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Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids

Guangming He1*, Beibei Chen23, Xuncheng Wang4, Xueyong Li25, Jigang Li12, Hang He1, Mei Yang1, Lu Lu6, Yijun Qi7, Xiping Wang6 and Xing Wang Deng12*

Author Affiliations

1 Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China

2 Department of Molecular, Cellular and Developmental Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA

3 Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China

4 Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Tsinghua Park No. 1, Haidian District, Beijing 100084, China

5 National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agriculture Sciences, No. 12 Zhongguancun South Street, Haidian District, Beijing 100081, China

6 College of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing 100875, China

7 National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China

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Genome Biology 2013, 14:R57  doi:10.1186/gb-2013-14-6-r57

Published: 12 June 2013

Additional files

Additional file 1:

Table S1: Summary of total reads obtained from all sequencing libraries.

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Additional file 2:

Figures S1 to 11. Figure S1: Mean levels of exons and introns in shoots and roots of reciprocal hybrids. Figure S2: Distribution of H3K36me3 levels within and around differentially expressed genes. Figure S3: Experimental validation of methylated DNA regions by genomic bisulfite sequencing. Figure S4: A representative genomic region on maize chromosome 1 showing integrated maps of transcription and epigenetic modifications. Figure S5: Tree view of hierarchical clustering of H3K9ac and H3K36me3 levels. Figure S6: Relationships of variations in H3K36me3 and gene expression between organs and between genotypes. Figure S7: Functional categories of genes upregulated in shoots and roots of hybrids. Figure S8: Correlation of allelic expression bias between shoots and roots of Mo17 ´ B73. Figure S9: Coverage of 21 nt, 22 nt, and 24 nt siRNA clusters in and around protein-coding genes. Figure S10: Distribution of 21 nt and 22 nt siRNA clusters on maize chromosome 1. Figure S11: Correlation between 22 nt siRNAs and DNA-methylation levels at the same genomic loci.

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Additional file 3:

Tables S2 and 3. Table S2: List of genes showing expression variation in shoots and roots of maize hybrids. Table S3: Number of small RNA reads associated with known maize microRNAs.

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Additional file 4:

Supplemental methods. Details of data processing and analyses.

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