Domain duplication, divergence, and loss events in vertebrate Msx paralogs reveal phylogenomically informed disease markers

<p>Abstract</p> <p>Background</p> <p>Msx originated early in animal evolution and is implicated in human genetic disorders. To reconstruct the functional evolution of Msx and inform the study of human mutations, we analyzed the phylogeny and synteny of 46 metazoan Msx proteins and tracked the duplication, diversification and loss of conserved motifs.</p> <p>Results</p> <p>Vertebrate Msx sequences sort into distinct Msx1, Msx2 and Msx3 clades. The sister-group relationship between <it>MSX1 </it>and <it>MSX2 </it>reflects their derivation from the 4p/5q chromosomal paralogon, a derivative of the original "MetaHox" cluster. We demonstrate physical linkage between Msx and other MetaHox genes (<it>Hmx</it>, <it>NK1</it>, <it>Emx</it>) in a cnidarian. Seven conserved domains, including two Groucho repression domains (N- and C-terminal), were present in the ancestral Msx. In cnidarians, the Groucho domains are highly similar. In vertebrate Msx1, the N-terminal Groucho domain is conserved, while the C-terminal domain diverged substantially, implying a novel function. In vertebrate Msx2 and Msx3, the C-terminal domain was lost. MSX1 mutations associated with ectodermal dysplasia or orofacial clefting disorders map to conserved domains in a non-random fashion.</p> <p>Conclusion</p> <p>Msx originated from a MetaHox ancestor that also gave rise to Tlx, Demox, NK, and possibly EHGbox, Hox and ParaHox genes. Duplication, divergence or loss of domains played a central role in the functional evolution of Msx. Duplicated domains allow pleiotropically expressed proteins to evolve new functions without disrupting existing interaction networks. Human missense sequence variants reside within evolutionarily conserved domains, likely disrupting protein function. This phylogenomic evaluation of candidate disease markers will inform clinical and functional studies.</p

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

<p>Abstract</p> <p>Background</p> <p>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).</p> <p>Results</p> <p>Using a combination of <it>in silico </it>queries and phylogenetic analyses, we found that a cluster of three PRD-class homeobox genes (<it>Homeobrain (hbn)</it>, <it>Rax (rx) </it>and <it>Orthopedia (otp)</it>) is present in cnidarians, insects and mollusks (a partial cluster comprising hbn and rx is present in the placozoan <it>Trichoplax adhaerens</it>). We failed to identify this 'HRO' cluster in deuterostomes; in fact, the <it>Homeobrain </it>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 <it>Nematostella vectensis</it>, and characterized their spatiotemporal expression using <it>in situ </it>hybridization. In <it>N. vectensis</it>, 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.</p> <p>Conclusion</p> <p>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 <it>Trichoplax</it>. Very similar clusters comprising these three genes exist in <it>Nematostella </it>and diverse protostomes. Interestingly, in chordates, one member of the ancestral cluster (<it>homeobrain</it>) has apparently been lost, and there is no linkage between <it>rx </it>and <it>orthopedia </it>in any of the vertebrates. In <it>Nematostella</it>, 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 ANTP-class homeobox clusters that have been widely conserved throughout animal evolution.</p

The cnidarian-bilaterian ancestor possessed at least 56 homeoboxes: evidence from the starlet sea anemone, Nematostella vectensis

BACKGROUND: Homeodomain transcription factors are key components in the developmental toolkits of animals. While this gene superclass predates the evolutionary split between animals, plants, and fungi, many homeobox genes appear unique to animals. The origin of particular homeobox genes may, therefore, be associated with the evolution of particular animal traits. Here we report the first near-complete set of homeodomains from a basal (diploblastic) animal. RESULTS: Phylogenetic analyses were performed on 130 homeodomains from the sequenced genome of the sea anemone Nematostella vectensis along with 228 homeodomains from human and 97 homeodomains from Drosophila. The Nematostella homeodomains appear to be distributed among established homeodomain classes in the following fashion: 72 ANTP class; one HNF class; four LIM class; five POU class; 33 PRD class; five SINE class; and six TALE class. For four of the Nematostella homeodomains, there is disagreement between neighbor-joining and Bayesian trees regarding their class membership. A putative Nematostella CUT class gene is also identified. CONCLUSION: The homeodomain superclass underwent extensive radiations prior to the evolutionary split between Cnidaria and Bilateria. Fifty-six homeodomain families found in human and/or fruit fly are also found in Nematostella, though seventeen families shared by human and fly appear absent in Nematostella. Homeodomain loss is also apparent in the bilaterian taxa: eight homeodomain families shared by Drosophila and Nematostella appear absent from human (CG13424, EMXLX, HOMEOBRAIN, MSXLX, NK7, REPO, ROUGH, and UNC4), and six homeodomain families shared by human and Nematostella appear absent from fruit fly (ALX, DMBX, DUX, HNF, POU1, and VAX)

Evaluating models for lithospheric loss and intraplate volcanism beneath the Central Appalachian Mountains

