Fig. 3

Most expressed functions and genes in the growth state of the incubations. A Expression values (TPM) of the 359 most expressed genes in “growth” samples pooled into custom categories, delineated to report each KO to a single category (see Table S1 for further details). B Fold change (FC) between “lag” and “growth” incubation states and TPM expression values of genes (KOs) annotated as peptidases, translocases (proton pumps), and CAZy enzymes. Dots representing FC larger than the average FC of housekeeping genes are colored in dark blue. KOs displaying overlap in functional annotations (i.e., different KOs associated to the same transcript) needed to be grouped into broader sets (asterisk, see Fig. S5 for further details). “Cysteine peptidases” include cathepsins B, F, H, K, L, O, and X, as well as KDEL-tailed endopeptidase and xylem cysteine peptidase; “aspartyl peptidase” includes cathepsins D and E, phytepsin and saccharopepsin; “serine peptidase” includes cathepsin A, serine carboxypeptidase-like clades I and II and vitellogenic carboxypeptidase-like protein. For CAZy enzymes, “GH7” groups cellulose 1,4-beta-cellobiosidase and cellulase