Genome-wide identification and characterization of long non-coding RNAs involved in the early somatic embryogenesis in Dimocarpus longan Lour

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.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5158-z) contains supplementary material, which is available to authorized users.

Transcriptome and Phytochemical Analyses Provide New Insights Into Long Non-Coding RNAs Modulating Characteristic Secondary Metabolites of Oolong Tea (Camellia sinensis) in Solar-Withering

“…Moreover, 68.22% of the lncRNAs contained only one exon, whereas 85.98% of the mRNAs comprised more than two exons. These observations are consistent with the findings of studies on maize (Li et al, 2014), kiwifruit (Tang et al, 2016), and longan (Chen et al, 2018a), which confirmed that lncRNAs contain fewer exons than the annotated mRNAs and that most plant lncRNAs contain one exon.…”

“…In Arabidopsis thaliana, the lncRNA IPS1, which is an eTM of ath-miR399, can inhibit the cleavage of PHO2 by ath-miR399 (Franco-Zorrilla et al, 2007). Similarly, several lncRNAs function by interacting with miRNAs in other plant species (Hao et al, 2015;Wang et al, 2015;Deng et al, 2018;Chen et al, 2018a). Furthermore, nta-eTMX27 in Nicotiana tabacum , osa-eTM160 in Oryza sativa (Wang et al, 2017a), lncRNA23468 in Solanum lycopersicum (Jiang et al, 2019), and LTCONS-00042843 in Dimocarpus longan (Chen et al, 2018a) are eTMs that modulate target gene expression by functioning as decoys for relevant miRNAs.…”

“…Similarly, several lncRNAs function by interacting with miRNAs in other plant species (Hao et al, 2015;Wang et al, 2015;Deng et al, 2018;Chen et al, 2018a). Furthermore, nta-eTMX27 in Nicotiana tabacum , osa-eTM160 in Oryza sativa (Wang et al, 2017a), lncRNA23468 in Solanum lycopersicum (Jiang et al, 2019), and LTCONS-00042843 in Dimocarpus longan (Chen et al, 2018a) are eTMs that modulate target gene expression by functioning as decoys for relevant miRNAs. The development of high-throughput sequencing and bioinformatics tools enabled the identification of many lncRNAs in several plant species, including model plants like A. thaliana (Yuan et al, 2016), O. sativa (Zhang et al, 2014;Wang et al, 2018a), and Brachypodium distachyon (Quattro et al, 2017), and also in horticultural plants such as S. lycopersicum (Zhu et al, 2015), Cucumis sativus (Hao et al, 2015), Musa itinerans (Liu et al, 2018a), D. longan (Chen et al, 2018a), and Citrus sinensis (Ke et al, 2019).…”

Transcriptome and phytochemical analyses provide new insights into long non-coding RNAs and characteristic secondary metabolites of oolong tea (Camellia sinensis) in solar-withering

“…This result is consistent with the findings in maize [3], kiwifruit [68] and longan [12], the lncRNAs contains fewer exons than annotated mRNAs and the majority of the lncRNAs in plants are single exon transcripts.…”

“…The mRNAs, miRNAs and lncRNAs qRT-PCR was performed by the LightCycler 480 platform (Roche Applied Sciences, Basel, Switzerland) with Transtart Tip Green qPCR SuperMix (TransGen Biotech, Beijing, China), respectively. The setting of qRT-PCR procedure and reaction system were both referred to the method of Chen et al [12]. The glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and β-actin genes were used as reference genes for mRNAs and lncRNAs normalization.…”