Abstract
BackgroundLong 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.ResultsIn 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).ConclusionAnalyses 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.
Highlights
Long non-coding RNAs are involved in variable cleavage, transcriptional interference, regulation of DNA methylation and protein modification
Illumina sequencing and identification of Long non-coding RNAs (lncRNAs) during early somatic embryogenesis (SE) in longan To investigate the regulatory roles of lncRNAs during early longan SE, lncRNAs obtained from embryogenic callus (EC), incomplete compact pro-embryogenic cultures (ICpEC) and globular embryos (GE) samples of longan were sequenced by Illumina HiSeq sequencing
The expressions of LTCONS-00053938, LTCONS-00050060, LTCONS-00022307, LTCONS-00037848 and LTCONS00021462 increased gradually from EC to ICpEC. These results indicated that different lncRNAs might be involved in the maintenance of different stages of longan SE, i.e. the eight lncRNAs of category I could be related to maintaining the pre-embryonic status of the EC, the four lncRNAs of category Polymerase II (II) could be related to maintaining the embryogenic status of the ICpEC, and the 12 lncRNAs of category III could be related to maintaining the embryonic status of the GE
Summary
Long non-coding RNAs (lncRNAs) are involved in variable cleavage, transcriptional interference, regulation of DNA methylation and protein modification. The regulation of lncRNAs in plant somatic embryos remains unclear. LncRNAs come from the intergenic, intronic or coding gene regions in the sense and antisense directions. According to their genomic transcriptional positions, lncRNAs can be grouped into three classes: antisense, intronic, and intergenic. It has been reported that lncRNAs play important regulatory roles at the gene transcriptional [2], post-transcriptional [3], translational [4] and epigenetic [5, 6] levels, and are involved in variable cleavage, transcriptional interference, regulation of DNA methylation and protein modification. While there have been a few reports on the regulation of lncRNAs in animal embryos, studies on lncRNAs in plant somatic embryogenesis (SE) have not been reported to date
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