Non-parsimonious evolution of hagfish Dlx genes
© Fujimoto et al.; licensee BioMed Central Ltd. 2013
Received: 5 September 2012
Accepted: 11 January 2013
Published: 19 January 2013
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© Fujimoto et al.; licensee BioMed Central Ltd. 2013
Received: 5 September 2012
Accepted: 11 January 2013
Published: 19 January 2013
The number of members of the Dlx gene family increased during the two rounds of whole-genome duplication that occurred in the common ancestor of the vertebrates. Because the Dlx genes are involved in the development of the cranial skeleton, brain, and sensory organs, their expression patterns have been analysed in various organisms in the context of evolutionary developmental biology. Six Dlx genes have been isolated in the lampreys, a group of living jawless vertebrates (cyclostomes), and their expression patterns analysed. However, little is known about the Dlx genes in the hagfish, the other cyclostome group, mainly because the embryological analysis of this animal is difficult.
To identify the hagfish Dlx genes and describe their expression patterns, we cloned the cDNA from embryos of the Japanese inshore hagfish Eptatretus burgeri. Our results show that the hagfish has at least six Dlx genes and one pseudogene. In a phylogenetic analysis, the hagfish Dlx genes and those of the lampreys tended to be excluded from the clade of the gnathostome Dlx genes. In several cases, the lamprey Dlx genes clustered with the clade consisting of two hagfish genes, suggesting that independent gene duplications have occurred in the hagfish lineage. Analysis of the expression of these genes showed distinctive overlapping expression patterns in the cranial mesenchymal cells and the inner ear.
Independent duplication, pseudogenization, and loss of the Dlx genes probably occurred in the hagfish lineage after its split from the other vertebrate lineages. This pattern is reminiscent of the non-parsimonious evolution of its morphological traits, including its inner ear and vertebrae, which indicate that this group is an early-branching lineage that diverged before those characters evolved.
The extant vertebrates are divided into two major groups, the jawed (gnathostomes) and the jawless vertebrates (agnathans). The two groups share a number of morphological characters (synapomorphies) that define the vertebrates, such as the neurogenic placode, neural crest, and their derivatives, including complex sense organs and a cranial skeleton [1–3]. These morphological characters are not seen in non-vertebrate chordates. To investigate the early phase of vertebrate evolution from a molecular perspective, the expression patterns of various developmental regulatory genes have been compared between the gnathostomes and the lamprey, one of the two extant groups of agnathans [4–14]. In contrast to the lamprey, little is known about the developmental processes of these morphological characters in the hagfish because their embryos have been unavailable until recently.
The cyclostomes are often recognized as a paraphyletic group in the fields of morphology and palaeontology [3, 15–17] because of the extraordinarily different morphologies of the hagfish and lampreys [18, 19]. In fact, the hagfish has been considered to lack a number of the vertebrate characters possessed by the lamprey, such as de-epithelialized and migrating neural crest cells, vertebral elements, a complex branchial basket, and multiple semicircular canals in the inner ear [18–22]. Based on the idea that these relatively simple morphological features of the hagfish represent the ancestral state of the vertebrates, this animal has tended to be placed at the base of the phylogenetic tree of the entire vertebrates [3, 15–17]. However, on various molecular phylogenetic trees, the hagfish tends to cluster with the lamprey in a monophyletic group, and this position is now widely accepted by researchers who are familiar with these molecular phylogenetic analyses [23–27]. This discrepancy between the molecular and morphological data has been a source of contention regarding the evolution of the early vertebrates, and there was no consensus on the phylogenetic position of the hagfish for about three decades .
Given the monophyly of the cyclostomes, it is conceivable that the molecular developmental mechanisms of the lampreys and hagfish evolved independently in each lineage after their divergence more than 400 million years ago , resulting in secondarily degenerate characters that are more marked in the hagfish lineage. In fact, this assumption is consistent, at the molecular level, with the evidence that the Xlox gene, one of the ParaHox genes responsible for organogenesis (including pancreas formation) in the gnathostomes, is pseudogenized in the genome of the Atlantic hagfish (Myxine glutinosa), which may correlate with the absence of some endocrine organs in the hagfish . This suggests that some molecular sequences and expression patterns could be secondarily degenerate for other hagfish genes that are involved in the developmental processes of the vertebrate morphological synapomorphies.
