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. 2010 Mar 4;5(3):e9519. doi: 10.1371/journal.pone.0009519

Figure 6. The transcriptome in non-functional, Fix− nodules of M. truncatula.

Figure 6

(A) PCA analysis of the microarray experiments. The two principal components and their fraction of the overall variability of the data (%) are shown on the x-axis and on the y-axis. Clusters of experiments are circled and annotated as “roots”, containing root samples and nodules from mutants Sm2011exoY, Sm1021bacA, TR3, TE7 and V1; “incipient nodules” containing wild type immature nodules; and “nodules” containing wild type nodules and nodules from the M. truncatula mutants TR183, TR36, TRV36, TRV43 and the S. meliloti mutants lpsB, nifA, fixJ, fixK, fixG and nifH. (B) Heat map of transcriptomes of nodulation mutants. The samples are annotated above the columns. The arborescence above the columns shows the similarities among the transcriptomes. The gene expression profiles that were identified in the wild type temporal analysis (see Figure 4) are indicated at the left. The colour coded scale bar for the relative levels of expression of the genes is indicated below the heat map. (C) RT-qPCR analysis of the expression patterns for 3 genes, selected among the ensemble, which exhibit expression profiles 5, 6, 7 and 8 and for genes expressed in all the mutants (common genes). The histograms are annotated with MtGI accession numbers. The samples in the histograms are as follows: J5 wild type roots, 1 (brown bars); nodules from TR3 induced by Sm1021, 2, and from TE7 induced by Sm1021, 3, (orange bars); nodules from J5 induced by Sm1021bacA, 4, (red bars); and nodules from TR36 induced by Sm1021, 5, and J5 wild type nodules induced by Sm1021, 6 (green bars). The relative expression levels correspond to the fold change relative to the sample with the lowest value (arbitrarily set to 1). The error bars correspond to the standard deviations for 3 biological repetitions.