Identification and characterization of miRNAome in tobacco (Nicotiana tabacum) by deep sequencing combined with microarray

Guo, Yushuang; Liu, Hanhua; Yang, Zhixiao; Chen, Jing; Sun, Yimin; Ren, Xueliang

doi:10.1016/j.gene.2012.04.002

Cited by 15 publications

(12 citation statements)

References 34 publications

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“…The size distribution of reads was not significantly different in the three libraries, and the majority of small RNAs were in the range from 18 to 24, with 24 nt as the most frequent size (Additional file 7). These results are consistent with previous studies in tobacco [32, 33] and similar to results reported for M. truncatula [34], maize [35], potato [36], tomato [37], Citrus trifoliate [38], Citrus sativus [39], Arabidopsis [40], and rice [41]. In order to remove rRNA, tRNA, snRNA, and snoRNA, all clean reads of three libraries were analyzed by BLAST against the Rfam database (See Methods section for details; these small RNAs accounted for 158,145, 197,174, and 1,943,313 total reads in CL, DL, and WL, respectively (Additional file 8).…”

Section: Resultssupporting

confidence: 94%

Integrated mRNA and microRNA analysis identifies genes and small miRNA molecules associated with transcriptional and post-transcriptional-level responses to both drought stress and re-watering treatment in tobacco

Chen

Zhang

et al. 2017

BMC Genomics

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BackgroundDrought stress is one of the most severe problem limited agricultural productivity worldwide. It has been reported that plants response to drought-stress by sophisticated mechanisms at both transcriptional and post-transcriptional levels. However, the precise molecular mechanisms governing the responses of tobacco leaves to drought stress and water status are not well understood. To identify genes and miRNAs involved in drought-stress responses in tobacco, we performed both mRNA and small RNA sequencing on tobacco leaf samples from the following three treatments: untreated-control (CL), drought stress (DL), and re-watering (WL).ResultsIn total, we identified 798 differentially expressed genes (DEGs) between the DL and CL (DL vs. CL) treatments and identified 571 DEGs between the WL and DL (WL vs. DL) treatments. Further analysis revealed 443 overlapping DEGs between the DL vs. CL and WL vs. DL comparisons, and, strikingly, all of these genes exhibited opposing expression trends between these two comparisons, strongly suggesting that these overlapping DEGs are somehow involved in the responses of tobacco leaves to drought stress. Functional annotation analysis showed significant up-regulation of genes annotated to be involved in responses to stimulus and stress, (e.g., late embryogenesis abundant proteins and heat-shock proteins) antioxidant defense (e.g., peroxidases and glutathione S-transferases), down regulation of genes related to the cell cycle pathway, and photosynthesis processes. We also found 69 and 56 transcription factors (TFs) among the DEGs in, respectively, the DL vs. CL and the WL vs. DL comparisons. In addition, small RNA sequencing revealed 63 known microRNAs (miRNA) from 32 families and 368 novel miRNA candidates in tobacco. We also found that five known miRNA families (miR398, miR390, miR162, miR166, and miR168) showed differential regulation under drought conditions. Analysis to identify negative correlations between the differentially expressed miRNAs (DEMs) and DEGs revealed 92 mRNA-miRNA interactions between CL and DL plants, and 32 mRNA-miRNA interactions between DL and WL plants.ConclusionsThis study provides a global view of the transcriptional and the post-transcriptional responses of tobacco under drought stress and re-watering conditions. Our results establish an empirical foundation that should prove valuable for further investigations into the molecular mechanisms through which tobacco, and plants more generally, respond to drought stress at multiple molecular genetic levels.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3372-0) contains supplementary material, which is available to authorized users.

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Section: Resultssupporting

confidence: 94%

Integrated mRNA and microRNA analysis identifies genes and small miRNA molecules associated with transcriptional and post-transcriptional-level responses to both drought stress and re-watering treatment in tobacco

Chen

Zhang

et al. 2017

BMC Genomics

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“…Conservation and diversity analysis of predicted miRNA families in various plant species demonstrates that a potential species-species miRNA link may exist 49 . Further study is needed to determine whether this link is related to biological evolution.…”

Section: Discussionmentioning

confidence: 99%

“…Compared with the rapidly increasing amount of information available for miRNAs in model and advanced plants 49 50 51 52 , little is known about miRNAs in the non-model lower seaweed C. crispus . Although over 35,000 miRNAs from 223 species have been submitted to the miRNA database (miRBase 21.0, June 2014; http://www.mirbase.org/ ) 53 , no miRNAs from C. crispus have been deposited.…”

