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Open Access Highly Accessed Research article

RNA-Seq improves annotation of protein-coding genes in the cucumber genome

Zhen Li1, Zhonghua Zhang2, Pengcheng Yan1, Sanwen Huang2, Zhangjun Fei3 and Kui Lin1*

Author Affiliations

1 College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Street, Beijing, 100875, China

2 Key Laboratory of Horticultural Crops Genetic Improvement of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics Technology, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancunnan Street, Beijing, 100081, China

3 Boyce Thompson Institute and USDA Robert W. Holley Center for Agriculture and Health, Cornell University, Tower Road Ithaca, New York, 14853-1801, USA

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BMC Genomics 2011, 12:540  doi:10.1186/1471-2164-12-540

Published: 2 November 2011

Additional files

Additional file 1:

Supplemental Tables and Figures. Table S1. Summary of the additional sequencing data from Cucumis sativus var. hardwickii and domestic Cucumis sativus var. sativus to reassembled the genome of Cucumis sativus var. sativus. Table S2. Statistics of cucumber genome ressembly. Table S3. Mapping RNA-seq reads onto the reassembled cucumber genome. Table S4. Prediction of non-coding RNAs in the two annotations. Table S5. Prediction and classification of transposable elements in the two annotations. Figure S1. Genes in annotVer 1.0 mapped to the same locus of the reassembly of cucumber genome. Figure S2. Two genes in annotVer 1.0 merged into one gene in annotVer 2.0. Figure S3. Genes in annotVer 1.0 and annotVer 2.0 mapped to the same locus but with different structures.

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