Expression patterns of anterior Hox genes in the polychaete Chaetopterus: correlation with morphological boundaries

Expression patterns for five Hox genes were examined by whole-mount in situ hybridization in larvae of Chaetopterus, a polychaete annelid with a tagmatized axial body plan. Phylogenetic analysis demonstrates that these genes are orthologs of the Drosophila genes labial, proboscipedia, zen, Deformed, and Sex combs reduced and are termed CH-Hox1, CH-Hox2, CH-Hox3, CH-Hox4, and CH-Hox5, respectively. Expression studies reveal a biphasic expression pattern. In early larval stages, well before any indications of segmental organization exist, a novel pattern of expression in bilateral posterior proliferating cell populations, corresponding to the teloblasts, was detected for each of the genes, with CH-Hox1 and CH-Hox2 expressed before the remaining three. In middle larval stages, all five genes are expressed in bilateral strips along the ventral midline, corresponding with the developing ventral nerve cord. In addition, CH-Hox1 and CH-Hox2 show strong expression at the foregut-midgut boundary. By late larval stages the expression is generally confined to the ventral CNS and ectoderm of the anterior parapodia. Anterior boundaries of expression are "colinear," at later larval stages, with CH-Hox2 expressed most rostrally, in the first segment, and anterior expression boundaries for CH-Hox1, CH-Hox3, CH-Hox4, and CH-Hox5 in segments 2, 3, 4, and 5, respectively. Like vertebrates and spiders, but unlike insects, CH-Hox3 participates in this colinear axial expression pattern. CH-Hox1 and CH-Hox2 have distinct posterior boundaries of expression in the ninth segment, which corresponds to a major morphological boundary, and may reflect a reorganization of Hox gene regulation related to the evolutionary reorganization of the Chaetopterus body plan.     

Genomic and gene regulatory signatures of cryptozoic adaptation: Loss of blue sensitive photoreceptors through expansion of long wavelength-opsin expression in the red flour beetle Tribolium castaneum

Background

Hox genes are expressed in specific domains along the anterior posterior body axis and define the regional identity. In most animals these genes are organized in a single cluster in the genome and the order of the genes in the cluster is correlated with the anterior to posterior expression of the genes in the embryo. The conserved order of the various Hox gene orthologs in the cluster among most bilaterians implies that such a Hox cluster was present in their last common ancestor. Vertebrates are the only metazoans so far that have been shown to contain duplicated Hox clusters, while all other bilaterians seem to possess only a single cluster.

Results

We here show that at least three Hox genes of the spider Cupiennius salei are present as two copies in this spider. In addition to the previously described duplicated Ultrabithorax gene, we here present sequence and expression data of a second Deformed gene, and of two Sex comb reduced genes. In addition, we describe the sequence and expression of the Cupiennius proboscipedia gene. The spider Cupiennius salei is the first chelicerate for which orthologs of all ten classes of arthropod Hox genes have been described. The posterior expression boundary of all anterior Hox genes is at the tagma border of the prosoma and opisthosoma, while the posterior boundary of the posterior Hox genes is at the posterior end of the embryo.

Conclusion

The presence of at least three duplicated Hox genes points to a major duplication event in the lineage to this spider, perhaps even of the complete Hox cluster as has taken place in the lineage to the vertebrates. The combined data of all Cupiennius Hox genes reveal the existence of two distinct posterior expression boundaries that correspond to morphological tagmata boundaries.     

家蚕Hox基因研究进展

Hox基因（homeobox genes）在昆虫躯体模式（body plan）的发育调控机制中扮演着重要角色,其表达具有严格的组织特异性和胚胎发育的程序性。家蚕Bombyx mori作为鳞翅目昆虫的代表,其Hox基因也陆续得到鉴定。在家蚕中存在一个拟复等位基因群--E群基因,其突变表型均与过剩斑纹和过剩附肢有关,这可能与Hox基因有着密切联系。家蚕全基因组测序完成后,发现其Hox基因簇中存在12个特有的homeobox基因（Bmshx1~Bmshx12）, 说明家蚕Hox基因可能具有独特的生物学意义。我们还利用家蚕基因芯片数据分析了Bmlab与Bmpb基因的组织表达特征。通过对家蚕Hox基因的研究,探索家蚕躯体模式建立机制,可望为解析其他鳞翅目昆虫的躯体模式的建立机制提供理论依据。本文就家蚕Hox基因的表达、功能及其与E群突变的关系等方面进行了综述。     

