Comparative genomics of Lbx loci reveals conservation of identical Lbx ohnologs in bony vertebrates

Abstract

Background

Lbx/ladybird genes originated as part of the metazoan cluster of Nk homeobox genes. In all animals investigated so far, both the protostome genes and the vertebrate Lbx1 genes were found to play crucial roles in neural and muscle development. Recently however, additional Lbx genes with divergent expression patterns were discovered in amniotes. Early in the evolution of vertebrates, two rounds of whole genome duplication are thought to have occurred, during which 4 Lbx genes were generated. Which of these genes were maintained in extant vertebrates, and how these genes and their functions evolved, is not known.

Results

Here we searched vertebrate genomes for Lbx genes and discovered novel members of this gene family. We also identified signature genes linked to particular Lbx loci and traced the remnants of 4 Lbx paralogons (two of which retain Lbx genes) in amniotes. In teleosts, that have undergone an additional genome duplication, 8 Lbx paralogons (three of which retain Lbx genes) were found. Phylogenetic analyses of Lbx and Lbx-associated genes show that in extant, bony vertebrates only Lbx1- and Lbx2-type genes are maintained. Of these, some Lbx2 sequences evolved faster and were probably subject to neofunctionalisation, while Lbx1 genes may have retained more features of the ancestral Lbx gene. Genes at Lbx1 and former Lbx4 loci are more closely related, as are genes at Lbx2 and former Lbx3 loci. This suggests that during the second vertebrate genome duplication, Lbx1/4 and Lbx2/3 paralogons were generated from the duplicated Lbx loci created during the first duplication event.

Conclusion

Our study establishes for the first time the evolutionary history of Lbx genes in bony vertebrates, including the order of gene duplication events, gene loss and phylogenetic relationships. Moreover, we identified genetic hallmarks for each of the Lbx paralogons that can be used to trace Lbx genes as other vertebrate genomes become available. Significantly, we show that bony vertebrates only retained copies of Lbx1 and Lbx2 genes, with some Lbx2 genes being highly divergent. Thus, we have established a base on which the evolution of Lbx gene function in vertebrate development can be evaluated.

Background

Ladybird/Lbx proteins are part of a clustered set of Nk transcription factors, which encompass the Nk4 protein tinman/Nkx2, the Nk3 protein bagpipe/Nkx3, ladybird/Lbx, C15/Tlx, and the Nk1 protein slouch/Nkx1 [1–4]. In protostome genomes, NK genes are organised into a cluster, which, along with the molecular phylogeny of Nk homeodomains, indicates that they originated via tandem duplications [2]. Indeed, the NK gene cluster is believed to be ancient, with aspects predating the divergence of sponges, cnidarians and bilaterians [5]. In deuterostomes, however, tight clustering has been lost with only Nkx4/Nkx3 and Lbx/Tlx linkages remaining in the cephalochordate amphioxus and in vertebrates [3].

Lbx genes have essential roles in development, including crucial functions in neural and mesodermal cell specification. In mammals and amphibians, Lbx1 controls the emigration of specialised, motile muscle precursors that give rise to limb and hypoglossal/tongue muscles, respectively [6–9]. In mouse embryos, Lbx1 is also required for the specification of several populations of dorsal spinal cord interneurons, which receive and process somatosensory information from the body [10–13]. Moreover, Lbx genes with a similar spinal cord expression pattern to mouse have been described in chick, zebrafish and the spotted dogfish and, in the case of zebrafish and chick, these genes are also expressed in muscle [14–16]. Interestingly, in Drosophila melanogaster, a protostome whose ancestors split from the deuterostome lineage over 500 million years ago, two tandem-duplicated ladybird/Lbx family members exist (ladybird early and ladybird late) that are also expressed in developing muscle and neural tissue and are required for the specification of subpopulations of myoblasts and neural cells [1, 17]. Thus, Lbx genes may have evolutionarily ancient functions in muscle and neural development.

Despite the intriguing similarities of some ladybird/Lbx genes, significant differences become apparent when considering all of the members of the Lbx family in different vertebrates. For example, mammals, including humans, have two Lbx genes [2] as does the chicken [15, 18], whereas Danio rerio has three Lbx genes (this report), and the genome sequencing project for Xenopus tropicalis has so far only revealed one Lbx gene (this report). In addition, the expression pattern of mammalian Lbx2 is distinct from that of Lbx1 (Lbx2 is expressed in the urogenital system, eye and brain) [19], whereas the two chicken Lbx genes and all zebrafish genes are co-expressed in migratory muscle precursors (K. R. Wotton and S. Dietrich, unpublished data). Yet the second chicken Lbx gene is not expressed in neural tissues [15, 18] while all three of the zebrafish genes are, albeit in distinct regions (K. E. Lewis, unpublished data). Consequently, the evolutionary and functional relationship of ladybird/Lbx genes is not clear.

It is generally believed that at the base of the vertebrate lineage, the entire genome was duplicated twice (2R hypothesis; [20]). This was followed by a further genome duplication in the ray-finned fish lineage at the base of the teleost radiation [21–23]. In all chordate relatives of vertebrates investigated so far, such as the urochordates Oikopleura dioica and Ciona intestinalis and the cephalochordate Branchiostoma floridae (amphioxus), only a single lbx gene has been found [3]. It is, therefore, safe to assume that prior to the two rounds of vertebrate genome duplication, only a single Lbx gene existed.

One prediction of the 2R hypothesis is that a 4:1 ratio of genes should have been present in an ancestral vertebrate when compared to their invertebrate relatives. However, with gene duplicates carrying redundant functions, many of these four copies (called ohnologs to indicate that they are paralogs that have originated by a process of whole-genome duplication – see [24, 25]) were lost. Yet, despite considerable interest in Lbx gene function in extant vertebrates, orthologies between Lbx genes have not been established. Therefore, it is not known whether different vertebrate lineages have lost the same, or different, Lbx ohnologs. This raises two alternative hypotheses for the differences that have been observed between vertebrate Lbx genes.

1. Different vertebrate lineages have retained different Lbx ohnologs with distinct expression patterns and/or functions

2. The same Lbx ohnologs have been maintained in all vertebrates with differences in expression or function being due to more recent neo- and/or sub- functionalisation.

To distinguish between these possibilities, we have used a number of bioinformatics approaches to characterise the organisation of Lbx loci in extant osteichthyan vertebrates and to determine the relationship of Lbx genes and genes associated with Lbx loci. Our studies identified non-NK genes that were acquired by Lbx/Tlx region(s) prior to, or during, the two rounds of vertebrate genome duplication and that hence, serve as signature genes for these loci. With the help of these signature genes, the remnants of all four Lbx/Tlx paralogons (eight in teleosts) were identified. Phylogenetic analyses of Lbx, Tlx and the co-localising non-Nk genes revealed that the first round of whole genome duplication in vertebrates created the ancestor of the Lbx1/Tlx1 and Lbx4/Tlx4 clusters plus the ancestor of the Lbx2/Tlx2 and Lbx3/Tlx3 clusters. After the second genome duplication, Lbx and Tlx genes were lost, such that before the split of the ray-finned and lobe-finned fish lineages only Lbx1/Tlx1, Lbx2/Tlx2 and Tlx3 genes were maintained. Gene loss also occurred after the additional genome duplication in the ray-finned fish lineage, leaving teleosts (including zebrafish and pufferfish) with two Lbx1 and Tlx3 genes but only one Lbx2, Tlx1 and Tlx2 gene. Since the amniote Lbx2 genes diverge much more in their coding sequences than the Lbx1 genes and the expression pattern of mouse Lbx2 is distinct from non-mammalian Lbx2 genes, we propose that amniote (or possibly sarcopterygian) Lbx2 genes have evolved at a faster rate and were subject to neofunctionalisation. Lbx1 genes on the other hand may have retained more features of the original chordate lbx gene.

