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Genome-wide identification and functional prediction of cold and/or drought-responsive lncRNAs in cassava

View Article: PubMed Central - PubMed

ABSTRACT

Cold and drought stresses seriously affect cassava (Manihot esculenta) plant growth and yield. Recently, long noncoding RNAs (lncRNAs) have emerged as key regulators of diverse cellular processes in mammals and plants. To date, no systematic screening of lncRNAs under abiotic stress and their regulatory roles in cassava has been reported. In this study, we present the first reference catalog of 682 high-confidence lncRNAs based on analysis of strand-specific RNA-seq data from cassava shoot apices and young leaves under cold, drought stress and control conditions. Among them, 16 lncRNAs were identified as putative target mimics of cassava known miRNAs. Additionally, by comparing with small RNA-seq data, we found 42 lncNATs and sense gene pairs can generate nat-siRNAs. We identified 318 lncRNAs responsive to cold and/or drought stress, which were typically co-expressed concordantly or discordantly with their neighboring genes. Trans-regulatory network analysis suggested that many lncRNAs were associated with hormone signal transduction, secondary metabolites biosynthesis, and sucrose metabolism pathway. The study provides an opportunity for future computational and experimental studies to uncover the functions of lncRNAs in cassava.

No MeSH data available.


Related in: MedlinePlus

Confirmation of the expression patterns of lncRNAs using quantitative RT-PCR.(A–L) The expression pattern of lncRNAs under cold or drought stress. The values shown are the means ± standard deviation of three replicates. MeACTIN was used as the reference gene.
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f4: Confirmation of the expression patterns of lncRNAs using quantitative RT-PCR.(A–L) The expression pattern of lncRNAs under cold or drought stress. The values shown are the means ± standard deviation of three replicates. MeACTIN was used as the reference gene.

Mentions: To further characterize cold- and/or drought- responsive lncRNAs listed in supplemental data S2 in cassava, 12 lncRNAs under cold and/or drought conditions were randomly selected and analyzed by real-time quantitative PCR (qRT-PCR). As shown in Fig. 4, the expression patterns of the stress-responsive lncRNAs as investigated by RNA-seq and qRT-PCR were relatively consistent with similar trends, suggesting that the lncRNA expression patterns based on RNA-seq data are reliable. The qRT-PCR results confirmed that 85% of lncRNAs (8 of the 12 detected lncRNAs) were cold- or drought- inducible in cassava. Among them, we found that three lncRNAs (lincRNA419, 207 and 234) were specifically up-regulated under the cold condition (Fig. 4A,B and C), while lincRNA101, 391 and 356 were uniquely up-regulated under the drought condition (Fig. 4D,E and F). The striking differences in the response pattern between the two treatments suggested that these lncRNAs may play different roles in cassava under the two types of stresses. Moreover, lincRNA28 and lincRNA105 were up-regulated after both cold and drought treatment (Fig. 4G,H), while four lncRNAs (lincRNA64, 350,182 and 392) were down-regulated under cold and/or drought treatment (Fig. 4I–L). The action mode of these lncRNAs in cassava will be further studied.


Genome-wide identification and functional prediction of cold and/or drought-responsive lncRNAs in cassava
Confirmation of the expression patterns of lncRNAs using quantitative RT-PCR.(A–L) The expression pattern of lncRNAs under cold or drought stress. The values shown are the means ± standard deviation of three replicates. MeACTIN was used as the reference gene.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5384091&req=5

f4: Confirmation of the expression patterns of lncRNAs using quantitative RT-PCR.(A–L) The expression pattern of lncRNAs under cold or drought stress. The values shown are the means ± standard deviation of three replicates. MeACTIN was used as the reference gene.
Mentions: To further characterize cold- and/or drought- responsive lncRNAs listed in supplemental data S2 in cassava, 12 lncRNAs under cold and/or drought conditions were randomly selected and analyzed by real-time quantitative PCR (qRT-PCR). As shown in Fig. 4, the expression patterns of the stress-responsive lncRNAs as investigated by RNA-seq and qRT-PCR were relatively consistent with similar trends, suggesting that the lncRNA expression patterns based on RNA-seq data are reliable. The qRT-PCR results confirmed that 85% of lncRNAs (8 of the 12 detected lncRNAs) were cold- or drought- inducible in cassava. Among them, we found that three lncRNAs (lincRNA419, 207 and 234) were specifically up-regulated under the cold condition (Fig. 4A,B and C), while lincRNA101, 391 and 356 were uniquely up-regulated under the drought condition (Fig. 4D,E and F). The striking differences in the response pattern between the two treatments suggested that these lncRNAs may play different roles in cassava under the two types of stresses. Moreover, lincRNA28 and lincRNA105 were up-regulated after both cold and drought treatment (Fig. 4G,H), while four lncRNAs (lincRNA64, 350,182 and 392) were down-regulated under cold and/or drought treatment (Fig. 4I–L). The action mode of these lncRNAs in cassava will be further studied.

View Article: PubMed Central - PubMed

ABSTRACT

Cold and drought stresses seriously affect cassava (Manihot esculenta) plant growth and yield. Recently, long noncoding RNAs (lncRNAs) have emerged as key regulators of diverse cellular processes in mammals and plants. To date, no systematic screening of lncRNAs under abiotic stress and their regulatory roles in cassava has been reported. In this study, we present the first reference catalog of 682 high-confidence lncRNAs based on analysis of strand-specific RNA-seq data from cassava shoot apices and young leaves under cold, drought stress and control conditions. Among them, 16 lncRNAs were identified as putative target mimics of cassava known miRNAs. Additionally, by comparing with small RNA-seq data, we found 42 lncNATs and sense gene pairs can generate nat-siRNAs. We identified 318 lncRNAs responsive to cold and/or drought stress, which were typically co-expressed concordantly or discordantly with their neighboring genes. Trans-regulatory network analysis suggested that many lncRNAs were associated with hormone signal transduction, secondary metabolites biosynthesis, and sucrose metabolism pathway. The study provides an opportunity for future computational and experimental studies to uncover the functions of lncRNAs in cassava.

No MeSH data available.


Related in: MedlinePlus