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Transcriptome Sequencing and Profiling of Expressed Genes in Phloem and Xylem of Ramie (Boehmeria nivea L. Gaud)
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 indus...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4213010/ https://www.ncbi.nlm.nih.gov/pubmed/25354139 http://dx.doi.org/10.1371/journal.pone.0110623 |
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author | Chen, Jianrong Liu, Fang Tang, Yinghong Yuan, Youmei Guo, Qingquan |
author_facet | Chen, Jianrong Liu, Fang Tang, Yinghong Yuan, Youmei Guo, Qingquan |
author_sort | Chen, Jianrong |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4213010 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-42130102014-11-05 Transcriptome Sequencing and Profiling of Expressed Genes in Phloem and Xylem of Ramie (Boehmeria nivea L. Gaud) Chen, Jianrong Liu, Fang Tang, Yinghong Yuan, Youmei Guo, Qingquan PLoS One Research Article 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. Public Library of Science 2014-10-29 /pmc/articles/PMC4213010/ /pubmed/25354139 http://dx.doi.org/10.1371/journal.pone.0110623 Text en © 2014 Chen et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Chen, Jianrong Liu, Fang Tang, Yinghong Yuan, Youmei Guo, Qingquan Transcriptome Sequencing and Profiling of Expressed Genes in Phloem and Xylem of Ramie (Boehmeria nivea L. Gaud) |
title | Transcriptome Sequencing and Profiling of Expressed Genes in Phloem and Xylem of Ramie (Boehmeria nivea L. Gaud) |
title_full | Transcriptome Sequencing and Profiling of Expressed Genes in Phloem and Xylem of Ramie (Boehmeria nivea L. Gaud) |
title_fullStr | Transcriptome Sequencing and Profiling of Expressed Genes in Phloem and Xylem of Ramie (Boehmeria nivea L. Gaud) |
title_full_unstemmed | Transcriptome Sequencing and Profiling of Expressed Genes in Phloem and Xylem of Ramie (Boehmeria nivea L. Gaud) |
title_short | Transcriptome Sequencing and Profiling of Expressed Genes in Phloem and Xylem of Ramie (Boehmeria nivea L. Gaud) |
title_sort | transcriptome sequencing and profiling of expressed genes in phloem and xylem of ramie (boehmeria nivea l. gaud) |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4213010/ https://www.ncbi.nlm.nih.gov/pubmed/25354139 http://dx.doi.org/10.1371/journal.pone.0110623 |
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