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Open Access Research article

Transcriptome profiling of peanut gynophores revealed global reprogramming of gene expression during early pod development in darkness

Han Xia1, Chuanzhi Zhao1, Lei Hou1, Aiqin Li1, Shuzhen Zhao1, Yuping Bi123, Jing An13, Yanxiu Zhao3, Shubo Wan12* and Xingjun Wang123*

Author Affiliations

1 High-Tech Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, PR China

2 College of Agriculture, Shandong University, Jinan 250100, PR China

3 College of Life Sciences, Shandong Normal University, Jinan 250014, PR China

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BMC Genomics 2013, 14:517  doi:10.1186/1471-2164-14-517

Published: 29 July 2013

Additional files

Additional file 1: Figure S1:

Length distribution of contigs (A), scaffolds (B) and unigenes (C), GAP of the unigenes (D).

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Additional file 2: Figure S2:

Length and GAP distribution of CDS predicted by BLAST (A, B) and ESTscan (C, D) program.

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Additional file 3: Figure S3-S12:

Genes identified in peanut transcriptome and the related pathways.

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Additional file 4: Figure S13:

Sequencing depth was saturated for gene identification. S1 (stage 1), aerial grown green gynophore; S2 (stage 2), white gynophore after soil penetration without ovary enlargement; S3 (stage 3), gynophore after soil penetration and ovary enlargement.

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Additional file 5: Figure S14:

Gene coverage analysis of S1, S2 and S3. S1 (stage 1), aerial grown green gynophore; S2 (stage 2), white gynophore after soil penetration without ovary enlargement; S3 (stage 3), gynophore after soil penetration and ovary enlargement.

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Additional file 6: Table S1:

Differentially expressed genes in S1 and S2. S1 (stage 1), aerial grown green gynophore; S2 (stage 2), white gynophore after soil penetration without ovary enlargement.

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Additional file 7: Table S2:

Differentially expressed genes in S1 and S3. S1 (stage 1), aerial grown green gynophore; S3 (stage 3), gynophore after soil penetration and ovary enlargement.

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Additional file 8: Table S3:

Gene-specific primers used in quantitative real-time PCR.

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Additional file 9: Table S4:

Verification of DGE results by qRT-PCR. The results showed the expression changes of 27 randomly selected genes. Three biological replicates, R1, R2 and R3 were used in this study. Average represent the mean of expression folds of S2/S1 or S3/S1; SD represent the standard derivation of the mean (n = 3); Seq Result denotes the DGE expression level.

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