Identification and characterization of microRNAs from citrus expressed sequence tags

Wu, Xiaomeng; Liu, Mei-Ya; Xu, Qiang; Guo, Wen‐Wu

doi:10.1007/s11295-010-0319-5

Cited by 17 publications

(8 citation statements)

References 72 publications

(72 reference statements)

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“…Total RNA extraction and qRT-PCR was carried out as previously (Liu et al 2007;Wu et al 2010 Table 2). In order to determine qPCR efficiency of miRNAs and the reference gene actin, tenfold serial dilutions of cDNA template (0.01, 0.1, 1, 10, 100 ng/lL) was amplified.…”

Section: Qrt-pcr Of Mirnas and Target Genesmentioning

confidence: 99%

Stage and tissue-specific modulation of ten conserved miRNAs and their targets during somatic embryogenesis of Valencia sweet orange

Liu

et al. 2010

Planta

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113

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Somatic embryogenesis (SE) is a remarkable process of plant somatic cells developing into an embryo capable of forming a complete plant. MiRNAs play important roles in plant development by regulating expression of their target genes, but its function in SE has rarely been studied. Herein, ten conserved miRNAs with critical functions in plant development are detected by stem-loop qRT-PCR in the SE system of Valencia sweet orange. Sixteen unigenes from citrus are predicted to be targeted by six of the miRNAs. Cleavage sites on 15 of these target mRNAs are mapped by 5'RACE, of which ten are reported in this study. Transcript abundances of the 16 target unigenes are detected by qRT-PCR during SE process. Stage and tissue-specific expressions of miRNAs and their targets suggest their possible modulation on SE of citrus callus: miR156, 168 and 171 exert regulatory function during somatic embryo induction process; miR159, 164, 390 and 397 are related to globular-shaped embryo formation; miR166, 167 and 398 are required for cotyledon-shaped embryo morphogenesis; in addition, target genes of miR164, 166 and 397 are associated with SE disability of nonembryogenic callus. Exploration of miRNA-mediated modulation on SE is expected to provide new insights into plant cell totipotency, as well as how to maintain and enhance the embryogenic capacity of somatic cells.

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Section: Qrt-pcr Of Mirnas and Target Genesmentioning

confidence: 99%

Stage and tissue-specific modulation of ten conserved miRNAs and their targets during somatic embryogenesis of Valencia sweet orange

Liu

et al. 2010

Planta

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113

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“…The growing interest in the role of small RNAs has resulted in a large number of publications that describe the microRNA population of various crop plants, including citrus [18][19][20]. Yet, studies relating to the physiological roles Fig.…”

Section: Discussionmentioning

confidence: 99%

Graft-induced Changes in MicroRNA Expression Patterns in Citrus Leaf Petioles

Tzarfati¹,

Ben‐Dor²,

Sela³

et al. 2013

TOPSJ

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Grafting is an important, widely used plant propagation technique but its physiological effects are as yet insufficiently understood. Recent studies indicate that movement of proteins and small RNAs through the graft union might be involved. MicroRNAs are known to play a significant role in regulation of higher plants’ developmental and metabolic traits. Extending this logic, we hypothesize that changes in activity of specific microRNAs are one of the mechanisms involved in physiological effects of grafting. The objective of the present study was to test this hypothesis. We determined the expression of a broad range of microRNAs in Citrus leaf petioles, as affected by grafting. Four stock/scion combinations (‘Merav’ mandarin and ‘Star Ruby‘ grapefruit scions X ‘Troyer’ citrange and ‘Volkamer’ lemon rootstocks), rootstock auto-grafts and plants of the variety used as rootstock (= non-grafted) were examined. Grafting caused a dramatic reduction in the expression of the major microRNAs, miR156 (and miR157), which appear to be associated with reduction of juvenility in perennial woody plants. This effect was strongest in hetero-grafts but evident also in auto-grafts. Expression of miR894 also declined upon grafting. Differences in the expression of miR397 were found among grafted scion cultivars, while in non-grafted rootstocks expression of miR397 was barely detectable. Bioinformatic analysis confirmed the presence of miR397 in the citrus genome, validated its sequence and demonstrated its ability to form a stem loop. The differences in miR397 expression might be related to specific copper and other micronutrient requirements of citrus stock-scion combinations.Thus, our results support the hypothesis, indicating the involvement of specific microRNAs in engendering physiological effects of grafting in Citrus. The precise, underlying mechanism needs to be elucidated.

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“…A wheat actin gene was selected to normalize the quantity of templates added in the PCR reactions for analyzing the expression of novel miRNAs using semi-quantitative RT-PCR [40]. Actin was also used as an endogenous control gene to normalize the expression of miRNAs in C. sinensis [41][42][43][44] and in tomato after inoculation with Phytophthora infestans [45]. Other stably expressed protein-coding genes, such as GAPDH or EF-1a, are also used as internal standards in miRNA quantitative studies [46,47].…”

Section: Introductionmentioning

confidence: 99%

Identification of Appropriate Reference Genes for Normalizing miRNA Expression in Citrus Infected by Xanthomonas citri subsp. citri

Lyu

et al. 2019

Genes

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MicroRNAs (miRNAs) are short noncoding RNA molecules that regulate gene expression at the posttranscriptional level. Reverse transcription-quantitative PCR (RT-qPCR) is one of the most common methods used for quantification of miRNA expression, and the levels of expression are normalized by comparing with reference genes. Thus, the selection of reference genes is critically important for accurate quantification. The present study was intended to identify appropriate miRNA reference genes for normalizing the level of miRNA expression in Citrus sinensis L. Osbeck and Citrus reticulata Blanco infected by Xanthomonas citri subsp. citri, which caused citrus canker disease. Five algorithms (Delta Ct, geNorm, NormFinder, BestKeeper and RefFinder) were used for screening reference genes, and two quantification approaches, poly(A) extension RT-qPCR and stem-loop RT-qPCR, were used to determine the most appropriate method for detecting expression patterns of miRNA. An overall comprehensive ranking output derived from the multi-algorithms showed that poly(A)-tailed miR162-3p/miR472 were the best reference gene combination for miRNA RT-qPCR normalization in citrus canker research. Candidate reference gene expression profiles determined by poly(A) RT-qPCR were more consistent in the two citrus species. To the best of our knowledge, this is the first systematic comparison of two miRNA quantification methods for evaluating reference genes. These results highlight the importance of rigorously assessing candidate reference genes and clarify some contradictory results in miRNA research on citrus.

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Identification and characterization of microRNAs from citrus expressed sequence tags

Cited by 17 publications

References 72 publications

Stage and tissue-specific modulation of ten conserved miRNAs and their targets during somatic embryogenesis of Valencia sweet orange

Stage and tissue-specific modulation of ten conserved miRNAs and their targets during somatic embryogenesis of Valencia sweet orange

Graft-induced Changes in MicroRNA Expression Patterns in Citrus Leaf Petioles

Identification of Appropriate Reference Genes for Normalizing miRNA Expression in Citrus Infected by Xanthomonas citri subsp. citri

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