College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210095, China.
BMC Plant Biol. 2019 Feb 11;19(1):64. doi: 10.1186/s12870-019-1672-7.
Long non-coding RNAs (lncRNAs) are transcripts more than 200 bp in length do not encode proteins. Up to the present, it has been reported that lncRNAs play an essential role in developmental processes through their regulatory functions. However, their characteristics, expression inheritance patterns, and functions in Prunus mume are quite unidentified.
In this present study, we exposed the specific characters of pistil development process between single pistil cv 'Qingjia No.2' (QJN2) and multiple pistils cv 'Da Yu' (DY). We found that early October is the key stage for pistil differentiation. The similarity epidermis was observed between two types of pistil. We also further investigated a complete pistil development lncRNA profiles through RNA-seq in Prunus mume. 2572 unique lncRNAs and 24,648 genes mapped to Prunus mume genome, furthermore, 591 novel lncRNAs were predicted. Both unique lncRNAs and novel lncRNAs are shorter in length than the mRNAs, and the overall expression level of lncRNAs was lower than mRNAs in Prunus mume. 186 known lncRNAs, 1638 genes and 89 novel lncRNAs were identified as significant differential expressed in QJN2 compared with DY. We predicted 421 target genes of differentially expressed known lncRNAs (DEKLs) and 254 target genes of differentially expressed novel lncRNAs (DENLs). 153 miRNAs were predicted interacted with 100 DEKLs while 112 miRNAs were predicted interacted with 55 DENLs. Further analysis of the DEKLs showed that the lncRNA of XR_514690.2 down-regulated its target ppe-miR172d, and up-regulated AP2, respectively. Meanwhile, the other lncRNA of TCONS_00032517 induced cytokinin negative regulator gene A-ARR expression via repressing its target miRNA ppe-miR160a/b in DY. At the same time we found that the AP2 expression was significantly up-regulated by zeatin (ZT) treatment in flower buds. Our experiments suggest that the two lncRNAs of XR_514690.2 and TCONS_00032517 might contribute the formation of multiple pistils in Prunus mume.
This study shows the first characterization of lncRNAs involved in pistil development and provides new indications to elucidate how lncRNAs and their targets play role in pistil differentiation and flower development in Prunus mume.
长链非编码 RNA（lncRNA）是长度超过 200bp 的转录本，不编码蛋白质。迄今为止，已有研究报道 lncRNA 通过其调控功能在发育过程中发挥重要作用。然而，lncRNA 在李属梅花中的特征、表达遗传模式和功能尚不清楚。
本研究通过比较单瓣梅花品种‘青梅 2 号’（QJN2）和多瓣梅花品种‘大渔’（DY）的雌蕊发育过程，揭示了雌蕊发育过程的特异性特征。我们发现 10 月初是雌蕊分化的关键阶段。两种类型的雌蕊具有相似的表皮。我们还通过 RNA-seq 进一步研究了梅花完整雌蕊发育的 lncRNA 图谱。在李属梅花基因组中，共鉴定到 2572 个特异 lncRNA 和 24648 个基因，进一步预测到 591 个新的 lncRNA。特异 lncRNA 和新的 lncRNA 的长度均短于 mRNAs，李属梅花中 lncRNA 的整体表达水平低于 mRNAs。在 QJN2 与 DY 比较中，鉴定到 186 个已知 lncRNA、1638 个基因和 89 个新的 lncRNA 显著差异表达。预测到 421 个差异表达已知 lncRNA（DEKLs）的靶基因和 254 个差异表达新 lncRNA（DENLs）的靶基因。预测到 153 个 miRNA 与 100 个 DEKLs 相互作用，112 个 miRNA 与 55 个 DENLs 相互作用。进一步分析 DEKLs 显示，lncRNA XR_514690.2 下调其靶基因 ppe-miR172d，上调 AP2，而另一个 lncRNA TCONS_00032517 通过抑制靶基因 miRNA ppe-miR160a/b 在 DY 中诱导细胞分裂素负调控基因 A-ARR 的表达。同时，我们发现在花蕾中，ZT 处理可显著上调 AP2 的表达。我们的实验表明，XR_514690.2 和 TCONS_00032517 这两个 lncRNA 可能有助于李属梅花形成多瓣。
本研究首次对参与雌蕊发育的 lncRNA 进行了特征描述，并为阐明 lncRNA 及其靶基因在李属梅花雌蕊分化和花发育中的作用提供了新的依据。
