Genome-wide identification and characterization of long non-coding RNAs involved in the early somatic embryogenesis in Dimocarpus longan Lour.
Genome-wide identification and characterization of long non-coding RNAs involved in the early somatic embryogenesis in Dimocarpus longan Lour.
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参与龙眼早期体细胞胚胎发生的长非编码RNA的全基因组鉴定和表征
DOI：
10.1186/s12864-018-5158-z
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发表时间：
2018-11-06
期刊：
影响因子：
4.4
通讯作者：
Lai Z
中科院分区：
文献类型：
--
作者：
Chen Y;Li X;Su L;Chen X;Zhang S;Xu X;Zhang Z;Chen Y;XuHan X;Lin Y;Lai Z
背景：长链非编码rna （lncRNAs）参与可变切割、转录干扰、DNA甲基化调控和蛋白质修饰。然而，lncrna在植物体细胞胚胎中的调控尚不清楚。龙眼体细胞胚胎发生（SE）系统是研究龙眼胚胎发育的良好系统。结果：本研究通过高通量测序鉴定了龙眼早期SE获得的7643个lncrna，其中表达了6005个。在表达的lncrna中，4790个在所有样本中发现，160个在胚性愈伤组织（EC）中特异性表达，154个在不完全胚性致密结构（ICpECs）中特异性表达，376个在球状胚（GEs）中特异性表达。我们对6005个表达的lncrna进行了注释，其中1404个lncrna属于506个非编码RNA （ncRNA）家族，4682个lncrna被预测为靶向蛋白质编码基因。目的基因包括5051个顺式调控的目的基因（5712对）和1605个反式调控的目的基因（3618对）。KEGG分析结果显示，这些lncrna的大部分差异表达靶基因（mrna）富集于龙眼SE早期的“植物-病原体相互作用”和“植物激素信号通路”中。实时荧光定量PCR证实，20个筛选出的lncrna表达存在显著差异，其中5个lncrna与生长素反应因子相关。与FPKM的表达趋势相比，qPCR中16个lncRNA的表达趋势相同。在lncRNA-miRNA-mRNA关系预测中，40个lncrna被预测为15个miRNA的etm， 7个lncrna被鉴定为潜在的miRNA前体。此外，我们通过mirna （miR172a, miR159a）的瞬时表达验证了lncRNA-miRNA-mRNA的调控关系。1和miR398a)。结论：龙眼SE早期lncrna分析显示，差异表达的lncrna参与SE各阶段的表达调控，并可能与mirna和mrna形成调控网络。这些发现提供了对lncrna的新认识，并为未来龙眼SE早期lncrna的功能分析奠定了基础。
Background:Long non-coding RNAs (lncRNAs) are involved in variable cleavage, transcriptional interference, regulation of DNA methylation and protein modification. However, the regulation of lncRNAs in plant somatic embryos remains unclear. The longan (Dimocarpus longan) somatic embryogenesis (SE) system is a good system for research on longan embryo development.Results:In this study, 7643 lncRNAs obtained during early SE in D. longan were identified by high-throughput sequencing, among which 6005 lncRNAs were expressed. Of the expressed lncRNAs, 4790 were found in all samples and 160 were specifically expressed in embryogenic callus (EC), 154 in incomplete embryogenic compact structures (ICpECs), and 376 in globular embryos (GEs). We annotated the 6005 expressed lncRNAs, and 1404 lncRNAs belonged to 506 noncoding RNA (ncRNA) families and 4682 lncRNAs were predicted to target protein-coding genes. The target genes included 5051 cis-regulated target genes (5712 pairs) and 1605 trans-regulated target genes (3618 pairs). KEGG analysis revealed that most of the differentially expressed target genes (mRNAs) of the lncRNAs were enriched in the "plant-pathogen interaction" and "plant hormone signaling" pathways during early longan SE. Real-time quantitative PCR confirmed that 20 selected lncRNAs showed significant differences in expression and that five lncRNAs were related to auxin response factors. Compared with the FPKM expression trends, 16 lncRNA expression trends were the same in qPCR. In lncRNA-miRNA-mRNA relationship prediction, 40 lncRNAs were predicted to function as eTMs for 15 miRNAs and 7 lncRNAs were identified as potential miRNA precursors. In addition, we verified the lncRNA-miRNA-mRNA regulatory relationships by transient expression of miRNAs (miR172a, miR159a.1 and miR398a).Conclusion:Analyses of lncRNAs during early longan SE showed that differentially expressed lncRNAs were involved in expression regulation at each SE stage, and may form a regulatory network with miRNAs and mRNAs. These findings provide new insights into lncRNAs and lay a foundation for future functional analysis of lncRNAs during early longan SE.
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影响因子：
14.9
作者：
Dai X;Zhao PX
通讯作者：
Zhao PX
影响因子：
4.6
作者：
Hardtke, CS;Ckurshumova, W;Berleth, T
通讯作者：
Berleth, T
影响因子：
4.2
作者：
ELHADRAMI, I;CARRON, MP;DAUZAC, J
通讯作者：
DAUZAC, J
影响因子：
14.9
作者：
Griffiths-Jones S;Grocock RJ;van Dongen S;Bateman A;Enright AJ
通讯作者：
Enright AJ
DOI：
10.1142/s0219720005001375
发表时间：
2005-08-01
影响因子：
1
作者：
Futschik, Matthias E.;Carlisle, Bronwyn
通讯作者：
Carlisle, Bronwyn