Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting soybean genotypes subjected to phosphate starvation
Background: Phosphorus (P) is essential for plant growth and development, and low-phosphorus (LP) stress is a major factor limiting the growth and yield of soybean. Long noncoding RNAs (lncRNAs) have recently been reported to be key regulators in the responses of plants to stress conditions, but the mechanism through which LP stress mediates the biogenesis of lncRNAs in soybean remains unclear.
Results: In this study, to explore the response mechanisms of lncRNAs to LP stress, we used the roots of two representative soybean genotypes that present opposite responses to P deficiency, namely, a P-sensitive genotype (Bogao) and a P-tolerant genotype (NN94156), for the construction of RNA sequencing (RNA-seq) libraries. In total, 4,166 novel lncRNAs, including 525 differentially expressed (DE) lncRNAs, were identified from the two genotypes at different P levels. GO and KEGG analyses indicated that numerous DE lncRNAs might be involved in diverse biological processes related to phosphate, such as lipid metabolic processes, catalytic activity, cell membrane formation, signal transduction, and nitrogen fixation. Moreover, lncRNA-mRNA-miRNA and lncRNA-mRNA networks were constructed, and the results identified several promising lncRNAs that might be highly valuable for further analysis of the mechanism underlying the response of soybean to LP stress.
Conclusions: These results revealed that LP stress can significantly alter the genome-wide profiles of lncRNAs, particularly those of the P-sensitive genotype Bogao. Our findings increase the understanding of and provide new insights into the function of lncRNAs in the responses of soybean to P stress.
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Table S8: List of primers used for qPCR of lncRNAs.
Table S7: The interested lncRNA-mRNA prediction for network construction.
Table S6: The mRNAs as targets of miRNA and lncRNA.
Table S5: KEGG pathway annotation of the predicted target mRNAs of DE lncRNAs in two comparisons.
Table S4: GO enrichment analysis of the targeted mRNAs of significantly DE lncRNAs in two comparisons.
Table S3: The target mRNAs of DE lncRNA in two comparisons.
Table S2. DE lncRNAs in different genotypes and P levels.
Table S1: Detailed information of identified lncRNAs in soybean roots.
Fig. S1: Number of up- and downregulated DE lncRNAs under LP and HP conditions in the two soybean genotypes.
Posted 13 Jan, 2021
On 05 Jan, 2021
On 31 Dec, 2020
Invitations sent on 31 Dec, 2020
On 31 Dec, 2020
On 31 Dec, 2020
On 01 Dec, 2020
Received 07 Oct, 2020
Received 07 Oct, 2020
On 16 Sep, 2020
Invitations sent on 15 Sep, 2020
On 15 Sep, 2020
On 31 Aug, 2020
On 30 Aug, 2020
On 30 Aug, 2020
On 27 Aug, 2020
Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting soybean genotypes subjected to phosphate starvation
Posted 13 Jan, 2021
On 05 Jan, 2021
On 31 Dec, 2020
Invitations sent on 31 Dec, 2020
On 31 Dec, 2020
On 31 Dec, 2020
On 01 Dec, 2020
Received 07 Oct, 2020
Received 07 Oct, 2020
On 16 Sep, 2020
Invitations sent on 15 Sep, 2020
On 15 Sep, 2020
On 31 Aug, 2020
On 30 Aug, 2020
On 30 Aug, 2020
On 27 Aug, 2020
Background: Phosphorus (P) is essential for plant growth and development, and low-phosphorus (LP) stress is a major factor limiting the growth and yield of soybean. Long noncoding RNAs (lncRNAs) have recently been reported to be key regulators in the responses of plants to stress conditions, but the mechanism through which LP stress mediates the biogenesis of lncRNAs in soybean remains unclear.
Results: In this study, to explore the response mechanisms of lncRNAs to LP stress, we used the roots of two representative soybean genotypes that present opposite responses to P deficiency, namely, a P-sensitive genotype (Bogao) and a P-tolerant genotype (NN94156), for the construction of RNA sequencing (RNA-seq) libraries. In total, 4,166 novel lncRNAs, including 525 differentially expressed (DE) lncRNAs, were identified from the two genotypes at different P levels. GO and KEGG analyses indicated that numerous DE lncRNAs might be involved in diverse biological processes related to phosphate, such as lipid metabolic processes, catalytic activity, cell membrane formation, signal transduction, and nitrogen fixation. Moreover, lncRNA-mRNA-miRNA and lncRNA-mRNA networks were constructed, and the results identified several promising lncRNAs that might be highly valuable for further analysis of the mechanism underlying the response of soybean to LP stress.
Conclusions: These results revealed that LP stress can significantly alter the genome-wide profiles of lncRNAs, particularly those of the P-sensitive genotype Bogao. Our findings increase the understanding of and provide new insights into the function of lncRNAs in the responses of soybean to P stress.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8