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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

Statistics of KEGG pathway enrichment.(A,B) KEGG pathway classification of DE-lncRNA-correlated differentially expressed genes under cold (A) and drought stress (B), respectively. The y-axis corresponds to KEGG pathway with a q-value ≤ 0.05, and the x-axis shows the enrichment ratio between the number of DEGs and all unigenes enriched in a particular pathway. The color of the dot represents q value, and the size of the dot represents the number of DEGs mapped to the reference pathways.
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f8: Statistics of KEGG pathway enrichment.(A,B) KEGG pathway classification of DE-lncRNA-correlated differentially expressed genes under cold (A) and drought stress (B), respectively. The y-axis corresponds to KEGG pathway with a q-value ≤ 0.05, and the x-axis shows the enrichment ratio between the number of DEGs and all unigenes enriched in a particular pathway. The color of the dot represents q value, and the size of the dot represents the number of DEGs mapped to the reference pathways.

Mentions: To further understand the function of stress-responsive lncRNAs, we performed co-expression analysis to identify trans-regulatory network of lncRNAs. In total, there were 12651 and 11133 protein-coding genes that were co-expressed with cold and drought responsive lncRNAs, respectively (Supplemental Data S7). GO (Gene Ontology) analysis of the genes in lncRNA trans-regulatory network was performed to explore their functions. We found 45 GO terms that were significantly enriched (P < 0.05), and 6 of these terms were associated with both cold and drought stress. For example, the top 10 enriched terms included sequence-specific DNA binding transcription factor activity, monooxygenase activity, tetrapyrrole binding activity, protein kinase activity, and phosphotransferase activity (Supplemental Figure S2). We also analyze the statistical enrichment of differentially expressed lncRNA target genes in KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway. Based on the results of significantly differentially expressed lncRNAs analysis, 8 and 6 pathways were found responsive to cold and drought stress, respectively (Fig. 8A,B, Supplemental Data S8). The most enriched pathways including plant hormone signal transduction, starch and sucrose metabolism, plant-pathogen interaction, biosynthesis of secondary metabolites and metabolic pathways. These results suggest that one of the principal roles of lncRNAs may be transcriptional regulation of gene expression, especially genes that involved in hormone signal transduction and secondary metabolic pathways. These findings provide a comprehensive view of cassava lncRNAs, which will enable in-depth functional analysis.


Genome-wide identification and functional prediction of cold and/or drought-responsive lncRNAs in cassava
Statistics of KEGG pathway enrichment.(A,B) KEGG pathway classification of DE-lncRNA-correlated differentially expressed genes under cold (A) and drought stress (B), respectively. The y-axis corresponds to KEGG pathway with a q-value ≤ 0.05, and the x-axis shows the enrichment ratio between the number of DEGs and all unigenes enriched in a particular pathway. The color of the dot represents q value, and the size of the dot represents the number of DEGs mapped to the reference pathways.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f8: Statistics of KEGG pathway enrichment.(A,B) KEGG pathway classification of DE-lncRNA-correlated differentially expressed genes under cold (A) and drought stress (B), respectively. The y-axis corresponds to KEGG pathway with a q-value ≤ 0.05, and the x-axis shows the enrichment ratio between the number of DEGs and all unigenes enriched in a particular pathway. The color of the dot represents q value, and the size of the dot represents the number of DEGs mapped to the reference pathways.
Mentions: To further understand the function of stress-responsive lncRNAs, we performed co-expression analysis to identify trans-regulatory network of lncRNAs. In total, there were 12651 and 11133 protein-coding genes that were co-expressed with cold and drought responsive lncRNAs, respectively (Supplemental Data S7). GO (Gene Ontology) analysis of the genes in lncRNA trans-regulatory network was performed to explore their functions. We found 45 GO terms that were significantly enriched (P < 0.05), and 6 of these terms were associated with both cold and drought stress. For example, the top 10 enriched terms included sequence-specific DNA binding transcription factor activity, monooxygenase activity, tetrapyrrole binding activity, protein kinase activity, and phosphotransferase activity (Supplemental Figure S2). We also analyze the statistical enrichment of differentially expressed lncRNA target genes in KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway. Based on the results of significantly differentially expressed lncRNAs analysis, 8 and 6 pathways were found responsive to cold and drought stress, respectively (Fig. 8A,B, Supplemental Data S8). The most enriched pathways including plant hormone signal transduction, starch and sucrose metabolism, plant-pathogen interaction, biosynthesis of secondary metabolites and metabolic pathways. These results suggest that one of the principal roles of lncRNAs may be transcriptional regulation of gene expression, especially genes that involved in hormone signal transduction and secondary metabolic pathways. These findings provide a comprehensive view of cassava lncRNAs, which will enable in-depth functional analysis.

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