Because the Dlx genes are crucial to the morphogenesis of the vertebrate synapomorphies, they may also be secondarily degenerate in the hagfish [38–42]. The Dlx genes, homeobox-containing transcription factors, are organized in convergently transcribed bi-gene clusters, which are linked to the Hox gene clusters in the genomes of the gnathostomes. For example, the six Dlx genes of mammals form three bi-gene clusters, Dlx1 Dlx2, Dlx3 Dlx4, and Dlx5 Dlx6, linked to the HoxD, HoxB, and HoxA clusters, respectively [43–47]. From the evidence that the chondrichthyan species have three Dlx bi-gene clusters, it is presumed that the common ancestor of the gnathostomes already had three bi-gene clusters, which seem to have derived from two rounds of genome duplication [44, 48]. More significantly, the Dlx genes show overlapping expression patterns in the synapomorphic characters of the gnathostomes; for example, in the forebrain, neural crest cells, and inner ear [40–42]. Almost all the Dlx genes are expressed in the ectomesenchymal cells derived from the cranial neural crest [41, 49, 50], and the expression of some Dlx genes is detected during the developmental processes of the inner ear [40, 42] in model gnathostome species, including the chicken, mouse, and zebrafish.
It has been demonstrated that the lamprey has at least six Dlx genes, designated DlxA F[13, 51]. At least four of these genes were generated by independent duplications unique to the lineage of either the lampreys or the cyclostomes. It is also known that DlxA–E display overlapping expression patterns in the cranial ectomesenchyme and some of them in the otic vesicles [7, 13, 14]. These data raise several simple questions. How many Dlx genes are there in the hagfish genome? Did the hagfish ancestor also undergo an independent duplication of the Dlx genes, as in the lamprey lineage?
The derivatives of the cranial ectomesenchyme and the otic vesicle are also clearly simpler in the hagfish than in the lampreys and gnathostomes at the morphological level [18, 30]. For example, the basket-like structure of the branchial skeleton is present in the lampreys but absent in the hagfish. There is also no vertical semicircular canal in the hagfish inner ear [18, 19]. These lines of evidence raise another question. Do the Dlx genes of the hagfish also show overlapping expression patterns in the cranial ectomesenchyme and otic vesicles, similar to those in the lamprey and gnathostomes?
To address these questions, we cloned the Dlx genes from embryonic materials of the Japanese inshore hagfish (E. burgeri) and analysed the gene expression patterns of the isolated hagfish Dlx genes using in situ hybridization. Here, we show that the hagfish has at least six Dlx genes, some of which arose from gene duplications unique to the hagfish lineage. Furthermore, some of the isolated hagfish Dlx genes are expressed in the cranial mesenchymal cells and otic vesicles with overlapping expression patterns, as reported in the lampreys and gnathostomes [6, 7, 13, 41, 42]. These results suggest that the Dlx genes were independently duplicated and then diverged in each of the hagfish and lamprey lineages, maintaining overlapping expression patterns.
From a comparison of the conserved regions of the amino acid sequences, it is expected that EbDlxΨ and EbDlx2/3/5B are closely related to each other, implying that they diverged recently in the hagfish lineage. However, we could not identify the phylogenetic position of this pseudogene from our data set, because of the paucity of informative amino acid site between EbDlxΨ and the other sequences (see Additional file 1). Therefore, we excluded EbDlxΨ from our phylogenetic analysis.
Molecular phylogenetic trees of the vertebrate Dlx genes were reconstructed using their homologues in two tunicate species (Ciona intestinalis and Oikopleura dioica) as outgroups. Although the positions of the tunicate Dlx homologues were not stable, these genes were excluded from the clades of the gnathostome and cyclostome Dlx genes in our phylogenetic trees (Figure 2). These outgroups are positioned on the internal branch connecting the Dlx1/4/6 and Dlx2/3/5 gene clades of the vertebrates on a phylogenetic tree consisting of 68 operational taxonomic units (Figure 2A). On this phylogenetic tree, EbDlx1/4/6C forms a cluster with DlxF of the lamprey with strong support, EbDlx2/3/5A and EbDlx2/3/5B cluster in a clade containing three lamprey genes (DlxA, -B, and -C), and EbDlx1/4/6A and -B cluster with two lamprey genes (DlxD and -E) (Figure 2A). Exceptionally, EbDlx2/3/5C was isolated from the other cyclostome Dlx genes on this phylogenetic tree.
