Identification and characterisation of microRNAs and their target genes in phosphate-starved Nicotiana benthamiana by small RNA deep sequencing and 5’RACE analysis

Huen, Amanda Kay; Bally, Julia; Smith, Penelope M. C.

doi:10.1186/s12864-018-5258-9

Cited by 30 publications

(26 citation statements)

References 67 publications

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“…Our results are consistent with sRNA sequencing data published for Arabidopsis [37,50] and Nicotiana benthamiana L. [72]. In both plant species, authors have shown that the number of various miR399 isomiRs was the most abundant in shoots and roots under low-Pi.…”

Section: Resultssupporting

confidence: 92%

Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

Sega

Kruszka

Bielewicz

et al. 2020

Preprint

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Background: Small RNAs (sRNAs) are 18–24 nt regulatory elements which are responsible for plant development regulation and participate in many plant stress responses. Insufficient inorganic phosphate (Pi) concentration triggers plant responses to balance the internal Pi level. Results: In this study, we describe Pi-starvation-responsive small RNAs and transcriptome changes in barley (Hordeum vulgare L.) using Next-Generation Sequencing (NGS) data derived from three different types of NGS libraries: (i) small RNAs, (ii) degraded RNAs, and (iii) functional mRNAs. We find that differentially and significantly expressed miRNAs (DEMs, p-value < 0.05) are represented by 162 (44.88 % of total differentially expressed small RNAs) molecules in shoot and 138 (7.14 %) in root; mainly various miR399 and miR827 isomiRs. The remaining small RNAs (i.e., those without perfect match to reference sequences deposited in miRBase) are considered as differentially expressed other sRNAs (DESs, Bonferroni correction). In roots, a more abundant and diverse set of other sRNAs (1796 unique sequences, 0.13 % from total unique reads obtained under low-Pi) contributes more to the compensation of low-Pi stress than that in shoots (199 unique sequences, 0.01 %). More than 80 % of differentially expressed other sRNAs are upregulated in both organs. Additionally, in barley shoots, upregulation of small RNAs is accompanied by strong induction of two nucleases (S1/P1 endonuclease and 3’-5’ exonuclease). This suggests that most small RNAs may be generated upon endonucleolytic cleavage to increase the internal Pi pool. Transcriptomic profiling of Pi-starved barley shoots identify 98 differentially expressed genes (DEGs). A majority of the DEGs possess characteristic Pi-responsive cis-regulatory elements (P1BS and/or PHO element), located mostly in the proximal promoter regions. GO analysis shows that the discovered DEGs primarily alter plant defense, plant stress response, nutrient mobilization, or pathways involved in the gathering and recycling of phosphorus from organic pools.Conclusions: Our results provide comprehensive data to demonstrate complex responses at the RNA level in barley to maintain Pi homeostasis and indicate that barley adapts to Pi scarcity through elicitation of RNA degradation. Novel P-responsive genes were selected as putative candidates to overcome low-Pi stress in barley plants.

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Section: Resultssupporting

confidence: 92%

Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

Sega

Kruszka

Bielewicz

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…In this work, the majority of DEMs represent various miR399 and miR827 isomiRs in both tested organs. Our results are consistent with sRNA sequencing data published for Arabidopsis [42,55] and Nicotiana benthamiana L. [93]. In both plant species, authors have shown that the number of various miR399 isomiRs was the most abundant in shoots and roots under low-Pi.…”

Section: Discussionsupporting

confidence: 92%

“…The well-known abiotic stress-responsive miR319c (21 nt) [6] was found to target various isoforms of GAMyb TF (HORVU3Hr1G079490, TargetSeek: score = 5, MFE = -34.6, PAREsnip2: score = 3, MFE = -35.4). The same predicted miR319 target has been previously found in RNA-Seq of Pi-starved tobacco plants [93]. Its targets, the plant GAMyb TFs, have been shown to activate gibberellin-responsive gene expression of α-amylase in barley [94,95].…”

