Phylogenetic analysis of hes genes in sarcopterygian. A The outline of phylogenetic tree in hes gene family. B The phylogenetic tree was constructed based on the amino acid sequences using the ML method. Bootstrap values for nodes are indicated (n = 100). Evolutionary analysis was conducted in RAxML. Blue and red letters indicate amniote and coelacanth genes, respectively. The abbreviation of animals are as follows: Hosa; human, Mumu; Mouse, Gaga; Chicken, Geja; Japanese gecko, Xetr; X. tropicalis, Xela; X. laevis, Lach; Coelacanth

Syntenic analysis of hes gene locus in sarcopterygian. The syntenies in frog (A), chicken (B), gecko (C) and coelacanth (D) are shown. Chromosome number is described as “XLA7L” in each panel. Pentagon arrows show genes with the 5′–3′ direction. Magenta shows hes gene and magenta with a broken line indicates a pseudogene. Orange or blue squares show the hes5.1 and hes5.3 cluster region, respectively. The broken lined circle shows “partial” hes gene

Phylogenetic analysis of teleost hes genes. The phylogenetic tree was constructed by ML method. hes genes except for hes5 (A), only hes5 genes (B). Red and blue letters indicate zebrafish/medaka and human hes genes, respectively. Hosa, human; Xela, Xenopus laevis; Xetr, Xenopus tropicalis; Dare, zebrafish; Orla, medaka

Comparison with hes gene locus among Xenopus, zebrafish and medaka. Chromosome number is described as “DRE23”. Pentagon arrows show genes a gene with 5′–3′ direction. Magenta shows hes gene. Broken arrow means same region (on DRE23). DRE, zebrafish; OLA, medaka; XLA, Xenopus laevis

Phylogenetic analysis of hes genes of several jawed vertebrates. The phylogenetic tree was constructed by ML method. hes genes except for hes5 (A), hes5 genes (B) of spotted gar, elephant shark, lamprey and amphioxus. Blue, red, purple and green letters indicate spotted gar, elephant shark, lamprey and amphioxus, respectively. Hosa, human; Xetr, Xenopus tropicalis; Leoc, spotted gar; Cami, elephant shark; Pema, lamprey; Brfl, amphioxus

Comparison with hes gene locus among Xenopus (A), spotted gar (B) and elephant shark (C). Pentagon arrows show genes with the 5′–3′ direction. Magenta shows hes gene and magenta with a broken line is a pseudo gene. Orange square shows the hes5-1 cluster region. Orange and blue square shows the hes5.1 and hes5.3 cluster region, respectively

Comprehensive phylogenetic analysis of hes genes except for hes5 (A) and hes5 genes (B) in jawed vertebrate. Evolutionary analysis was conducted in RAxML. Human HEYL, X.tropicalis hey2 and sponge (Amphimedon queenslandica) HEY1-like gene sequences were used as an outgroup. The outline of B is described in B’. Hosa, human; Mumu, Mouse; Gaga, Chicken; Geja, Japanese gecko; Xetr, Xenopus tropicalis; Lach, Coelacanth; Dare, zebrafish; Orla, medaka; Leoc, spotted gar; Cami, elephant shark; Amqu, sponge

Syntenic and phylogenetic analysis of Tibetan frog hes5 genes. A Synteny analysis around hes5 locus in Xenopus laevis and Nanorana parkeri. *: the gene lacks WPRW motif (the gene was deleted from the following phylogenetic analysis (B)). B Phylogenetic tree analysis of hes5 genes of Xenopus laevis, Xenopus tropicalis and Nanorana parkeri. The phylogenetic tree was constructed by ML method

Evolutionary acquisition of hes5 genes and the hes5 cluster. Phylogenetic tree of jawed vertebrate (left). The table shows the number of hes5 genes that were classified to the hes5.1 or hes5.3 cluster and the number of hes5 genes that were not classified to the two clusters. The phylogenetic analysis was conducted using full-length amino acid sequences