Characterization of Hox genes in the bichir,Polypterus palmas

It has been suggested that the increase in the number of Hox genes may have been one of the key events in vertebrate evolution. Invertebrates have one Hox cluster, while mammals have four. Interestingly, the number of Hox gene clusters is greater in the teleost fishes, zebrafish and medaka, than in mouse and human. The greater number of Hox clusters in the teleosts suggests that Hox gene duplication events have occurred during the radiation of ray-finned fishes. The question is when the Hox gene duplication event(s) that lead to seven Hox clusters in the teleosts actually occurred.We have addressed this question by studying the Hox genes in the bichir, Polypterus palmas. A preliminary PCR-estimation of the number of Hox genes suggests that Polypterus has five different Hox9 cognate group genes, which may be an indication of more than four Hox clusters in the bichir.     

Modulating Hox gene functions during animal body patterning

With their power to shape animal morphology, few genes have captured the imagination of biologists as the evolutionarily conserved members of the Hox clusters have done. Recent research has provided new insight into how Hox proteins cause morphological diversity at the organismal and evolutionary levels. Furthermore, an expanding collection of sequences that are directly regulated by Hox proteins provides information on the specificity of target-gene activation, which might allow the successful prediction of novel Hox-response genes. Finally, the recent discovery of microRNA genes within the Hox gene clusters indicates yet another level of control by Hox genes in development and evolution.     

Genome Duplications and Accelerated Evolution of Hox Genes and Cluster Architecture in Teleost Fishes

The early origin of four vertebrate Hox gene clusters duringthe evolution of gnathostomes was likely caused by two consecutiveduplications of the entire genome and the subsequent loss ofindividual genes. The presumed conserved and important rolesof these genes in tetrapods during development led to the generalassumption that Hox cluster architecture had remained unchangedsince the last common ancestor of all jawed vertebrates. Butrecent data from teleost fishes reveals that this is not thecase. Here, we present an analysis of the evolution of vertebrateHox genes and clusters, with emphasis on the differences betweenthe Hox A clusters of fish (actinopterygian) and tetrapod (sarcopterygian)lineages. In contrast to the general conservation of genomicarchitecture and gene sequence observed in sarcopterygians,the evolutionary history of actinopterygian Hox clusters likelyincludes an additional (third) genome duplication that initiallyincreased the number of clusters from four to eight. We document,for the first time, higher rates of gene loss and gene sequenceevolution in the Hox genes of fishes compared to those of landvertebrates. These two observations might suggest that two differentmolecular evolutionary strategies exist in the two major vertebratelineages. Preliminary data from the African cichlid fish Oreochromisniloticus compared to those of the pufferfish and zebrafishreveal important differences in Hox cluster architecture amongfishes and, together with genetic mapping data from Medaka,indicate that the third genome duplication was not zebrafish-specific,but probably occurred early in the history of fishes. Each descendingfish lineage that has been characterized so far, distinctivelymodified its Hox cluster architecture through independent secondarylosses. This variation is related to the large body plan differencesobserved among fishes, such as the loss of entire sets of appendagesand ribs in some lineages.     

Hox gene duplication in fish

The study of Hox gene clusters continues to serve as a paradigm for those interested in vertebrate genome evolution. Recent exciting discoveries about Hox gene composition in fishes challenges conventional views about vertebrate Hox gene evolution, and has initiated lively debates concerning the evolutionary events making the divergence of the major vertebrate lineages. Comparative analyses indicate that Hox cluster duplications occurred in early vertebrate evolution, and again within the order Cypriniformes of teleost fish. Loss of Hox genes was more widespread than duplication during fish evolution.     

