The fates of zebrafish Hox gene duplicates

In his 1970 book, Susumu Ohno stressed the importance of gene duplication in the evolution of the vertebrate genome and body plan. He elaborated the idea that duplication events provide novel genetic material on which evolution may act. Data are accumulating to show that extensive duplication events, perhaps incorporating the duplication of entire genomes, occurred in the lineage leading to teleost fishes. These duplications may have been pivotal in the explosive radiation of this highly successful vertebrate group. Thus, the teleosts provide us with an ideal opportunity to investigate the fates and functions of duplicated genes. A convenient system for these studies is the zebrafish, Danio rerio, which has become a popular genetic and embryological model.     

No more than 14: the end of the amphioxus Hox cluster

The Hox gene cluster has been a key paradigm for a generation of developmental and evolutionary biologists. Since its discovery in the mid-1980's, the identification, genomic organization, expression, colinearity, and regulation of Hox genes have been immediate targets for study in any new model organism, and metazoan genome projects always refer to the structure of the particular Hox cluster(s). Since the early 1990's, it has been dogma that vertebrate Hox clusters are composed of thirteen paralogous groups. Nonetheless, we showed that in the otherwise prototypical cephalochordate amphioxus (Branchiostoma floridae), the Hox cluster contains a fourteenth Hox gene, and very recently, a 14(th) Hox paralogous group has been found in the coelacanth and the horn shark, suggesting that the amphioxus cluster was anticipating the finding of Hox 14 in some vertebrate lineages. In view of the pivotal place that amphioxus occupies in vertebrate evolution, we thought it of considerable interest to establish the limits of its Hox gene cluster, namely resolution of whether more Hox genes are present in the amphioxus cluster (e.g., Hox 15). Using two strategies, here we report the completion and characterization of the Hox gene content of the single amphioxus Hox cluster, which encompasses 650 kb from Hox1 to Evx. Our data have important implications for the primordial Hox gene cluster of chordates: the prototypical nature of the single amphioxus Hox cluster makes it unlikely that additional paralogous groups will be found in any chordate lineage. We suggest that 14 is the end.     

Hox genes: Downstream “effectors” of retinoic acid signaling in vertebrate embryogenesis

One of the major regulatory challenges of animal development is to precisely coordinate in space and time the formation, specification, and patterning of cells that underlie elaboration of the basic body plan. How does the vertebrate plan for the nervous and hematopoietic systems, heart, limbs, digestive, and reproductive organs derive from seemingly similar population of cells? These systems are initially established and patterned along the anteroposterior axis (AP) by opposing signaling gradients that lead to the activation of gene regulatory networks involved in axial specification, including the Hox genes. The retinoid signaling pathway is one of the key signaling gradients coupled to the establishment of axial patterning. The nested domains of Hox gene expression, which provide a combinatorial code for axial patterning, arise in part through a differential response to retinoic acid (RA) diffusing from anabolic centers established within the embryo during development. Hence, Hox genes are important direct effectors of retinoid signaling in embryogenesis. This review focuses on describing current knowledge on the complex mechanisms and regulatory processes, which govern the response of Hox genes to RA in several tissue contexts including the nervous system during vertebrate development.     

应用PRINS技术定位黄鳝Hox基因的研究

Hox基因是近年来发现的支持基因组复制进化理论的最有力的证据。该研究应用引物原位延伸 (PRINS)技术 ,在黄鳝有丝分裂染色体标本上开展Hox基因的定位研究。研究结果表明 ,在黄鳝染色体组中可能存在有 6个Hox基因簇 ,这些基因簇分别位于黄鳝第 1、2、3、6、8和 10号染色体 ,相对着丝粒距离分别为 2 8 2 4± 2 88、4 5 5±1 39、13 89± 2 0 3、74 32± 1.86、38 0 3± 2 .4 1和 5 8 18± 2 0 5。该研究定位黄鳝Hox基因将有助于挖掘黄鳝染色体的来源和进化特征 ,并为基因组复制进化理论提供黄鳝这一特化物种的细胞遗传学证据。     

Hox genes from the Polystomatidae (Platyhelminthes, Monogenea)

Hox genes form a multigenic family that play a fundamental role during the early stages of development. They are organised in a single cluster and share a 60 amino acid conserved sequence that corresponds to the DNA binding domain, i.e. the homeodomain. Sequence conservation in this region has allowed investigators to explore Hox diversity in the metazoan lineages. Within parasitic flatworms only homeobox sequences of parasite species from the Cestoda and Digenea have been reported. In the present study we surveyed species of the Polyopisthocotylea (Monogenea) in order to clarify Hox identification and diversification processes in the neodermatan lineage. From cloning of degenerative PCR products of the central region of the homeobox, we report one ParaHox and 25 new Hox sequences from 10 species of the Polystomatidae and one species of the Diclidophoridae, which extend Hox gene diversity from 46 to 72 within Neodermata. Hox sequences from the Polyopisthocotylea were annotated and classified from sequence alignments and Bayesian inferences of 178 Hox, ParaHox and related gene families recovered from all available parasitic platyhelminths and other bilaterian taxa. Our results are discussed in the light of the recent Hox evolutionary schemes. They may provide new perspectives to study the transition from turbellarians to parasitic flatworms with complex life-cycles and outline the first steps for evolutionary developmental biological approaches within platyhelminth parasites.     

