Comparative transcriptomics of stem bark reveals genes associated with bast fiber development in Boehmeria nivea L. Gaud (ramie)

Abstract Background: Boehmeria nivea L. Gaud (Ramie) produces one of the longest natural fibers in nature. The bark of ramie is the raw material for fiber and primarily includes the entire phloem tissue of the plant stem. Therefore, identifying the molecular regulation of phloem development is important for the understanding of bast fiber biosynthesis and improvement in fiber quality in ramie. Results: In this study, we collected top bud (TB), bark from internode elongating region (ER) and bark from internode fully elongated region (FER) from the ramie variety Zhongzhu No. 1. Histological study indicated that these samples contain phloem tissues at different developmental and maturation stages, with a higher degree of maturation of phloem tissue in FER. RNA sequencing (RNA-seq) was performed to identify differentially expressed genes (DEGs) among these three samples. The de novo transcriptome was assembled and unigenes were identified. The DEGs among TB, ER and FER were analyzed, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) studies revealed clear differences in gene expression between ER and FER. Some unigenes for secondary cell wall biosynthesis were up-regulated in both ER and FER, and other cell wall components or cell wall modification related genes showed differential expression between ER and FER. In addition, ethylene activating pathway and gibberellins biosynthesis varied among samples in a stage dependent pattern. Conclusions: Both morphological study and gene expression analysis supported a burst of phloem and vascular development processes during the fiber maturation in the ramie stem. Two types of phytohormons, ethylene and gibberellin, might be involved in. Our findings provide novel insights into the phloem development and fiber maturation in ramie, which could be useful for fiber improvement in ramie and other fiber crops.