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. 2022 Aug 1:13:932926.
doi: 10.3389/fpls.2022.932926. eCollection 2022.

Integration of small RNA, degradome, and transcriptome sequencing data illustrates the mechanism of low phosphorus adaptation in Camellia oleifera

Affiliations

Integration of small RNA, degradome, and transcriptome sequencing data illustrates the mechanism of low phosphorus adaptation in Camellia oleifera

Juanjuan Chen et al. Front Plant Sci. .

Abstract

Phosphorus (P) is an indispensable macronutrient for plant growth and development, and it is involved in various cellular biological activities in plants. Camellia oleifera is a unique high-quality woody oil plant that grows in the hills and mountains of southern China. However, the available P content is deficient in southern woodland soil. Until now, few studies focused on the regulatory functions of microRNAs (miRNAs) and their target genes under low inorganic phosphate (Pi) stress. In this study, we integrated small RNA, degradome, and transcriptome sequencing data to investigate the mechanism of low Pi adaptation in C. oleifera. We identified 40,689 unigenes and 386 miRNAs by the deep sequencing technology and divided the miRNAs into four different groups. We found 32 miRNAs which were differentially expressed under low Pi treatment. A total of 414 target genes of 108 miRNAs were verified by degradome sequencing. Gene ontology (GO) functional analysis of target genes found that they were related to the signal response to the stimulus and transporter activity, indicating that they may respond to low Pi stress. The integrated analysis revealed that 31 miRNA-target pairs had negatively correlated expression patterns. A co-expression regulatory network was established based on the profiles of differentially expressed genes. In total, three hub genes (ARF22, WRKY53, and SCL6), which were the targets of differentially expressed miRNAs, were discovered. Our results showed that integrated analyses of the small RNA, degradome, and transcriptome sequencing data provided a valuable basis for investigating low Pi in C. oleifera and offer new perspectives on the mechanism of low Pi tolerance in woody oil plants.

Keywords: Camellia oleifera; co-expression network; integration analysis; low phosphorus stress; miRNA.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
(A) Changes in phenotype. (B) Root/shoot ratio. (C) Pi content. (D) Acid phosphate. Bars indicate means ± SE (n = 4). P-values were obtained from t-tests between LP and NP condition. **P < 0.01.
FIGURE 2
FIGURE 2
Summary of the classification of the four identified groups of miRNAs in C. oleifera. Counts MIRb, the counts of miRNAs from miRBase; expression level, low indicates < 10; middle indicates > 10 but less than average; high indicates over average.
FIGURE 3
FIGURE 3
Phosphorus (Pi) deficiency and miRNAs in C. oleifera. (A) Differential expressed miRNAs in five different low Pi treatment durations (CK, 1, 3, 7, and 30 days) by miRNAs hierarchical clustering. Red indicates higher levels of miRNAs and green indicates lower levels of miRNAs. The names of the samples are shown at the bottom. The original expression values of the miRNAs were normalized using Z-score normalization. The absolute signal intensity ranges from −1.5 to +1.5, with corresponding color changes from green to red. (B) The number of differentially expressed miRNAs under Pi deficiency compared with the control.
FIGURE 4
FIGURE 4
Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional classification of identified target genes. (A) GO enrichment analysis for targets of DE miRNAs under conditions of phosphate (Pi) starvation. (B) KEGG Enrichment Analysis for Targets of DE miRNAs under conditions of Pi starvation.
FIGURE 5
FIGURE 5
Combined view of expression levels between differentially expressed miRNAs (A) and their target genes (B) in C. oleifera at five different Pi treatment durations. The original expression values of miRNAs and their target genes were normalized by Z-score normalization.
FIGURE 6
FIGURE 6
Expression correlation between miRNAs and their targets at five different Pi treatment durations. (A) mtr-miR160a/ARF18; (B) athMIR472p3_2ss6TG18AG/FOL2; (C) gmamiR403a_R + 1_2ss20TC21GT/AGO2; (D) mtr-miR172a/RAP2-7; (E) ptc-miR160h_1ss15CG/ARF22; (F) ath-miR858b/MYB6; (G) mtr-MIR2592ao-p5_2ss1AT18TC/WRKY53; (H) mtr-miR171d/SCL6; The blue and red lines indicate miRNAs and the target abundance, respectively, based on the RT-qPCR results.
FIGURE 7
FIGURE 7
Co-expression subnetwork of ARF22, WRKY53, and SCL6. Red-colored letter denotes key hub gene; blue-colored letter denotes key miRNA; six different colored circles represent six different categories.

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