Integrated transcriptome and small RNA sequencing in revealing miRNA-mediated regulatory network of floral bud break in Prunus mume

Abstract

MicroRNAs is one class of small non-coding RNAs that play important roles in plant growth and development. Though miRNAs and their target genes have been widely studied in many plant species, their functional roles in floral bud break and dormancy release in woody perennials is still unclear. In this study, we applied transcriptome and small RNA sequencing together to systematically explore the transcriptional and post-transcriptional regulation of floral bud break in P. mume. Through expression profiling, we identified a few candidate genes and miRNAs during different developmental stage transitions. In total, we characterized 1,553 DEGs associated with endodormancy release and 2,084 DEGs associated with bud flush. Additionally, we identified 48 known miRNAs and 53 novel miRNAs targeting genes enriched in biological processes such as floral organ morphogenesis and hormone signaling transudation. We further validated the regulatory relationship between differentially expressed miRNAs and their target genes combining computational prediction, degradome sequencing, and expression pattern analysis. Finally, we integrated weighted gene co-expression analysis and constructed miRNA-mRNA regulatory networks mediating floral bud flushing competency. In general, our study revealed the miRNA-mediated networks in modulating floral bud break in P. mume. The findings will contribute to the comprehensive understanding of miRNA-mediated regulatory mechanism governing floral bud break and dormancy cycling in wood perennials.

WGCNA Reveals Genes Associated with Lignification in the Secondary Stages of Wood Formation

“…Transcriptome sequencing can reveal the relative relationships between genes at the molecular level and is an important tool for studying gene regulation, gene expression, as well as epigenetic and other molecular-level issues [21][22][23][24][25]. Weighted gene co-expression network analysis, which has been widely used in the field of biology [26][27][28][29], has also been used to explore the complex relationships between genes. In this study, we used the WGCNA to explore the transcriptome sequencing results from horizontal and vertical classification of wood formation.…”

Genome-Wide Identification of Callose Synthase Family Genes and Their Expression Analysis in Floral Bud Development and Hormonal Responses in Prunus mume

“…Prunus is among the most important genera in the Rosaceae family due to its economic value as common fruit and for its ornamental value [ 23 ]. Within this genus, Prunus mume is recognized as the most early flowering tree species, which can bloom under low temperatures in early spring [ 24 ]. The flower buds of Prunus mume initiate in late summer, followed by leaf drop and establishment of dormancy triggered by short daylength and low temperature.…”

Transcriptome Sequencing and WGCNA Reveal Key Genes in Response to Leaf Blight in Poplar

“…Weighted gene co-expression network analysis (WGCNA), which is capable of extracting associated genes from phenotypic data, is widely used for exploring the complex relationships among different kinds of genes [ 18 , 19 , 20 , 21 , 22 , 23 ]. In this study, we sampled the poplar leaves with inoculation of Alternaria alternate fungus for 0 h, 12 h, 24 h, 48 h and 72 h, respectively.…”