Analysis of protein kinase families misregulated in cht7. a) ML phylogeny of the kinase domain of 43 protein kinases encoded by genes that are differentially expressed (log₂-fold change >1, P-adj < 0.05) in cht7 at ≥5 timepoints along with kinase domains retrieved from 122 known protein kinases. Confidence of branches was tested by aLRT branch support. Refer to Materials and methods for details. Cr, Chlamydomonas reinhardtii; At, Arabidopsis; Lt, Lotus japonicus; Mt, Medicago truncatula; Ps, Pisum sativum; Nt, Nicotiana tabacum; Ll, Lilium longiflorum; Os, Oryza sativa; Pp, Physcomitrella patience; CCaMK, Ca2+/CaM-dependent protein kinase; CIPK, CBL-interacting protein kinase; CDK and CPK, calcium-dependent protein kinases; CNK, Chlamydomonas NIMA-related kinase; NEK, NIMA-related Kinase; GSK3, glycogen synthase kinase 3. b–f) Expression of genes encoding MAPK3K-related kinases (b), ALKs (c), and cluster 1–3 potential protein kinases (d–f) in cht7 (orange), WT (black), and CHT7-HA::cht7 (gray) across all timepoints. Y-axis: normalized read count. See also Supplementary Data 1, Tables 3 and 4.