To increase the number of informative amino acid sites for the phylogenetic analysis and to improve the resolution of the phylogenetic tree, we separately analysed the Dlx1/4/6 and Dlx2/3/4 clade genes with/without the outgroups (Figure 2B, C; Additional File 2). The clade of EbDlx1/4/6C and the lamprey DlxF gene was located at the most basal position of the vertebrate Dlx1/4/6 gene clade on the phylogenetic tree that included the outgroups (Figure 2B). To maximize the number of informative amino acid sites used in the phylogenetic inference, we excluded the sequences that produced extremely long branches (all tunicate Dlx homologues, gnathostome Dlx4 and −6, EbDlx1/4/6C, and lamprey DlxF genes) from the alignment. On this phylogenetic tree, four Dlx genes of the cyclostomes formed a single clade, in which two EbDlx1/4/6 genes clustered with a high bootstrap value (Additional file 2A). The cluster containing the lamprey DlxD and DlxE genes was located next to the hagfish cluster, although the bootstrap value was not very high. This phylogenetic tree indicates that the duplication that produced EbDlx1/4/6A and EbDlx1/4/6B occurred in the hagfish lineage after its separation from the lamprey lineage.
The tree topology of the Dlx2/3/5 subfamily also suggested an independent gene duplication in the hagfish lineage (Figure 2C; Additional file 2). The cluster containing EbDlx2/3/5A and EbDlx2/3/5B formed a sister group with the cluster containing lamprey DlxA and DlxC, with high bootstrap support. This cluster was located at the basal position of the Dlx2/3/5 clade (Figure 2C). In the phylogenetic tree without outgroups, the clade containing EbDlx2/3/5A, EbDlx2/3/5B, lamprey DlxA, and DlxC had a high supporting value in all the phylogenetic methods used (Additional file 2), suggesting that independent gene duplications had occurred in both the lamprey and hagfish lineages. This phylogenetic tree also suggested that the EbDlx2/3/5C and lamprey DlxB genes are most closely related to each other (Additional file 2).
In the middle-pharyngula embryo, transcripts of EbDlx1/4/6A, EbDlx2/3/5A, and EbDlx2/3/5C were detected in the mesenchymal cells between the pharyngeal endoderm and the surface ectoderm, which are presumptive cranial neural crest cells (Figure 3). Although not as distinct as the expression patterns of those three genes, EbDlx1/4/6B and EbDlx2/3/5B tended to be detected in the lateral ventral part of the epithelial cells of the otic vesicles (Additional file 3). In the late-pharyngula embryo at the pre-otic level, which contains the trabecular cartilage (indicated by the arrowhead in Figure 1B; Figure 4A), transcripts of EbDlx1/4/6A, EbDlx2/3/5B, and EbDlx2/3/5C were detected (Figure 4B-D). The signal for EbDlx1/4/6A was detected in the mesenchymal cells of the primordium of the tendons of the vagina of the clavatus, which is one of the tissues of the hagfish feeding apparatus (Figure 4B). The expression of EbDlx2/3/5B was observed in different mesenchymal cells of the primordial tendons and cartilages, including the tendons of the clavatus muscle and the vagina of the clavatus, the basal cartilage, and the cartilage that comprises the trabecula, dorsal longitudinal bar, and extrapalato-quadrate (Figure 4C). A highly intense EbDlx2/3/5C signal was detected in the mesenchyme located on the ventral aspects of the pharynx and the basal cartilage (Figure 4D). At the level of the inner ear (Figure 1B, arrow), EbDlx1/4/6B and EbDlx2/3/5B showed distinct expression patterns in the auditory capsule (Figure 5). EbDlx2/3/5B was expressed broadly throughout the auditory capsule with homogeneous intensity (Figure 5B, E), whereas EbDlx1/4/6B showed a strong signal on the lateral side of the auditory capsule (Figure 5C, F).
The expression pattern of EbDlxΨ is broad, and no specific signals were detected in the middle-pharyngula stage. In the late-pharyngula stage, this pseudogene showed specific expression patterns in the cranial cartilages and inner ear (Additional file 3).
In this study, we successfully isolated seven hagfish cDNAs, whose deduced amino acid sequences show significant similarity to the Dlx sequences of the jawed vertebrates. Our molecular phylogenetic analyses suggested that six of these with intact open reading frames are homologues of the Dlx genes reported for other vertebrates, and the other is a transcribed pseudogene with a nonsense nucleotide substitution. We also analysed the expression patterns of all six isolated genes in middle- and late-pharyngula hagfish embryos. From our results, we deduced the common ancestral state and evolutionary processes of the Dlx genes in the cyclostome lineage, based on our previous knowledge of the molecular phylogeny and gene expression patterns of the Dlx genes of the lampreys and gnathostomes [7, 13, 14, 38–42].
