Genome-wide identification and characterization of cadmium-responsive microRNAs and their target genes in radish (Raphanus sativus L.) roots

Xu, Liang; Wang, Yan; Zhai, Limin; Xu, Yuanyuan; Wang, Liangju; Zhu, Xiaoming; Gong, Yiqin; Yu, Rugang; Limera, Cecilia; Liu, Liwang

doi:10.1093/jxb/ert240

Cited by 118 publications

(123 citation statements)

References 67 publications

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“…Transcriptomes, however, cannot capture true pre-miRNA sequences because the latter are very short and devoid of poly-A tails; consequently, the sequences mapped by miRNA were likely pri-miRNAs [57]. Based on the hairpin structural characteristics of pre-miRNA, pre-miRNA sequences could subsequently be obtained from pri-miRNA sequences using bioinformatics approaches [27,28].…”

Section: Discussionmentioning

confidence: 99%

Identification and Target Prediction of MicroRNAs in Ulmus pumila L. Seedling Roots under Salt Stress by High-Throughput Sequencing

Zhu¹,

Yang²,

Liu³

et al. 2016

Forests

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MicroRNAs (miRNAs) are a class of endogenous small RNAs with important roles in plant growth, development, and environmental stress responses. Ulmus pumila L., a deciduous broadleaved tree species of northern temperate regions, is widely distributed in central and northern Asia and has important economic and ecological value. With the spread and aggravation of soil salinization, salt stress has become a major abiotic stress affecting the normal growth and development of U. pumila. However, the influence of salt stress on U. pumila miRNA expression has not been investigated. To identify miRNAs and predict their target mRNA genes under salt stress, three small RNA libraries were generated and sequenced from roots of U. pumila seedlings treated with various concentrations of NaCl corresponding to no salt stress, light short-term salt stress, and medium-heavy long-term salt stress. Integrative analysis identified 254 conserved miRNAs representing 29 families and 49 novel miRNAs; 232 potential targets of the miRNAs were also predicted. Expression profiling of miRNAs between libraries was performed, and the expression of six miRNAs was validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Our findings provide an overview of potential miRNAs and corresponding targets involved in regulating U. pumila salt defense responses. These results lay the foundation for further research into molecular mechanisms involved in salt stress resistance in U. pumila and other Ulmaceae species.

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Section: Discussionmentioning

confidence: 99%

Identification and Target Prediction of MicroRNAs in Ulmus pumila L. Seedling Roots under Salt Stress by High-Throughput Sequencing

Zhu¹,

Yang²,

Liu³

et al. 2016

Forests

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“…Using Illumina technology, the identification of potential cadmium-responsive miRNAs and their target genes in radish (Raphanus sativus L.) roots has been performed (Xu et al 2013b). SMRT technology by Pacific Biosciences was used with the aim of identifying circular RNAs using transcriptome analysis.…”

Section: Study Of Epigenetic Regulationmentioning

confidence: 99%

Application of next-generation sequencing in plant breeding

Vlk¹,

Řepková²

2017

Czech J. Genet. Plant Breed.

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In the past decade, next-generation sequencing (NGS) platforms have changed the impact of sequencing on our knowledge of crop genomes and gene regulation. These techniques are today acquiring a great potential in metagenomic and agrigenomic research while showing prospects for their utilization in plant breeding. We can now obtain new and beneficial information about gene regulation on the cellular as well as whole-plant level through RNA-sequencing and subsequent expression analyses of genes participating in plant defence reactions to pathogens and in abiotic stress tolerance. NGS has facilitated the development of methods to genotype very large numbers of single-nucleotide polymorphisms. Genotyping-by-sequencing and whole-genome resequencing can lead to the development of molecular markers suited to studies of genetic relationships among breeding materials, creation of detailed genetic mapping of targeted genes and genome-wide association studies. Plant genotyping can benefit plant breeding through selection of individuals resistant to climatic stress and to pathogens causing substantial losses in agriculture.

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“…Differentially expressed miRNAs were examined using qPCR with SYBR green (Xu et al 2013 Fig. 1 a, b Preliminary analysis of the reads of schistosomula from Wistar rats and BALB/c mice (Wang et al 2010).…”

Section: Validation Of Mirna Expression With Quantitative Pcr (Qpcr) mentioning

confidence: 99%

Comparative characterization of microRNAs in Schistosoma japonicum schistosomula from Wistar rats and BALB/c mice

Peng

Hong²,

Fu³

et al. 2015

Parasitol Res

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More than 40 kinds of mammals in China are known to be naturally infected with Schistosoma japonicum (S. japonicum) (Peng et al. Parasitol Res 106:967-76, 2010). Compared with permissive BALB/c mice, rats are less susceptible to S. japonicum infection and are considered to provide an unsuitable microenvironment for parasite growth and development. MicroRNAs (miRNAs), via the regulation of gene expression at the transcriptional and post-transcriptional levels, may be responsible for developmental differences between schistosomula in these two rodent hosts. Solexa deep-sequencing technology was used to identify differentially expressed miRNAs from schistosomula isolated from Wistar rats and BALB/c mice 10 days post-infection. The deep-sequencing analysis revealed that nearly 40 % of raw reads (10.37 and 10.84 million reads in schistosomula isolated from Wistar rats and BALB/c mice, respectively) can be mapped to selected mirs in miRBase or in species-specific genomes. Further analysis revealed that several miRNAs were differentially expressed in schistosomula isolated from these two rodents; 18 were downregulated (by <2-fold) and 23 were up-regulated (>2-fold) (expression levels in rats compare with those in mice). Additionally, three novel miRNAs were primarily predicted and identified. Among the 41 differentially expressed miRNAs, 4 miRNAs had been identified with specific functions in schistosome development or host-parasite interaction, such as sexual maturation (sja-miR-1, sja-miR-7-5p), embryo development (sja-miR-36-3p) in schistosome, and pathogenesis of schistosomiasis (sja-bantam). Then, the target genes were mapped, filtered, and correlated with a set of genes that were differentially expressed genes in schistosomula isolated from mice and rats, which we identified in a S. japonicum oligonucleotide microarray analysis in a previous study. Gene Ontology (GO) analysis of the predicted target genes of 13 differentially expressed miRNAs revealed that they were involved in some important biological pathways, such as metabolic processes, the regulation of protein catabolic processes, catalytic activity, oxidoreductase activity, and hydrolase activity. The study presented here includes the first identification of differentially expressed miRNAs between schistosomula in mice or rats. Therefore, we hypothesized that the differentially expressed miRNAs may affect the development, growth, and maturation of the schistosome in its life cycle. Our analysis suggested that some differentially expressed miRNAs may impact the survival and development of the parasite within a host. This study increases our understanding of schistosome development and host-parasite interactions.

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Genome-wide identification and characterization of cadmium-responsive microRNAs and their target genes in radish (Raphanus sativus L.) roots

Cited by 118 publications

References 67 publications

Identification and Target Prediction of MicroRNAs in Ulmus pumila L. Seedling Roots under Salt Stress by High-Throughput Sequencing

Identification and Target Prediction of MicroRNAs in Ulmus pumila L. Seedling Roots under Salt Stress by High-Throughput Sequencing

Application of next-generation sequencing in plant breeding

Comparative characterization of microRNAs in Schistosoma japonicum schistosomula from Wistar rats and BALB/c mice

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