Results

Identification of Lbxgenes in extant Osteichthyes

To reconstruct the phylogeny of vertebrate Lbx genes we first attempted to identify the complete set of these genes in representatives of extant Osteichthyes. For this, BLAST-searches of sequence databases were carried out, using the known human and mouse Lbx1 and Lbx2, chicken Lbx1 and Lbx3, Xenopus laevis Lbx1 and zebrafish Lbx1 sequences as query sequences [1, 2, 4, 9, 14, 15, 18, 19]. To obtain outgroups for these phylogenetic analyses, we also searched the databases for lbx/ladybird sequences in invertebrate deuterostomes, including the cephalochordate Branchiostoma floridae (amphioxus), the urorchordates Oikopleura dioica and Ciona intestinalis, and the echinoderm Strongylocentrotus purpuratus (purple sea urchin); moreover we included sequences from various protostomes. Our search confirmed the presence of two distinct Lbx genes in placental mammals and marsupials (human, mouse, dog, cattle, opossum), one Lbx gene in the still incompletely sequenced platypus and Anole lizard genomes, and two Lbx genes in the chicken. Only one Lbx gene was found for the frog Xenopus tropicalis. On the other hand, besides the gene so far known as zebrafish lbx1 [14], two novel lbx genes were identified in this organism. Three Lbx genes were also identified in the teleosts Takifugu rubripes (fugu), Tetraodon nigroviridis, Gasterosteus aculeatus (stickleback), and two genes in Oryzias latipes (Medaka), while only one lbx/ladybird gene was retrieved for the invertebrate deuterostomes.

Phylogenetic analysis of osteichthyan Lbxprotein sequences

To determine the evolutionary relationship between osteichthyan Lbx genes, we first determined the phylogenetic relationship of Lbx proteins (Fig. 1). For this purpose, amino acid sequences were aligned and analysed, using maximum likelihood methods. We found that the vertebrate Lbx sequences were assigned to two distinct groups. The first group encompassed the known human, mouse, chicken and frog Lbx1 proteins. In addition, this group contained the two novel zebrafish Lbx proteins, encoded by the genes located on chromosomes 13 and 1, the fugu Lbx proteins whose genes are on scaffolds 52 and 62, the Tetraodon protein encoded by the Lbx gene on chromosome 18, the stickleback proteins with genes on groups VI and IX and the medaka protein encoded by the gene on chromosome 1.

Figure 1

Molecular phylogenetic analysis of Lbx sequences. The tree shows a maximum likelihood analysis of Lbx protein sequences. Dark grey boxes indicate orthologous groups while light grey boxes indicate gene linkage. Bootstrap values below 70 have been removed. Only two Tetraodon Lbx proteins are included as the third sequence (found on scaffold 8483) is incomplete. Note that the Lbx sequences separate into two clear groups, Lbx1 and Lbx2, which are supported by bootstrap values of 79 and 83 (boxed), respectively. The chicken protein previously denoted as Lbx3 [18], the zebrafish protein previously denoted as Lbx1 [14] and one of the fugu, Tetraodon, stickleback and medaka sequences group with mammalian Lbx2 sequences. The two novel zebrafish Lbx sequences and the remaining teleost sequences group with mammalian, chicken and frog Lbx1. The tree shows significantly longer branch lengths for the Lbx2 proteins indicating that these sequences may be evolving at a quicker rate than the Lbx1 proteins. For common names of species see additional file 2.

The second group contained all of the mammalian Lbx2 proteins, the chicken protein currently known as Lbx3, the zebrafish protein so far named Lbx1 and encoded by the gene on chromosome 14, together with the Lbx sequences encoded by genes on fugu scaffold 70, Tetraodon chromosome 20, stickleback group IV and medaka scaffold 1066. The division into two distinct groups of Lbx proteins was supported by high bootstrap values. Our phylogenetic analysis shows significantly longer branch lengths for the amniote Lbx2 proteins, indicating that these Lbx2 genes have probably evolved at a quicker rate than the Lbx1 genes. No evidence was found for distinct Lbx3/4 proteins.

Comparison of genomic Lbxloci in Osteichthyes

It is generally held that in the lineage leading to jawed vertebrates, two rounds of whole genome duplication occurred, followed by a further genome duplication in the lineage leading to teleosts [20–23, 26]. Thus, theoretically, if no gene loss has occurred, four Lbx genes should be detectable in extant tetrapods and eight in teleost fish. However, our phylogenetic analyses suggest that only two Lbx genes were retained after the second vertebrate genome duplication and before the genome duplication in ray-finned fish. To confirm these results and to further analyse the orthology of the various vertebrate Lbx genes, we compared the organisation of genes associated with the vertebrate Lbx loci, reasoning that orthologous Lbx genes would share a similar chromosomal environment, while paralogous genes would exhibit a distinct arrangement of the locus (see [27–29] for examples).

Since the human genome information is the most accurate and complete, we began by recording the genes that according to the NCBI Map Viewer database are located in the environment of human LBX1 and 2 genes (Fig. 2). Subsequently, we looked for remnants of the LBX3 and 4 loci, initially by searching the human genome for paralogues of the genes co-localising with LBX1 and 2. We then identified and determined the arrangement of genes characteristic for each of these four paralogons in the genomes of other mammals, the chicken, the frog Xenopus tropicalis and the five teleosts (Fig. 3 and additional file 1).

Figure 2

Human paralogons of the LBX/TLX cluster loci. Schematic representation of the four human LBX/TLX paralogons plus paralogous genes occurring at the NKX3.2 locus, deduced from analysis of the human genome using NCBI map viewer Homo sapiens Build 36.2 (September 2006). Genes are represented by boxes with gene names appearing above and gene subfamilies indicated by numbers inside. Letters on the far left indicate paralogon designation, while chromosomal locations are indicated on the far right. Numbers between genes are approximate intergenic distances in Kb. Background shading indicates paralogous genes. Blue and red dots indicate sites of inversions. Note that LOXL1, AUP1 and PCGF1 genes appear only at the LBX2 locus and KAZALD1, POLL, DPCD, FBXW4 and MGEA5 appear only at the LBX1 locus. BTRC, FGF, NPM and KCNIP genes are linked with LBX and TLX genes at more than one locus, suggesting that these genes were acquired by the LBX/TLX cluster during or before the two rounds of vertebrate genome duplication. Also note that a KCNIP4 and a SLIT2 gene are associated with NKX3.2 on chromosome 4. A KCNIP3 gene is located on the long arm of chromosome2, however at a distance to LBX2, suggesting that it is not an original component of the LBX2 paralogon.

