Figure 6

Phylogenetic analysis of LHY and CCA1 (A), PRR family (B), GI (C), and ZTL, LKP2 and FKF1 (D) in plants. The neighbor-joining method [77] was used to construct the phylogenetic trees. The names of genes isolated from Japanese cedar (Cryptomeria japonica) start with Cj. Other species names are abbreviated as follows: Ac, Allium cepa (onion); At, Arabidopsis thaliana (thale cress); Bd, Brachypodium distachyon (purple false brome); Cr, Chlamydomonas reinhardtii (green alga); Cs, Chrysanthemum seticuspe f. boreale (chrysanthemum); Csa, Castanea sativa (chestnut); Cv, Chlamydomonas variabilis (green alga); Gm, Glycine max (soybean); Lg, Lemna gibba (gibbous duckweed); Lp, Lemna paucicostata (duckweed); Mc, Mesembryanthemum crystallinum (common iceplant); Mt, Medicago truncatula (barrel medic); Na, Nicotiana attenuata (coyote tobacco); Ot, Ostreococcus tauri (picoplankton); Osj, Oryza sativa (Japanese rice); Pa, Picea abies (Norway spruce); Pp, Physcomitrella patens subsp. patens (moss); Pps, Pinus pinaster (maritime pine); Ps, Picea sitchensis (Sitka spruce); Psy, Pinus sylvestris (Scots pine); Pt, Populus trichocarpa (black cottonwood); Pv, Phaseolus vulgaris (common bean); Rc, Ricinus communis (castor bean); Sb, Sorghum bicolor (sorghum); Sl, Solanum lycopersicum (tomato); Sm, Selaginella moellendorffii (lycophyte); Ta, Triticum aestivum (bread wheat); Th, Thellungiella halophila (salt cress); Vv, Vitis vinifera (wine grape); Zm, Zea mays (maize). The number following the species name indicates its NCBI accession number. The amino acid sequences of PpCCA1a and PpCCA1b are from Okada et al. [41]. Arabidopsis MYB protein (AAS09982), O. tauri APRR-like protein (AAU14274), S. moellendorffii GI protein (XP_002961231) and Arabidopsis F-box kelch-repeat protein (NP_564592) were used as the outgroups of each phylogenetic tree.