Phylogenetic trees of full-length CCCH domain proteins from Populus,Arabidopsisand rice. All CCCH proteins of Populus (91), Arabidopsis (68) and rice (67) were divided into five distinct subfamilies (CCCH-a to CCCH-e) based on the types of CCCH motif. Each protein in subfamily CCCH-a has 1–3 C-X7-C-X5-C-X3-H motif (s), CCCH-b has 1–6 C-X8-C-X5-C-X3-H, CCCH-c has 2–3 C-X7-C-X5-C-X3-H and C-X8-C-X5-C-X3-H, CCCH-d has 1 C-X5-C-X4-C-X3-H and 1 C-X7,8,10-C-X5-C-X3-H, whereas CCCH-e has 1–6 other non-conventional CCCH motifs. The unrooted tree was constructed based on the full-length protein sequences using MEGA 4.0. Numbers at nodes indicate the percentage bootstrap scores and only bootstrap values higher than 50 % from 1,000 replicates are shown. The percentages in the bracket represent protein sequence similarity range for each subfamily, which were obtained using the Smith-Waterman algorithm. Populus CCCH proteins were marked with the red dots. The scale bar corresponds to 0.05 or 0.1 estimated amino acid substitutions per site.
Chai et al. BMC Genomics 2012 13:253 doi:10.1186/1471-2164-13-253