Figure 3

Genomic organisation of human LBX/TLX cluster paralogons and putative orthologous counterparts. Genomic organisation of human (Hs) Lbx/Tlx paralogons and the putative orthologous counterparts identified in Mus musculus (Mm), Xenopus tropicalis (Xt), Gallus gallus (Gg), Danio rerio (Dr), Tetraodon nigroviridis (Tn) and Takifugu rubripes (Fr). For simplicity, only three teleosts are included in this figure: additional data for Oryzias latipes (medaka) and Gasterosteus aculeatus (stickleback) can be found in additional file 1. The main genes characteristic of each paralogon are included in the figure; additional genes and linked genes found further away can be found in additional file 1. Schematic representations of the orthologous genomic regions are depicted in panels 1–4, which correspond to human paralogons 1–4 in figure 2. Gene orthology is indicated by colour code and was inferred from molecular phylogenetics (see additional files). Genes appearing in more than one orthologous region are underlined. Numbers at the ends of each line indicate chromosome (chr) or scaffold (s) numbers. A parallel red line marks gaps in the sequence, while triple black lines indicate large intergenic distances. Blue dots mark sites of inversions, red arrows the end of a contig. Boxes off-line represent genes for which genomic sequences are incomplete; where no chromosome or scaffold number is given, no linkage data is available. In some cases, "missing" genes can be found on different scaffolds or chromosomes. This data is shown in additional file 1. In addition, we do not show the dispersed 2^nd teleost Lbx2 paralogon that no longer contains an Lbx or Tlx gene, but this information is included in additional file 1. The genes our phylogenetic analysis identified as Lbx1 are found in a similar genomic environment, linked to orthologs of the genes present at the human LBX1/TLX1 locus. In addition, non-mammalian Lbx1 genes are linked to the Slc2a15 gene not found at any other Lbx locus. Lbx2 genes are linked to Loxl3, Aup1 and Pcgf1 genes (genomic information incomplete for chicken and frog), while Tlx3 genes are linked to the orthologs of human KCNIP1, NMP1, FGF18 and BTRC2. In teleosts, Fgf24 and Npm4 are part of the Lbx2 locus, while in all species examined, Fgf17 and Npm2 are no longer linked to Lbx/Tlx genes.

Lbxloci in humans

Human LBX1 has previously been mapped to chromosome 10, 1.7 Mb distant from NKX2.3 [2, 4]. LBX1 is tightly linked to the related Nk-type homeobox gene TLX1 (Fig. 2 and Additional file 1). This is followed by the Kazal-type serine peptidase inhibitor domain 1 gene KAZALD1, the LOXL4 gene encoding a Lysyl oxidase like protein and the SLIT1 gene encoding an axon guidance molecule. Moving in the opposite direction, LBX1 is linked to a Beta-transducin repeat containing gene (BTRC1, a F-box and WD repeat domain 11 type gene), the DNA polymerase lambda gene (POLL), the Deleted in a mouse model of Primary Ciliary Dyskinesia gene (DPCD), the F-box and WD repeat domain containing 4 gene (FBXW4), the Fibroblast growth factor 8 gene (FGF8), the Nucleophosmin 3 gene (NPM3), the Meningioma expressed antigen 5 gene (MGEA5), the gene encoding a Kv channel interacting protein 2 (KCNIP2), and further away, the gene encoding the Lim domain binding protein LDB1 and the NKX1.2 gene (Figs 2 &3).

Human LBX2 has been mapped to chromosome 2, and is linked to TLX2 ([2, 4]; Fig. 2). Neither of these genes are associated with other NK genes, suggesting that they have translocated from their original cluster [2, 3]. LBX2 and TLX2 are separated by the PCGF1 gene, which encodes a polycomb group ring finger. Facing away from PCGF1 and TLX2, LBX2 is linked to genes that encode Dynactin subunit 1 (DCTN1) and the Tetratricopeptide repeat protein 31 (TTC31). TLX2 on the other side is flanked by the DEAQ box 1 (DQX1) gene which encodes for an ATP-dependent RNA helicase, the gene encoding Ancient ubiquitous protein 1 (AUP1), the HTRA1 gene which encodes for a high temperature requiring serine protease, the LOXL3 gene, DOK1 which encodes for the Docking downstream of Tyrosine kinase 1 protein, and a gene encoding the uncharacterised protein NP620159.2. Thus, the human LBX1 and LBX2 loci are quite distinct (Fig. 2). However, they both harbour TLX genes, in line with the idea that Lbx and Tlx genes were linked in the original bilaterian cluster of Nk-type homebox genes [2, 3]. Moreover, both LBX loci include LOXL genes.

In humans, a further TLX gene exists 1.4 Mb distant from NKX2.5 on chromosome 5, thought to be a remnant of the third cluster of NK genes, which, after the second vertebrate genome duplication, lost its cognate LBX gene ([3]; Fig. 2, Additional file 1). Investigating the organisation of this former LBX3/TLX3 locus, we found that TLX3 is on one side linked to the gene that encodes for Ran-binding protein 17 (RANBP17, a member of the Exportin protein family), the gene encoding for the gamma-aminobutyric acid receptor (GABRP), a further KCNIP gene, KCNIP1, the Lymphocyte cytosolic protein gene LCP2, the Forkhead transcription factor gene FOXI1, the Dedicator of cytokinesis gene DOCK2, the coil-coil domain encoding CCDC99 gene, followed by SLIT3. On the other side, TLX3 is linked to NMP1, FGF18, FBXW11/BTRC2, and further away from the TLX3 gene, NKX2.5, MSX2 and DOK3. The order of NMP1, FGF18 and FBXW11/BTRC2 is reversed compared to the paralogous genes at the LBX1/TLX1 locus. However, it is remarkable that for both the LBX1/TLX1 and LBX3/TLX3 paralogons, the NPM and FGF genes are closely linked, separated by sequences of only 5 and 9 kb, respectively. Taken together, our data suggests that Kcnip, Fbxw11/Btrc2, Slit, Loxl, Dok and the closely associated Fgf-Npm genes are hallmarks of Lbx/Tlx loci.

To identify remnants of the fourth LBX locus, we searched the human genome for additional, linked KCNIP, BTRC/FBXW11, SLIT, LOXL, DOK and FGF-NPM sequences. No further homologues of BTRC/FBXW11 genes were identified. However, we found:

- FGF17 and NPM2 closely linked to DOK2 and about 1.8 Mb distant from LOXL2, NKX2.6 and NKX3.1 on chromosome 8, which also carries NKX6.3

- Linked KCNIP4-SLIT2 genes 7.7 Mb distant from NKX3.2 on chromosome 4

- KCNIP3 on the long arm of chromosome 2, however 20.9 Mb distant from and hence probably not a genuine part of the LBX2-TLX2 region.

A previous report suggested that LBX2/TLX2 may once have belonged to the NKX2.6-NKX3.1 region on chromosome 8 [3]. However, the presence of LOXL and DOK genes at both the LBX2 locus and the NKX2.6-NKX3 locus is not consistent with this idea. KCNIP4-SLIT2 were found linked to the Prominin gene PROM1, so far not associated with LBX/TLX loci. However, as KCNIP3 is also linked to PROM2, this suggests that Prom genes may once have belonged to Lbx/Tlx containing regions. Taken together, these observations suggest that the LBX2/TLX2 region may have originated from the NKX3.2 containing cluster on chromosome 4, while FGF17-NPM2 linked to LOXL2 and DOK2 represent the remnants of the fourth LBX/TLX region associated with NKX2.6 and 3.1 on chromosome 8.

Lbxloci in other mammals

Investigating the arrangement of genes at Lbx loci in additional placental mammals (mouse, dog and cattle), a marsupial (opossum) and a monotreme (platypus), we found that the loci are arranged in the same fashion as in humans (Fig. 3, Additional file 1 and data not shown). The exception is the platypus Lbx2/Tlx2 locus, whose existence could not be confirmed as genes linked to this paralogon in other mammals were found on short, unlinked and poorly characterised DNA fragments. Moreover, in mouse and Monodelphis, Prom2-Kcnip3 are not on the same chromosome as the Lbx2 locus, supporting the idea that these genes secondarily intercalated into the Lbx2 carrying chromosome in the lineage leading to humans.

