Transcriptome-wide identification and characterization of microRNAs in diverse phases of wood formation in Populus trichocarpa.

Ruiqi Wang,Shuanghui Tian,Zhigang Wei,Muhammad Saqib,Huaxin Zhang,He Cheng,Yingying Liu,Cong Liu,Hairong Wei,Mengxuan Reng

doi:10.1093/g3journal/jkab195

Abstract

We applied miRNA expression profiling method to Populus trichocarpa stems of the three developmental stages, primary stem (PS), transitional stem (TS), and secondary stem (SS), to investigate miRNA species and their regulation on lignocellulosic synthesis and related processes. We obtained 892, 872, and 882 known miRNAs and 1727, 1723, and 1597 novel miRNAs, from PS, TS, and SS, respectively. Comparisons of these miRNA species among different developmental stages led to the identification of 114, 306, and 152 differentially expressed miRNAs (DE-miRNAs), which had 921, 2639, and 2042 candidate target genes (CTGs) in the three respective stages of the same order. Correlation analysis revealed 47, 439, and 71 DE-miRNA-CTG pairs of high negative correlation in PS, TS, and SS, respectively. Through biological process analysis, we finally identified 34, 6, and 76 miRNA-CTG pairs from PS, TS, and SS, respectively, and the miRNA target genes in these pairs regulate or participate lignocellulosic biosynthesis-related biological processes: cell division and differentiation, cell wall modification, secondary cell wall biosynthesis, lignification, and programmed cell death processes. This is the first report on an integrated analysis of genome-wide mRNA and miRNA profilings during multiple phases of poplar stem development. Our analysis results imply that individual miRNAs modulate secondary growth and lignocellulosic biosynthesis through regulating transcription factors and lignocellulosic biosynthetic pathway genes, resulting in more dynamic promotion, suppression, or regulatory circuits. This study advanced our understanding of many individual miRNAs and their essential, diversified roles in the dynamic regulation of secondary growth in woody tree species.

Highlights

MicroRNAs are small, non-coding RNAs that have important regulatory functions in plant growth and development
To identify the miRNAs involved in diverse phases of wood formation, we performed high-throughput sequencing of small RNA libraries generated from primary stem (PS), transitional stem (TS), and secondary stem (SS), and obtained 15,374,878, 15,653,777, and 11,989,204 high-quality reads, respectively
‘Glycine, serine and threonine metabolism’, which is reported to be related to cell wall synthesis and cell wall remodelling pathways[82], was the typical pathway in the middle phase of wood formation, while the ‘Biosynthesis of secondary metabolites’ and ‘Phenylalanine metabolism’ are typical pathways in the late phase of wood formation[78,79,80]. These results demonstrate that the DE-miRNAs of PS vs TS, PS vs SS, and TS vs SS played various roles in the diverse phases of wood formation by regulating candidate target genes (CTGs), which are regulators and structural genes involved in diverse biological processes and pathways of wood formation

Summary

Introduction

MicroRNAs (miRNAs) are small, non-coding RNAs that have important regulatory functions in plant growth and development. We applied miRNA expression profiling method to the Populus trichocarpa trunks of the three distinct developmental stages defined as the primary stem (PS), transitional stem (TS), and secondary stem (SS) to investigate the miRNA species, their dynamic regulation and functions during the transitions of wood formation in different developmental stages at the genome-wide scale by Solexa sequencing. Wood formation is a complexly continuous biological process involved in multiple molecular mechanisms to precisely control the collaborative expressions of many genes related to different processes of wood formation[1,2,3]. Extensive efforts have been made to unravel the molecular regulatory mechanisms of wood formation, a genome-wide profiling of both miRNAs and mRNAs across multiple developmental stages of wood formation may shed more lights on the underlying regulatory mechanisms

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Results

Discussion

Conclusion