Hox Genes from the Tapeworm Taenia asiatica (Platyhelminthes: Cestoda)

Hox genes are important in forming the anterior-posterior body axis pattern in the early developmental stage of animals. The conserved nature of the genomic organization of Hox genes is well known in diverse metazoans. To understand the Hox gene architecture in human-infecting Taenia tapeworms, we conducted a genomic survey of the Hox gene using degenerative polymerase chain reaction primers in Taenia asiatica. Six Hox gene orthologs from 276 clones were identified. Comparative analysis revealed that T. asiatica has six Hox orthologs, including two lab/Hox1, two Hox3, one Dfd/Hox4, and one Lox2/Lox4. The results suggest that Taenia Hox genes may have undergone independent gene duplication in two Hox paralogs. The failure to detect Post1/2 orthologs in T. asiatica may suggest that sequence divergence or the secondary loss of the posterior genes has occurred in the lineage leading to the cestode and trematode.     

Position-specific and non-colinear expression of the planarian posterior (Abdominal-B-like) gene

Hox genes are pivotal molecules in the control of morphogenesis along the anterior-posterior (AP) axis in various bilaterians. Planarians are key animals for understanding the evolution of the bilaterian body plan. Furthermore, they are also known for their strong regeneration ability and are thought to use the Hox genes in the process of reconstruction of the AP axis. In the present paper, the identification and analysis of expression of two posterior (Abdominal-B-like) genes, DjAbd-Ba and DjAbd-Bb, is reported in the planarian Dugesia japonica. DjAbd-Ba is expressed in the entire tail region and its anterior boundary is the posterior pharyngeal region. In contrast, DjAbd-Bb is expressed in several types of cells throughout the body. During regeneration, the expression of DjAbd-Ba rapidly recovers a pattern similar to that in the normal worm. These findings suggest the possibility that DjAbd-Ba is involved in the specification of the tail region. The anterior boundary of the expression domain of the posterior gene DjAbd-Ba is anterior to the domains of the central genes Plox4-Dj and Plox5-Dj. These expression patterns of planarian Hox genes seem out of the rule of spatial colinearity and may reflect an ancestral feature of bilaterian Hox genes.     

2R or not 2R: Testing hypotheses of genome duplication in early vertebrates

The widely popular hypothesis that there were two rounds of genome duplication by polyploidization early in vertebrate history (the 2R hypothesis) has been difficult to test until recently. Among the lines of evidence adduced in support of this hypothesis are relative genome size, relative gene number, and the existence of genomic regions putatively duplicated during polyploidization. The availability of sequence for a substantial portion of the human genome makes possible the first rigorous tests of this hypothesis. Comparison of gene family size in the human genome and in invertebrate genomes shows no evidence of a 4:1 ratio between vertebrates and invertebrates. Furthermore, explicit phylogenetic tests for the topology expected from two rounds of polyploidization have revealed alternative topologies in a substantial majority of human gene families. Likewise, phylogenetic analyses have shown that putatively duplicated genomic regions often include genes duplicated at widely different times over the evolution of life. The 2R hypothesis thus can be decisively rejected. Rather, current evidence favors a model of genome evolution in which tandem duplication, whether of genomic segments or of individual genes, predominates.     

Synchronous and early activation of planarian Hox genes and the re-specification of body axes during regeneration in Dugesia (G.) tigrina (Turbellaria; Tricladida)

Seven Hox cluster-related genes (Dthox-A to -G) have been isolated from the freshwater triclad Dugesia (G.) tigrina, their sequence compared to other Hox genes and their expression in intact and regenerating organisms analyzed by whole mount in situ hybridization. Sequence comparison analyses show high similarities of D. tigrina Hox genes to anterior and medial groups of coelomate Hox genes. Expression analyses show very early, synchronous, and overlapping expression of Dthox -A, -E, -G and -F in anterior, posterior and lateral regenerative tissues. At one hour of regeneration all Dthox genes studied showed a neat, clear expression at the wound boundary. Later, as the blastema grows, the expression area expands to more proximal regions covering the blastema and the distal postblastema regions. Blastemas formed by intercalary regeneration also show a synchronous expression of the same Hox genes though the onset of activation is much delayed. The finding that the same set of Hox genes is synchronously activated in anterior, posterior, intercalary and lateral regeneration is in sharp contrast to its well established role in specifying antero-posterior pattern during embryonic development. The implications of these results as regards ancestral versus co-opted roles of Hox genes in development and regeneration are discussed. This revised version was published online in July 2006 with corrections to the Cover Date.     