It also remains to be ascertained whether the bi-gene cluster structure of the Dlx genes has been conserved in the cyclostomes during the entire course of their evolution. Given that the bi-gene clusters were already present before the divergence of the cyclostomes and gnathostomes [44, 51, 54, 55], it is reasonable to assume that the ancestral cyclostome Dlx genes were also present in bi-gene clusters (Figure 6). Our data show that the expression domains of the hagfish Dlx genes overlap (Figures 3 and 5). The expression of EbDlx1/4/6A, EbDlx2/3/5A, and EbDlx2/3/5C was detected in the pharyngeal mesenchymal cells of the middle-pharyngula embryo (Figure 3), as is seen in the lampreys and gnathostomes [7, 13, 14]. A number of conserved cis-acting regulatory elements that are shared by two different Dlx genes and contribute to their overlapping expression patterns in the pharyngeal mesenchymal cells have been identified in the intergenic regions of the gnathostome Dlx gene clusters [56–58]. Therefore, it seems plausible that the hagfish Dlx genes that show overlapping expression patterns in the pharyngeal mesenchymal cells have retained the ancestral bi-gene clusters, with conservation of these cis-acting regulatory elements (the blue boxed arrows and the dashed line in Figure 6).
In this context, it is worth considering the evolutionary relationships between the two rounds of whole-genome duplication, the number of Dlx genes, and their linkage to other genes. Based on the presumption that the Hox cluster and its associated genes (including the Dlx genes), the so-called the “core-Hox paralogon”, were increased by the two rounds of genomic duplication in the common ancestor of the vertebrates [46, 47], the two Dlx genes in each bi-gene cluster are also thought to have been duplicated twice, consequently producing eight Dlx genes in total, including the two hypothetical genes (Dlx7 and Dlx8) in the genome of the common vertebrate ancestor. To explain why sharks and mammals have only six Dlx genes (Dlx1–6), it is assumed that the two hypothetical Dlx genes (Dlx7 and Dlx8) that should have been linked to the HoxC cluster and Col2A1 were lost before the radiation of the extant gnathostomes . This raises the question of whether this loss predated the split of the cyclostome lineage from the gnathostome lineage and, if not, whether the genomes of the modern cyclostome species have retained Dlx7 and Dlx8. To answer this question, further investigation of their whole genomes is required, with particular consideration of whether the Dlx genes are localized in the genomic regions containing the HoxC cluster and Col2A1 genes in the cyclostome genomes. To investigate all these issues, the whole-genome sequence of the hagfish is required.
Recent progress in phylogenetic analysis has allowed us to construct reliable phylogenetic trees, and these trees support the monophyly of the cyclostomes [25–27, 34, 59]. However, identifying the orthology and resolving the molecular phylogeny of many cyclostome genes remain challenging . In fact, our study has shown that the evolutionary processes of the hagfish Dlx genes cannot be explained by any simple parsimonious assumption based on a one-to-one orthology between the hagfishes, lampreys, and gnathostomes. Non-parsimonious evolutionary processes with “hidden paralogy”, involving ancient gene duplications followed by lineage-specific gene losses, have been proposed for several genes, including Cdx and Bmp2/4/16. Therefore, we must be cautious in applying the parsimonious assumption to the evolutionary processes of other cyclostome genes. This caution also seems applicable to the hagfish morphological characters, such as the inner ear and cranial skeleton [19, 30], in which the embryonic function of the Dlx genes is implicated, although these morphological characters have long been interpreted as plesiomorphic in the classical “Vertebrata”, excluding the hagfishes, based on parsimonious assumptions in the field of palaeontology [15–17].
Our study has shown that the hagfish has retained at least six intact protein-coding Dlx genes and a single pseudogene. Conventional molecular phylogenetic methods suggest that four of these were generated by independent gene duplications in the hagfish lineage. These data indicate that more than half the Dlx genes of the hagfish are paralogous to the Dlx genes of the lampreys and gnathostomes, suggesting a complex gene phylogeny, possibly involving lineage-specific gene losses. The hagfish Dlx genes show overlapping embryonic expression patterns, as previously observed in the lampreys and gnathostomes. Our data indicate that the evolutionary processes of the hagfish Dlx genes cannot be explained by a simple evolutionary scenario inferred according to the principle of maximum parsimony.
