BambooGDB, a bamboo genome database with comprehensive functional annotation and extensible analysis platform. The de novo sequenced genome data by Bamboo Genome Project, full-length cDNA and RNA-seq data for moso bamboo (Phyllostachys edulis, once-used Latin name was Phyllostachys heterocycla) together composed the main contents of this database. Based on these sequence data, a comprehensive function annotation for bamboo genome was made. Besides, an analytical platform providing visualization of genomic data, protein-protein interactions network, pathway analysis and comparative genomic analysis was also constructed. Moreover, diverse and powerful search tools and a convenient browser were incorporated to facilitate the navigation of these data.
BambooGDB is developed with the following features briefly:
- Providing genome sequence of moso bamboo with comprehensive functional annotations under multi-levels (such as gene, protein function and protein structure);
- Presenting comparative analyses between bamboo and its relative plants by OrthoMCL algorithm and BLAST;
- Integrating and exhibiting multi-level results from published studies on moso bamboo such as expression data and microRNA data;
- Data visualization, including genomic data, heterozygous SNPs, RNA-Seq data and full length-cDNA data using GBrowse (version 2);
- Other tools composed of retrieve sequences, protein-protein interaction and pathway analysis are available for user.
1. Peng, Z., Lu, Y., Li, L., Zhao, Q., Feng, Q., Gao, Z., .. & Jiang, Z*. (2013) The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla). Nature genetics, 45, 456-461, 461e451-452.
2. Zhao, H., Peng, Z., Fei, B., Li, L., Hu, T., Gao, Z*., Jiang, Z*. (2014) BambooGDB: a bamboo genome database with functional annotation and an analysis platform.Database Vol.2014:article ID:bau006.
3. Zhao, H., Chen, D., Peng, Z., Wang, L. and Gao, Z*. (2013) Identification and Characterization of MicroRNAs in the Leaf of Ma Bamboo (Dendrocalamus latiflorus) by Deep Sequencing. PloS one, 8, e78755.
4. Peng, Z., Zhang C., Zhang Y., Hu T., Mu S., Li X., Gao, J*. (2013) Transcriptome Sequencing and Analysis of the Fast Growing Shoots of Moso Bamboo (Phyllostachys edulis). PloS one, 8, e78944.