Lbxloci in the chicken

As the information on the chicken genome is still fragmentary, the localisation of chicken Lbx genes could not be determined with certainty. However, chicken chromosome 6 contains a region that is syntenic with the LBX1 region on Human chromosome 10, encompassing Kazald1, Tlx1, Btrc, Poll, Dpcd, Fbxw4, Fgf8, Nmp3, Mgea5 and Kcnip2 in the same order as the human genes (Fig. 3). Loxl4, Slit1 and further genes located in the wider environment of the mammalian Lbx1 locus were also identified, with gene groups displaying a similar arrangement in the chicken and in mammals (Additional file 1). Furthermore, we identified sequences 300 bp upstream and 2.2 kb downstream of the two Lbx1 exons, which are conserved between the mammalian Lbx1 loci and the putative chicken Lbx1 site; in the chicken these regions flank a region that has not been fully sequenced yet (data not shown). Thus, it is likely that this area on chromosome 6 indeed harbours the Lbx1 gene. As will become relevant below, in the chicken the Btrc1 gene is separated from the Poll gene by the Slc2a15 gene (our name) encoding a solute carrier (Fig. 3).

The Lbx2-type gene so far named Lbx3 [18] is situated on a short contig not assigned to a chromosome (Fig. 3). However, Aup1, Htra2, Loxl3, the gene encoding NP620159.2, together with a further Mgea gene, were found on the so far poorly-characterised contig 242 assigned to chromosome 4; all genes are arranged in the same order as the corresponding genes at the Lbx2/Tlx2 containing region of mammalian chromosomes (Fig. 3; Additional file 1). Moreover, separated by sequence gaps, these genes are linked to the Dctn1 gene, which is downstream of Lbx2 in mammals. Significantly, this chromosome also carries genes associated with the NKX3.2 locus in humans, adding weight to the hypothesis that Lbx2 genes were once associated with this particular NK cluster.

Tlx3 was found on chicken chromosome 13 in a region syntenic with the TLX3 containing region of human chromosome 5 and grouped with Fbxw11/Btrc2, Fgf18, Npm1, Ranbp17, Gabrp, Kcnip1, Foxi1, Lcp2, Dock2, Ccdc99 and Slit3 in the same fashion as mammalian Tlx3. In agreement with this being the third Lbx/Tlx paralogon, other members of the NK cluster associated with this paralogon are also found on chick chromosome 13 (Additional file 1).

Finally, a representative of Fgf17 could not be identified, but Npm2, Dok2 and Loxl2 were found on chromosome 22, in a region syntenic to the FGF17-NPM2 region on human chromosome 8 and linked to Nkx2.8 and 6.3 (Fig. 3 and Additional file 1). Notably, this region is also linked to Prom2, a gene in mammals associated with Kcnip3 (Kcnip3 was not found in the chicken). This finding supports the idea that Kcnip3-Prom2 are not an original component of the Lbx2/Tlx2 paralagon but instead probably belong to the fourth Lbx/Tlx paralagon.

Lbx loci in Xenopus tropicalis

In the frog, both Lbx1 and the Kazald1, Tlx1, Btrc, Poll, Dpcd, Fbxw4, Fgf8, Nmp3, Mgea5 and Kcnip2 genes typical for the amniote Lbx1 locus were found on scaffold 238 (Fig. 3 and Additional file 1). As in the chicken, the Slc2a15 gene was located between Btrc and Poll, suggesting that the solute carrier gene was present in the original Lbx1 locus and was lost from this location in the lineage leading to mammals.

A Tlx2 gene was found on the scaffold 2223, but this scaffold does not contain any further genes associated with Lbx/Tlx paralagons (Fig. 3 and Additional files). Similarly, an isolated Pcgf1 gene was found on scaffold 47. Searches for Loxl3 and Aup genes were unsuccessful. Thus, the existence of a Lbx2/Tlx2 locus could not be determined. However, linked Tlx3, Gabrp, Kcnip1, Foxi, Dock2 and Ccdc99 genes were found on scaffold 313, suggesting that a Lbx3/Tlx3 locus exists in frogs (Fig. 3).

As in chicken, we did not find a Xenopus tropicalis ortholog of Fgf17, but we detected Npm2 and Dok2 on scaffold 34, linked to each other and arranged in the same order as the corresponding genes surrounding human and chicken Npm2. Notably, as in amniotes, these genes are also linked to Nkx6.3 (Additional file 1). Moreover, scaffold 30 contains linked Loxl2, Nkx3.1, Nkx2.6, Prom2 and Kcnip3 genes, which in amniotes, with the exception of Prom2-Kcnip3 that have translocated to a different chromosome in placental mammals, are linked to Fgf17, Npm2, Dok2 and Nkx6.3 (Additional file 1). Taken together, this suggests that all of these genes belong to the same Nkx3.1, 2.6 and 6.3 containing cluster.

Lbxloci in teleost fish

For teleosts, we expected to find chromosomal arrangements corresponding to that of tetrapods, if, in line with our analysis of Lbx proteins, only two Lbx bearing loci were present prior to the genome duplication in the ray-finned fish lineage. Alternatively, if in teleosts Lbx3 and Lbx4 genes were maintained, they should be embedded in distinct loci, with Lbx3 next to Tlx3, Kcnip1, Npm1, Fgf18 and Btrc2 and/or Lbx4 near to Fgf17 and Npm2.

We found for the two novel Lbx1-type teleost genes that the organisation of their gene loci fell into two classes. The genes on zebrafish chromosome 13, Tetraodon scaffolds 8483 and 13770, fugu scaffold 52 and stickleback group VI are surrounded by Tlx1 (sequence incomplete for Tetraodon), Slc2a15, Fbxw4 and Fgf8, thus bearing the hallmarks of the tetrapod Lbx1/Tlx1 locus (Fig. 3 and additional files). The same arrangement of genes was found on medaka chromosome 15, with a sequence gap at the place where the lbx gene is expected to be. Significantly, in all of these teleosts the order of genes is identical to that of the equivalent tetrapod genes, with the exception of an inversion between the Tlx1 and Fgf8 region (Figure 3). The Lbx genes on zebrafish chromosome 1, Tetraodon chromosome 18 (sequence incomplete), fugu scaffold 62, stickleback group IX and medaka chromosome 1 are linked to a second Slc2a15 gene, and to Poll, Dpcd and a second Fgf8-type gene (there is a sequence gap at the position of the Fgf8 gene in Tetraodon), thus also bearing hallmarks of the tetrapod Lbx1/Tlx1 locus (Fig. 3 and additional files). Both stickleback and medaka loci are accompanied by Kcnip2 and Mgea5 genes; for stickleback group VI and medaka chromosome 15, these genes are also associated with Npm3 and Slit1, while linked Npm3-Mgea5 genes were found on zebrafish chromosome 13. Moreover, all of the teleost Lbx1-type loci are associated with gene groups found in the wider environment of Lbx1 loci in amniotes (Additional file 1). Taken together, these findings support the idea that all of these fish have two Lbx1/Tlx1 paralogons, although in many cases there has been reciprocal gene loss following the teleost-specific whole genome duplication

