Transcriptome/Degradome-Wide Identification of R. glutinosa miRNAs and Their Targets: The Role of miRNA Activity in the Replanting Disease

Li, Ming Jie; Yang, Yan; Chen, Xin Jian; Wang, Feng Qing; Wen, Lin; Yan, Yijin; Zeng, Lei; Yang, Shuo; Zhang, Zhongyi

doi:10.1371/journal.pone.0068531

Cited by 20 publications

(18 citation statements)

References 53 publications

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“…Here, a non-redundant R. glutinosa transcriptome contained 87,665 transcripts from two sets of roots and leaves have constructed in our previous study (Li et al, 2013). Approximately 1.97% transcript sequences were found to carry at least one SSR locus (≥18 bp), similar to the 2.8% prevalence in barley (Fraser et al, 2004), 3.2% in wheat (Parida et al, 2006), 3.83% in Ramie (Liu et al, 2013).…”

Section: Discussionmentioning

confidence: 86%

“…In this study, a high-capacity R. glutinosa transcriptome derived from different organs using highthroughput sequencing technology (Li et al, 2013) was built to provide basic support for the development. Meanwhile, Polymorphism level of novel R. glutinosa EST-SSR markers was finely identified based on same R. glutinosa species from different ecological regions.…”

Section: Introductionmentioning

confidence: 99%

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SSR Development and Utilization with Rehmannia glutinosa Transcriptome

Li¹,

Yang²,

Feng³

et al. 2016

IJAB

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Rehmannia glutinosa Libosch is a well-known medicinal plant in China. Despite its common use, very few molecular markers are available for this species, severely impeding any improvement of key agronomic traits. In this study, gene-based SSR (simple sequence repeat) markers were mined from the R. glutinosa transcriptome, assembled from leaf and root libraries, to obtain polymorphic information content (PIC). A total of 1,812 SSR (≥18 bp) loci were identified from 1,747 transcripts, in which 1,018 transcripts had significant homology to known proteins, and 35 transcripts were identified as non-coding RNA. Of all SSR loci, AG/GT was the most frequent SSRs repeat type, and bias of base composition presented SSRs loci from noncoding RNA. A set of 279 SSR primers (≥20 bp) were synthesized, of which 204 were successfully amplified in the Wen85-5 genome and 91 had a polymorphic information content between 0.33 and 0.90. Seven pairs of polymorphic SSR primers were selected to evaluate the genetic diversity of 36 R. glutinosa germplasms, and results demonstrated that cultivars are differ considerably from wild strains and that distinct genetic relationships exist among wild strains. The SSRs identified in this study provide critical information for future R. glutinosa breeding.

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Section: Discussionmentioning

confidence: 86%

Section: Introductionmentioning

confidence: 99%

SSR Development and Utilization with Rehmannia glutinosa Transcriptome

Li¹,

Yang²,

Feng³

et al. 2016

IJAB

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“…While some hundreds of miRNA sequences have been identified in Arabidopsis thaliana and rice (Reinhart et al, 2002;Gielen et al, 2016), only 37 R. glutinosa ones have been lodged in the database so far Li et al, 2013). In the study, the application of NGS has identified 18 novel miRNA families of R. glutinosa roots, which enriched the species' sRNA information.…”

Section: Discussionmentioning

confidence: 99%

“…In the study, the application of NGS has identified 18 novel miRNA families of R. glutinosa roots, which enriched the species' sRNA information. An earlier comparison of miRNAs and their mRNA targets between plants growing in fresh soil and second-year plants suggested that miRNAs were likely involved in replanting disease Li et al, 2013). Here, the survey has been extended to plants grown for a third and fourth year.…”

Section: Discussionmentioning

confidence: 99%

“…They are intimately involved in the adaptive response to both abiotic and biotic stress, and are regulated by complex gene networks (Kumar, 2014;Feng et al, 2015;Niu et al, 2016). A number of miRNAs have been associated already with the expression of replanting disease in a second-year crop of R. glutinosa whole plants Li et al, 2013). Although this finding has been taken to imply that they play a regulatory role in the onset of the disease, preliminarily screening some miRNAsresponsive replanting disease, it is still unclear about which miRNAs play a vital role in response to the disease.…”