ftz evolution: findings, hypotheses and speculations (response to DOI 10.1002/bies.201100019)

In a recent paper, Merabet and Hudry discuss models explaining the functional evolution of fushi tarazu (ftz) from an ancestral homeotic to a pair-rule segmentation gene in Drosophila. As most of the experimental work underlying these models comes from our research, we wish to reply to Merabet and Hudry providing an explanation of the experimental approaches and logical framework underlying them. We review experimental data that support our hypotheses and discuss misconceptions in the literature. We emphasize that the change in ftz function required changes in both expression pattern and protein function and review the evidence that these functional changes involved a switch in cofactor-interaction motifs during arthropod radiations. While agreeing with Merabet and Hudry that protein context likely contributes to Ftz function, we argue that until supporting evidence for alternative mechanisms is obtained, the role of cofactor-interaction motifs in driving a functional switch remains compelling.     

Discrimination in partnership: compartment-specific interactions of Hox proteins

Journal of Genetics -     

Hox genes in sea spiders (Pycnogonida) and the homology of arthropod head segments

The pycnogonids (or sea spiders) are an enigmatic group of arthropods, classified in recent phylogenies as a sister-group of either euchelicerates (horseshoe crabs and arachnids), or all other extant arthropods. Because of their bizarre morpho-anatomy, homologies with other arthropod taxa have been difficult to assess. We review the main morphology-based hypotheses of correspondence between anterior segments of pycnogonids, arachnids and mandibulates. In an attempt to provide new relevant data to these controversial issues, we performed a PCR survey of Hox genes in two pycnogonid species, Endeis spinosa and Nymphon gracile, from which we could recover nine and six Hox genes, respectively. Phylogenetic analyses allowed to identify their orthology relationships. The Deformed gene from E. spinosa and the abdominal-A gene from N. gracile exhibit unusual sequence divergence in their homeodomains, which, in the latter case, may be correlated with the extreme reduction of the posterior region in pycnogonids. Expression patterns of two Hox genes (labial and Deformed) in the E. spinosa protonymphon larva are discussed. The anterior boundaries of their expression domains favour homology between sea spider chelifores, euchelicerates chelicerae and mandibulate (first) antennae, in contradistinction with previously proposed alternative schemes such as the protocerebral identity of sea spider chelifores or the absence of a deutocerebrum in chelicerates. In addition, while anatomical and embryological evidences suggest the possibility that the ovigers of sea spiders could be a duplicated pair of pedipalps, the Hox data support them as modified anterior walking legs, consistent with the classical views.Supplementary material is available for this article at and is accessible for authorized users.Guest editors Jean Deutsch and Gerhard Scholtz     

Functional divergence in protein (family) sequence evolution

As widely used today to infer function, the homology search is based on the neutral theory that sites of greatest functional significance are under the strongest selective constraints as well as lowest evolutionary rates, and vice versa. Therefore, site-specific rate changes (or altered selective constraints) are related to functional divergence during protein (family) evolution. In this paper, we review our recent work about this issue. We show a great deal of functional information can be obtained from the evolutionary perspective, which can in turn be used to facilitate high throughput functional assays. The emergence of evolutionary functional genomics is also indicated. The related software DIVERGE can be obtained form http://xgu1.zool.iastate.edu.     

Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth

Gene duplication plays important roles in organismal evolution, because duplicate genes provide raw materials for the evolution of mechanisms controlling physiological and/or morphological novelties. Gene duplication can occur via several mechanisms, including segmental duplication, tandem duplication and retroposition. Although segmental and tandem duplications have been found to be important for the expansion of a number of multigene families, the contribution of retroposition is not clear. Here we show that plant SKP1 genes have evolved by multiple duplication events from a single ancestral copy in the most recent common ancestor (MRCA) of eudicots and monocots, resulting in 19 ASK (Arabidopsis SKP1-like) and 28 OSK (Oryza SKP1-like) genes. The estimated birth rates are more than ten times the average rate of gene duplication, and are even higher than that of other rapidly duplicating plant genes, such as type I MADS box genes, R genes, and genes encoding receptor-like kinases. Further analyses suggest that a relatively large proportion of the duplication events may be explained by tandem duplication, but few, if any, are likely to be due to segmental duplication. In addition, by mapping the gain/loss of a specific intron on gene phylogenies, and by searching for the features that characterize retrogenes/retrosequences, we show that retroposition is an important mechanism for expansion of the plant SKP1 gene family. Specifically, we propose that two and three ancient retroposition events occurred in lineages leading to Arabidopsis and rice, respectively, followed by repeated tandem duplications and chromosome rearrangements. Our study represents a thorough investigation showing that retroposition can play an important role in the evolution of a plant gene family whose members do not encode mobile elements.