Identification and characterization of long non-coding RNAs involved in the formation and development of poplar adventitious roots

Liu, Sian; Sun, Zimou; Xu, Meng

doi:10.1016/j.indcrop.2018.03.071

Cited by 46 publications

(49 citation statements)

References 65 publications

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“…However, the molecular mechanisms underlying the differences in the total polyphenol, total flavonoid, and catechin contents in the SW and IW remain unclear. Moreover, previous studies concluded that lncRNAs play important regulatory roles at the transcript level (Liu et al, 2018b;Lin et al, 2019;Varshney et al, 2019). However, there has been relatively little research on the lncRNAs in tea plants, with no published reports regarding the regulatory mechanisms of lncRNAs related to the processing of tea leaves.…”

Section: Discussion the Expression Levels Of The Identified Differentmentioning

confidence: 99%

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

Zhu

Zhang

et al. 2019

Front. Plant Sci.

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Oolong tea is a popular and semi-fermented beverage. During the processing of tea leaves, withering is the first indispensable process for improving flavor. However, the roles of long non-coding RNAs (lncRNAs) and the characteristic secondary metabolites during the withering of oolong tea leaves remain unknown. In this study, phytochemical analyses indicated that total polyphenols, flavonoids, catechins, epigallocatechin (EGC), catechin gallate (CG), gallocatechin gallate (GCG), epicatechin gallate (ECG), and epigallocatechin gallate (EGCG) were all less abundant in the solar-withered leaves (SW) than in the fresh leaves (FL) and indoor-withered leaves (IW). In contrast, terpenoid, jasmonic acid (JA), and methyl jasmonate (MeJA) contents were higher in the SW than in the FL and IW. By analyzing the transcriptome data, we detected 32,036 lncRNAs. On the basis of the Kyoto Encyclopedia of Genes and Genomes analysis, the flavonoid metabolic pathway, the terpenoid metabolic pathway, and the JA/MeJA biosynthesis and signal transduction pathway were enriched pathways. Additionally, 63 differentially expressed lncRNAs (DE-lncRNAs) and 23 target genes were identified related to the three pathways. A comparison of the expression profiles of the DE-lncRNAs and their target genes between the SW and IW revealed four up-regulated genes (FLS, CCR, CAD, and HCT), seven up-regulated lncRNAs, four down-regulated genes (4CL, CHI, F3H, and F3'H), and three downregulated lncRNAs related to flavonoid metabolism; nine up-regulated genes (DXS, CMK, HDS, HDR, AACT, MVK, PMK, GGPPS, and TPS), three up-regulated lncRNAs, and six down-regulated lncRNAs related to terpenoid metabolism; as well as six upregulated genes (LOX, AOS, AOC, OPR, ACX, and MFP2), four up-regulated lncRNAs, and three down-regulated lncRNAs related to JA/MeJA biosynthesis and signal transduction. These results suggested that the expression of DE-lncRNAs and their targets involved in the three pathways may be related to the low abundance of the total polyphenols, flavonoids, and catechins (EGC, CG, GCG, ECG, and EGCG) and the

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Section: Discussion the Expression Levels Of The Identified Differentmentioning

confidence: 99%

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

Zhu

Zhang

et al. 2019

Front. Plant Sci.

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“…Genomic DNA was extracted from newly expanded leaves via a DNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). Total RNA was subsequently extracted via an RNAprep Pure Plant Kit (Tiangen, Beijing, China) (Liu, Sun & Xu, 2018). Full cDNA sequences of TcARF6 were identified according to the manual provided with a SMARTer Rapid Amplification of cDNA Ends (RACE) 5′/3′ Kit (Clontech, Mountain View, CA, USA), with slight modifications (Wang et al, 2018a;2018b;Cheng et al, 2017).…”

Section: Sequence Cloningmentioning

confidence: 99%

ARF family identification in Tamarix chinensis reveals the salt responsive expression of TcARF6 targeted by miR167