For the third of the teleost Lbx genes, namely the gene currently known as zebrafish Lbx1 on chromosome 14 and the Lbx genes on Tetraodon chromosome 20, fugu scaffold 70, stickleback group IV and medaka scaffold 1066, we found an environment reminiscent of the mammalian Lbx2 locus, with the Lbx genes being separated from a Tlx gene by Pcgf1 (Fig. 3). The exception is the medaka scaffold 1066, which is a short fragment that only contains the Lbx and Pcgf genes. Different from that of mammals, an Fgf24-Npm4 gene set was found between the Lbx and Tlx genes. In the wider environment of the Lbx-Pcgf1-Fgf24-Npm4-Tlx gene set, we found two types of arrangement (Additional file 1). On zebrafish chromosome 14, the genes are associated with Aup1 and Loxl3, reminiscent of the mammalian Lbx2/Tlx2 paralagon. The genes on fugu scaffold 70, Tetraodon chromosome 20 and stickleback group IV, are associated with Nanos1, Limch1, Phox2b, Tmem33, Bbs7, Anxa5, Fgfbp, Prom1, Tapt1, Ldb2 (Lbx1 side) and Adad1, Spata5, Ankrd50, Leprot1, Srp72, Arl9, Hop, Sec24B (Tlx side); the ultracontigs 115 and 117 and chromosome 10 of medaka harbour the same genes in the same order. Notably, the genes surrounding the Lbx-Pcgf-Fgf-Npm-Tlx group in fugu, Tetraodon, stickleback and medaka are also found on zebrafish chromsome 14, while Aup1 is found on stickleback group IV and medaka chromosome 10 (Additional file 1), i.e. all of these genes were located in the wider environment of the Lbx-Pcgf-Fgf-Npm-Tlx locus. Taken together, our data suggest that, despite substantial gene rearrangements, these chromosomal regions in teleosts are Lbx2/Tlx2 paralogons. Interestingly, the genes closely associated with fugu, Tetraodon, stickleback and medaka Lbx2, including the Fgfbp-Prom1-Tapt1-Ldb2-Anxa5 genes, are linked with the Nkx3.2 locus on human chromosome 4 and chicken chromosome 4, consistent with our proposal that the mammalian Lbx2 genes were originally part of the Nkx3.2 cluster (additional file 1).

Searching for remnants of the second teleost Lbx2 paralagon, we found Loxl3, a further Nanos1 gene and Ttc31 on Tetraodon chromosome 10, fugu scaffold 338, stickleback group XV and medaka chromosome 22. Dok1-NP620159.2-Sema4f genes were found on Tetraodon scaffold 7074, fugu scaffold 186, stickleback group VII and medaka chromosome 18; in stickleback and medaka these genes were also linked to Kcnip4-Gba3-Gpr125, which in tetrapods co-localise with Nkx3.2 (Additional file 1; the scaffolds were too short to determine whether this linkage also exists for fugu and Tetraodon). Finally, at a distance from the second Lbx1 locus on zebrafish chromosome 1, Tetraodon chromosome 18, fugu scaffold 17, stickleback group IX and medaka chromosome 1, we found Slit2 and a second group of Fgfbp-Prom1-Tapt1-Anxa5 genes linked to Fbxw7, which in humans are all associated with the LBX2 locus. Thus, it seems that the second teleost Lbx2 paralagon has dispersed, with parts having translocated to one of the Lbx1 carrying chromosomes.

For Tlx3 genes, two types of arrangements were identified (Additional file 1). On zebrafish chromosome 14, fugu scaffold 160, Tetraodon chromosome 1, stickleback group IV and medaka chromosome 10, i.e. inserted into the Lbx2 containing chromosome, Tlx3 is on one side linked to Kcnip1, and on the other linked to the Hrh2 gene encoding a Histamine receptor, Dock2 and, slightly more distant, Fgf18 and Fbxw11. On zebrafish chromosome 10, fugu scaffold 6, Tetraodon chromosome 7, stickleback group VII and medaka chromosome 14, Hrh2 is linked with Kncip1, Npm1 and in the case of zebrafish, Tlx3b, Fgf18 and Fbxw11, suggesting that remnants of the two Tlx3 loci created by the teleost-specific genome duplication still exist.

Finally, searching for additional Btrc, Prom, Loxl, Slit, Dok, Kcnip, and Fgf-Npm genes as indicators of other possible Lbx/Tlx paralogons, we identified linked Npm2-Dok2-Fgf17 genes on zebrafish chromosome 8, linked Fgf17-Loxl2-Kcnip3 genes on stickleback group XIII, and linked Kcnip3-Loxl2-Dok2 genes on Tetraodon chromosome 12 and medaka chromosome 9. A second set of linked Kcnip3-Loxl2-Dok2 genes was identified on zebrafish chromosome 10 and a second set of Loxl2 and Kcnip3 genes in a conserved environment but split between two chromosomes were also identified for the other four fish species. Notably, additional genes were also identified that co-localise with Loxl2, Dok2, Kcnip3, Fgf17 and Npm2 genes both in teleosts and tetrapods, including orthologs of Nkx2.6 (Additional file 1 and data not shown), supporting the idea that all these genes once belonged to the same locus, which in tetrapods still encompasses Nkx 2.6, 3.1 and 6.3.

Phylogenetic relationship of signature genes for Lbx/Tlxparalogons

Characterising Lbx/Tlx loci in tetrapods, we found evidence for three distinct paralogons, with the possibility of Fgf17-Npm2 representing the remnant of the fourth. In teleosts, the arrangement of Lbx1/Tlx1 and Tlx3 genes closely follows the pattern observed in tetrapods. However, the putative teleost Lbx2/Tlx2 paralogon (genes currently named Lbx1 and Tlx3a in zebrafish) includes additional Fgf-Npm genes. Moreover, all of the teleosts except zebrafish show a somewhat divergent organisation of genes in the chromosomal regions surrounding the Lbx2/Tlx2 loci. Furthermore, the duplicate Lbx2 paralogon and the two Fgf17-Npm2 paralogons are poorly preserved in teleosts. Therefore, to further confirm the evolutionary relationship of the Lbx loci and our assignment of genes to specific paralogons, we carried out a comprehensive phylogenetic analysis of protein sequences encoded by the genes in the various Lbx/Tlx regions. For this, we BLAST-searched sequence databases for related sequences and built phylogenetic trees which included various invertebrate outgroups (Additional file 2).

Phylogenetic relationship of genes co-localising with several Lbxparalogons

Btrc/Fbxw11, Mgea, Kazald, Ldb and Prom genes occurred at two, Tlx, Loxl, Slit and Dok genes at three and Kcnip, and the linked Fgf-Npm genes at four putative Lbx loci in tetrapods. If our assignment of Lbx/Tlx paralogons is correct, then the genes that we have assigned to particular paralogons should group together. In addition, if the fundamental lay-out of Lbx/Tlx paralogons was established in vertebrates before the divergence of lobe-finned and ray-finned fish and the additional genome duplication in the ray-finned fish lineage, then the teleost protein sequences should group with the tetrapod proteins. If, however, distinct Lbx/Tlx loci were maintained in the lineage leading to lobe-finned fish/tetrapods and ray-finned fish/teleosts, then our phylogenetic analysis should reveal additional groups of genes.

With the exception of Dok2 sequences, which seem to have become highly diverged, all of our analyses supported our assignment of the different Lbx/Tlx paralogons (discussed in detail in Additional file 2). Notably, our analyses of Ldb and Prom1 genes also support our model that the tetrapod Lbx2 loci was originally located in the Nkx3.2 containing cluster: the Ldb2 sequences, which are associated with Lbx2 in teleosts and with the now Lbx-less locus carrying Nkx3.2 in tetrapods group together, as do the Prom1 genes which are linked to Ldb2-Tapt-Anxa5 genes and hence, to the current plus the dispersed Lbx2 and Nkx3.2 loci (Fig 3). In addition, our analyses of Prom2, Tlx, Kcnip, Fgf and Npn genes shows that orthologues associated with the Lbx1 and Lbx4 paralogons are more closely related to each other than to orthologues associated with the Lbx2 and Lbx3 paralogons and vice versa. This is most informative for the genes where four paralogues are still linked to potential Lbx loci in extant vertebrates (Fgf, Npm and Kcnip genes). In these cases, we found that Kcnip1 and Kcnip4 genes are more closely related to each other than to Kcnip2 and 3. Similarly, Fgf8 sequences are closely related to Fgf17 sequences, and Fgf24 sequences are closely related to Fgf18. Finally, the Npm3-Npm2 and Npm4-Npm1 sequences are more closely related to each other, respectively (Additional file 2). Taken together, this suggests that the Lbx1/4 paralogons and the Lbx2/3 paralagons arose from different ancestral Lbx loci generated during the first vertebrate genome duplication.

