Evolution of hes gene family in vertebrates: the hes5 cluster genes have specifically increased in frogs
BMC Ecology and Evolution volume 21, Article number: 147 (2021)
hes genes are chordate homologs of Drosophila genes, hairy and enhancer of split, which encode a basic helix-loop-helix (bHLH) transcriptional repressor with a WRPW motif. Various developmental functions of hes genes, including early embryogenesis and neurogenesis, have been elucidated in vertebrates. However, their orthologous relationships remain unclear partly because of less conservation of relatively short amino acid sequences, the fact that the genome was not analyzed as it is today, and species-specific genome duplication. This results in complicated gene names in vertebrates, which are not consistent in orthologs. We previously revealed that Xenopus frogs have two clusters of hes5, named “the hes5.1 cluster” and “the hes5.3 cluster”, but the origin and the conservation have not yet been revealed.
Here, we elucidated the orthologous and paralogous relationships of all hes genes of human, mouse, chicken, gecko, zebrafish, medaka, coelacanth, spotted gar, elephant shark and three species of frogs, Xenopus tropicalis (X. tropicalis), X. laevis, Nanorana parkeri, by phylogenetic and synteny analyses. Any duplicated hes5 were not found in mammals, whereas hes5 clusters in teleost were conserved although not as many genes as the three frog species. In addition, hes5 cluster-like structure was found in the elephant shark genome, but not found in cyclostomata.
These data suggest that the hes5 cluster existed in the gnathostome ancestor but became a single gene in mammals. The number of hes5 cluster genes were specifically large in frogs.
hes genes are chordate homologs of Drosophila hairy and enhancer of split genes, which encode the basic helix-loop-helix (bHLH) transcriptional repressor . These genes are known to have various developmental functions, including Notch signaling target and neurogenesis , somitogenesis, and early development of the presumptive midbrain-hindbrain boundary (pre-MHB) [3, 4].
Many hes-related genes have been reported in various species. For instance, mammals including human and mouse have seven hes genes, and these genes are considered to form gene family [5, 6]. However, the orthologous relationship between species is not still well-known because, for instance, most of hes-related genes in zebrafish and medaka are not called as hes, but her, hairy-related gene . It is thought that these intricate naming is caused partly by the large number of the genes and these sequences are relatively small to compare (their total size of the proteins are around 200 aa).
Recently, a number of vertebrate genomic analyses including frogs, Xenopus laevis (X. laevis) and X. tropicalis, have been reported. Xenopus includes diploid to dodecaploid species, although polyploidy is considered to be rare in amniotes. X. tropicalis has a diploid genome, and X. laevis has an allotetraploid genome . The genomic analysis showed that the allotetraploidization was caused by interspecific crosses between two species that have a diploid genome. Thus, X. laevis has two subgenomes, called L and S [9, 10].
We previously identified all hes genes of X. tropicalis and X. laevis by phylogenetic analysis and synteny analysis . In brief, for X. tropicalis, we revealed the phylogenetic and synteny relationships of all the 18 hes genes with human hes genes, and renamed them properly. X. laevis has 37 hes genes: 18 homeologs, one laevis-specific gene, hes5.7, and a pseudogene, hes7.4. Although the number of genes doubled after allotetraploidization, the homeologs of hes genes, except for hes2, have been conserved in X. laevis. In addition, Xenopus frogs have more than two paralogs of hes5, hes6, and hes7 genes, in contrast to human hes genes. In particular, the number of hes5 genes in Xenopus is quite high. Interestingly, they form two clusters, which we call “the hes5.1 cluster” and “the hes5.3 cluster”.
Clustered genes such as the Hox gene cluster, human β-globin gene cluster, and human growth hormone (hGH)/chorionic somatomammotropin gene cluster are considered to be formed as a result of gene duplication and divergence [12, 13], and have various notable functions with unique regulatory mechanisms. Similarly, some of hes genes are known to be indispensable in neurogenesis , and most of hes genes are well conserved. In addition, they make two gene clusters at least in Xenopus. This implies that the hes5 cluster also plays an important role during embryogenesis as other cluster genes.