Anterior boundaries of Hox gene expression in mesoderm-derived structures correlate with the linear gene order along the chromosome

The developmental expression patterns of four genes, Hox 1.1, Hox 1.2, Hox 1.3 and Hox 3.1, were examined by in situ hybridization to serial embryonic sections. The three genes of the Hox 1 cluster, used in this study, map to adjacent positions along chromosome 6, whereas the Hox 3.1 gene maps to the Hox 3 cluster on chromosome 15. The anterior expression limits in segmented mesoderm varied among the four genes examined. Interestingly, a linear correlation exists between the position of the gene along the chromosome and the extent of anterior expression. Genes that are expressed more posterior are also more restricted in their expression in other mesoderm-derived tissues. The order of expression anterior to posterior was determined as: Hox 1.3, Hox 1.2, Hox 1.1 and Hox 3.1. Similarly, genes of the Drosophila Antennapedia and Bithorax complex specifying segment identity also exhibit anterior expression boundaries that correlate with gene position. The data suggest that Hox genes may specify positional information along the anterior-posterior axis during the formation of the body plan.     

Developmental Data and Phylogenetic Systematics: Evolution of the Vertebrate Limb

Among the primary contributions of phylogenetic systematicsto the synthesis of developmental biology and evolution arephylogenetic hypotheses. Phylogenetic hypotheses are criticalin interpreting the patterns of evolution of developmental genesand processes, as are morphological data. Using a robust phylogeny,the evolutionary history of individual morphological or developmentalfeatures can be traced and ancestral conditions inferred. Multiplecharacters (e.g., morphological and developmental) can be mappedtogether on the phylogeny, and patterns of character associationcan be quantified and tested for correlation. Using the vertebrate forelimb as an example, I show that bymapping accurate morphological data (homologous skeletal elementsof the vertebrate forelimb) onto a phylogeny, an alternativeinterpretation of Hox gene expression emerges. Teleost fishesand tetrapods may share no homologous skeletal elements in theirforelimbs, and thus similarities and differences in Hox patternsduring limb development must be reinterpreted. Specifically,the presence of the phase III Hox pattern in tetrapods may notbe correlated with digits but rather may simply be the normalexpression pattern of a metapterygium in fishes. This exampleillustrates the rigorous hypotheses that can be developed usingmorphological data and phylogenetic methods. "Creating a general reference system and investigating the relationsthat extend from it to all other possible and necessary systemsin biology is the task of systematics." (Hennig, 1966, p.7)     

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 Genes and Segmental Patterning of the Vertebrate Hindbrain

SYNOPSIS. Pattern formation in the developing hindbrain andcranio-facial region has been studied in a range of vertebrateorganisms. The developing hindbrain is transiently segmentedinto units termed rhombomeres which correspond with domainsof gene expression, lineage restriction and neuronal organizationand serve to coordinate the migration of cranial neural crestinto the adjacent branchial arches. In this paper I review thecellular and molecular events underlying both hindbrain segmentationand the acquisition of segmental identity, consolidating recentresults from different model systems. Data suggesting that thevertebrate Hox genes play an important role in specifying positionalvalue to the rhombomeres and cranial neural crest are also examined.I compare expression patterns of the Hox genes between speciesand consider the mechanisms involved in controlling their appropriatespatial regulation. In addition I describe a recently characterizedzebraflsh hindbrain segmentation mutant, Valentino; morphological,cellular and gene expression data for this mutant are helpingto further our understanding of hindbrain patterning.     

Differential regulation of ParaHox genes by retinoic acid in the invertebrate chordate amphioxus (Branchiostoma floridae)

The ParaHox cluster is the evolutionary sister to the Hox cluster. Like the Hox cluster, the ParaHox cluster displays spatial and temporal regulation of the component genes along the anterior/posterior axis in a manner that correlates with the gene positions within the cluster (a feature called collinearity). The ParaHox cluster is however a simpler system to study because it is composed of only three genes. We provide a detailed analysis of the amphioxus ParaHox cluster and, for the first time in a single species, examine the regulation of the cluster in response to a single developmental signalling molecule, retinoic acid (RA). Embryos treated with either RA or RA antagonist display altered ParaHox gene expression: AmphiGsx expression shifts in the neural tube, and the endodermal boundary between AmphiXlox and AmphiCdx shifts its anterior/posterior position. We identified several putative retinoic acid response elements and in vitro assays suggest some may participate in RA regulation of the ParaHox genes. By comparison to vertebrate ParaHox gene regulation we explore the evolutionary implications. This work highlights how insights into the regulation and evolution of more complex vertebrate arrangements can be obtained through studies of a simpler, unduplicated amphioxus gene cluster.     