Discussion

Ladybird/Lbx genes are crucial regulators of metazoan neural and muscle cell specification [6–9]. Yet before this study, it was difficult to evaluate the basic role of Lbx genes in vertebrate development and evolution, as it was unclear exactly how many Lbx genes exist in different vertebrates and how these genes are phylogenetically related to each other. The 2R hypothesis predicts that early in the vertebrate lineage, four ohnologs were generated for each gene in the genome; for teleosts, descendants of ray-finned fish, a further genome duplication should have produced eight gene copies [3, 20–23, 26, 30–38]. However four ohnologs are seldom found in vertebrate genomes, suggesting that gene loss has played an important part in genome evolution. In recent years, two Lbx genes were identified in amniotes, one in frogs and one in the teleost Danio rerio [1, 2, 9, 14, 15, 18, 19]. One of the amniote Lbx genes and the Lbx genes identified in frog and zebrafish had been reported to be Lbx1 genes, while the second of the amniote Lbx genes had been suggested to represent distinct Lbx2 (mammals) and Lbx3 genes (birds) with rather divergent expression and function [18, 19]. This suggested that Lbx1, 2 and 3 genes were retained in amniotes up to the split of mammalian and avian lineages, while despite their additional genome duplication ray-finned fish seemed to have experienced a near-complete extinction of Lbx genes. However, previous Lbx gene assignments were sometimes based on limited sequence comparisons, and neither a comprehensive phylogenetic analysis nor a comparative genomic analysis of vertebrate Lbx genes had been carried out. Therefore, it remained unclear whether more Lbx genes had yet to be found and whether these genes were survivors of Lbx1, 2, 3 or 4 genes.

In this study, we searched vertebrate sequence databases for Lbx genes and determined their phylogenetic relationships. Moreover, we investigated the organisation of Lbx gene loci, identified signature genes linked to these loci and established the phylogenetic relationships of these genes. Our study confirms the existence of two Lbx genes in amniotes, while only one Lbx gene was found, thus far, in Xenopus tropicalis. However, we were able to detect novel Lbx genes in teleosts. Yet, we found no species with the predicted set of four (lobe-finned fish lineage) or eight (ray-finned fish lineage) Lbx genes. Thus, in all bony vertebrates, some Lbx genes have been lost. Nevertheless, tracing the signature genes linked to different Lbx loci, we were able to identify remnants of all four Lbx paralogons in tetrapods and all eight Lbx paralogons in teleosts. However, only Lbx1 and Lbx2-type loci retained Lbx genes; no evidence for surviving Lbx3 or Lbx4 genes was found. With cognate tetrapod and fish paralogons displaying a high degree of similarity, this suggests that Lbx3 and 4 genes were lost before the split of the lobe-finned and ray-finned fish lineages. Finally, our phylogenetic and synteny analyses revealed that Lbx-associated genes in Lbx1-Lbx4 paralogons and in Lbx2-Lbx3 paralogons, respectively, are more closely related. This suggests that Lbx1 and Lbx4 paralogons originated from one, and Lbx2 and Lbx3 paralogons from the other, parental paralogon generated during the first round of vertebrate genome duplication.

Two novel Lbxgenes were identified in teleosts

Our searches of genomic databases identified two novel Lbx genes in zebrafish, and three Lbx genes in Takifugu rubripes (fugu), Tetraodon nigroviridis and Gasterosteus aculeatus (stickleback). Oryzias latipes (medaka) carries two Lbx genes, with a sequence gap at the expected position of the third. Taken together, this suggests that teleosts share the same set of 3 Lbx genes.

Phylogenetic analyses grouped the two novel zebrafish Lbx proteins, two of the three fugu, Tetraodon and stickleback proteins and one of the medaka proteins with the tetrapod Lbx1 sequences. Conversely, the zebrafish protein currently known as Lbx1, the remaining fugu, Tetraodon, stickleback and medaka sequences and the chicken protein so far called Lbx3 all grouped with the mammalian Lbx2 sequences. The bipartite separation of Lbx sequences was supported by high bootstrap values, suggesting that in all extant Osteichthyes, only Lbx1 and Lbx2 type genes were maintained, with teleosts harbouring duplicates of Lbx1.

Traces of four Lbxloci were identified in tetrapods

Prior to the two rounds of vertebrate genome duplication, the NK clusters broke up and non-NK genes were acquired by these loci ([3] and this study). Our analysis shows that tetrapod Lbx1 is invariantly linked to Tlx1, Kazald1, Btrc, Slc2a15, Poll, Dpcd, Fbxw4, Fgf8, Npm3, Mgea5, Kcnip2, Ldb, Loxl4 and Slit1 with Slc2a15 being lost in mammals. The assignment of Lbx2-type genes was more problematic, due to incomplete sequence information for chicken and frog. For mammals however, Lbx2 was found linked to Tlx2, Pcgf1, Aup1, Loxl3 and Dok1, and linked Loxl and Aup genes were also identified for chicken (distribution of signature genes for Lbx loci shown in Table 1).

Table 1 Distribution of paralogous genes at the four Lbx-Tlx loci.

The linking of Lbx with Tlx genes was not unexpected, given its maintenance in the otherwise fragmented amphioxus nk cluster [3]. Yet tetrapods harbour a third Tlx gene, suggesting that a third, previously Lbx3-containing paralogon still exists [39–41]. Indeed, tetrapod Tlx3 sequences form a phylogenetic group distinct from Tlx1 and Tlx2 sequences, supporting the idea that this gene did not arise from a single gene duplication event. Moreover, Tlx3 loci share the same organisation amongst tetrapods and encompass Btrc2, Fgf18, Npm1, Kcnip1, and Slit3, which according to our phylogenetic analysis are paralogues of the genes found at the Lbx1 site. Thus, while Lbx3 itself was lost from the Tlx3 locus, a number of genes that must have been acquired by the Nk cluster prior to the two rounds of vertebrate genome duplication are still present.

Using the previously identified signature genes linked to the Lbx/Tlx loci as query sequences, we also identified remnants of the fourth Lbx paralogon. Interestingly, both the Lbx1/Tlx1 and the Tlx3 locus contain closely linked Fgf-Npm genes, and an additional pair of tightly linked Fgf-Npm genes, namely Fgf17 and Npm2, was found in mammals, linked to Dok2, Loxl2, Nkx3.1 and 2.6. Linked Loxl2-Dok2-Npm2 sequences were also found in the chicken genome, and in the frog, linked Dok2-Npm2 genes and Loxl2-Nkx3.1-Nkx2.6 genes were found on two, possibly neighbouring scaffolds. In some tetrapods the Loxl2-Nkx3.1-Nkx2.6 genes were also linked to Prom2 and Kcnip3. This suggests that Prom2-Kcnip3 initially belonged to the fourth Lbx paralogon that contains Fgf17-Npm2 as well as Dok2-Loxl2-Nkx3.1-Nkx2.6 genes, while the placement of Prom2-Kcnip3 on the same chromosome but at a distance to Lbx2 in humans, cattle and dog (but not mouse) is probably a result of a more recent transposition event. In summary, presence of a number of signature genes for Lbx loci linked to Nkx2.6 and Nkx3.1 suggests that this region is the ancestral home of the lost Lbx4-Tlx4 genes.