To understand the evolution and role of hes genes in vertebrates, especially the clustered hes genes, it is important to identify all hes genes and reveal the orthologous relationship. In this study, we have elucidated orthologous and paralogous relationships of the hes gene family using phylogenetic and synteny analyses of human, mouse, chicken, zebrafish, medaka, three frog species (X. tropicalis, X. laevis and Nanorana parkeri), Gekko japonicus, coelacanth, spotted gar, elephant shark, lamprey, and amphioxus. From these analyses, we revealed that hes genes are specifically increased in frogs, and also discussed the evolution of the two hes5 clusters.
Classification of hes genes in sarcopterygian
Our previous studies on the identification of hes genes have shown that there are ten hes5 paralogs in X. laevis, which we refer to as "the hes5.1 cluster" or "the hes5.3 cluster" . To determine when the hes5 clusters emerged, we first performed a phylogenetic analysis of sarcopterygian hes5 genes (Fig. 1, Additional file 1: Fig. S2; complete tree was shown in Additional file 1: Fig. S4). Maximum likelihood (ML) phylogenetic tree construction revealed that all the hes5 genes we examined were assigned in a single clade with a high bootstrap value (Fig. 1A). In the hes5 clade, the genes, Hosahes5, Mumuhes5, Gagahes5chr21-3 (the name means “Gaga” (Gallus gallus) “hes5” gene located on “chr21” (chromosome 21), gene number “3”, Fig. 2B), Gejahes5sc135-1 (Gejahes5 on scaffold 135, number 1, Fig. 2C), which are human (Homo sapiens), mouse (Mus musculus), chick (Gallus gallus), and gecko (Gekko japonicus) genes, formed a single clade with a high bootstrap value. Interestingly, Xenopus hes5.3-5.9 formed a monophyletic group, suggesting that gene duplication of hes5.3-5.9 occurred independently (Fig. 1B, blue letters). In Coelacanth (Latimeria chalumnae (Lach)), one of hes5 genes formed a single clade (Lachhes5sc00059), three genes (Lachhes5sc00001, Lachhes5sc00319 and Lachhes5sc00199) formed a clade with Xenopus hes5.3-5.9 although the bootstrap value was too low. This result suggests that three coelacanth genes may be related to the hes5.3 cluster.
Next, to examine the presence of the hes5 clusters in other species, we analyzed synteny of hes5 locus in chicken, geckos, and coelacanth genomes (synteny of other hes genes are shown in Additional file 1: Fig. S1A, C). In the chicken genome, hes5 genes were located on a single chromosome, chromosome 21 (Fig. 2B). In gecko, synteny around hes5 was observed in scaffolds 135 and 31595 (Fig. 2C). In coelacanth, we found four hes5 genes in scaffold00199, 00001, 00319, and 00059 (Fig. 2D). Hes5chr21-1~3 genes in chick, hes5sc135-1~2, and hes5-like genes in gecko, and hes5sc00319 gene in coelacanth were all located next to pank4, similar to Xenopus hes5.1 cluster genes. This suggests that these genes correspond to the hes5.1 cluster (orange background). In chicken and gecko, however, there were no hes5 genes between nol9 and zbtb48 (the hes5 genes located between these genes are defined as hes5.3 cluster genes in Xenopus, blue background). In contrast, the coelacanth Lachhes5sc00199 gene was located near nol9. This result suggested that coelacanth Lachhes5sc00199 may be homologous to the hes5.3 cluster gene. In coelacanth, Lachhes5sc00001 was found near chd5 (Fig. 2D). In Xenopus, chd5 (chd5-like) was located next to rnf207 near the hes5 clusters, suggesting the relevance of the coelacanth gene to the hes5 clusters. Lachhes5c00059 was found near ppil2, which is located on the 1st chromosome in Xenopus, indicating that the synteny was different from other hes5 genes. Phylogenetic analysis also indicated that Lachhes5sc00059 was first divided in the hes5 gene family (Fig. 1B), suggesting a distinct evolution of this gene. Together with these results, it is suggested that all the hes5 genes of chicken and gecko are classified to the hes5.1 cluster, whereas coelacanth hes5 genes belong to the hes5.1 and hes5.3 clusters.
