Figure 2. Proteomics in High-Ploidy Species Enhanced by Assignment of Proteins to Orthogroups. Also Figure S1.

(A) Number of proteins assigned per orthogroup for each plant species in our study colored by ploidy. Shaded ovals at left represent subgenome organization.

(B) Fold increase (x-axis) in peptide spectral matches that identify unique orthogroups vs. unique proteins. Each bar represents a single fractionation experiment conducted on the species named at left and color-coded by ploidy as in (A).

(C) The number of observed proteins (left plot) or orthogroups (right plot) experimentally observed (in blue) compared to the possible total in the proteome (gray). Note that relative coverage per species is a function of the amount of data collected from that species in this study.

(D) Our data set is sufficient to identify the majority of orthogroups possible by this method. Each dot represents the number of orthogroups identified (y-axis) in a subsample of n experiments (x-axis), with sampling repeated ten times per each n.

(E) Orthogroups with more than two proteins were approximately equally likely to be represented by a single dominant protein as not, regardless of ploidy.

(F) Orthogroups observed by mass spectra (green) represent those with higher mRNA abundances (TPM, transcripts per million, log scale; data from (Panchy et al., 2014)), as shown for Chlamydomonas. Gray represents orthogroups not observed in our study.

(G) Log-scale protein abundances (y-axis) show expected correlation with RNA abundances (x-axis, Transcripts per million; same as in (F)) in Chlamydomonas, however with numerous outliers, notably, RuBisCo (green dot).