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Discovery and analysis of microRNAs in Leymus chinensis under saline-alkali and drought stress using high-throughput sequencing.

Zhai J, Dong Y, Sun Y, Wang Q, Wang N, Wang F, Liu W, Li X, Chen H, Yao N, Guan L, Chen K, Cui X, Yang M, Li H - PLoS ONE (2014)

Bottom Line: From these data we identified 132 known miRNAs and 16 novel miRNAs candidates.This is the first study to demonstrate differentially expressed miRNAs in L. chinensis under saline-alkali and drought stress.These findings may help explain the saline-alkaline and drought stress responses in L. chinensis.

View Article: PubMed Central - PubMed

Affiliation: Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, China; College of Life Sciences, Jilin Agricultural University, Changchun, Jilin, China.

ABSTRACT
Leymus chinensis (Trin.) Tzvel. is a perennial rhizome grass of the Poaceae (also called Gramineae) family, which adapts well to drought, saline and alkaline conditions. However, little is known about the stress tolerance of L. chinensis at the molecular level. microRNAs (miRNAs) are known to play critical roles in nutrient homeostasis, developmental processes, pathogen responses, and abiotic stress in plants. In this study, we used Solexa sequencing technology to generate high-quality small RNA data from three L. chinensis groups: a control group, a saline-alkaline stress group (100 mM NaCl and 200 mM NaHCO3), and a drought stress group (20% polyethylene glycol 2000). From these data we identified 132 known miRNAs and 16 novel miRNAs candidates. For these miRNAs we also identified target genes that encode a broad range of proteins that may be correlated with abiotic stress regulation. This is the first study to demonstrate differentially expressed miRNAs in L. chinensis under saline-alkali and drought stress. These findings may help explain the saline-alkaline and drought stress responses in L. chinensis.

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Analysis of potential targets in L. chinensis.A: Characterization of candidate miRNA expression levels under saline-alkali and drought stress by qRT-PCR; B: Comparison of predicted target expression levels under saline-alkali and drought stress by qRT-PCR; C: Cleavage site analysis of GW_13268 by 5′ RACE PCR.
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pone-0105417-g005: Analysis of potential targets in L. chinensis.A: Characterization of candidate miRNA expression levels under saline-alkali and drought stress by qRT-PCR; B: Comparison of predicted target expression levels under saline-alkali and drought stress by qRT-PCR; C: Cleavage site analysis of GW_13268 by 5′ RACE PCR.

Mentions: We analyzed the expression of the predicted targets of known L. chinensis miRNAs using published transcriptome sequencing data [13]. Under saline-alkaline stress, we observed no change in the expression for four predicted targets, GW_c49847, GW_c34555, GW_rep_c87771 and GW_c41075, while 109 predicted targets were up- or down-regulated. Among them, 68 had similar expression patterns to the miRNAs that regulate them (table S4, table S7). We then analyzed five miRNAs (miR164a, miR172b, miR444a, miR1120 and miR1318) and their predicted targets (from the 68 described above) by qRT-PCR. After considering the miRNA expression patterns, seven target genes showed a moderate increase in expression under both saline–alkaline and drought conditions (Figure 5A, 5B). Finally, analysis of GW_c13268 by 5′-RACE revealed an mRNA fragment consistent with miRNA-guided cleavage in agreement with previous results obtained for predicted targets of known miRNAs (Figure 5C).


Discovery and analysis of microRNAs in Leymus chinensis under saline-alkali and drought stress using high-throughput sequencing.

Zhai J, Dong Y, Sun Y, Wang Q, Wang N, Wang F, Liu W, Li X, Chen H, Yao N, Guan L, Chen K, Cui X, Yang M, Li H - PLoS ONE (2014)

Analysis of potential targets in L. chinensis.A: Characterization of candidate miRNA expression levels under saline-alkali and drought stress by qRT-PCR; B: Comparison of predicted target expression levels under saline-alkali and drought stress by qRT-PCR; C: Cleavage site analysis of GW_13268 by 5′ RACE PCR.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4219666&req=5

pone-0105417-g005: Analysis of potential targets in L. chinensis.A: Characterization of candidate miRNA expression levels under saline-alkali and drought stress by qRT-PCR; B: Comparison of predicted target expression levels under saline-alkali and drought stress by qRT-PCR; C: Cleavage site analysis of GW_13268 by 5′ RACE PCR.
Mentions: We analyzed the expression of the predicted targets of known L. chinensis miRNAs using published transcriptome sequencing data [13]. Under saline-alkaline stress, we observed no change in the expression for four predicted targets, GW_c49847, GW_c34555, GW_rep_c87771 and GW_c41075, while 109 predicted targets were up- or down-regulated. Among them, 68 had similar expression patterns to the miRNAs that regulate them (table S4, table S7). We then analyzed five miRNAs (miR164a, miR172b, miR444a, miR1120 and miR1318) and their predicted targets (from the 68 described above) by qRT-PCR. After considering the miRNA expression patterns, seven target genes showed a moderate increase in expression under both saline–alkaline and drought conditions (Figure 5A, 5B). Finally, analysis of GW_c13268 by 5′-RACE revealed an mRNA fragment consistent with miRNA-guided cleavage in agreement with previous results obtained for predicted targets of known miRNAs (Figure 5C).

Bottom Line: From these data we identified 132 known miRNAs and 16 novel miRNAs candidates.This is the first study to demonstrate differentially expressed miRNAs in L. chinensis under saline-alkali and drought stress.These findings may help explain the saline-alkaline and drought stress responses in L. chinensis.

View Article: PubMed Central - PubMed

Affiliation: Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, China; College of Life Sciences, Jilin Agricultural University, Changchun, Jilin, China.

ABSTRACT
Leymus chinensis (Trin.) Tzvel. is a perennial rhizome grass of the Poaceae (also called Gramineae) family, which adapts well to drought, saline and alkaline conditions. However, little is known about the stress tolerance of L. chinensis at the molecular level. microRNAs (miRNAs) are known to play critical roles in nutrient homeostasis, developmental processes, pathogen responses, and abiotic stress in plants. In this study, we used Solexa sequencing technology to generate high-quality small RNA data from three L. chinensis groups: a control group, a saline-alkaline stress group (100 mM NaCl and 200 mM NaHCO3), and a drought stress group (20% polyethylene glycol 2000). From these data we identified 132 known miRNAs and 16 novel miRNAs candidates. For these miRNAs we also identified target genes that encode a broad range of proteins that may be correlated with abiotic stress regulation. This is the first study to demonstrate differentially expressed miRNAs in L. chinensis under saline-alkali and drought stress. These findings may help explain the saline-alkaline and drought stress responses in L. chinensis.

Show MeSH
Related in: MedlinePlus