Abstract
Ramie (Boehmeria nivea L. Gaud) is a highly versatile herbaceous plant which is widely cropped in southern China. The success of this herbaceous plant relies on wide use in modern industry. Understanding the profiling of expressed genes in phloem and xylem of ramie is crucial for improving its industrial performance. Herein, we uncover the transcriptome profile in phloem and xylem in present study. Using Illumina paired-end sequencing technology, 57 million high quality reads were generated. De novo assembly yielded 87,144 unigenes with an average length of 635 bp. By sequence similarity searching for public databases, a total of 32,541 (41.77%) unigenes were annotated for their function. Among these genes, 57,873 (66.4%) and 28,678 (32.9%) unigenes were assigned to categories of Gene Ontology and Orthologous Groups database, respectively. By searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG), 18,331 (21.0%) unigenes were mapped to 125 pathways. The metabolic pathways were assigned the most unigene (4,793, 26.2%). Furthermore, Pol II and Pol III subunits as well as the genes of Galactose metabolism pathway had higher expression in phloem compared to xylem. In addition, fatty acid metabolism pathway genes showed more abundant in xylem than phloem. These results suggest that high activities of RNA synthesis and Galactose metabolism pathway promises fiber synthesis in phloem. The present study is the initial exploration to uncover the fiber biosynthesis difference between phloem and xylem in ramie through the analysis of deep sequencing data.
Highlights
Ramie (Boehmeria nivea) is one of the most widely cropped herbaceous plants in southern China which provides important natural fiber for industry, including packing materials, fishing nets, filter cloths, industrial fuel and bio-fertilizers [1,2,3]
Unigenes were produced by realignment of paired-end reads to contigs, and the contigs in one transcript which assembled with not extended on the end were considered as unigenes
The strict controlled sequential changes of gene expression are required for tissue differentiation during plant development
Summary
Ramie (Boehmeria nivea) is one of the most widely cropped herbaceous plants in southern China which provides important natural fiber for industry, including packing materials, fishing nets, filter cloths, industrial fuel and bio-fertilizers [1,2,3]. As in other plants, phloem and xylem are two different complex tissues which plays crucial role in transporting food and water in plant [4]. In modern industry, these two tissues have different uses. Bast fibers in phloem of ramie are one of the best clothing materials which are the second usage clothing materials in China except cotton fiber [5,6] while, lignin in xylem is great raw material for industrial ethanol production and suitable material for bio-fertilizers after fermentation [7,8]. Several studies have been focus on the mechanisms of phloem and xylem development in ramie [6,9,10,11]. To better understand the differentiation of the net work genes between phloem and xylem, high-throughput technology needs to be employed
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