Hox gene expression in larval development of the polychaetes Nereis virens and Platynereis dumerilii (Annelida, Lophotrochozoa)

The bilaterian animals are divided into three great branches: the Deuterostomia, Ecdysozoa, and Lophotrochozoa. The evolution of developmental mechanisms is less studied in the Lophotrochozoa than in the other two clades. We have studied the expression of Hox genes during larval development of two lophotrochozoans, the polychaete annelids Nereis virens and Platynereis dumerilii. As reported previously, the Hox cluster of N. virens consists of at least 11 genes (de Rosa R, Grenier JK, Andreeva T, Cook CE, Adoutte A, Akam M, Carroll SB, Balavoine G, Nature, 399:772–776, 1999; Andreeva TF, Cook C, Korchagina NM, Akam M, Dondua AK, Ontogenez 32:225–233, 2001); we have also cloned nine Hox genes of P. dumerilii. Hox genes are mainly expressed in the descendants of the 2d blastomere, which form the integument of segments, ventral neural ganglia, pre-pygidial growth zone, and the pygidial lobe. Patterns of expression are similar for orthologous genes of both nereids. In Nereis, Hox2, and Hox3 are activated before the blastopore closure, while Hox1 and Hox4 are activated just after this. Hox5 and Post2 are first active during the metatrochophore stage, and Hox7, Lox4, and Lox2 at the late nectochaete stage only. During larval stages, Hox genes are expressed in staggered domains in the developing segments and pygidial lobe. The pattern of expression of Hox cluster genes suggests their involvement in the vectorial regionalization of the larval body along the antero-posterior axis. Hox gene expression in nereids conforms to the canonical patterns postulated for the two other evolutionary branches of the Bilateria, the Ecdysozoa and the Deuterostomia, thus supporting the evolutionary conservatism of the function of Hox genes in development. Milana Kulakova, Nadezhda Bakalenko and Elena Novikova contributed equally to this work.     

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.     

Exploring the myriapod body plan: expression patterns of the ten Hox genes in a centipede

The diversity of the arthropod body plan has long been a fascinating subject of study. A flurry of recent research has analyzed Hox gene expression in various arthropod groups, with hopes of gaining insight into the mechanisms that underlie their evolution. The Hox genes have been analyzed in insects, crustaceans and chelicerates. However, the expression patterns of the Hox genes have not yet been comprehensively analyzed in a myriapod. We present the expression patterns of the ten Hox genes in a centipede, Lithobius atkinsoni, and compare our results to those from studies in other arthropods. We have three major findings. First, we find that Hox gene expression is remarkably dynamic across the arthropods. The expression patterns of the Hox genes in the centipede are in many cases intermediate between those of the chelicerates and those of the insects and crustaceans, consistent with the proposed intermediate phylogenetic position of the Myriapoda. Second, we found two 'extra' Hox genes in the centipede compared with those in DROSOPHILA: Based on its pattern of expression, Hox3 appears to have a typical Hox-like role in the centipede, suggesting that the novel functions of the Hox3 homologs zen and bicoid were adopted somewhere in the crustacean-insect clade. In the centipede, the expression of the gene fushi tarazu suggests that it has both a Hox-like role (as in the mite), as well as a role in segmentation (as in insects). This suggests that this dramatic change in function was achieved via a multifunctional intermediate, a condition maintained in the centipede. Last, we found that Hox expression correlates with tagmatic boundaries, consistent with the theory that changes in Hox genes had a major role in evolution of the arthropod body plan.     

Conserved boundary elements from the Hox complex of mosquito,Anopheles gambiae

The conservation of hox genes as well as their genomic organization across the phyla suggests that this system of anterior–posterior axis formation arose early during evolution and has come under strong selection pressure. Studies in the split Hox cluster of Drosophila have shown that proper expression of hox genes is dependent on chromatin domain boundaries that prevent inappropriate interactions among different types of cis-regulatory elements. To investigate whether boundary function and their role in regulation of hox genes is conserved in insects with intact Hox clusters, we used an algorithm to locate potential boundary elements in the Hox complex of mosquito, Anopheles gambiae. Several potential boundary elements were identified that could be tested for their functional conservation. Comparative analysis revealed that like Drosophila, the bithorax region in A. gambiae contains an extensive array of boundaries and enhancers organized into domains. We analysed a subset of candidate boundary elements and show that they function as enhancer blockers in Drosophila. The functional conservation of boundary elements from mosquito in fly suggests that regulation of hox genes involving chromatin domain boundaries is an evolutionary conserved mechanism and points to an important role of such elements in key developmentally regulated loci.     