Hox Gene Loss during Dynamic Evolution of the Nematode Cluster

HOX GENES ARE IMPORTANT: their central role in anterior-posterior patterning provides a framework for molecular comparison of animal body plan evolution. The nematode Caenorhabditis elegans stands out as having a greatly reduced Hox gene complement. To address this, orthologs of C. elegans Hox genes were identified in six species from across the Nematoda, and they show that rapid homeodomain sequence evolution is a general feature of nematode Hox genes. Some nematodes express additional Hox genes belonging to orthology groups that are absent from C. elegans but present in other bilaterian animals. Analysis of the genomic environment of a newly identified Brugia malayi Hox6-8 ortholog (Bm-ant-1) revealed that it lay downstream of the Bm-egl-5 Hox gene and that their homeodomain exons are alternately cis spliced to the same 5' exon. This organization may represent an intermediate state in Hox gene loss via redundancy. The Hox clusters of nematodes are the product of a dynamic mix of gene loss and rapid sequence evolution, with the most derived state observed in the model C. elegans.     

Chromosomal mapping of ANTP class homeobox genes in amphioxus: piecing together ancestral genomes

Homeobox genes encode DNA-binding proteins, many of which are implicated in the control of embryonic development. Evolutionarily, most homeobox genes fall into two related clades: the ANTP and the PRD classes. Some genes in ANTP class, notably Hox, ParaHox, and NK genes, have an intriguing arrangement into physical clusters. To investigate the evolutionary history of these gene clusters, we examined homeobox gene chromosomal locations in the cephalochordate amphioxus, Branchiostoma floridae. We deduce that 22 amphioxus ANTP class homeobox genes localize in just three chromosomes. One contains the Hox cluster plus AmphiEn, AmphiMnx, and AmphiDll. The ParaHox cluster resides in another chromosome, whereas a third chromosome contains the NK type homeobox genes, including AmphiMsx and AmphiTlx. By comparative analysis we infer that clustering of ANTP class homeobox genes evolved just once, during a series of extensive cis-duplication events of genes early in animal evolution. A trans-duplication event occurred later to yield the Hox and ParaHox gene clusters on different chromosomes. The results obtained have implications for understanding the origin of homeobox gene clustering, the diversification of the ANTP class of homeobox genes, and the evolution of animal genomes.     

Hox gene complexity in medaka fish may Be similar to that in pufferfish rather than zebrafish.

Changes in number and the genomic organization of Hox genes have played an important role in metazoan body-plan evolution. They make cluster(s), and in vertebrates, each cluster contains different number of Hox genes that have been classified into 13 groups. There are 39 Hox genes in four clusters on different chromosomes in the mammalian genome. In the fish, while 31 Hox genes in four clusters have been identified in pufferfish Fugu rubripes, 47 Hox genes in seven clusters exist in the zebrafish Danio rerio. To estimate the evolutionary origin of Hox organization in ray-finned fishes, we searched for Hox genes in the medaka fish Oryzias latipes, with a taxon thought to be widely separated from those of pufferfish and zebrafish. We synthesized various mixed oligonucleotides that can work as group-specific primers for PCR, then cloned and sequenced amplified fragments. Numbers of Hox genes identified in the present study were 2 for group 1, 2 for group 2, 1 for group 3, 3 for group 4, 6 for groups 5-7, 2 for group 8, 4 for group 9, 3 for group 10, 1 for group 12, and 3 for group 13. The primers specific for group 11 did not function in this study. Thus, at least 27 Hox genes are present in medaka genome, suggesting that the Hox gene complexity of the medaka genome is similar to that of the pufferfish rather than the zebrafish.     

The "fish-specific" Hox cluster duplication is coincident with the origin of teleosts

The Hox gene complement of zebrafish, medaka, and fugu differs from that of other gnathostome vertebrates. These fishes have seven to eight Hox clusters compared to the four Hox clusters described in sarcopterygians and shark. The clusters in different teleost lineages are orthologous, implying that a "fish-specific" Hox cluster duplication has occurred in the stem lineage leading to the most recent common ancestor of zebrafish and fugu. The timing of this event, however, is unknown. To address this question, we sequenced four Hox genes from taxa representing basal actinopterygian and teleost lineages and compared them to known sequences from shark, coelacanth, zebrafish, and other teleosts. The resulting gene genealogies suggest that the fish-specific Hox cluster duplication occurred coincident with the origin of crown group teleosts. In addition, we obtained evidence for an independent Hox cluster duplication in the sturgeon lineage (Acipenseriformes). Finally, results from HoxA11 suggest that duplicated Hox genes have experienced diversifying selection immediately after the duplication event. Taken together, these results support the notion that the duplicated Hox genes of teleosts were causally relevant to adaptive evolution during the initial teleost radiation.     

