A conserved cluster of three PRD-class homeobox genes (homeobrain, rx and orthopedia) in the Cnidaria and Protostomia

Abstract

Background: Homeobox genes are a superclass of transcription factors with diverse developmental regulatory functions, which are found in plants, fungi and animals. In animals, several Antennapedia (ANTP)-class homeobox genes reside in extremely ancient gene clusters (for example, the Hox, ParaHox, and NKL clusters) and the evolution of these clusters has been implicated in the morphological diversification of animal bodyplans. By contrast, similarly ancient gene clusters have not been reported among the other classes of homeobox genes (that is, the LIM, POU, PRD and SIX classes).Results: Using a combination of in silico queries and phylogenetic analyses, we found that a cluster of three PRD-class homeobox genes (Homeobrain (hbn), Rax (rx) and Orthopedia (otp)) is present in cnidarians, insects and mollusks (a partial cluster comprising hbn and rx is present in the placozoan Trichoplax adhaerens). We failed to identify this 'HRO' cluster in deuterostomes; in fact, the Homeobrain gene appears to be missing from the chordate genomes we examined, although it is present in hemichordates and echinoderms. To illuminate the ancestral organization and function of this ancient cluster, we mapped the constituent genes against the assembled genome of a model cnidarian, the sea anemone Nematostella vectensis, and characterized their spatiotemporal expression using in situ hybridization. In N. vectensis, these genes reside in a span of 33 kb with the same gene order as previously reported in insects. Comparisons of genomic sequences and expressed sequence tags revealed the presence of alternative transcripts of Nv-otp and two highly unusual protein-coding polymorphisms in the terminal helix of the Nv-rx homeodomain. A population genetic survey revealed the Rx polymorphisms to be widespread in natural populations. During larval development, all three genes are expressed in the ectoderm, in non-overlapping territories along the oral-aboral axis, with distinct temporal expression. Conclusion:We report the first evidence for a PRD-class homeobox cluster that appears to have been conserved since the time of the cnidarian-bilaterian ancestor, and possibly even earlier, given the presence of a partial cluster in the placozoan Trichoplax. Very similar clusters comprising these three genes exist in Nematostella and diverse protostomes. Interestingly, in chordates, one member of the ancestral cluster (homeobrain) has apparently been lost, and there is no linkage between rx and orthopedia in any of the vertebrates. In Nematostella, the spatial expression of these three genes along the body column is not colinear with their physical order in the cluster but the temporal expression is, therefore, using the terminology that has been applied to the Hox cluster genes, the HRO cluster would appear to exhibit temporal but not spatial colinearity. It remains to be seen whether the mechanisms responsible for the evolutionary conservation of the HRO cluster are the same mechanisms responsible for cohesion of the Hox cluster and other ANT...

Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs

“…Although much less studied than the Hox, ParaHox and NK clusters, the trio of hbn, rx and otp constitutes a well-conserved PRD-homeobox gene cluster whose organization has been maintained in many protostome genomes (Mazza et al, 2010). Together, these results reveal that xiphosuran genomes contain paralogous arrays of genes that are well known for being single copy in other animal species.…”

“…Multiple gene copies in the three sequenced horseshoe crab genomes were also found for representatives from other homeobox clusters found in other bilaterians, such as the ParaHox, Hbn/Otp/Rx and NK clusters (additional file 1, Zhong and Holland, 2011a;Hui et al, 2008Hui et al, , 2012Mazza et al, 2010). Although much less studied than the Hox, ParaHox and NK clusters, the trio of hbn, rx and otp constitutes a well-conserved PRD-homeobox gene cluster whose organization has been maintained in many protostome genomes (Mazza et al, 2010).…”

“…Unlike ANTP class genes, PRD genes are usually dispersed; however, two PRD-homeobox clusters have been proposed-the mammalian Rhox homeobox gene cluster (MacLean et al, 2005) and a conserved cluster containing homeobrain, rx and orthopedia (Mazza et al, 2010).…”

Mechanisms of tentacle morphogenesis in the sea anemoneNematostella vectensis

“…Once budded, planula larvae express a subset of genes in the buds, such as PaxA (Magie et al, 2005) (green), between the buds, such as homeobrain (Mazza et al, 2010) (red), and encircling the buds, such as Delta (Marlow et al, 2012) (orange). Patterning becomes more complicated at the primary polyp stage, when some genes are expressed along the length of the tentacle, such as muscle LIM and Rx (Martindale et al, 2004;Mazza et al, 2010) (green), or at the tips of the tentacles, such as sprouty ) (yellow).…”

The characterization of larval homology: transcriptomic insights into the origin and evolution of animal life cycles

“…Jackson et al 2005, Dunn et al 2007, Rentzsch et al 2008, Mazza et al 2010, Santagata et al 2012, Marlow et al 2014. Specifically, studies have examined the similarities of bilaterian larval gut development, illustrating that expression patterns, such as of Brachyury, otx, and goosecoid, are conserved between protostome and deuterostome larvae (Arendt et al 2001).…”