Open Access Highly Accessed Research article

Deep sequencing reveals the complex and coordinated transcriptional regulation of genes related to grain quality in rice cultivars

R C Venu1, M V Sreerekha1, Kan Nobuta2, André Beló2, Yuese Ning4, Gynheung An3, Blake C Meyers2 and Guo-Liang Wang14*

  • * Corresponding author: Guo-Liang Wang wang.620@osu.edu

  • † Equal contributors

Author Affiliations

1 Department of Plant Pathology, The Ohio State University, Columbus OH-43210, USA

2 Delaware Biotechnology Institute, University of Delaware, Newark DE-19711, USA

3 Crop Biotech Institute, Kyung Hee University, Youngin 446-701, Republic of Korea

4 State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China

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BMC Genomics 2011, 12:190  doi:10.1186/1471-2164-12-190

Published: 14 April 2011

Additional files

Additional file 1:

Filter results of the five MPSS and SBS libraries. A) A total of 39,288 distinct 17-base expressed signatures from the five MPSS libraries were processed according to three filters: significance, reliability, and genomic match. B) Similarly, 397,543 signatures from the five SBS libraries were also processed using these same filters as previously described by Meyers et al. [45].

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Additional file 2:

Classification of the MPSS and SBS signatures from the five libraries based on their location on the annotated gene (hits = 1) (See Meyers et al. 2004 [45]for details).

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Additional file 3:

List of expressed grain quality related genes identified in 6 days old developing seeds by MPSS and SBS technologies.

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Additional file 4:

List of five fold up and down-regulated genes, antisense and alternate transcripts. A: List of genes commonly identified by MPSS and SBS technologies. Five fold up- and down-regulated genes, antisense and alternate transcripts are presented. B: Genes identified by SBS technology. Five fold up- and down-regulated genes, antisense and alternate transcripts are listed. C: Genes identified by MPSS technology. Five fold up- and down-regulated genes, antisense and alternate transcripts are listed.

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Additional file 5:

Network of lysine and aspartate family amino acid biosynthesis and degradation. http://www.gramene.org webcite. Only the genes with 5-fold up- or down-regulation in Cypress (PSC) or Ilpumbyeo (PSI) compared with that in LaGrue or YR15965 are shown. The positive number in parenthesis indicates up-regulation and the negative number in parenthesis indicates down-regulation. The first value in parenthesis shows the fold change in expression either in LaGrue or YR15965, and the second value shows the fold change in expression in Nipponbare. The italicized and underlined bold number before the parenthesis shows the MPSS/SBS signature class [45]. Green indicates that the gene was identified by SBS only. Red indicates that the gene was identified by MPSS only. Blue indicates that the gene was identified by both MPSS and SBS.

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Additional file 6:

Five fold up and down regulated transcription factors identified by MPSS, SBS and both.

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Additional file 7:

Conserved cis elements in the promoter region of the highly induced genes (≥50 fold) in Cypress (compared to LaGrue and Nipponbare) and Ilpumbyeo (compared to YR15965 and Nipponbare) that are involved in seed development.

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