The Hox Paradox: More complex(es) than imagined

An understanding of the origin of different body plans requires knowledge of how the genes and genetic pathways that control embryonic development have evolved. The Hox genes provide an appealing starting point for such studies because they play a well-understood causal role in the regionalization of the body plan of all bilaterally symmetric animals. Vertebrate evolution has been characterized by gene, and possibly genome, duplication events, which are believed to have provided raw genetic material for selection to act upon. It has recently been established that the Hox gene organization of ray-finned fishes, such as the zebrafish, differs dramatically from that of their lobe-finned relatives, a group that includes humans and all the other widely used vertebrate model systems. This unusual Hox gene organization of zebrafish is the result of a duplication event within the ray-finned fish lineage. Thus, teleosts, such as zebrafish, have more Hox genes arrayed over more clusters (or "complexes") than do tetrapod vertebrates. Here, I review our understanding of Hox cluster architecture in different vertebrates and consider the implications of gene duplication for Hox gene regulation and function and the evolution of different body plans.     

Missing link in the evolution of Hox clusters

Hox cluster has key roles in regulating the patterning of the antero-posterior axis in a metazoan embryo. It consists of the anterior, central and posterior genes; the central genes have been identified only in bilaterians, but not in cnidarians, and are responsible for archiving morphological complexity in bilaterian development. However, their evolutionary history has not been revealed, that is, there has been a "missing link". Here we show the evolutionary history of Hox clusters of 18 bilaterians and 2 cnidarians by using a new method, "motif-based reconstruction", examining the gain/loss processes of evolutionarily conserved sequences, "motifs", outside the homeodomain. We successfully identified the missing link in the evolution of Hox clusters between the cnidarian-bilaterian ancestor and the bilaterians as the ancestor of the central genes, which we call the proto-central gene. Exploring the correspondent gene with the proto-central gene, we found that one of the acoela Hox genes has the same motif repertory as that of the proto-central gene. This interesting finding suggests that the acoela Hox cluster corresponds with the missing link in the evolution of the Hox cluster between the cnidarian-bilaterian ancestor and the bilaterians. Our findings suggested that motif gains/diversifications led to the explosive diversity of the bilaterian body plan.     

Differential evolution of the 13 Atlantic salmon Hox clusters

Hox cluster organization represents a valuable marker to study the effects of recent genome duplication in salmonid fish (25-100 Mya). Using polymerase chain reaction amplification of cDNAs, BAC library screening, and genome walking, we reconstructed 13 Hox clusters in the Atlantic salmon containing 118 Hox genes including 8 pseudogenes. Hox paralogs resulting from the genome duplication preceding the radiation of ray-finned fish have been much better preserved in salmon than in other model teleosts. The last genome duplication in the salmon lineage has been followed by the loss of 1 of the 4 HoxA clusters. Four rounds of genome duplication after the vertebrate ancestor salmon Hox clusters display the main organizational features of vertebrate Hox clusters, with Hox genes exclusively that are densely packed in the same orientation. Recently, duplicated Hox clusters have engaged a process of divergence, with several cases of pseudogenization or asymmetrical evolution of Hox gene duplicates, and a marked erosion of identity in noncoding sequences. Strikingly, the level of divergence attained strongly depends on the Hox cluster pairs rather than on the Hox genes within each cluster. It is particularly high between both HoxBb clusters and both HoxDa clusters, whereas both HoxBa clusters remained virtually identical. Positive selection on the Hox protein-coding sequences could not be detected.     