Adult male and female E. burgeri were collected in the Japan Sea off Shimane and Yamaguchi. The male and female individuals were maintained in an aquarium tank and a cage in the sea according to published methods [29, 30, 32]. From 2008 to 2009, 42 hagfish embryos were obtained in the aquarium tank and the cage. We gave identification numbers to these embryos  and staged them according to Dean’s figures and descriptions . Among these embryos, the middle- and late-pharyngula stage embryos (#0903 and #B04, respectively) were selected as the most appropriate embryos for histological analysis and the analysis of the expression patterns of the Dlx genes.
Molecular cloning and sequencing were performed according to a previous report . A single pharyngula-stage embryo, which was obtained in 2007 , was used for total RNA extraction by using TRIzol Reagent (Invitrogen, Japan). Degenerate RT–PCR was performed to amplify the fragment of cDNA encoding the conserved homeobox region of the Dlx amino acid sequence, using three different degenerate primer sets (Additional file 4). The PCR products were isolated on a 2% agarose gel, and the individual bands were excised from the gel. The amplified PCR fragments containing the conserved homeobox regions of the Dlx genes were independently ligated with the TOPO TA Cloning Dual Promoter Kit (Invitrogen) and transformed into Escherichia coli DH5α. In total, more than 12 clones were picked from each population of clones and sequenced using an ABI 3130XL automated sequencer (Applied Biosystems, Japan). To determine the full-length cDNA sequences, the 5′ and 3′ ends were amplified with a GeneRacer kit (Invitrogen) with specific primers (Additional file 4) and sequenced with the method described above. Sequence traces were aligned with CodonCode Aligner (CodonCode Corporation, Dedham, MA, USA). To confirm the stop codon site in EbDlxΨ, PCR and sequencing were performed with three different cDNA samples, which were isolated from different hagfish embryos, using specific primers (Additional file 4). The sequence data were submitted to the DDBJ database [DDBJ:AB679710–AB679716].
A multiple sequence alignment of the Dlx genes derived from representative vertebrate species was constructed with the CLUSTALW multiple alignment program  (also see Additional file 1) and refined by visual inspection. Based on this alignment, molecular phylogenetic analyses were performed using three different methods: the neighbour-joining (NJ), maximum likelihood (ML), and Bayesian inference (BI) methods. The NJ and ML trees were constructed with 1000 bootstrap replications. JTT and WAG models were used to construct the NJ and ML trees, respectively. The BI analyses were based on two independent runs of two million generations, with samples taken from every 100 generations. Each run consisted of one cold and three heated chains. The NJ, ML, and BI analyses were performed with MEGA , PhyML , and MrBayes , respectively.
The hagfish embryos and adult specimens were fixed by immersion in Serra’s fixative, processed for paraffin sectioning by standard methods, and sectioned to 6–10 μm. A single section was place on a glass slide, and the adjacent sections were used for haematoxylin and eosin staining and in situ hybridization. The probes were prepared and in situ hybridizations were conducted based on previous reports [30, 66]. In situ hybridization was performed in a Ventana automated machine (Roche Diagnostics, Japan). To detect the signals, a BlueMap NBT/BCIP substrate kit was used, and the samples were counterstained with a nuclear Fast Red equivalent reagent, ISH Red (Roche Diagnostics). We performed several pilot in situ hybridization experiments using the olfactory epithelial tissues of the adult hagfish, because the olfactory epithelium is known to express several Dlx genes in mammals [67, 68] (Additional file 5). The research followed internationally recognized guidelines. We received ethical approval from RIKEN Kobe Institute Safety Center.
SF is a technical assistant and YO is a doctoral student in the Laboratory for Evolutionary Morphology at the Center for Developmental Biology (CDB). KGO initiated this study in the same laboratory but now holds an independent position at the Yilan Marine Research Station, ICOB, Academia Sinica in Taiwan. S. Kuraku is the leader of the Genome Resource and Analysis Unit at CDB. S. Kuratani is the director of the Laboratory for Evolutionary Morphology at CDB.
We are grateful to Captain Osamu Kakitani and the members of the Fishery Association in Gotsu City and to Kiyomi Kayano (Director, Sekikatsu Inc.) for their assistance in collecting the hagfish. We also thank Fumiaki Sugahara at the Laboratory for Evolutionary Morphology, CDB, RIKEN, for maintaining the aquariums, and the staff of Yilan Marine Station, ICOB, Academia Sinica, for their assistance with administrative support. Finally, we wish to express our deep gratitude to Kenta Sumiyama and Kyle Martin for their advice on the experimental strategy. This research was supported by Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science (JSPS), Ministry of Education, Culture, Sports, Science, and Technology of Japan, and NSC grant 101-2311-B-001-001-MY2 from the National Science Council of Taiwan.
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