Comparison of hes genes between teleosts and Xenopus
It is known that whole genome duplication (WGD) occurred 500 million year ago in the common ancestor of vertebrates. Additionally, in teleost, another WGD occurred 3.7 million years ago after divergence from the common ancestor of gnathostomes [14, 15]. Thus, in teleost genome, the two loci having similar gene order to each other on different chromosomes are called doubly conserved synteny (DCS), are found and the fact that the gene is doubly conserved even after WGD suggests that it has an important function . In zebrafish (Danio rerio) and medaka (Japanese ricefish, Oryzias latipes), hes genes have not been well characterized, especially the orthologous relationship between species. Indeed, many genes that seem to be hes orthologues were named as "her" genes. Therefore, we attempted to identify the orthologous relationship of teleost hes genes based on phylogenetic analysis by their amino acid sequences. By our phylogenetic analysis, we found that many zebrafish and medaka “her” genes formed clades with Xenopus hes genes (Fig. 3A; complete tree is shown in Additional file 1: Fig. S5; detailed gene annotations are shown in Additional file 1: Table S1). Zebrafish her6 and medaka her6, her6.2 formed a single clade with Xenopus hes1. Medaka her4 and zebrafish her9 were located near Xenopus hes4 clade. Orlaher8.2 and Dareher8.2, 8a showed high similarity with Xenopus hes6.2. Dareher13, Darehes6, Orlahes62of2, and orlahes6 belonged to a clade of Xenopus hes6.1 and human hes6 genes. The genes annotated as hes3 and hes2 in zebrafish, medaka, and Xenopus belonged to each homologous clade. her5, 7 of both medaka and zebrafish belonged to Xenopus hes7.1 clade, whereas zebrafish her1, her11, and medaka her7 belonged to Xenopus hes7.3 clade.
About hes5 genes, many homologous genes were found in both zebrafish and medaka, Dareher4.1-her4.4, two genes named Dareher4.2, Dareher2, 12, 15.1-15.2, and Orlaher4.2, 12 (Fig. 3B). These genes formed teleost-specific monophyly among the large hes5 clade. Thus, it is not clear which Xenopus hes5 cluster zebrafish/medaka hes5 belongs to.
We next performed synteny analysis around her4.1-4.4, 12 and her2, 15.1-15.2 to clarify whether these genes formed clusters similar to Xenopus hes5.1 and hes5.3 clusters (the synteny of other teleost hes genes were shown in Additional file 1: Fig. S1B, D). In the zebrafish genome, her4.1-4.4, 12 cluster and her2, 15.1-15.2 cluster were present on chromosomes 23 and 11, respectively. dnajc11 and rnf207 genes were found in the genomic region around the clusters. Icmt, kcnab2, nol9, and chd5 genes located in Xenopus hes5 locus were also found on either chromosome 23 (DRE23) or chromosome 11 (DRE11). These results suggested that DCSs were found in the hes5 region of the zebrafish genome. Near the her2, 15 cluster on DRE11, dnajc11, which is located near the hes5.3 cluster in Xenopus, was found (Fig. 4A). However, other typical features of the hes5.3 cluster were not observed in the locus. For instance, nol9 or zbtb48 was not located near the hes2, 15 locus. On DRE23, the her4.1-4.4, 12 cluster was located between emc1 and icmt (Fig. 4A). Icmt gene was located near hes3 (hes3.L) gene in Xenopus (Fig. 4B). No her or hes gene was found between the locus of zbtb48 and nol9, as in the chicken (Fig. 2B). From these results, it was difficult to determine whether the her4.1-4.4, 12 cluster corresponds to the hes5.1 cluster or hes5.3 cluster in Xenopus. It should be pointed out that the sequence homology of the zebrafish genes with Xenopus hes5 genes appeared to be higher with the hes5.1 cluster genes than with the hes5.3 cluster genes (Table 1), suggesting that her2, 15 and her 4.1-4.4, 12 genes of zebrafish might correspond to the hes5.1 cluster genes in Xenopus. In medaka, her7 gene was found to be located near grik5, which was located near the hes5.1 cluster in Xenopus (Fig. 4C). However, phylogenetic analysis showed that OLA her7 was in Xenopus hes7.1 subclade (Fig. 3A). On the other hand, OLA her4.4 and her12 were located on medaka chromosome 7 around the following genes, espn, acot7, and hes2.2, which were located near the hes5.3 cluster in Xenopus. No hes-related genes were located between nol9 and zbtb48 (Fig. 4D, medaka chromosome 1) although similar gene order to Xenopus hes5 region was also observed around the locus (Fig. 4D).
