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De Novo Assembly of Expressed Transcripts and Global Transcriptomic Analysis from Seedlings of the Paper Mulberry (Broussonetia kazinoki x Broussonetia papyifera)
The paper mulberry is one of the multifunctional tree species in agroforestry systems and is also commonly utilized in traditional medicine in China and other Asian countries. However, little is known about its molecular genetics, which hinders research on and exploitation of this valuable resource....
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Public Library of Science
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4029624/ https://www.ncbi.nlm.nih.gov/pubmed/24848504 http://dx.doi.org/10.1371/journal.pone.0097487 |
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author | Xianjun, Peng Linhong, Teng Xiaoman, Wang Yucheng, Wang Shihua, Shen |
author_facet | Xianjun, Peng Linhong, Teng Xiaoman, Wang Yucheng, Wang Shihua, Shen |
author_sort | Xianjun, Peng |
collection | PubMed |
description | The paper mulberry is one of the multifunctional tree species in agroforestry systems and is also commonly utilized in traditional medicine in China and other Asian countries. However, little is known about its molecular genetics, which hinders research on and exploitation of this valuable resource. To discern the correlation between gene expression and the essential properties of the paper mulberry, we performed a transcriptomics analysis, assembling a total of 37,725 unigenes from 54,638,676 reads generated by RNA-seq. Among these, 22,692 unigenes showed greater than 60% similarity with genes from other species. The lengths of 13,566 annotated unigenes were longer than 1,000 bp. Functional clustering analysis with COG (Cluster of Orthologous Groups) revealed that 17,184 unigenes are primarily involved in transcription, translation, signal transduction, carbohydrate metabolism, secondary metabolism, and energy metabolism. GO (Gene Ontology) annotation suggests enrichment of genes encoding antioxidant activity, transporter activity, biosynthesis, metabolism and stress response, with a total of 30,659 unigenes falling in these categories. KEGG (Kyoto Encyclopedia of Genes and Genomes) metabolic pathway analysis showed that 7,199 unigenes are associated with 119 metabolic pathways. In addition to the basic metabolism, these genes are enriched for plant pathogen interaction, flavonoid metabolism and other secondary metabolic processes. Furthermore, differences in the transcriptomes of leaf, stem and root tissues were analyzed and 7,233 specifically expressed unigenes were identified. This global expression analysis provided novel insights about the molecular mechanisms of the biosynthesis of flavonoid, lignin and cellulose, as well as on the response to biotic and abiotic stresses including the remediation of contaminated soil by the paper mulberry. |
format | Online Article Text |
id | pubmed-4029624 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-40296242014-05-28 De Novo Assembly of Expressed Transcripts and Global Transcriptomic Analysis from Seedlings of the Paper Mulberry (Broussonetia kazinoki x Broussonetia papyifera) Xianjun, Peng Linhong, Teng Xiaoman, Wang Yucheng, Wang Shihua, Shen PLoS One Research Article The paper mulberry is one of the multifunctional tree species in agroforestry systems and is also commonly utilized in traditional medicine in China and other Asian countries. However, little is known about its molecular genetics, which hinders research on and exploitation of this valuable resource. To discern the correlation between gene expression and the essential properties of the paper mulberry, we performed a transcriptomics analysis, assembling a total of 37,725 unigenes from 54,638,676 reads generated by RNA-seq. Among these, 22,692 unigenes showed greater than 60% similarity with genes from other species. The lengths of 13,566 annotated unigenes were longer than 1,000 bp. Functional clustering analysis with COG (Cluster of Orthologous Groups) revealed that 17,184 unigenes are primarily involved in transcription, translation, signal transduction, carbohydrate metabolism, secondary metabolism, and energy metabolism. GO (Gene Ontology) annotation suggests enrichment of genes encoding antioxidant activity, transporter activity, biosynthesis, metabolism and stress response, with a total of 30,659 unigenes falling in these categories. KEGG (Kyoto Encyclopedia of Genes and Genomes) metabolic pathway analysis showed that 7,199 unigenes are associated with 119 metabolic pathways. In addition to the basic metabolism, these genes are enriched for plant pathogen interaction, flavonoid metabolism and other secondary metabolic processes. Furthermore, differences in the transcriptomes of leaf, stem and root tissues were analyzed and 7,233 specifically expressed unigenes were identified. This global expression analysis provided novel insights about the molecular mechanisms of the biosynthesis of flavonoid, lignin and cellulose, as well as on the response to biotic and abiotic stresses including the remediation of contaminated soil by the paper mulberry. Public Library of Science 2014-05-21 /pmc/articles/PMC4029624/ /pubmed/24848504 http://dx.doi.org/10.1371/journal.pone.0097487 Text en © 2014 Xianjun 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 Xianjun, Peng Linhong, Teng Xiaoman, Wang Yucheng, Wang Shihua, Shen De Novo Assembly of Expressed Transcripts and Global Transcriptomic Analysis from Seedlings of the Paper Mulberry (Broussonetia kazinoki x Broussonetia papyifera) |
title |
De Novo Assembly of Expressed Transcripts and Global Transcriptomic Analysis from Seedlings of the Paper Mulberry (Broussonetia kazinoki x Broussonetia papyifera) |
title_full |
De Novo Assembly of Expressed Transcripts and Global Transcriptomic Analysis from Seedlings of the Paper Mulberry (Broussonetia kazinoki x Broussonetia papyifera) |
title_fullStr |
De Novo Assembly of Expressed Transcripts and Global Transcriptomic Analysis from Seedlings of the Paper Mulberry (Broussonetia kazinoki x Broussonetia papyifera) |
title_full_unstemmed |
De Novo Assembly of Expressed Transcripts and Global Transcriptomic Analysis from Seedlings of the Paper Mulberry (Broussonetia kazinoki x Broussonetia papyifera) |
title_short |
De Novo Assembly of Expressed Transcripts and Global Transcriptomic Analysis from Seedlings of the Paper Mulberry (Broussonetia kazinoki x Broussonetia papyifera) |
title_sort | de novo assembly of expressed transcripts and global transcriptomic analysis from seedlings of the paper mulberry (broussonetia kazinoki x broussonetia papyifera) |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4029624/ https://www.ncbi.nlm.nih.gov/pubmed/24848504 http://dx.doi.org/10.1371/journal.pone.0097487 |
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