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. 2022 Jun 14:13:923183.
doi: 10.3389/fpls.2022.923183. eCollection 2022.

Integrative mRNA and Long Noncoding RNA Analysis Reveals the Regulatory Network of Floral Bud Induction in Longan (Dimocarpus longan Lour.)

Fan Liang  1 , Yiyong Zhang  1 , Xiaodan Wang  1 , Shuo Yang  1 , Ting Fang  1 , Shaoquan Zheng  2 , Lihui Zeng  1
Affiliations

Integrative mRNA and Long Noncoding RNA Analysis Reveals the Regulatory Network of Floral Bud Induction in Longan (Dimocarpus longan Lour.)

Fan Liang et al. Front Plant Sci. .

Abstract

Longan (Dimocarpus longan Lour.) is a tropical/subtropical fruit tree of significant economic importance. Floral induction is an essential process for longan flowering and plays decisive effects on the longan yield. Due to the instability of flowering, it is necessary to understand the molecular mechanisms of floral induction in longan. In this study, mRNA and long noncoding RNA (lncRNA) transcriptome sequencing were performed using the apical buds of fruiting branches as materials. A total of 7,221 differential expressions of mRNAs (DEmRNAs) and 3,238 differential expressions of lncRNAs (DElncRNAs) were identified, respectively. KEGG enrichment analysis of DEmRNAs highlighted the importance of starch and sucrose metabolic, circadian rhythms, and plant hormone signal transduction pathways during floral induction. Combining the analysis of weighted gene co-expression network (WGCNA) and expression pattern of DEmRNAs in the three pathways, specific transcriptional characteristics at each stage during floral induction and regulatory network involving co-expressed genes were investigated. The results showed that sucrose metabolism and auxin signal transduction may be crucial for the growth and maturity of autumn shoots in September and October (B1-B2 stage); starch and sucrose metabolic, circadian rhythms, and plant hormone signal transduction pathways participated in the regulation of floral bud physiological differentiation together in November and December (B3-B4 stage) and the crosstalk among three pathways was also found. Hub genes in the co-expression network and key DEmRNAs in three pathways were identified. The circadian rhythm genes FKF1 and GI were found to activate SOC1gene through the photoperiod core factor COL genes, and they were co-expressed with auxin, gibberellin, abscisic acid, ethylene signaling genes, and sucrose biosynthesis genes at B4 stage. A total of 12 hub-DElncRNAs had potential for positively affecting their distant target genes in three putative key pathways, predominantly in a co-transcriptional manner. A hypothetical model of regulatory pathways and key genes and lncRNAs during floral bud induction in longan was proposed finally. Our studies will provide valuable clues and information to help elucidate the potential molecular mechanisms of floral initiation in longan and woody fruit trees.

Keywords: WGCNA; floral bud induction; long noncoding RNA; longan; mRNA; transcriptome.

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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
Morphological characteristics of the apical bud during floral bud induction in longan. (A–E) Morphological characteristics of apical buds at B1, B2, B3, B4, and B5 stages, respectively.
Figure 2
Figure 2
Characterization and statistical analysis of candidate mRNAs and lncRNAs. (A) Statistics of novel mRNA and annotated mRNA. The horizontal axis indicates the number of mRNAs. (B) Venn diagram of candidate lncRNAs. (C) Classification of the identified lncRNAs. (D) FPKM distribution of mRNA and lncRNA transcripts. (E–G) Characterization of annotated mRNA, novel mRNA, and novel lncRNA transcripts. The horizontal axis of the density plot from left to right indicates total length (left), ORF length (middle), and the number of exons (right) of annotated mRNA, novel mRNA, and novel lncRNA transcripts, respectively.
Figure 3
Figure 3
Up- and down-regulated numbers of DEmRNAs and DElncRNAs and KEGG enrichment analysis of DEmRNAs at different stages. (A) The number of up-regulated and down-regulated DEmRNAs. (B) The number of up-regulated and down-regulated DElncRNAs. (C–F) KEGG enrichment analysis of DEmRNAs in B2_vs_B1, B3_vs_B2, B4_vs_B3, and B5_vs_B4. The horizontal axis shows -log10(p). The vertical axis shows pathways of enrichment.
Figure 4
Figure 4
Co-expression network analysis of DEmRNAs and DElncRNAs. (A) Heatmaps showing correlation of module eigengenes at different stages of floral induction in longan. Pearson correlation coefficient is given in each module for the different stages and is colored from blue to red according to the scores. The MEpurple, MEyellow, MEblack, Medarkred, and MEblue modules (Pearson's correlation coefficient >0.75 or <-0.5 and p < 0.05) with stars are closely related to the floral induction in longan. (B) KEGG enrichment analysis and transcriptional changes of DEmRNAs in the MEpurple, MEyellow, MEblack, MEdarkred, and MEblue modules. The selected module KEGG enriched pathways are visualized by different colors. (C,D) Visualization of the central coexpression network in MEyellow and MEblue modules associated with B4 stage. The size of nodes indicates connectivity. The width of the line indicates the strength of the correlation.
Figure 5
Figure 5
DEmRNAs and DElncRNAs in sucrose metabolism and signaling pathway. (A) Transcriptional changes in DEmRNAs associated with sucrose metabolism. (B) Expression profiles of hub-DElncRNAs and their target genes related to the sucrose metabolism based on the transcriptome data. Transcriptional change levels were normalized by log2transformed (FPKM + 1). (C) Co-expression network of genes involved in sucrose biosynthesis and metabolism in MEblack and Medarkred (pink nodes). Different nodes represent different types of genes, and edges connect co-expression genes.
Figure 6
Figure 6
DEmRNAs and DElncRNAs in photoperiod and circadian clock pathways. (A) Transcriptional trends of DEmRNAs in photoperiod and circadian clock pathway and visualized as heatmaps. (B) DEmRNAs targeted by hub-DElncRNAs. Expression profiles of hub-DElncRNAs and their target genes related to photoperiod and circadian clock based on the transcriptome data. Transcriptional change levels were normalized by log2transformed (FPKM + 1).
Figure 7
Figure 7
DEmRNAs and DElncRNAs in auxin, gibberellin (GAs), and ethylene (ETH) biosynthesis and signal transduction pathways. (A) Transcriptional changes of genes associated with auxin, GAs, and ETH at different stages visualized as heatmaps. (B) Expression profiles of hub-DElncRNAs and their target genes related to the phytohormone biosynthesis and signal transduction based on the transcriptome data. Transcriptional change levels were normalized by log2transformed (FPKM + 1).
Figure 8
Figure 8
Potential regulatory modes of lncRNAs. (A) Comparison of co-expression correlations between neighboring lncRNA-mRNA and random lncRNA-mRNA groups. Significant differences between the two groups were analyzed using Duncan's test. (B) Quantity distribution of transcription factors (TFs) included in two example modules (MEblue and MEyellow). (C,E,G) Three representative binding motifs in lncRNA sequences from MEyellow and MEblue modules. (D,F,H) Functional analysis of 3 representative lncRNA-binding motifs using GOMO tool.
Figure 9
Figure 9
Consistency analysis of RNA-Seq and qRT-PCR data. (A) Verification of the consistency of RNA-Seq data and qRT-PCR of 12 DEmRNAs. (B) Verification of the consistency of RNA-Seq data and qRT-PCR of 5 DElncRNAs. The different letters (a, b, c, d) show significant differences at the p < 0.05 level based on Duncan's test.
Figure 10
Figure 10
A hypothetical model showing three genetic pathways regulating floral bud induction in longan.
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