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confidence: 99%

Identification and Characterization of miRNAs in Chondrus crispus by High-Throughput Sequencing and Bioinformatics Analysis

Gao

Nan

Song³

et al. 2016

Sci Rep

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Chondrus crispus, an economically and medicinally important red alga, is a medicinally active substance and important for anti-tumor research. In this study, 117 C. crispus miRNAs (108 conserved and 9 novel) were identified from 2,416,181 small-RNA reads using high-throughput sequencing and bioinformatics methods. According to the BLAST search against the miRBase database, these miRNAs belonged to 110 miRNA families. Sequence alignment combined with homology searching revealed both the conservation and diversity of predicted potential miRNA families in different plant species. Four and 19 randomly selected miRNAs were validated by northern blotting and stem-loop quantitative real-time reverse transcription polymerase chain reaction detection, respectively. The validation rates (75% and 94.7%) demonstrated that most of the identified miRNAs could be credible. A total of 160 potential target genes were predicted and functionally annotated by Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes analysis. We also analyzed the interrelationship of miRNAs, miRNA-target genes and target genes in C. crispus by constructing a Cytoscape network. The 117 miRNAs identified in our study should supply large quantities of information that will be important for red algae small RNA research.

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“…Currently, the development of high-throughput sequencing and bioinformatic approaches have enabled the identification of large sets of miRNAs that occur in certain tissues, cells or at particular stages. Using the above mentioned techniques, the miRNA collections have been identified from many species, including model organisms or important food crops [28,37,40,48,49]. One of the vegetables that is significant in some countries due to its health and economic benefits is the Brassica oleracea var.…”

Section: Discussionmentioning

confidence: 99%

High-throughput sequencing identification of novel and conserved miRNAs in the Brassica oleracea leaves

et al. 2013

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BackgroundPlant microRNAs are short (~21 nt) non-coding molecules that regulate gene expression by targeting the mRNA cleavage or protein translation inhibition. In this manner, they play many important roles in the cells of living organisms. One of the plant species in which the entire set of miRNAs has not been yet completely identified is Brassica oleracea var. capitata (cabbage). For this reason and for the economic and nutritional importance of this food crop, high-throughput small RNAs sequencing has been performed to discover the novel and conserved miRNAs in mature cabbage leaves.ResultsIn this study, raw reads generated from three small RNA libraries were bioinformatically processed and further analyzed to select sequences homologous to known B. oleracea and other plant miRNAs. As a result of this analysis, 261 conserved miRNAs (belonging to 62 families) have been discovered. MIR169, MIR167 and MIR166 were the largest miRNA families, while the highest abundance molecules were miR167, miR166, miR168c and miR157a. Among the generated sequencing reads, miRNAs* were also found, such as the miR162c*, miR160a* and miR157a*. The unannotated tags were used in the prediction and evaluation of novel miRNAs, which resulted in the 26 potential miRNAs proposal. The expressions of 13 selected miRNAs were analyzed by northern blot hybridization. The target prediction and annotation for identified miRNAs were performed, according to which discovered molecules may target mRNAs encoding several potential proteins – e.g., transcription factors, polypeptides that regulate hormone stimuli and abiotic stress response, and molecules participating in transport and cell communication. Additionally, KEGG maps analysis suggested that the miRNAs in cabbage are involved in important processing pathways, including glycolysis, glycerolipid metabolism, flavonoid biosynthesis and oxidative phosphorylation.ConclusionsConclusively, for the first time, the large set of miRNAs was identified in mature cabbage leaves. Potential targets designation for these miRNAs may suggest their essential role in many plants primary biological processes. Presented study not only supplements the knowledge about B. oleracea miRNAs, but additionally it may be used in other research concerning the improvement of the cabbage cultivation.

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Identification and characterization of miRNAome in tobacco (Nicotiana tabacum) by deep sequencing combined with microarray

Cited by 15 publications

References 34 publications

Integrated mRNA and microRNA analysis identifies genes and small miRNA molecules associated with transcriptional and post-transcriptional-level responses to both drought stress and re-watering treatment in tobacco

Integrated mRNA and microRNA analysis identifies genes and small miRNA molecules associated with transcriptional and post-transcriptional-level responses to both drought stress and re-watering treatment in tobacco

Identification and Characterization of miRNAs in Chondrus crispus by High-Throughput Sequencing and Bioinformatics Analysis

High-throughput sequencing identification of novel and conserved miRNAs in the Brassica oleracea leaves

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