Open Access Highly Accessed Research article

Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RNA-Seq

Chao Feng1, Ming Chen2, Chang-jie Xu1, Lin Bai2, Xue-ren Yin1, Xian Li1, Andrew C Allan3, Ian B Ferguson13 and Kun-song Chen1*

  • * Corresponding author: Kun-song Chen akun@zju.edu.cn

  • † Equal contributors

Author Affiliations

1 Laboratory of Fruit Quality Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou 310058, P. R. China

2 Department of Bioinformatics/The State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China

3 The Horticulture and Food Research Institute of New Zealand, Private Bag 92169, Auckland, New Zealand

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BMC Genomics 2012, 13:19  doi:10.1186/1471-2164-13-19

Published: 13 January 2012

Additional files

Additional File 1:

Length and gap distribution of Contigs, Scaffolds and UniGenes from each library of Chinese bayberry cv. Biqi.

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Additional File 2:

Overview of the length, gap and depth distribution of Chinese bayberry UniGenes. (A) Length distribution, (B) Gap percentage (ratio of number of 'N' to UniGene length) distribution, (C) Depth distribution, (D) Length distribution of deduced amino acid sequences.

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Additional File 3:

GO classification of Chinese bayberry UniGenes.

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Additional File 4:

Pathway annotation of Chinese bayberry UniGenes.

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Additional File 5:

Ascorbic acid biosynthesis pathway in Chinese bayberry. The number of UniGenes is shown besides each step.

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Additional File 6:

COG classification of Chinese bayberry UniGenes.

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Additional File 7:

Clustering analysis of differentially expressed UniGenes.

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Additional File 8:

Co-expression relationships of differentially expressed UniGenes. Top 12 related UniGenes are shown in this Table.

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Additional File 9:

Dynamic Interactive pathway analysis on bayberry fruit during ripening. This flash file shows the dynamic changes in absolute expression magnitude of specific gene families from 75 DAF to 80 DAF and finally 85 DAF. The expression was summed from all members encoding a gene from the same family, identified through KO id. The lines with 10 different colors from blue to red show the absolute expression magnitude, with the RPKM values 0-10, 10-20, 20-40, 40-80, 80-160, 160-320, 320-640, 640-1280, 1280-2560, and over 2560 represented by color 1 to 10, respectively.

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Additional File 10:

Expression annotation and functional annotation of UniGenes shown in Figure 5B and Figure 6B.

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Additional File 11:

The branch of co-expression network related with UniGenes in the anthocyanin biosynthesis pathway. The UniGenes encoding anthocyanin biosynthesis enzymes and related co-expressed UniGenes are indicated with yellow and pink red circles, respectively, and a line is drawn between co-expressed genes.

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Additional File 12:

Top BLAST results of Chinese bayberry sucrose transport protein (SUT) to Arabidopsis and other plants based on amino sequence.

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Additional File 13:

A PERL program applied in the p-value calculation.

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