Characterization of conserved and novel microRNAs and their targets, including a TuMV‐induced TIR–NBS–LRR class <i>R</i> gene‐derived novel miRNA in Brassica

He, Xiangfeng; Fang, Yuanyuan; Feng, Lei; Guo, Hui‐Shan

doi:10.1016/j.febslet.2008.06.011

Cited by 207 publications

(145 citation statements)

References 31 publications

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“…Of the 186 miRNAs belonging to 55 families identified in the present study 15 miRNAs belonging to 10 families were reported previously (He et al, 2008); thus, the remaining 40 miRNA families in our study are newly identified. Furthermore, we identified more members belonging to those previously reported B. rapa miRNA families.…”

Section: Identification Of Novel B Rapa and Brassica Lineagespecificsupporting

confidence: 55%

“…Furthermore, we identified more members belonging to those previously reported B. rapa miRNA families. He et al (2008) identified 1 member each for miRNA families 157, 159, 164, 167, 390, and 1885 and 2 members each for miRNA families 160, 172 and 398; only miRNA family 171 had 3 identified members (He et al, 2008). In the present study, we identified 15 members each for BrMiR 159 and 172; 6 for miRNA 164; 8 for miRNA 160; 4 for miRNA 167; 7 for miRNA 390; and 3 for miRNA 398 (Table 2).…”

Section: Identification Of Novel B Rapa and Brassica Lineagespecificsupporting

confidence: 55%

“…brassica-rapa.org, http://www.brassica.info). Although a previous study reports the identification of few miRNAs in B. rapa (He et al, 2008), their presence remains largely unknown in this species. An increasing number of genomic/DNA sequences in the form of GSS, EST, mRNA, and cDNA are being deposited into the NCBI database every day.…”

Section: Discussionmentioning

confidence: 93%

“…However, despite a growing number of informations regarding miRNAs for specific gene expression regulation, miRNAs in Brassica species -especially B. rapa -are largely unknown despite a previous study reporting few miRNAs in this species (He et al, 2008). The systematic identification and characterization of miRNAs in B. rapa would help to elucidate the background of a large amount of genetic and morphological diversity that might have resulted in part to the differential gene expression regulated by miRNAs within and between B. rapa subspecies.…”

Section: Introductionmentioning

confidence: 99%

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Identification of Potential microRNAs and Their Targets in Brassica rapa L.

Dhandapani

Ramchiary

Pavlidis

et al. 2011

Molecules and Cells

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MicroRNAs (miRNAs) are recently discovered, noncoding, small regulatory RNA molecules that negatively regulate gene expression. Although many miRNAs are identified and validated in many plant species, they remain largely unknown in Brassica rapa (AA 2n =, 20). B. rapa is an important Brassica crop with wide genetic and morphological diversity resulting in several subspecies that are largely grown for vegetables, oilseeds, and fodder crop production. In this study, we identified 186 miRNAs belonging to 55 families in B. rapa by using comparative genomics. The lengths of identified mature and pre-miRNAs ranged from 18 to 22 and 66 to 305 nucleotides, respectively. Comparison of 4 nucleotides revealed that uracil is the predominant base in the first position of B. rapa miRNA, suggesting that it plays an important role in miRNA-mediated gene regulation. Overall, adenine and guanine were predominant in mature miRNAs, while adenine and uracil were predominant in pre-miRNA sequences. One DNA sequence producing both sense and antisense mature miRNAs belonging to the BrMiR 399 family, which differs by 1 nucleotide at the, 20 th position, was identified. In silico analyses, using previously established methods, predicted 66 miRNA target mRNAs for 33 miRNA families. The majority of the target genes were transcription factors that regulate plant growth and development, followed by a few target genes that are involved in fatty acid metabolism, glycolysis, biotic and abiotic stresses, and other cellular processes. Northern blot and qRT-PCR analyses of RNA samples prepared from different B. rapa tissues for 17 miRNA families revealed that miRNAs are differentially expressed both quantitatively and qualitatively in different tissues of B. rapa.

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Section: Identification Of Novel B Rapa and Brassica Lineagespecificsupporting

confidence: 55%

Section: Identification Of Novel B Rapa and Brassica Lineagespecificsupporting

confidence: 55%

Section: Discussionmentioning

confidence: 93%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Identification of Potential microRNAs and Their Targets in Brassica rapa L.

Dhandapani

Ramchiary

Pavlidis

et al. 2011

Molecules and Cells

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show abstract

“…The remaining 35% (83/237) of unmatched small RNAs were likely to be specific to Brassica. For example, bra-miR1885, which can be induced specifically by Turnip mosaic virus (TuMV) infection and has been found to target TIR-NBS-LRR class disease-resistant protein-coding gene sequences [21], was identified to be a Brassica-specific novel miRNA [22]. Bna-miR1140, a newly discovered candidate miRNA family, has also been found to be possibly unique to Brassica [23].…”

Section: Introductionmentioning

confidence: 99%

Identification of microRNAs potentially involved in male sterility of Brassica campestris ssp. chinensis using microRNA array and quantitative RT-PCR assays

Jiang

Yang

et al. 2013

Cellular and Molecular Biology Letters

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microRNAs (miRNAs) are a class of newly identified, noncoding, small RNA molecules that negatively regulate gene expression. Many miRNAs are reportedly involved in plant growth, development and stress response processes. However, their roles in the sexual reproduction mechanisms in flowering plants remain unknown. Pollen development is an important process in the life cycle of a flowering plant, and it is closely related to the yield and quality of crop seeds. This study aimed to identify miRNAs involved in pollen development. A microarray assay was conducted using the known complementary sequences of plant miRNAs as probes on inflorescences of a sterile male line (Bcajh97-01A) and a fertile male line (Bcajh97-01B) of the Brassica campestris ssp. chinensis cv. 'Aijiaohuang' genic male sterility sister line system (Bcajh97-01A/B). The results showed that 44 miRNAs were differently expressed in the two lines. Of these, 15 had over 1.5-fold changes in their transcript levels, with 9 upregulated and 6 downregulated miRNAs in inflorescences of 'Bcajh97-01A' sterile line plants. We then focused on 3 of these 15 miRNAs (miR158, miR168 and miR172). Through computational methods, 13 family members were predicted for these 3 miRNAs and 22 genes were predicted to be their candidate target genes. By using 5' modified RACE, 2 target genes of miR168 and 5 target genes of miR172 were identified. Then, qRT-PCR was applied to verify the existence and expression patterns of the 3 miRNAs in the flower buds at five developmental stages. The results were generally consistent with those of the microarray. Thus, this study may give

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