Classification of hes genes in gnathostomata
To determine the origin of the hes5 cluster, we carried out phylogenetic analysis with spotted gar (Lepisosteus oculatus), elephant shark (Callorhinchus milii), lamprey (Petromyzon marinus), and amphioxus (Branchiostoma floridae) (Fig. 5A, B, Additional file 1: Fig. S3; the complete tree is shown in Additional file 1: Fig. S6). As a result, genes of hes7 and hes5 were clearly separated from the other genes with high bootstrap values. First, we counted the number of hes genes in these species except for hes7- and hes5-classified genes, although the bootstrap values were low. Spotted gar was suggested to have two hes3, two hes7, and three hes6 (Fig. 5A, shown in red letter). Elephant shark had one hes1, hes2, hes4, and hes6 (Fig. 5A, shown in blue letter). In lamprey, there were one hes4, three hes2, and one hes3 (Fig. 5A, shown in purple letter). In amphioxus, hairy A-G genes were found, but were formed a single clade (Fig. 5A, shown in green letter).
In the hes5 clade, both spotted gar and elephant shark possessed four genes (Fig. 5B), but all the genes were separately classified to the Xenopus genes (Fig. 5B, red and blue letters). From the results, we could not identify the homologous relationship of hes5 genes between Xenopus, gar and elephant shark. In addition, no putative hes5 genes were found in lamprey and amphioxus.
Next, we compared the gene order on the genome around Xenopus hes5 cluster locus in spotted gar and elephant shark. In linkage group (LG) 25 of the spotted gar, four hes5-like genes were located next to pank4, but no hes5 (-like) genes were found near nol9 (Fig. 6B). This suggests that gar had a hes5 cluster, and the cluster was closer to the hes5.1 cluster than to the hes5.3 cluster in Xenopus. In contrast, three of four hes5 genes (hes5-like) in elephant shark were clustered near nol9 on KI635912.1 (Fig. 6C). This suggests that the clustered genes might be related to the hes5.3 cluster in Xenopus. In addition, the gene named her3 was located near pank4, which is located near the hes5.1 cluster in Xenopus, on HMISc93. Although the gene may have been given a wrong name because the sequence lacking WPRW domain, the synteny analysis suggests that the gene might be the homolog of hes5, and thus, a gene classified to the hes5.1 cluster might be conserved in elephant shark. Another hes5 gene in elephant shark was located next to ppil2. The order of the two genes was conserved in coelacanth (Fig. 2D), but not in Xenopus. One possible explanation for this is that the common ancestor of teleost and cartilaginous fishes had another hes5 next to ppil2, but later lost the gene.
Evolutionary phylogenetic relationships of hes gene in gnathostomes
To further confirm the classification, we performed a phylogenetic analysis with human hey genes, which are reported to be close to hes genes, as an outgroup (Fig. 7A: complete tree is shown in Additional file 1: Fig. S7) . As it can be seen from the low bootstrap values in the hes clades, the phylogenetic tree was not solved well. However, as we already discussed above, eight zebrafish genes (her4.1-4.4, her12, her15.1-15.2), two medaka genes (Orlaher4.2, 12), and three gar genes formed a single clade with Xenopus hes5.1-5.2 (Fig. 7B, B’). However, a monophyletic group including Xenopus hes5.3-5.10, three coelacanth hes5 (LachSc00001, 00119, 00319), Zebrafish her2, and one gar hes5 (LeocLG25-1) was formed (Fig. 7B, B’), even though LachSc00319 and LeocLG25-1 showed syntenic similarity with the hes5.1 cluster (Figs. 2D, 6B).