Evolution of the echinoderm Hox gene cluster

SUMMARY Extant echinoderms are members of an ancient and highly derived deuterostome phylum. The composition and arrangement of their Hox gene clusters are consequently of interest not only from the perspective of evolution of development, but also in terms of metazoan phylogeny and body plan evolution. Over the last decade numerous workers have reported partial Hox gene sequences from a variety of echinoderms. In this paper we used a combined methods approach to analyze phylogenetic relationships between 68 echinoderm Hox homeodomain fragments, from species of five extant classes—two asteroids, one crinoid, one ophiuroid, one holothuroid, and three echinoids. This analysis strengthens Mito and Endo's (2000) proposition that the ancestral echinoderm's Hox gene cluster contained at least eleven genes, including at least four posterior paralogous group genes. However, representatives of all paralogous groups are not known from all echinoderm classes. In particular, these data suggest that echinoids may have lost a posterior group Hox gene subsequent to the divergence of the echinoderm classes. Evolution of the highly derived echinoderm body plan may have been accompanied by class-specific duplication, diversification and loss of Hox genes.     

Hox clusters of the bichir (Actinopterygii, Polypterus senegalus) highlight unique patterns of sequence evolution in gnathostome phylogeny

Teleost fishes have extra Hox gene clusters owing to shared or lineage-specific genome duplication events in rayfinned fish (actinopterygian) phylogeny. Hence, extrapolating between genome function of teleosts and human or even between different fish species is difficult. We have sequenced and analyzed Hox gene clusters of the Senegal bichir (Polypterus senegalus), an extant representative of the most basal actinopterygian lineage. Bichir possesses four Hox gene clusters (A, B, C, D); phylogenetic analysis supports their orthology to the four Hox gene clusters of the gnathostome ancestor. We have generated a comprehensive database of conserved Hox noncoding sequences that include cartilaginous, lobe-finned, and ray-finned fishes (bichir and teleosts). Our analysis identified putative and known Hox cis-regulatory sequences with differing depths of conservation in Gnathostoma. We found that although bichir possesses four Hox gene clusters, its pattern of conservation of noncoding sequences is mosaic between outgroups, such as human, coelacanth, and shark, with four Hox gene clusters and teleosts, such as zebrafish and pufferfish, with seven or eight Hox gene clusters. Notably, bichir Hox gene clusters have been invaded by DNA transposons and this trend is further exemplified in teleosts, suggesting an as yet unrecognized mechanism of genome evolution that may explain Hox cluster plasticity in actinopterygians. Taken together, our results suggest that actinopterygian Hox gene clusters experienced a reduction in selective constraints that surprisingly predates the teleost-specific genome duplication.     

Ciona intestinalis ParaHox genes: evolution of Hox/ParaHox cluster integrity,developmental mode,and temporal colinearity

The Hox gene cluster, and its evolutionary sister the ParaHox gene cluster, pattern the anterior-posterior axis of animals. The spatial and temporal regulation of the genes seems to be intimately linked to the gene order within the clusters. In some animals the tight organisation of the clusters has disintegrated. We note that these animals develop in a derived fashion relative to the norm of their respective lineages. Here we present the genomic organisation of the ParaHox genes of Ciona intestinalis, and note that tight clustering has been lost in evolution. We present a hypothesis that the Hox and ParaHox clusters are constrained as ordered clusters by the mechanisms producing temporal colinearity; when temporal colinearity is no longer needed or used during development, the clusters can fall apart. This disintegration may be mediated by the invasion of transposable elements into the clusters, and subsequent genomic rearrangements.     

