Transcriptome analysis of leaf tissue of Raphanus sativus by RNA sequencing.
Raphanus sativus is not only a popular edible vegetable but also an important source of medicinal compounds. However, the paucity of knowledge about the transcriptome of R. sativus greatly impedes better understanding of the functional genomics and medicinal potential of R. sativus. In this study, t...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2013-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3827192?pdf=render |
| _version_ | 1811336628415758336 |
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| author | Libin Zhang Haibo Jia Yongtai Yin Gang Wu Heng Xia Xiaodong Wang Chunhua Fu Maoteng Li Jiangsheng Wu |
| author_facet | Libin Zhang Haibo Jia Yongtai Yin Gang Wu Heng Xia Xiaodong Wang Chunhua Fu Maoteng Li Jiangsheng Wu |
| author_sort | Libin Zhang |
| collection | DOAJ |
| description | Raphanus sativus is not only a popular edible vegetable but also an important source of medicinal compounds. However, the paucity of knowledge about the transcriptome of R. sativus greatly impedes better understanding of the functional genomics and medicinal potential of R. sativus. In this study, the transcriptome sequencing of leaf tissues in R. sativus was performed for the first time. Approximately 22 million clean reads were generated and used for transcriptome assembly. The generated unigenes were subsequently annotated against gene ontology (GO) database. KEGG analysis further revealed two important pathways in the bolting stage of R.sativus including spliceosome assembly and alkaloid synthesis. In addition, a total of 6,295 simple sequence repeats (SSRs) with various motifs were identified in the unigene library of R. sativus. Finally, four unigenes of R. sativus were selected for alignment with their homologs from other plants, and phylogenetic trees for each of the genes were constructed. Taken together, this study will provide a platform to facilitate gene discovery and advance functional genomic research of R. sativus. |
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| format | Article |
| id | doaj.art-48cd2cdca3e94b82927e5fb4acaacb0b |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-13T17:42:17Z |
| publishDate | 2013-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-48cd2cdca3e94b82927e5fb4acaacb0b2022-12-22T02:37:07ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-01811e8035010.1371/journal.pone.0080350Transcriptome analysis of leaf tissue of Raphanus sativus by RNA sequencing.Libin ZhangHaibo JiaYongtai YinGang WuHeng XiaXiaodong WangChunhua FuMaoteng LiJiangsheng WuRaphanus sativus is not only a popular edible vegetable but also an important source of medicinal compounds. However, the paucity of knowledge about the transcriptome of R. sativus greatly impedes better understanding of the functional genomics and medicinal potential of R. sativus. In this study, the transcriptome sequencing of leaf tissues in R. sativus was performed for the first time. Approximately 22 million clean reads were generated and used for transcriptome assembly. The generated unigenes were subsequently annotated against gene ontology (GO) database. KEGG analysis further revealed two important pathways in the bolting stage of R.sativus including spliceosome assembly and alkaloid synthesis. In addition, a total of 6,295 simple sequence repeats (SSRs) with various motifs were identified in the unigene library of R. sativus. Finally, four unigenes of R. sativus were selected for alignment with their homologs from other plants, and phylogenetic trees for each of the genes were constructed. Taken together, this study will provide a platform to facilitate gene discovery and advance functional genomic research of R. sativus.http://europepmc.org/articles/PMC3827192?pdf=render |
| spellingShingle | Libin Zhang Haibo Jia Yongtai Yin Gang Wu Heng Xia Xiaodong Wang Chunhua Fu Maoteng Li Jiangsheng Wu Transcriptome analysis of leaf tissue of Raphanus sativus by RNA sequencing. PLoS ONE |
| title | Transcriptome analysis of leaf tissue of Raphanus sativus by RNA sequencing. |
| title_full | Transcriptome analysis of leaf tissue of Raphanus sativus by RNA sequencing. |
| title_fullStr | Transcriptome analysis of leaf tissue of Raphanus sativus by RNA sequencing. |
| title_full_unstemmed | Transcriptome analysis of leaf tissue of Raphanus sativus by RNA sequencing. |
| title_short | Transcriptome analysis of leaf tissue of Raphanus sativus by RNA sequencing. |
| title_sort | transcriptome analysis of leaf tissue of raphanus sativus by rna sequencing |
| url | http://europepmc.org/articles/PMC3827192?pdf=render |
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