AMS-dependent and independent regulation of anther transcriptome and comparison with those affected by other Arabidopsis anther genes
1 Department of Biology and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, PA 16802, USA
2 Intercollege Graduate Program of Cell and Developmental Biology, the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, PA 16802, USA
3 State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
4 Plant and Microbial Biology Department, University of California, Berkeley, CA 94720, USA
BMC Plant Biology 2012, 12:23 doi:10.1186/1471-2229-12-23Published: 15 February 2012
Additional file 1:
Figure S1. Correlation coefficients between signal intensities from wild-type and the ams anther replicates. Pearson's correlation coefficients were larger than 0.96 between pair of the biological replicates from the ams and wild type anther, indicating that the results were highly reproducible. Figures S2 & S3. GO annotation of genes up- and down-regulated in ams. GO categorization of genes differentially expressed in the ams mutant compared with wild type. The enriched groups were shown in different color with P-value provided. Figures S4-S11. The genes involved in different metabolic pathways that were activated or repressed in ams compared with wild type. Red color represents genes activated while green color represents genes repressed in ams compared with wild type. The overview of metabolism activities was shown in supplemental figure 4. Figure 5, 6, 7, 8-11 showed expression shifts of genes involved in secondary metabolism, regulatory pathways, receptor-like-kinase pathway, transcriptional regulation, protein trafficking, stress response, ubiquitin and autophagy dependent degradation pathway. Figure S12. Real-time PCR results consistent with microarray data. Six genes were verified using real-time PCR. The bars in blue represent the real-time RT-PCR results while red the microarray results. All the numbers shown in this figure are the fold changes of expression intensities in other tissues compared with anther. "infl" is the abbreviation of inflorescence.
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Additional file 2:
Genes differentially expressed in anther and inflorescences from the ams mutant. This additional file contains information about genes differentially expressed in the ams anther and inflorescences compared with wild type. Column sequence, abbreviation and the version of annotation are as those used as in table 1 and all the other supplemental tables. All expression values are log2 ratio.
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Additional file 3:
GO categorization of different clusters based on expression pattern. This additional file contains information about numbers of genes in each GO category. The enriched categories were highlighted in red color.
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Additional file 4:
Genes differentially expressed in the ams mutant with putative function in exocytosis, transportation, ubiquitination and stress reaction. This additional file contains information about genes involved in different pathways with elevated expression levels in ams.
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Additional file 5:
Genes defined as specifically or preferentially expressed in early anther or preferentially expressed in reproductive tissue. This additional file contains information about genes preferentially expressed in only anther or reproductive tissues compared with roots, stems, leaves, siliques.
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Additional file 6:
Genes expressed in stamen, early anther and pollen. This additional file contains information about the expression levels of gene in different organs.
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Additional file 7:
Genes differentially expressed in spl, ems1 or/and the ams mutants. This additional file contains information about the expression levels of gene differentially expressed in the three mutants.
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Additional file 8:
Expression pattern of MADS, MYB, bHLH, WRKY, bZIP, AP2/ERF and NAC families. This additional file contains information about the expression levels of different gene families.
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