BnTIR: an online transcriptome platform for exploring RNA‐seq libraries for oil crop Brassica napus
To investigate the dynamic gene expression during B. napus development and provide an easy access visualization of the expression levels of B. napus genes, we performed RNA-seq for 91 different tissue samples including root, seedling, stem, 1st-23rd leaves from the main branch, flower buds (2 and 4...
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| Published in | Plant biotechnology journal Vol. 19; no. 10; pp. 1895 - 1897 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
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Southampton
John Wiley & Sons, Inc
01.10.2021
John Wiley and Sons Inc |
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| Online Access | Get full text |
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| Abstract | To investigate the dynamic gene expression during B. napus development and provide an easy access visualization of the expression levels of B. napus genes, we performed RNA-seq for 91 different tissue samples including root, seedling, stem, 1st-23rd leaves from the main branch, flower buds (2 and 4 mm), flower tissues (sepal, petal, filament, and pollen), silique walls (2–60 day after flowering (DAF), with 2-day intervals) and seeds (14–64 DAF, with 2-day intervals) (Figure 1a). BnTIR is a refined transcriptome platform for Brassica napus. (a) Summary of statistics for transcriptome sequencing of diverse tissue types of B. napus. (b) The homepage of BnTIR. (c) Architecture of BnTIR database, including data source layer, middleware layer, and application layer. (d) eFP viewer. (e) Tissue expression viewer. (f) Co-expression viewer. (g) JBrower viewer. (h) Blast module. (i) Gene index module. (j) Sequence fetch module. (k) Transcription factor module. (l–o) A case of application of BnTIR, including the phylogenetic tree and expression profile of BAN and their four B. napus homolog genes (l); expression comparison of B. napus BAN homolog genes in seed and silique wall (m); the co-expression network of homolog genes of BAN (n); and expression profile of co-expressed genes of BAN (o). According to PlantTFDB, the information of 58 TF families in B. napus is also provided in the tool interface (Figure 1k; http://planttfdb.gao-lab.org/). |
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| AbstractList | To investigate the dynamic gene expression during B. napus development and provide an easy access visualization of the expression levels of B. napus genes, we performed RNA-seq for 91 different tissue samples including root, seedling, stem, 1st-23rd leaves from the main branch, flower buds (2 and 4 mm), flower tissues (sepal, petal, filament, and pollen), silique walls (2–60 day after flowering (DAF), with 2-day intervals) and seeds (14–64 DAF, with 2-day intervals) (Figure 1a). BnTIR is a refined transcriptome platform for Brassica napus. (a) Summary of statistics for transcriptome sequencing of diverse tissue types of B. napus. (b) The homepage of BnTIR. (c) Architecture of BnTIR database, including data source layer, middleware layer, and application layer. (d) eFP viewer. (e) Tissue expression viewer. (f) Co-expression viewer. (g) JBrower viewer. (h) Blast module. (i) Gene index module. (j) Sequence fetch module. (k) Transcription factor module. (l–o) A case of application of BnTIR, including the phylogenetic tree and expression profile of BAN and their four B. napus homolog genes (l); expression comparison of B. napus BAN homolog genes in seed and silique wall (m); the co-expression network of homolog genes of BAN (n); and expression profile of co-expressed genes of BAN (o). According to PlantTFDB, the information of 58 TF families in B. napus is also provided in the tool interface (Figure 1k; http://planttfdb.gao-lab.org/). |
| Author | Dai, Cheng Wei, Lulu Lu, Shaoping Wang, Xuemin Yu, Pugang Yu, Liangqian Yang, Zhiquan Wang, Jing Zhang, Shuntai Zhang, Yuting Zhou, Yongming Liu, Dongxu Yang, Yanjun Zhao, Hu Yao, Xuan Yang, Qing‐Yong Guo, Liang Chen, Guanqun |
| AuthorAffiliation | 5 Department of Agricultural, Food and Nutritional Science University of Alberta Edmonton AB Canada 7 Donald Danforth Plant Science Center St. Louis MO USA 2 Hubei Key Laboratory of Agricultural Bioinformatics College of Informatics Huazhong Agricultural University Wuhan China 3 Hubei Hongshan Laboratory Wuhan China 4 College of Humanities & Social Science Huazhong Agricultural University Wuhan China 1 National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University Wuhan China 6 Department of Biology University of Missouri‐St. Louis St. Louis MO USA |
| AuthorAffiliation_xml | – name: 4 College of Humanities & Social Science Huazhong Agricultural University Wuhan China – name: 2 Hubei Key Laboratory of Agricultural Bioinformatics College of Informatics Huazhong Agricultural University Wuhan China – name: 5 Department of Agricultural, Food and Nutritional Science University of Alberta Edmonton AB Canada – name: 3 Hubei Hongshan Laboratory Wuhan China – name: 6 Department of Biology University of Missouri‐St. Louis St. Louis MO USA – name: 7 Donald Danforth Plant Science Center St. Louis MO USA – name: 1 National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University Wuhan China |
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| Title | BnTIR: an online transcriptome platform for exploring RNA‐seq libraries for oil crop Brassica napus |
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