Wang

et al. 2020

PeerJ

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Auxin response factors (ARFs) are important transcription factors (TFs) that are differentially expressed in response to various abiotic stresses. The important roles of ARFs and small RNA-ARF pathways in mediating plant growth and stress responses have emerged in several recent studies. However, no studies on the involvement of ARFs in tamarisk trees, which are resistant to salinity, have been conducted. In this study, systematic analysis revealed 12 TcARF genes belonging to five different groups in Tamarix chinensis. The microRNA response elements of miR160, which belongs to group I and miR167, which belongs to group III, were conserved in terms of their location and sequence. Moreover, digital gene expression profiles suggested that a potential miR167 target gene, TcARF6, was rapidly expressed in response to salt stress. Cloning of TcARF6 revealed that TcARF6 could be an activation TF with a glutamine-rich region and expression pattern analysis revealed that the expression of TcARF6 was significantly downregulated specifically in the roots. A significant negative correlation in the expression pattern of tch-miR167/TcARF6 indicated that this module may play a key role in the response to salt stress. Overall, these results provide basic information on the posttranscriptional regulation of TcARF6 for future investigations of the T. chinensis salt-stress response.

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“…2c and d). This phenomenon has also been observed in humans, Sus scrofa, Populus and Gossypium hirsutum [30,34,[72][73][74]. In addition, in the study of maize and red clover, fusion events tended to arise inter-chromosomally rather than intra-chromosomally [22,24].…”

Section: Discussionmentioning

confidence: 63%

“…Single-molecule long-read sequencing technology (SMRT), which was developed by Paci c Biosciences (PacBio), has recently been used effectively to discover lncRNAs, comprehensively analyse AS and APA, detect fusion genes, correct misannotated gene models and discover novel genes in animals and plants [23,[26][27][28][29][30][31][32][33][34]. However, the shortcomings of SMRT are its high error rate (~13%) and low throughput [26,31].…”

Section: Introductionmentioning

confidence: 99%

Gene co-expression analysis and tissue-specific gene identification in Liriodendron chinense via hybrid sequencing

Tu¹,

Shen²,

Wen³

et al. 2020

Preprint

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Background Liriodendron chinense (Hemsl.) Sarg. is an economically and ecologically important deciduous tree species that has been studied for many years. Although the complete L. chinense genome has been sequenced, the gene co-expression modules and tissue-specific genes of L. chinense remain unknown. Results Here, we used the bracts, petals, sepals, stamens, pistils, leaves, and the shoot apex of L. chinense as materials and analysed their gene co-expression modules and tissue-specific genes via hybrid sequencing. We identified 3,032 DEGs between the floral and vegetative tissues and 2,126 tissue-specific genes. By using WGCNA analysis, we identified 13 gene co-expression modules, and KEGG pathway enrichment analysis revealed that tissue-specific genes and genes from different modules were enriched in different pathways. Genes associated with plant defence were highly expressed in the bracts, genes participating in plant hormone signal transduction were highly expressed in the shoot apex, and genes participating in photosynthesis were highly expressed in the leaves, petals and sepals. Moreover, we identified 10 MIKC-type MADS-box genes that were classified as member of the AP3/PI, SVP, SEP, AG/SHP/STK, AGL12, SOC1 and TM8 subfamily. Phylogenetic analysis showed that the expression profiles of these ten genes were consistent with those reported in Arabidopsis and Populus , indicating that these genes are highly conserved evolutionarily and related to floral and vegetative tissue development. The small number of MIKC-type MADS-box genes in L. chinense was probably owing to its incomplete genome annotation. Conclusions In this work, we provided a reference transcriptome for L. chinense research by using hybrid sequencing. We identified 2,126 tissue-specific genes and 3,032 DEGs that contributed greatly to the functional differences between vegetative organs and floral organs. By using WGCNA analysis, 13 gene co-expression modules and 52 hub genes from six co-expression modules of interest were identified. Moreover, we identified 10 MIKC-type MADS-box genes that might be related to the development and growth regulation of floral and vegetative organs. These findings will improve our understanding of gene co-expression, tissue specific genes and flower development model of L. chinense .

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Identification and characterization of long non-coding RNAs involved in the formation and development of poplar adventitious roots

Cited by 46 publications

References 65 publications

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

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

ARF family identification in Tamarix chinensis reveals the salt responsive expression of TcARF6 targeted by miR167

Gene co-expression analysis and tissue-specific gene identification in Liriodendron chinense via hybrid sequencing

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