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De Novo Transcriptome of Brassica juncea Seed Coat and Identification of Genes for the Biosynthesis of Flavonoids
Brassica juncea, a worldwide cultivated crop plant, produces seeds of different colors. Seed pigmentation is due to the deposition in endothelial cells of proanthocyanidins (PAs), end products from a branch of flavonoid biosynthetic pathway. To elucidate the gene regulatory network of seed pigmentat...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3747200/ https://www.ncbi.nlm.nih.gov/pubmed/23990927 http://dx.doi.org/10.1371/journal.pone.0071110 |
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author | Liu, Xianjun Lu, Ying Yuan, Yuhui Liu, Shuyan Guan, Chunyun Chen, Sheyuan Liu, Zhongsong |
author_facet | Liu, Xianjun Lu, Ying Yuan, Yuhui Liu, Shuyan Guan, Chunyun Chen, Sheyuan Liu, Zhongsong |
author_sort | Liu, Xianjun |
collection | PubMed |
description | Brassica juncea, a worldwide cultivated crop plant, produces seeds of different colors. Seed pigmentation is due to the deposition in endothelial cells of proanthocyanidins (PAs), end products from a branch of flavonoid biosynthetic pathway. To elucidate the gene regulatory network of seed pigmentation in B. juncea, transcriptomes in seed coat of a yellow-seeded inbred line and its brown-seeded near- isogenic line were sequenced using the next-generation sequencing platform Illumina/Solexa and de novo assembled. Over 116 million high-quality reads were assembled into 69,605 unigenes, of which about 71.5% (49,758 unigenes) were aligned to Nr protein database with a cut-off E-value of 10(−5). RPKM analysis showed that the brown-seeded testa up-regulated 802 unigenes and down-regulated 502 unigenes as compared to the yellow-seeded one. Biological pathway analysis revealed the involvement of forty six unigenes in flavonoid biosynthesis. The unigenes encoding dihydroflavonol reductase (DFR), leucoantho-cyanidin dioxygenase (LDOX) and anthocyanidin reductase (ANR) for late flavonoid biosynthesis were not expressed at all or at a very low level in the yellow-seeded testa, which implied that these genes for PAs biosynthesis be associated with seed color of B. juncea, as confirmed by qRT-PCR analysis of these genes. To our knowledge, it is the first time to sequence the transcriptome of seed coat in Brassica juncea. The unigene sequences obtained in this study will not only lay the foundations for insight into the molecular mechanisms underlying seed pigmentation in B.juncea, but also provide the basis for further genomics research on this species or its allies. |
format | Online Article Text |
id | pubmed-3747200 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-37472002013-08-29 De Novo Transcriptome of Brassica juncea Seed Coat and Identification of Genes for the Biosynthesis of Flavonoids Liu, Xianjun Lu, Ying Yuan, Yuhui Liu, Shuyan Guan, Chunyun Chen, Sheyuan Liu, Zhongsong PLoS One Research Article Brassica juncea, a worldwide cultivated crop plant, produces seeds of different colors. Seed pigmentation is due to the deposition in endothelial cells of proanthocyanidins (PAs), end products from a branch of flavonoid biosynthetic pathway. To elucidate the gene regulatory network of seed pigmentation in B. juncea, transcriptomes in seed coat of a yellow-seeded inbred line and its brown-seeded near- isogenic line were sequenced using the next-generation sequencing platform Illumina/Solexa and de novo assembled. Over 116 million high-quality reads were assembled into 69,605 unigenes, of which about 71.5% (49,758 unigenes) were aligned to Nr protein database with a cut-off E-value of 10(−5). RPKM analysis showed that the brown-seeded testa up-regulated 802 unigenes and down-regulated 502 unigenes as compared to the yellow-seeded one. Biological pathway analysis revealed the involvement of forty six unigenes in flavonoid biosynthesis. The unigenes encoding dihydroflavonol reductase (DFR), leucoantho-cyanidin dioxygenase (LDOX) and anthocyanidin reductase (ANR) for late flavonoid biosynthesis were not expressed at all or at a very low level in the yellow-seeded testa, which implied that these genes for PAs biosynthesis be associated with seed color of B. juncea, as confirmed by qRT-PCR analysis of these genes. To our knowledge, it is the first time to sequence the transcriptome of seed coat in Brassica juncea. The unigene sequences obtained in this study will not only lay the foundations for insight into the molecular mechanisms underlying seed pigmentation in B.juncea, but also provide the basis for further genomics research on this species or its allies. Public Library of Science 2013-08-19 /pmc/articles/PMC3747200/ /pubmed/23990927 http://dx.doi.org/10.1371/journal.pone.0071110 Text en © 2013 Liu 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 Liu, Xianjun Lu, Ying Yuan, Yuhui Liu, Shuyan Guan, Chunyun Chen, Sheyuan Liu, Zhongsong De Novo Transcriptome of Brassica juncea Seed Coat and Identification of Genes for the Biosynthesis of Flavonoids |
title |
De Novo Transcriptome of Brassica juncea Seed Coat and Identification of Genes for the Biosynthesis of Flavonoids |
title_full |
De Novo Transcriptome of Brassica juncea Seed Coat and Identification of Genes for the Biosynthesis of Flavonoids |
title_fullStr |
De Novo Transcriptome of Brassica juncea Seed Coat and Identification of Genes for the Biosynthesis of Flavonoids |
title_full_unstemmed |
De Novo Transcriptome of Brassica juncea Seed Coat and Identification of Genes for the Biosynthesis of Flavonoids |
title_short |
De Novo Transcriptome of Brassica juncea Seed Coat and Identification of Genes for the Biosynthesis of Flavonoids |
title_sort | de novo transcriptome of brassica juncea seed coat and identification of genes for the biosynthesis of flavonoids |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3747200/ https://www.ncbi.nlm.nih.gov/pubmed/23990927 http://dx.doi.org/10.1371/journal.pone.0071110 |
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