Since two hes5 clusters with a high number of genes was conserved in two Xenopus species, we next examined the possibility of conservation in frogs. To determine this, we analyzed another frog species, Tibetan frog (Nanorana parkeri). From the synteny analysis, many hes5-like genes were found to be clustered on the genomes: two hes5-like genes were located next to pank4, and six hes5-like genes were located between nol9 and zbtb48 (although TAS1R1 was inserted into the hes gene cluster locus, which was not found around the hes5.1 or hes5.3 cluster in Xenopus) (Fig. 8A). These results suggest that the two hes5 genes on Scaffold815 of Tibetan frog are classified to the hes5.1 cluster and the other six genes on Scaffold5 are to the hes5.3 cluster. Consistently, phylogenetic analysis showed that two Tibetan frog hes5 formed a single clade with the hes5.1 cluster genes of Xenopus and the other Tibetan frog hes5 genes formed a clade with Xenopus hes5.4-5.9, the hes5.3 cluster genes (Fig. 8B: complete tree was shown in Additional file 1: Fig. S8). These results suggest that the two hes5 clusters are conserved among frogs.
Our study showed that hes5 gene was absent in lamprey and amphioxus, but was existed in Gnathostomata, suggesting that the gene was acquired at the common ancestor of Gnathostomata (Figs. 5, 9). However, there are still other possibilities. Eight hairy genes have been reported in amphioxus, at least four of which have conserved gene expression patterns in vertebrates (in the central nervous system, presomitic mesoderm, somites, notochord, and gut) . Considering from this, it is also possible that other hes genes (hairy) substitute for hes5 function in these species.
We found that elephant shark possessed hes5 (Figs. 5B, 9). Interestingly, synteny analysis indicated that three hes5 genes might be the orthologue of the hes5.3 cluster in Xenopus (Fig. 6C). In addition, a putative hes5.1 cluster gene, which is named as her3, existed near pank4 in the shark (Fig. 6C). In contrast, no hes5-related gene was found in amphioxus and lamprey (Fig. 9). These results suggest that a common ancestor of gnathostomata acquired both hes5.1 and hes5.3 genes.
In spotted gar, we could not identify any genes that belong to the hes5.3 cluster, although we could find many hes5-like genes, which belong to the hes5.1 cluster (Figs. 6B, 9). We wonder how it is evolved: one possible explanation is that, when the ancestor evolved into cartilaginous fishes and neopterygii, the genes called three hes5-like genes in the shark near nol9 (the hes5.3 cluster) was translocated to the locus next to pank4 and partially duplicated. Another possibility is that her3 (the hes5.1 cluster) was duplicated, and three hes5-like genes (the hes5.3 cluster) in elephant shark were lost in the spotted gar. Unfortunately, we could not obtain direct evidence for these possibilities from phylogenetic analysis (Fig. 5).
The hes5.1 and hes5.3 cluster seemed to be conserved in both teleost and neopterygian (Figs. 4, 6). On the other hand, although many hes5 genes were existed in coelacanths (Fig. 2), no cluster was found.From this point of view, what is characteristic of coelacanths is the presence of hes5, in which only the synteny of elephant shark is preserved, so the evolution of hes5 is different between sarcopterygians and cartilaginous fishes, and only sarcopterygians and cartilaginous fishes seem to have preserved hes5 differently from other animals. Although further analysis for the connection of the scaffold is needed, the genes in the coelacanth are possibly the prototype of the hes5.1 and hes5.3 cluster genes. All amniote hes5 genes seemed to be classified to the hes5.1 cluster, and not the hes5.3 cluster (Figs. 1, 2, 9), suggesting that the hes5.3 clusters was lost after branching into amniotes.
We further performed gene structure analysis: the number of exons in the coding regions of each hes5 gene as Zhou et al. . In both X. tropicalis and X. laevis, almost all hes5 consisted of three exons, except for hes5.8. On the other hand, hes5 genes of many actinopterygian including zebrafish, medaka, and spotted gar genes possessed two exons in coding region (Table 2). This might reflect that hes5 genes in actinopteryozoa and osteichthyes were increased in an independent manner.
