Evolutionary dynamics of linc<scp>RNA</scp> transcription in nine citrus species

Ke, Lili; Zhou, Zhi; Xu, Xiwen; Wang, Xia; Liu, Yuanlong; Xu, Yuantao; Huang, Yue; Wang, Zhen; Deng, Xiuxin; Chen, Lingling; Xu, Qiang

doi:10.1111/tpj.14279

Cited by 25 publications

(20 citation statements)

References 52 publications

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“…Target mimicking of miRNA is one of the most important mechanisms of lncRNAs regulating the plant development 11,42 . In other plant species, such as chickpea, Arabidopsis, citrus, rice, canola and maize, it was shown that lncRNAs also could act as miRNA targets, miRNA precursors or endogenous target mimics 34,[42][43][44][45][46] . To sum up, the interaction between lncRNAs and miRNAs could be an important posttranscriptional regulatory mechanism for gene regulation in the developing seeds of Jatropha.…”

Section: Identification Of J Curcas Lncrnas and The Characteristic Fmentioning

confidence: 99%

Identification and characterization of long non-coding RNA (lncRNA) in the developing seeds of Jatropha curcas

Yan

Yang

2020

Sci Rep

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Long non-coding RNAs (lncRNAs) play critical roles in plant development. However, the information of lncRNAs in Jatropha curcas remains largely unexplored. Thus, an attempt has been made in J. curcas to identify 1,850 lncRNAs based on deep sequencing of developing seeds at three typical stages. About ten percent lncRNAs (196 lncRNAs) were differentially expressed lncRNAs during seed developing process. Together with reverse transcription quantitative real-time PCR, the lncRNA expression analyses revealed the stage-specific expression patterns of some novel lncRNAs in J. curcas. The target genes of lncRNAs were annotated for their roles in various biological processes such as gene expression, metabolism, and cell growth. Besides, 10 lncRNAs were identified as the precursors of microRNAs and 26 lncRNAs were predicted to be the targets of Jatropha miRNAs. A total of 31 key lncRNAs play critical roles in the seed developing process in the context of cell growth and development, lipid metabolism, and seed maturation. Our study provides the first systematic study of lncRNAs in the developing seeds of J. curcas and facilitates the functional research of plant lncRNAs and the regulation of seed development. Jatropha curcas is a perennial tree belonging to Euphorbiaceae family and its seed has a high content of oil which can be used as biodiesel 1,2. Gene expression profiles have been analyzed by several efforts in the developing seeds of Jatropha in order to understand the molecular processes of oil metabolism and seed development 3-6. The whole genome sequence of J. curcas have been sequenced and assembled independently by Japan, China and South Korea, and these efforts lay a solid foundation for further exploration of the non-coding RNAs of J. curcas 7-9. Non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are functional transcripts that are not translated into proteins but usually function to regulate the expression of other genes. Studies demonstrate that lncRNAs regulate gene expression in plants by DNA methylation and chromatin remodeling, and in some cases, they act as miRNA sponges to enhance the expression of mRNA targeted by miRNA 10. A great body of evidence indicates that lncRNAs function in both nuclear and cytoplasmic compartments and play essential regulatory roles in plant development processes (the development of pollen, fiber and lateral root; photomorphogenesis), plant reproduction processes (vernalization, flowering time and male sterility), and plant stress responses 11-15. The role of lncRNAs in plant seed development has been acknowleged in recent years, as much effort has been made to identify the lncRNAs from seeds in many plants, including maize 16-18 , Brassica napus 19 , tree peony 20 , castor bean 21 , pigeonpea 22 , Ginkgo biloba 23 , and rice 24. In maize, lncRNAs might play a part in the complex regulation of genetic imprinting during maize endosperm development 17 , and lncRNAs probably have function in lipid metabolism regulation of Brassica napus and tree p...

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Section: Identification Of J Curcas Lncrnas and The Characteristic Fmentioning

confidence: 99%

Identification and characterization of long non-coding RNA (lncRNA) in the developing seeds of Jatropha curcas

Yan

Yang

2020

Sci Rep

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“…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). Moreover, lncRNAs in plants help regulate secondary metabolism and stress responses Zhang et al, 2018;Liu et al, 2018a;Wang et al, 2019a).…”

Section: Introductionmentioning

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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“…by high-throughput sequencing, of which the number varied from tens to tens of thousands 59 . In citrus, we only found that Ke et al 60 identified 1238 (Citrus paradisi) to 3285 (Atalantia buxifolia) lncRNAs in nine citrus species, and Wang et al 61 identified a total of 6584 potential lncRNAs in trifoliate orange. In addition, Zeng et al 62 identified 558 potential circRNAs in trifoliate orange.…”

Section: Possible Function Of Lncrna and Circrna In Citrus Cu Toxicitymentioning

confidence: 66%

Construction of a ceRNA regulatory network in Ziyang xiangcheng (Citrus junos Sieb. ex Tanaka) based on whole-genome transcriptome profiling of mRNAs, lncRNAs, miRNAs and circRNAs under Cu toxicity

Fu¹,

Zhang²,

Qiu³

et al. 2019

Preprint

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Background Copper (Cu) toxicity has become a potential threat for citrus production, but little is known about related mechanisms. This study aims to uncover the global molecular response of mRNAs, long non-coding RNAs (lncRNAs), circular RNAs (circRNAs) and microRNAs (miRNAs) to Cu toxicity and to construct their competing endogenous RNAs (ceRNAs) network in citrus.Results In this study, tolerance of four commonly used rootstocks to Cu toxicity was first evaluated, and ‘Ziyang Xiangcheng’ (Citrus junos ) was proved to be tolerant rootstock. Then the Cu-treated and -untreated root (CuR, CKR) and leaf (CuL, CKL) of ‘Ziyang Xiangcheng’ was selected to perform whole-genome transcriptome sequencing. In total, 5734 and 222 mRNAs, 164 and 5 lncRNAs, 45 and 17 circRNAs, and 147 and 130 miRNAs were identified to be differentially expressed (DE) in CuR/CKR and CuL/CKL, respectively. Gene ontology enrichment analysis of these DEmRNAs and targets of DElncRNAs and DEmiRNAs showed that most were annotated to oxidation-reduction, phosphorylation, membrane, and ion binding. The ceRNA network was constructed with the predicted DEmRNAs-DEmiRNAs and DElncRNAs-DEmiRNAs pairs, which further revealed regulatory roles of these DERNAs in Cu toxicity.Conclusions A large number of mRNAs, lncRNAs, circRNAs, and miRNAs were altered in response to Cu toxicity in citrus, and they may play crucial roles in mitigation of Cu toxicity through the ceRNA regulatory network.

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Evolutionary dynamics of lincRNA transcription in nine citrus species

Cited by 25 publications

References 52 publications

Identification and characterization of long non-coding RNA (lncRNA) in the developing seeds of Jatropha curcas

Identification and characterization of long non-coding RNA (lncRNA) in the developing seeds of Jatropha curcas

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

Construction of a ceRNA regulatory network in Ziyang xiangcheng (Citrus junos Sieb. ex Tanaka) based on whole-genome transcriptome profiling of mRNAs, lncRNAs, miRNAs and circRNAs under Cu toxicity

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