Functional evolution of Hox proteins in arthropods

It is presumed that the evolution of morphological diversity in animals and plants is driven by changes in the developmental processes that govern morphology, hence basically by changes in the function and/or expression of a defined set of genes that control these processes. A large body of evidence has suggested that changes in developmental gene regulation are the predominant mechanisms that sustain morphological evolution, being much more important than the evolution of the primary sequences and functions of proteins. Recent reports challenge this idea by highlighting functional evolution of Hox proteins during the evolutionary history of arthropods.     

Additional hox clusters in the zebrafish: divergent expression patterns belie equivalent activities of duplicate hoxB5 genes

SUMMARY The evolution of metazoan body plans has involved changes to the Hox genes, which are involved in patterning the body axis and display striking evolutionary conservation of structure and expression. Invertebrates contain a single Hox cluster whereas tetrapods possess four clusters. The zebrafish has seven unlinked hox clusters, a finding that is difficult to reconcile with the notion that genomic complexity, reflected by Hox cluster number, and morphological complexity are causally linked, as the body plan of the zebrafish is not obviously more complex than that of the mouse or human. Why have the additional hox genes in zebrafish been conserved? To address the role of these additional zebrafish hox genes, we have examined the duplicate hoxB5 genes, hoxB5a, and hoxB5b. Conservation of gene duplicates can occur when one gene acquires a new function (neofunctionalization), or when the ancestral function is divided between the two duplicates (subfunctionalization). hoxB5a and hoxB5b are expressed in distinct domains, and their combined expression domain is strikingly similar to that of single Hoxb5 genes in other species. The biochemical functions encoded by the two genes were studied by overexpression, which resulted in identical developmental defects in the anterior hindbrain and cranial neural crest, suggesting strongly that hoxB5a and hoxB5b have equivalent biochemical properties with respect to early development. From these studies, we conclude that conservation of hoxB5a and hoxB5b is likely the result of division of the ancestral Hoxb5 function between the two genes, without significant changes in biochemical activity. These results suggest a resolution to the conundrum of the extra hox genes and clusters in the zebrafish, since if any of the additional hox genes in the zebrafish are similarly subfunctionalized, they are unlikely to supply novel genetic functions. Thus, the morphological complexity potentially conferred by the majority of additional zebrafish hox clusters may not be substantially greater than that conferred by the four tetrapod clusters.     

Hox gene duplications correlate with posterior heteronomy in scorpions

The evolutionary success of the largest animal phylum, Arthropoda, has been attributed to tagmatization, the coordinated evolution of adjacent metameres to form morphologically and functionally distinct segmental regions called tagmata. Specification of regional identity is regulated by the Hox genes, of which 10 are inferred to be present in the ancestor of arthropods. With six different posterior segmental identities divided into two tagmata, the bauplan of scorpions is the most heteronomous within Chelicerata. Expression domains of the anterior eight Hox genes are conserved in previously surveyed chelicerates, but it is unknown how Hox genes regionalize the three tagmata of scorpions. Here, we show that the scorpion Centruroides sculpturatus has two paralogues of all Hox genes except Hox3, suggesting cluster and/or whole genome duplication in this arachnid order. Embryonic anterior expression domain boundaries of each of the last four pairs of Hox genes (two paralogues each of Antp, Ubx, abd-A and Abd-B) are unique and distinguish segmental groups, such as pectines, book lungs and the characteristic tail, while maintaining spatial collinearity. These distinct expression domains suggest neofunctionalization of Hox gene paralogues subsequent to duplication. Our data reconcile previous understanding of Hox gene function across arthropods with the extreme heteronomy of scorpions.     

Selection on coding regions determined Hox7 genes evolution

The important role of Hox genes in determining the regionalization of the body plan of the vertebrates makes them invaluable candidates for evolutionary analyses regarding functional and morphological innovation. Gene duplication and gene loss led to a variable number of Hox genes in different vertebrate lineages. The evolutionary forces determining the conservation or loss of Hox genes are poorly understood. In this study, we show that variable selective pressures acted on Hox7 genes in different evolutionary lineages, with episodes of positive selection occurring after gene duplications. Tests for functional divergence in paralogs detected significant differentiation in a region known to modulate HOX7 protein activity. Our results show that both positive and negative selection on coding regions are influencing Hox7 genes evolution.