生的数据有助于更深入地理解lncRNAs在银杏乃至植物胚胎发育中的作用。