Section: Pi-responsive Motifs Found In the Promoters Of Degssupporting

confidence: 68%

Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

Sega

Kruszka

Bielewicz

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Small RNAs (sRNAs) are 20–30 nt regulatory elements which are responsible for plant development regulation and participate in many plant stress responses. Insufficient inorganic phosphate (Pi) concentration triggers plant responses to balance the internal Pi level. Results: In this study, we describe Pi-starvation-responsive small RNAs and transcriptome changes in barley (Hordeum vulgare L.) using Next-Generation Sequencing (NGS) RNA-Seq data derived from three different types of NGS libraries: (i) small RNAs, (ii) degraded RNAs, and (iii) functional mRNAs. We find that differentially and significantly expressed miRNAs (DEMs, p-value < 0.05) are represented by 162 (44.88 % of total differentially expressed small RNAs) molecules in shoot and 138 (7.14 %) in root; mainly various miR399 and miR827 isomiRs. The remaining small RNAs (i.e., those without perfect match to reference sequences deposited in miRBase) are considered as differentially expressed other sRNAs (DESs, p-value Bonferroni correction < 0.05). In roots, a more abundant and diverse set of other sRNAs (DESs, 1796 unique sequences, 0.13 % from total unique reads obtained under low-Pi) contributes more to the compensation of low-Pi stress than that in shoots (DESs, 199 unique sequences, 0.01 %). More than 80 % of differentially expressed other sRNAs are up-regulated in both organs. Additionally, in barley shoots, up-regulation of small RNAs is accompanied by strong induction of two nucleases (S1/P1 endonuclease and 3’-5’ exonuclease). This suggests that most small RNAs may be generated upon endonucleolytic cleavage to increase the internal Pi pool. Transcriptomic profiling of Pi-starved barley shoots identifies 98 differentially expressed genes (DEGs). A majority of the DEGs possess characteristic Pi-responsive cis-regulatory elements (P1BS and/or PHO element), located mostly in the proximal promoter regions. GO analysis shows that the discovered DEGs primarily alter plant defense, plant stress response, nutrient mobilization, or pathways involved in the gathering and recycling of phosphorus from organic pools.Conclusions: Our results provide comprehensive data to demonstrate complex responses at the RNA level in barley to maintain Pi homeostasis and indicate that barley adapts to Pi-starvation through elicitation of RNA degradation. Novel P-responsive genes were selected as putative candidates to overcome low-Pi stress in barley plants.

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“…The use of phosphorus fertilizers has alleviated the problem, but it is rapidly depleted as a non-renewable natural resource, and lead to serious environmental pollution (Tong et al, 2017). Therefore, a substantial number of studies based on nextgeneration sequencing have documented the molecular responses of different plant species under Pideficient conditions (O′Rourke et al, 2013;Gho et al, 2018;Huen et al, 2018). Previously, we reported temporal transcriptome responses to Pi starvation in Masson pine seedlings and found that most transcripts were stably and gradually up-or downregulated within 48 d of Pi starvation (Fan et al, 2014).…”

Section: Discussion 10mentioning

confidence: 93%

Integrated mRNA and miRNA expression profiling analyses of Pinus massoniana roots and shoots in response to phosphate deficiency

Fan¹,

Shang²,

Ding³

et al. 2020

Preprint

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Background Masson pine ( Pinus massoniana ) is primarily present in subtropical and tropical areas of China, which are severely deficient in inorganic phosphate (Pi). Although some studies identified transcriptomic and proteomic responses to Pi deficiency in Masson pine seedlings, different tissues, especially the roots, that exhibit primary responses to low-Pi stress, have not been well studied. To shed further light on the complex responses of Masson pine to Pi deficiency, a spatiotemporal experiment was performed to identify differentially expressed mRNAs and miRNAs under Pi-deficient conditions. Results Spatiotemporal analyses of 72 RNA sequencing libraries provided a comprehensive overview of the dynamic responses of Masson pine to low-Pi stress. Differentially expressed gene analysis revealed several high-affinity phosphate transporters and nitrate transporters, reflecting the crosstalk between nitrate and Pi homeostasis in plants. The MYB family was the most abundant transcription factor family identified. miRNA differential expression analysis identified several families that were associated with Pi deficiency, such as miR399. In addition, some other families, including novel miRNA families in Masson pine, were dramatically changed in response to Pi starvation. GO and KEGG analyses of these mRNAs and targets of miRNAs indicated that metabolic processes were most enriched under Pi deficiency. Conclusions This study provided abundant spatiotemporal transcriptomic information to functionally dissect the response of Masson pine seedlings to Pi deficiency, which will aid in further elucidation of the biological regulatory mechanisms of pines in response to low-Pi stress.

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Identification and characterisation of microRNAs and their target genes in phosphate-starved Nicotiana benthamiana by small RNA deep sequencing and 5’RACE analysis

Cited by 30 publications

References 67 publications

Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

Integrated mRNA and miRNA expression profiling analyses of Pinus massoniana roots and shoots in response to phosphate deficiency

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