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 Pro: a specialized database for clusters and networks of homeobox genes

It is now clear that the homeobox motif is well conserved across metazoan phyla. It has been established experimentally that a subset of genes containing this motif plays key roles in the orchestration of gene expression during development. Auto- and cross-regulatory functional interactions join homeobox genes into genetic networks. We have developed a specialized database HOX-Pro in order to arrange all available data on structure, function, phylogeny and evolution of Hox genes, Hox clusters and Hox networks. Its primary location is http://www.iephb.nw.ru/hoxpro. The database is also mirrored at http://www.mssm.edu/molbio/hoxpro. The HOX-Pro database is aimed at: (i) analysis and classification of regulatory and coding regions in diverse homeobox and related genes; (ii) comparative analysis of organization of 'Hox-based' genetic networks in the sea urchin Strongylocentrotus purpuratus, the fruit fly Drosophila melanogaster and the mouse Mus musculus; and (iii) analysis of phylogeny and evolution of homeobox genes and clusters.     

Classification and nomenclature of all human homeobox genes

Background

The homeobox genes are a large and diverse group of genes, many of which play important roles in the embryonic development of animals. Increasingly, homeobox genes are being compared between genomes in an attempt to understand the evolution of animal development. Despite their importance, the full diversity of human homeobox genes has not previously been described.

Results

We have identified all homeobox genes and pseudogenes in the euchromatic regions of the human genome, finding many unannotated, incorrectly annotated, unnamed, misnamed or misclassified genes and pseudogenes. We describe 300 human homeobox loci, which we divide into 235 probable functional genes and 65 probable pseudogenes. These totals include 3 genes with partial homeoboxes and 13 pseudogenes that lack homeoboxes but are clearly derived from homeobox genes. These figures exclude the repetitive DUX1 to DUX5 homeobox sequences of which we identified 35 probable pseudogenes, with many more expected in heterochromatic regions. Nomenclature is established for approximately 40 formerly unnamed loci, reflecting their evolutionary relationships to other loci in human and other species, and nomenclature revisions are proposed for around 30 other loci. We use a classification that recognizes 11 homeobox gene 'classes' subdivided into 102 homeobox gene 'families'.

Conclusion

We have conducted a comprehensive survey of homeobox genes and pseudogenes in the human genome, described many new loci, and revised the classification and nomenclature of homeobox genes. The classification scheme may be widely applicable to homeobox genes in other animal genomes and will facilitate comparative genomics of this important gene superclass.     

Homeobox genes in vertebrate evolution.

A wide range of anatomical features are shared by all vertebrates, but absent in our closest invertebrate relatives. The origin of vertebrate embryogenesis must have involved the evolution of new regulatory pathways to control the development of new features, but how did this occur? Mutations affecting regulatory genes, including those containing homeobox sequences, may have been important: for example, perhaps gene duplications allowed recruitment of genes to new roles. Here I ask whether comparative data on the genomic organization and expression patterns of homeobox genes support this hypothesis. I propose a model in which duplications of particular homeobox genes, followed by the acquisition of gene-specific secondary expression domains, allowed the evolution of the neural crest, extensive organogenesis and craniofacial morphogenesis. Specific details of the model are amenable to testing by extension of this comparative approach to molecular embryology.     

Molecular cloning and characterization of homeo-box-containing genes from Atlantic salmon

As the most primitive group among vertebrates, fish might serve as a model system when studying the genetic regulation of embryogenesis in higher animals. To identify genes important for early development, we have constructed a genomic library from Atlantic salmon (Salmo salar) and screened it with homeobox-containing probes from Drosophila melanogaster. Five different salmon homeoboxes were isolated. Two of these were located in the same clone, separated by only 7.5 kb. This demonstrates the presence of clustered homeobox genes in fish. The two clustered homeoboxes were sequenced and shown to be closely related to the ANT-C/BX-C class of Drosophila, being about 80% homologous to the Ultrabithorax gene (Ubx) homeobox. One of the clustered genes appears to be the salmon equivalent of the mouse Hox-2.1 gene, indicating that some of the vertebrate homeobox-containing genes are conserved in evolution. A more diverged homeobox that shares only 60% homology with Ubx, was also sequenced. In analogy to Drosophila, therefore, the salmon genome contains more than one class of homeoboxes. In addition, Northern-blot experiments demonstrated that two of the homeobox genes are expressed in salmon embryos, suggesting their importance for proper development.     

Extensive chordate and annelid macrosynteny reveals ancestral homeobox gene organization

Genes with the homeobox motif are crucial in developmental biology and widely implicated in the evolution of development. The Antennapedia (ANTP)-class is one of the two major classes of animal homeobox genes, and includes the Hox genes, renowned for their role in patterning the anterior-posterior axis of animals. The origin and evolution of the ANTP-class genes are a matter of some debate. A principal guiding hypothesis has been the existence of an ancient gene Mega-cluster deep in animal ancestry. This hypothesis was largely established from linkage data from chordates, and the Mega-cluster hypothesis remains to be seriously tested in protostomes. We have thus mapped ANTP-class homeobox genes to the chromosome level in a lophotrochozoan protostome. Our comparison of gene organization in Platynereis dumerilii and chordates indicates that the Mega-cluster, if it did exist, had already been broken up onto four chromosomes by the time of the protostome-deuterostome ancestor (PDA). These results not only elucidate an aspect of the genome organization of the PDA but also reveal high levels of macrosynteny between P. dumerilii and chordates. This implies a very low rate of interchromosomal genome rearrangement in the lineages leading to P. dumerilii and the chordate ancestor since the time of the PDA.     