Combined-method phylogenetic analysis of Hox and ParaHox genes of the metazoa

The clustered Hox genes show a conserved role in patterning the body axis of bilaterian metazoans. Increasingly, a broader phylogenetic sampling of non-model system organisms is being examined to detect a correlation, if any, between Hox gene evolution, and body plan innovations. To assess how Hox gene expression and function evolve with changing cluster arrangements, we must be able to reliably assign gene orthologies between Hox genes. Recent evidence suggests that a four-gene proto-Hox cluster duplicated to form the precursor of the present cluster and an additional sister-cluster, the ParaHox group. Here, phylogenetic methods are used to determine Hox-gene orthologies and to infer probable clustering events leading to the current bilaterian Hox complement. This analysis supports the ParaHox hypothesis and gives first confirmation that ind (intermediate neuroblasts defective) is an anterior ParaHox ortholog from protostomes. This analysis supports a proto-Hox cluster of four genes in which the central-class member of the ParaHox cluster may have been lost. It is also proposed here that ancestral diploblasts had central-class members of both Hox and ParaHox clusters. Primitive Hox gene ancestors are estimated by phylogenetic methods and found to have no strong affinity to any particular class of extant Hox members.     

Hox, ParaHox, ProtoHox: facts and guesses

The Hox gene cluster has captivated the imagination of evolutionary and developmental biologists worldwide. In this review, the origin of the Hox and ParaHox gene clusters by duplication of a ProtoHox gene cluster, and the changes in their gene numbers in major Metazoan Transitions are reviewed critically. Re-evaluation of existing data and recent findings in Cnidarians, Acoels, and critical stages of vertebrate evolution suggest alternative scenarios for the origin, structure, and changes in Hox gene numbers in relevant events of Metazoan evolution. I discuss opposing views and propose that (i) the ProtoHox cluster had only two genes, and not four as commonly believed: a corollary is that the origin of Bilaterians was coincident with the invention of new Hox and ParaHox gene classes, which may have facilitated such a transition; (ii) the ProtoHox cluster duplication was a cis duplication event, rather than a trans duplication event, as previously suggested, and (iii) the ancestral vertebrate cluster possessed 14 Hox genes, and not the 13 generally assumed. These hypotheses could be verified or refuted in the near future, but they may help critical discussion of the evolution of the Hox/ParaHox family in the metazoan kingdom.     

Hox基因及其进化机制的研究进展

Hox基因是生物体内一类重要的发育调控基因家族.Hox基因高度保守,通常成簇存在,编码一类转录因子,在个体胚胎发育中起着重要的调控作用.近期研究表明,基因复制、基因序列变异及选择压力对Hox基因簇的产生和进化有重要作用,同时调节元件和协同进化对Hox基因的进化也有重要影响.     

Hox cluster organization in the jawless vertebrate Petromyzon marinus

Large-scale gene amplifications may have facilitated the evolution of morphological innovations that accompanied the origin of vertebrates. This hypothesis predicts that the genomes of extant jawless fish, scions of deeply branching vertebrate lineages, should bear a record of these events. Previous work suggests that nonvertebrate chordates have a single Hox cluster, but that gnathostome vertebrates have four or more Hox clusters. Did the duplication events that produced multiple vertebrate Hox clusters occur before or after the divergence of agnathan and gnathostome lineages? Can investigation of lamprey Hox clusters illuminate the origins of the four gnathostome Hox clusters? To approach these questions, we cloned and sequenced 13 Hox cluster genes from cDNA and genomic libraries in the lamprey, Petromyzon marinus. The results suggest that the lamprey has at least four Hox clusters and support the model that gnathostome Hox clusters arose by a two-round-no-cluster-loss mechanism, with tree topology [(AB)(CD)]. A three-round model, however, is not rigorously excluded by the data and, for this model, the tree topologies [(D(C(AB))] and [(C(D(AB))] are most parsimonious. Gene phylogenies suggest that at least one Hox cluster duplication occurred in the lamprey lineage after it diverged from the gnathostome lineage. The results argue against two or more rounds of duplication before the divergence of agnathan and gnathostome vertebrates. If Hox clusters were duplicated in whole-genome duplication events, then these data suggest that, at most, one whole genome duplication occurred before the evolution of vertebrate developmental innovations.