Open Access Highly Accessed Research article

Meiosis-specific gene discovery in plants: RNA-Seq applied to isolated Arabidopsis male meiocytes

Changbin Chen1*, Andrew D Farmer2, Raymond J Langley24, Joann Mudge2, John A Crow2, Gregory D May2, James Huntley23, Alan G Smith1 and Ernest F Retzel2*

Author Affiliations

1 Department of Horticultural Science, University of Minnesota, 1970 Folwell Avenue, St. Paul, MN 55108, USA

2 National Center for Genome Resources, 2935 Rodeo Park Drive E., Santa Fe, NM 87505, USA

3 Illumina Inc., Hayward, California 94545, USA

4 Immunology, Lovelace Respiratory Research Institute, 2425 Ridgecrest Drive SE, Albuquerque, NM 87108, USA

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BMC Plant Biology 2010, 10:280  doi:10.1186/1471-2229-10-280

Published: 17 December 2010

Additional files

Additional file 1:

Table S1. Transcript profiling of genes that function in meiosis. Transcript profiling of 68 previously reported genes that function in meiosis. Showing the signal intensity by reads per million reads. M = meiocyte, A = anther, S = seedling.

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Additional file 2:

Figure S1. Parallel plot to demonstrate the similarity of technical replicates. Showing high similarity of technical replicates. Red--anther; green--meiocyte; blue--seedling. In this figure, no technical replicates for seedlings were presented.

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Additional file 3:

Supplementary Figure S2. Figure S2. Scatterplot matrix to demonstrate the correlations among all samples. The pairs plots show the correlations among all samples. Anther_control = anthers; Anther_meiosis = meiocytes.

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Additional file 4:

Table S2. A list of MGI genes that are preferentially expressed in meiocytes. SN = serial number, MGI = mitochondrial genomic insertion, M = meiocyte, A = anther.

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Additional file 5:

Supplementary Table S3. Table S3. A list of differentially expressed TEs in meiocytes and anthers. The list of differentially expressed TEs in meiocytes and anthers, the label of "--" refers to zero (0) reads from anther. In addition to the mRNA signal intensity of read counts (normalized as reads per million reads), this table also provides gene ID, transposon ID, transposon family and super family. The shaded rows are genes that down-regulated in meiocytes and preferentially expressed in anthers. M = meiocyte, A = anther.

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Additional file 6:

Figure S3. Distribution of expressed mRNAs in meiocytes among gene function categories. Percentage of gene distribution and raw data are presented next to each category.

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Additional file 7:

Figure S4. Distribution of expressed TEs in meiocytes among gene function categories. Treemaps of expressed TEs in meiocytes generated by REVIGO. In each category, the size of the rectangle is proportional to the population of functional groups. A. Biological process. B. Cellular component. C. Molecular function.

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Additional file 8:

Table S4. A list of differentially expressed TEs in meiocytes and seedlings. The list of differentially expressed TEs in meiocytes and seedlings, the label of "--" refers to zero (0) reads from seedling. The shaded rows are genes that down-regulated in meiocytes and preferentially expressed in seedlings. M = meiocyte, S = seedling.

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