Isolation of Hox cluster genes from insects reveals an accelerated sequence evolution rate

Among gene families it is the Hox genes and among metazoan animals it is the insects (Hexapoda) that have attracted particular attention for studying the evolution of development. Surprisingly though, no Hox genes have been isolated from 26 out of 35 insect orders yet, and the existing sequences derive mainly from only two orders (61% from Hymenoptera and 22% from Diptera). We have designed insect specific primers and isolated 37 new partial homeobox sequences of Hox cluster genes (lab, pb, Hox3, ftz, Antp, Scr, abd-a, Abd-B, Dfd, and Ubx) from six insect orders, which are crucial to insect phylogenetics. These new gene sequences provide a first step towards comparative Hox gene studies in insects. Furthermore, comparative distance analyses of homeobox sequences reveal a correlation between gene divergence rate and species radiation success with insects showing the highest rate of homeobox sequence evolution.     

Ancient linkage of a POU class 6 and an anterior Hox-like gene in cnidaria: implications for the evolution of homeobox genes

Linkage analyses in metazoan genomes suggest two ancestral arrays for the majority of homeobox genes. The related homeobox genes and chromosomal regions that are dispersed in extant species derived possibly from only two single common ancestor regions. One proposed ancestral array, designated as ANTP mega-array, contains most of the ANTP class homeobox genes; the second, named the contraHox super-paralogon, would consist of the classes PRD, POU, LIM, CUT, prospero, TALE and SIX. Here, we report the tight linkage of a POU class 6 gene to an anterior Hox-like gene in the hydrozoan Eleutheria dichotoma and discuss its possible significance for the evolution of homeobox genes. POU class 6 genes also seem to be ancestrally linked to the HoxC and A clusters in vertebrates, despite POU homeobox genes belonging to the contraHox paralogon. Hence, the much tighter linkage of a POU class 6 gene to an anterior Hox-like gene in a cnidarian is possibly the evolutionary echo of an ancestral genomic region from which most metazoan homeobox classes emerged.     

The genesis and evolution of homeobox gene clusters

Once called the 'Rosetta stone' of developmental biology, the homeobox continues to fascinate both evolutionary and developmental biologists. The birth of the homeotic, or Hox, gene cluster, and its subsequent evolution, has been crucial in mediating the major transitions in metazoan body plan. Comparative genomics studies indicate that the more recently discovered ParaHox and NK clusters were linked to the Hox cluster early in evolution, and that together they constituted a 'megacluster' of homeobox genes that conspicuously contributed to body-plan evolution.     

Homeobox Genes in the Rodent Pineal Gland: Roles in Development and Phenotype Maintenance

The pineal gland is a neuroendocrine gland responsible for nocturnal synthesis of melatonin. During early development of the rodent pineal gland from the roof of the diencephalon, homeobox genes of the orthodenticle homeobox (Otx)- and paired box (Pax)-families are expressed and are essential for normal pineal development consistent with the well-established role that homeobox genes play in developmental processes. However, the pineal gland appears to be unusual because strong homeobox gene expression persists in the pineal gland of the adult brain. Accordingly, in addition to developmental functions, homeobox genes appear to be key regulators in postnatal phenotype maintenance in this tissue. In this paper, we review ontogenetic and phylogenetic aspects of pineal development and recent progress in understanding the involvement of homebox genes in rodent pineal development and adult function. A working model is proposed for understanding the sequential action of homeobox genes in controlling development and mature circadian function of the mammalian pinealocyte based on knowledge from detailed developmental and daily gene expression analyses in rats, the pineal phenotypes of homebox gene-deficient mice and studies on development of the retinal photoreceptor; the pinealocyte and retinal photoreceptor share features not seen in other tissues and are likely to have evolved from the same ancestral photodetector cell.     

Genome-wide identification, classification, evolutionary expansion and expression analyses of homeobox genes in rice

Homeobox genes play a critical role in regulating various aspects of plant growth and development. In the present study, we identified a total of 107 homeobox genes in the rice genome and grouped them into ten distinct subfamilies based upon their domain composition and phylogenetic analysis. A significantly large number of homeobox genes are located in the duplicated segments of the rice genome, which suggests that the expansion of homeobox gene family, in large part, might have occurred due to segmental duplications in rice. Furthermore, microarray analysis was performed to elucidate the expression profiles of these genes in different tissues and during various stages of vegetative and reproductive development. Several genes with predominant expression during various stages of panicle and seed development were identified. At least 37 homeobox genes were found to be differentially expressed significantly (more than two-fold; P < 0.05) under various abiotic stress conditions. The results of the study suggest a critical role of homeobox genes in reproductive development and abiotic stress signaling in rice, and will facilitate the selection of candidate genes of agronomic importance for functional validation.