Duplicates of the four tetrapod-type Lbx loci were identified in teleosts, with two Lbx1 genes and one Lbx2gene still present

In teleosts, the two novel, putative Lbx1 genes were found in two types of genomic settings, both of which contained signature genes for the tetrapod Lbx1 locus. Genes that occurred at only one of the novel teleost Lbx sites formed monophyletic groups with their tetrapod counterparts. Importantly, Slc2a15 and Fgf8 genes, which were found at both of the teleost loci as well as the tetrapod Lbx1 sites, also formed single groups, indicating that the two novel Lbx loci in teleosts arose from a common Lbx1-containing ancestor. Consequently, tetrapod Lbx1 genes and the two novel teleost Lbx genes are orthologs.

Similar to the Lbx1 paralogons, the relationship of the now Lbx-less Tlx3 loci could readily be established. Teleosts harbour one locus containing Slit3, Kcnip1, Tlx3, Fgf18 and Btrc2 genes in the same order as found at the tetrapod Tlx3 site, with the exception of Tetraodon whose Slit3 gene intercalated between Kcnip1 and Fgf18. Notably, this Tlx3 locus is found on the same chromosome, but with different integration sites, as the gene we propose to rename Lbx2, suggesting extensive transposition between Lbx/Tlx loci in teleosts. The second Tlx3 locus contains Kcnip1-Npm1 and in zebrafish also Tlx3b, plus a second copy of Fgf18 and Btrc2. Further shared genes were found in the environment of the tetrapod and teleost Tlx3 loci; genes at these sites, including the Tlx genes themselves, grouped together in our phylogenetic analyses. This suggests that teleost Tlx3 and Tlx3b are orthologs of the tetrapod Tlx3 genes. The high degree of locus conservation also suggests that the basic lay out of this Tlx3 paralogon, including the elimination of Lbx3, was established prior to the teleost-specific genome duplication.

In the zebrafish, the gene currently known as lbx1 but placed with mammalian Lbx2 in our phylogenetic analyses was found in a genomic environment bearing the hallmarks of the mammalian Lbx2 locus, being linked with Pcgf1, a Tlx gene currently named Tlx3a, Aup1 and Loxl3. These genes formed monophyletic groups with the cognate genes at the mammalian Lbx2 locus, with teleost Tlx3a grouping with mammalian Tlx2. This suggests that this locus is indeed a Lbx2 paralogon. In fugu, Tetraodon, stickleback and medaka, the third Lbx gene was also linked to Pcgf1 and a Tlx2-type gene, although Aup was located at a distance or in case of Tetraodon, on a different chromosome. The latter seems to be a result of a secondary rearrangement of the locus, as aup is linked to lbx in amphioxus and hence, was part of lbx loci before the split of cephalochordate-vertebrate lineages (aup and lbx are both found on Scaffold 294 of the Branchiostoma floridae v1.0 genome at the JGI. See Availability and requirements section for URL). Nevertheless, all of the teleost Lbx2 loci encompassed a Fgf24-Npm4 set between Pcgf1 and Tlx2. Moreover, genes associated with Prom1 and directly linked to fugu, Tetraodon, stickleback and medaka Lbx2 were found in the same order in the wider environment of the zebrafish Lbx-Pcgf1-Tlx set. Phylogenetic analyses indicated that these genes are orthologs, suggesting that the teleost Lbx2 loci are variations on the same theme.

In fugu, Tetraodon, stickleback and medaka, the Lbx2 gene was directly adjacent to Nanos1, which is not linked to the mammalian Lbx2 gene. In mammals on the other side, the Lbx2-Pcgf1-Tlx2 set was flanked by Ttc31 and Loxl3-Dok1-Np620159.2-Sema4f. Yet in these four teleosts, a second Nanos1 gene was identified, linked to Loxl3, Dok1, Np620159.2, Sema4f and Ttc31. Moreover, a duplicate of the Prom1-linked gene set was found at the same site. A similar arrangement of genes was also detected in the zebrafish, distributed however between two chromosomes and with individual genes missing from the set. Phylogenetic analyses grouped the genes with the cognate genes at the mammalian and teleost Lbx2-bearing sites, suggesting that this location is the second, now Lbx2/Tlx2-less Lbx2 paralogon in teleosts. As will become relevant below, this locus encompassed Slit2, Kcnip4 and Fbxw7, associated with the Lbx-free Nkx3.2 locus in tetrapods.

Establishing whether teleosts carry duplicates of the possible fourth Lbx paralogon was more problematic as unfortunately, some of the genes suggestive of this paralogon (namely Fgf17, Npm2, Dok2, Loxl2, Prom2, Kcnip3) reside on rather small scaffolds and hence, linkage could not always be established. However, all five teleosts harboured two sets of Loxl2-Kcnip3 genes. One of the sets was associated with Dok2 and in stickleback, also with Fgf17. Moreover, Npm2-Dok2-Fgf17 were found together on zebrafish chromosome 8. Phylogenetic analyses grouped Fgf17, Npm2, Loxl2, Kcnip3 genes with their namesakes from tetrapod genomes. This suggests that, although less well preserved, two copies of the putative fourth Lbx paralogon still exist in extant teleosts.

The mammalian Lbx2 locus has translocated from the NK cluster containing Nkx3.2

Previous studies of human Nk genes showed that remnants of two Nk clusters have been preserved, with chromosome 10 carrying LBX1 and TLX1 linked to NKX2.3 and NKX1.2, and chromosome 5 carrying TLX3 linked to NKX2.5 [3]. More partial remnants of two further Nk clusters have also been identified, one on chromosome 8 with NKX2.6 and NKX3.1 and one on chromosome 4 with NKX3.2 and NKX1.1. However, no LBX or TLX genes are linked to these regions.

A previous study, based primarily on the human genome, proposed that the Nkx2.6, 3.1 and 6.3 paralogon (located on human chromosome 8) might be the ancestral location of Lbx2 and Tlx2 (now located on human chromosome 2) [3]. By a process of elimination, this would further suggest that Lbx4 and Tlx4 were lost from the NKX3.2 paralogon (currently located on human chromosome 4). Consistent with this hypothesis, paralogs of a few genes (Kcnip, Prom, Add, Adra2) are represented at both the Lbx2 and the Nk3.2 loci in mammals, suggesting that these two loci have derived from separate Lbx/Tlx paralogons. However, phylogenetic analysis of these gene families shows that the mammalian genes linked to the Lbx2 loci group with frog, chicken and/or teleost genes associated with Fgf17 and Npm2 loci (see phylogenetic analysis and discussion in Additional file 2). This suggests that these genes may have translocated to the mammalian Lbx2 loci from the putative 4^th Lbx/Tlx paralogon (e.g. the genes now on human chromosome 2 may have originally been linked to the Tlx/Lbx paralogon now on human chromosome 8).

