Figure 4.

Functional categorization, subcellular localization, and hierarchical clustering of differentially abundant proteins upon E. arvense spore germination. (A) A total of 80 proteins were classified into 11 functional categories. The percentage of proteins in different functional categories are shown in the pie. (B) Subcellular localization categories of proteins predicted based on softwares and literature. The numbers of proteins with different locations are shown in the pie. Chl, chloroplast; Cyt, cytoplasm; Gol, Golgi apparatus; Mit, mitochondria; Nuc, nucleus; Pox, peroxisome. (C,D) Dendrogram of 80 differentially abundant proteins obtained by hierarchical clustering analysis. The columns represent different spore germination stages, including MS, mature spores; RS, rehydrated spores; DCS, double-celled spores; GS, germinated spores; SPC, spores with protonemal cells. The rows represent individual proteins. Three main clusters (I–III) and subclusters of II and III (II-1, II-2, III-1, and III-2) are shown on the left side. Functional categories indicated by capital letters, spot numbers, and protein name abbreviations are listed on the right side. The scale bar indicates log (base 2) transformed protein abundance ratios ranging from -13.0 to 3.0. The ratio was calculated as protein abundance at MS stage divided by abundance each stage, respectively. The increased and decreased proteins are represented in red and green, respectively. The color intensity increases with increasing abundant differences. Undetected proteins are indicated in gray. Abbreviations for functional categories: A, Photosynthesis; B, Carbohydrate and energy metabolism; C, Other metabolisms; D, Signaling and vesicle trafficking; E, Cell structure; F, Cell cycle; G, Transcription related; H, Protein synthesis; I, Protein folding and processing; J, Protein degradation; K, Stress and defense. Detailed information on protein names and abbreviations can be found in Table 1.