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cDNA LIBRARY CONSTRUCTION |
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| Contact us |
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Addr:300 Fenglin Road Shanghai,200032 P.R China |
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When using the RAPESEED, please cite the following reference:
Wu, G.Z., Shi, Q.M., Niu, Y., Xing, M.Q., Xue, H.W. "Shanghai RAPESEED Database: a resource for functional genomics studies of seed development and fatty acid metabolism of Brassica. Nucleic Acids Research,2008,36: D1044-D1047; doi:10.1093/nar/gkm780 |
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Click here to download all the EST information.
Click here to download the original BLASTx results of all the ESTs.
Click here to download the Gene Ontology annotation.
Large-scale sequencing of expressed sequence tags (ESTs) has been widely used for gene identifications, comparative analysis among different species, and generation of physical map and genetic markers.
Rapeseed embryos at different developmental stages (Figure 1) were collected to construct two cDNA libraries using materials at 3-9 day after pollination or 11-19 day after pollination. After normalization and sequencing, ~16,000 and 6,000 ESTs were sequenced from library 1 and 2, respectively, and finally 6637 and 1825 unique (total 8462) ESTs were obtained, ranging at sizes of 158-1398 bp.
Annotating ESTs through BASTX against the non-redundant protein database results in the functional identification of 6892 sequences (E-value < 1.0E-5), of which 6420 ones are by Arabidopsis and only 262 are by Brassica species. Through Gene Ontology (GO) analysis, annotated ESTs were further functionally classified into three sections: molecular function, biological process, and cellular component. Among the section of molecular function, genes encoding peptides with catalytic activity, binding activity and transporter activity are the three major parts and account for nearly 80% of all classified genes, indicating the active protein metabolisms in early-developing B. napus seeds.
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Figure B. napus Embryos at Different Development Stages.
Delopmental changes of B. napus embryos after pollination, those at different stages are collected for cDNA library construction (3-9 DAP or 11-17 DAP respectively) and cDNA chip hybridization (7, 9, 12, 17, 19, 21, 25 and 31 DAP, respectively).
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