The number of hes5 genes is specifically high in frogs, especially the hes5.3 cluster genes. To estimate the duplication process, comparison of the transcriptional direction is considered important . As we previously reported, the directions of hes5.5, 5.6, 5.7, and 5.9 are same. Phylogenetic analysis also indicated that these genes were closely mapped in the tree (Fig. 1A), suggesting that these genes may share a common origin, and may be tandemly duplicated in Xenopus. Phylogenetic analysis also indicated that hes5.1, hes5.2, and hes5.10 showed high similarity (Fig. 1B, 3B, 5B, and 7B). This result suggests another possibility that hes5.10 duplicated from hes5.1/5.2.
In general, hes5 functions downstream of Notch signaling and inhibits neuronal differentiation [19, 20]. RNA-seq analysis revealed that the expression of almost all hes5 genes is high during the gastrula and neurula stages, at which Notch signaling is activated, in Xenopus . These results imply that the function of hes5 is possibly conserved between mouse and Xenopus. Thus, how these duplicated hes5 genes work in neurogenesis remains to be investigated, and this may elucidate the significance of the higher number of hes5 genes in the frogs.
In this study, to reveal the evolutionary process of hes genes, we elucidatedthe orthologous relationship of hes genes in vertebrates using phylogenetic and synteny analyses. In addition, we estimated the evolutionary origins of the two hes5 clusters, which have been found in Xenopus. Although hes5 genes were found in other jawed vertebrates, the number of hes5 genes was higher in frogs. The rudiment of the two clusters was found in elephant shark, suggesting that ancestral species of chondrichthyans might have the origin of these clusters. These findings go a step further in the research on the function of all hes genes in vertebrates as well as the understanding of the evolutionary process of large gene clusters.
Protein sequencing comparison
A multiple alignment of protein sequence of hes genes were visualized with MUSCLE .
Phylogenetic analysis was performed using RAxML (v8.2.0) . Multiple alignments of protein sequence were carried out using MAFFT (v7.221)  with the auto strategy. Unaligned regions were trimmed with TrimAl (v1.2rev59)  using the gappyout option and phylogeny trees were constructed by the maximum likelihood method with PROTGAMMAAUTO.
Annotation of genes: GenBank accessions of hes genes
Genomic synteny of hes genes was analyzed using genome assemblies of X. laevis (v9.1), X. tropicalis (v9) from Xenopus genome project (http://viewer.shigen.info/Xenopus/).
hes5 genes are as follows: hes5chr21-1 ID: 419390. hes5chr21-2 ID: 107057363. hes5chr21-3 ID: 419,392. hes5sc135-1 ID: 107122264. hes5Sc135-2 ID: 107122267. Lach hes5Sc00059 ID: 102346872. hes5Sc00199 ID: 102346203. Lepisosteus oculatus hes5 LG25-1 ID: 102684766. hes5LG25-2 ID: 102684967. hes5 LG25-3 ID: 102683774. hes5LG25-4 ID: 102685165. Callorhinchus milii hes5Sc221 ID: 103188596. hes5Sc58-2 ID: 103181452. hes5Sc58-3 ID: 103181453. hes5Sc58-1 ID: 103181414.
Availability of data and materials
All data is presented within the manuscript including supplemental materials.
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Dr. Yuuri Yasuoka (RIKEN, Yokohama) for comments on the methods for the analyses.
This work was supported in part by management expenses grants from the University of Tokyo.
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Additional file 1: Table S1. The list of hes genes in Danio rerio and Oryzias latipes. Figure S1. Syntenic comparison with hes1, 6 and hes7 gene loci. Figure S2. Multiple alignment of amino acid sequences of hes5. Figure S3. Multiple alignment of amino acid sequence of lamprey (Pema) and amphioxus (Brfl) hes genes. Figure S4. Detail phylogenetic tree of hes genes in sarcopterygian. Figure S5. Detail phylogenetic tree of hes genes in teleosts. Figure S6. Detail phylogenetic tree of hes genes in jawed vertebrates. Figure S7. Detail phylogenetic tree of all hes5 genes we observed. Figure S8. Detail phylogenetic tree of all hes5 genes in Tibetan frog.
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Kuretani, A., Yamamoto, T., Taira, M. et al. Evolution of hes gene family in vertebrates: the hes5 cluster genes have specifically increased in frogs. BMC Ecol Evo 21, 147 (2021). https://doi.org/10.1186/s12862-021-01879-6