Consistent with this second interpretation our data suggests that the ancestral location of the LBX2/TLX2 paralogon now located on human chromosome 2 was the NKX3.2 paralogon on human chromosome 4 (as shown in Fig. 3). The evidence for this is several fold. Firstly, we have identified four distinct Fgf and Npm genes, with Fgf8-Npm3 demarcating Lbx1/Tlx1 loci, Fgf18-Npm1 the Tlx3 loci, Fgf24-Npm4 the preserved teleost Lbx2/Tlx2 locus and Fgf17-Npm2 genes associated with tetrapod and teleost Nkx2.6-3.1-6.3 genes. Secondly, paralogous Loxl and Dok genes are present at both the Lbx2 locus and the Nkx2.6-3.1-6.3 locus, suggesting that these two loci have evolved from different paralogons. Thirdly, amniote orthologs of genes associated with the two teleost Lbx2 loci such as Fbxw7, Ldb2, Prom1, Slit1 and Kcnip4 co-localise with Nkx3.2, and these amniote and teleost genes fall into the same phylogenetic groups. Fourthly, the Lbx2 locus is still associated with Nkx3.2 genes in teleosts, and possibly, also in the chicken (the signature genes linked to the Lbx2 locus are assigned to chromosome 4, but their position is not determined). All together, this strongly suggests that the mammalian Lbx2-Tlx2 locus was once located in the Nk cluster containing Nkx3.2 and that Lbx4 and Tlx4 were lost from the Nkx2.6-3.1-6.3 paralogon that contains fgf17 and npm2.

Lbx4-Tlx4were lost prior to the third genome duplication in ray-finned fish

If the assignment of Lbx2-Tlx2 to the Nkx3.2 carrying Nk cluster is correct then, as discussed above, the Nk cluster containing Nkx2.6, 3.1 and 6.3 (and fgf17 and npm2) is the former location of the Lbx4-Tlx4 paralogon. This idea is supported by the presence of a number of signature genes for Lbx loci at this site. Moreover, genes at this locus do not group with paralogues accompanying other Lbx loci; most notably, the Fgf-Npm and Kcnip genes located here constitute distinct phylogenetic groups. Taken together, this suggests that different to Lbx2-Tlx2 genes, Lbx4-Tlx4 genes did not translocate to another chromosome. Rather, they were lost from this fourth NK cluster. Significantly, both teleosts and tetrapods retained a similar set of genes from this locus. This indicates that the basic lay-out of the paralogon, including the elimination of its Lbx and Tlx genes, was probably established in an ancestor of the Osteichthyes (i.e. prior to the split of the lobe-finned and ray-finned fish lineages).

Lbx loci in extant vertebrates arose from Lbx1/4 and Lbx2/3precursors

Our study shows that of the genes associated with Lbx-Tlx loci, Fgf, Npm and Kcnip genes still exist in four copies, inferring that indeed, the original chordate locus was duplicated twice in the lineage leading to vertebrates. Phylogenetic analyses indicated that Fgf8 genes found in the Lbx1/Tlx1 paralogon and Fgf17, found in the Lbx4/Tlx4 paralogon, are more closely related than Fgf24 found in the intact teleost Lbx2/Tlx2 paralogon and Fgf18 found in the Lbx3/Tlx3 paralogon. Similarly, Npm4 (teleost Lbx2/Tlx2 paralogon) and Npm1 (Lbx3/Tlx3 paralogon) are closely related to each other, distinguished from Npm1 (Tlx3 paralogon) and Npm4 (teleost Lbx2 paralogon), A similar grouping was found for Kcnip genes, with Kcnip1 (Tlx3 paralogon) and Kcnip4 (teleost Lbx2 and tetrapod Nkx3.2 loci) being the most closely related. This pair-wise grouping is supported by high bootstrap values and suggests that during the second vertebrate genome duplication, Lbx1 and Lbx4 paralogons arose from one of the Lbx-Tlx loci generated by the initial duplication event and Lbx2 and Lbx3 paralogons arose from the other duplicated locus. Consistent with this model, Tlx2 and Tlx3 genes are rather similar and are easily distinguished from the Tlx1 genes associated with Lbx1.

Basic roles of Lbx1 genes and neofunctionalisation of mammalian Lbx2genes

Our analysis shows that the organisation of orthologous Lbx/Tlx paralogons is very similar in extant bony vertebrates, suggesting that the main compositions of the paralogons were established before the divergence of lobe-finned and ray-finned fish. This infers that Osteichthyes had only two types of Lbx genes. Expression analyses and functional studies on Lbx1 type genes suggest that they all play a role in dorsal spinal cord and muscle development [6–16]. Interestingly, the zebrafish and chicken Lbx2 genes are still expressed in muscle precursors, and zebrafish lbx2 is also expressed in the spinal cord [14, 18]. In contrast, mouse Lbx2 is not expressed in these regions, rather labelling the urogenital system, eye and brain [19]. Amniote Lbx2 proteins also show the most divergent sequences. This suggests that amniote (or potentially sarcopterygian) Lbx2 genes have evolved at a faster rate than their anamniote (or non-sarcopterygian) orthologs, and undergone neofunctionalisation. Other Lbx2 genes, however, may have retained aspects of ancestral Lbx expression and function, which seems to be tied to the formation of specific neural and muscle cell types.

Conclusion

We have identified remnants of all four Lbx/Tlx paralogons in extant bony vertebrates. Phylogenetic analyses of Lbx, Tlx and non-NK genes at these loci revealed that the first round of whole genome duplication in vertebrates created the ancestor of the Lbx1/Tlx1 and Lbx4/Tlx4 paralogons and the ancestor of the Lbx2/Tlx2 and Lbx3/Tlx3 paralogons (Fig. 4). After the second genome duplication, Lbx and Tlx genes were lost, such that before the split of the ray-finned fish/teleost and lobe-finned fish/tetrapod lineages only Lbx1/Tlx1, Lbx2/Tlx2 and Tlx3 genes were maintained. In the ray-finned fish lineage, genome duplication and subsequent gene loss left teleosts with two Lbx1, one Lbx2 and two Tlx3 loci. Since the amniote Lbx2 genes show divergent amino acid sequences and expression patterns, we propose that these Lbx2 genes have been evolving at a faster rate and were subject to neofunctionalisation. Lbx1 genes on the other hand may have retained more features of the original chordate lbx gene.

Figure 4

A model of the evolution of the vertebrate Lbx/Tlx loci. Lbx loci in extant vertebrates arose from a region containing an Lbx, Tlx, Fgf8/17/24/18 and an Npm gene. After one round of whole genome duplication (1R WGD) Lbx1/4 and Lbx2/3 precursors were produced linked to Fgf8/17 – Npm2/3 and Fgf24/18 – Npm4/1 precursors, respectively. During the second round of whole genome duplication (2R WGD), four loci where produced. By the time of the divergence of the lobed-fined and ray-finned fish, the Lbx4, Tlx4 and Lbx3 genes (shown in grey) had been lost.

Methods

Regions surrounding the human LBX/TLX cluster loci were searched using NCBI Map Viewer build 36.2. To identify further paralagous genes, BLAST searches with putative protein sequences were conducted against the human genome, and putative positive targets were further characterised by molecular phylogenetics to resolve orthologous and paralagous relationships. Each of the genes from the putative human paralogons was cross-referenced by BLAST against the following NCBI genome assemblies; Mus musculus (build 37.1), Gallus gallus (build 2.1) and Danio rerio (Zv6) on NCBI map viewer. The Xenopus tropicalis (v4.1) and fugu rubripes (v4.0) genomes were searched at the Joint Genome Institute genome portal, and the Tetraodon nigroviridis (v8), Oryzias latipes (MEDAKA1) and Gasterosteus aculeatus (BROAD S1) genomes were searched via the Ensembl server. Putative target sequences were further analysed by molecular phylogenetics, to establish orthologous and paralogous relationships and to reaffirm our original classification of human sequences. For molecular phylogenetic analyses, protein sequences were first aligned, (with invertebrate outgroup sequences included where possible) using ClustalX and edited by eye [42]. Phylogenetic analyses were then carried out using maximum likelihood implemented by ClustalX [42], and by PHYML [43, 44].

Availability and requirements

JGI: http://genome.jgi-psf.org/Brafl1/Brafl1.home.html