Section: Introductionmentioning

confidence: 99%

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The miRNAomes in Rehmannia glutinosa Roots Exposed to Different Levels of Replanting Disease Pressure

Yang¹,

Li²,

Yan-jie³

2017

IJAB

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To cite this paper: Yang, Y., M. Li and Y. Yi, 2017. The miRNAomes in Rehmannia glutinosa roots exposed to different levels of replanting disease pressure. AbstractRoot development in the medicinal plant Rehmannia glutinosa is severely disordered by replanting disease, which occurs when it is grown in the same soils over consecutive seasons. Following the demonstration of changes to the miRNAome of the R. glutinosa plants in the second year of cultivation, a fuller experiment was organized to track the root miRNAomes over four successive plantings. Four small RNA libraries were generated from the roots of one year's planted (free of replanting disease) and 2-4 years' continuous cultivation (replanting disease) R. glutinosa plants, respectively. Sequencing of these libraries revealed the presence of 18 novel and 344 conserved miRNA families. The abundance of many of the miRNAs varied between the four libraries, consistent with the notion that replanting disease reflects the outcome differential miRNA transcription. A combined bioinformatic and degradome sequencing approach allowed the identification of 69 differentially abundant (DA) miRNA targets, leading to the recognition that particular miRNA/target modules may be important for the expression of the disease. The expression profiles of 28 key miRNAs and their targets implied that the longer years of continuous cultivation was extended, the more severe tendency of these profiles' changes would be. The indication was that the miRNAs-responsive continuous cultivation pressure reprogrammed gene expression patterns, which disordered hormone signaling, repressed core mechanisms, weakened stress tolerance and resulted in forming the disease in R. glutinosa. In conclusion, the key miRNAs involved in important roles of replanting disease and were a crucial basis for exploration in the disease forming repertoire.

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Transcriptome analysis reveals metabolic alteration due to consecutive monoculture and abiotic stress stimuli in Rehamannia glutinosa Libosch

et al. 2017

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We deeply investigated the mechanism underlying metabolic regulation in response to consecutive monoculture (replanting disease) and different abiotic stresses that unfolded the response mechanism to consecutive monoculture problem through RNA-seq analysis. The consecutive monoculture problem (CMP) resulted of complex environmental stresses mediated by multiple factors. Previous studies have noted that multiple stress factors in consecutive monoculture soils or plants severely limited the interpretation of the critical molecular mechanism, and made a predict that the specifically responding factor was autotoxic allelochemicals. To identify the specifically responding genes, we compared transcriptome changes in roots of Rehamannia glutinosa Libosch using consecutive monoculture, salt, drought, and ferulic acid as stress factors. Comparing with normal growth, 2502, 2672, 2485, and 1956 genes were differentially expressed in R. glutinosa under consecutive monoculture practice, salt, drought, and ferulic acid stress, respectively. In addition, 510 genes were specifically expressed under consecutive monoculture, which were not present under the other stress conditions. Integrating the biological and enrichment analyses of the differentially expressed genes, the result demonstrated that the plants could alter enzyme genes expression to reconstruct the complicated metabolic pathways, which used to tolerate the CMP and abiotic stresses. Furthermore, most of the affected pathway genes were closely related to secondary metabolic processes, and the influence of consecutive monoculture practice on the transcriptome genes expression profile was very similar to the profile under salt stress and then to the profile under drought stress. The outlined schematic diagram unfolded the putative signal regulation mechanism in response to the CMP. Genes that differentially up- or down-regulated under consecutive monoculture practice may play important roles in the CMP or replanting disease in R. glutinosa.

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Transcriptome/Degradome-Wide Identification of R. glutinosa miRNAs and Their Targets: The Role of miRNA Activity in the Replanting Disease

Cited by 20 publications

References 53 publications

SSR Development and Utilization with Rehmannia glutinosa Transcriptome

SSR Development and Utilization with Rehmannia glutinosa Transcriptome

The miRNAomes in Rehmannia glutinosa Roots Exposed to Different Levels of Replanting Disease Pressure

Transcriptome analysis reveals metabolic alteration due to consecutive monoculture and abiotic stress stimuli in Rehamannia glutinosa Libosch

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