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Long, M. D., Wagner, L. S., King, S. D., Evans, R. L., Mazza, S. E., Byrnes, J. S., Johnson, E. A., Kirby, E., Bezada, M. J., Gazel, E., Miller, S. R., Aragon, J. C., & Liu, S. Evaluating models for lithospheric loss and intraplate volcanism beneath the Central Appalachian Mountains. Journal of Geophysical Research: Solid Earth, 126(10), (2021): e2021JB022571, https://doi.org/10.1029/2021JB022571.The eastern margin of North America has been shaped by a series of tectonic events including the Paleozoic Appalachian Orogeny and the breakup of Pangea during the Mesozoic. For the past ∼200 Ma, eastern North America has been a passive continental margin; however, there is evidence in the Central Appalachian Mountains for post-rifting modification of lithospheric structure. This evidence includes two co-located pulses of magmatism that post-date the rifting event (at 152 and 47 Ma) along with low seismic velocities, high seismic attenuation, and high electrical conductivity in the upper mantle. Here, we synthesize and evaluate constraints on the lithospheric evolution of the Central Appalachian Mountains. These include tomographic imaging of seismic velocities, seismic and electrical conductivity imaging along the Mid-Atlantic Geophysical Integrative Collaboration array, gravity and heat flow measurements, geochemical and petrological examination of Jurassic and Eocene magmatic rocks, and estimates of erosion rates from geomorphological data. We discuss and evaluate a set of possible mechanisms for lithospheric loss and intraplate volcanism beneath the region. Taken together, recent observations provide compelling evidence for lithospheric loss beneath the Central Appalachians; while they cannot uniquely identify the processes associated with this loss, they narrow the range of plausible models, with important implications for our understanding of intraplate volcanism and the evolution of continental lithosphere. Our preferred models invoke a combination of (perhaps episodic) lithospheric loss via Rayleigh-Taylor instabilities and subsequent small-scale mantle flow in combination with shear-driven upwelling that maintains the region of thin lithosphere and causes partial melting in the asthenosphere.The authors acknowledge support from the U.S. National Science Foundation EarthScope and GeoPRISMS programs via grants EAR-1460257 (R. L. Evans), EAR-1249412 (E. Gazel), EAR-1249438 (E. A. Johnson), EAR-1250988 (S. D. King), EAR-1251538 (E. Kirby), and EAR-1251515 (M. D. Long). The collection and dissemination of most of the geophysical data and models discussed in this study were facilitated by the Incorporated Research Institutions for Seismology (IRIS). The facilities of the IRIS Consortium are supported by the United States National Science Foundation under Cooperative Agreement EAR-1261681

Pre-Bilaterian Origins of the Hox Cluster and the Hox Code: Evidence from the Sea Anemone, Nematostella vectensis

BACKGROUND: Hox genes were critical to many morphological innovations of bilaterian animals. However, early Hox evolution remains obscure. Phylogenetic, developmental, and genomic analyses on the cnidarian sea anemone Nematostella vectensis challenge recent claims that the Hox code is a bilaterian invention and that no “true” Hox genes exist in the phylum Cnidaria. METHODOLOGY/PRINCIPAL FINDINGS: Phylogenetic analyses of 18 Hox-related genes from Nematostella identify putative Hox1, Hox2, and Hox9+ genes. Statistical comparisons among competing hypotheses bolster these findings, including an explicit consideration of the gene losses implied by alternate topologies. In situ hybridization studies of 20 Hox-related genes reveal that multiple Hox genes are expressed in distinct regions along the primary body axis, supporting the existence of a pre-bilaterian Hox code. Additionally, several Hox genes are expressed in nested domains along the secondary body axis, suggesting a role in “dorsoventral” patterning. CONCLUSIONS/SIGNIFICANCE: A cluster of anterior and posterior Hox genes, as well as ParaHox cluster of genes evolved prior to the cnidarian-bilaterian split. There is evidence to suggest that these clusters were formed from a series of tandem gene duplication events and played a role in patterning both the primary and secondary body axes in a bilaterally symmetrical common ancestor. Cnidarians and bilaterians shared a common ancestor some 570 to 700 million years ago, and as such, are derived from a common body plan. Our work reveals several conserved genetic components that are found in both of these diverse lineages. This finding is consistent with the hypothesis that a set of developmental rules established in the common ancestor of cnidarians and bilaterians is still at work today

Figure 10

<p>Phylogenetic mapping of Hox expression. The neighbor-joining and Bayesian phylogenies (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000153#pone-0000153-g002" target="_blank">Figure 2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000153#pone.0000153.s001" target="_blank">S1</a>) were pared to remove all bilaterian sequences. The strict consensus topology shown here depicts the relative relationships among <i>Nematostella</i> sequences. Each of the <i>Nematostella</i> Hox-related sequences is coded according to whether its expression is restricted along the primary (O/A) body axis or the secondary (directive) body axis (Y = yes; N = no). A yellow Y in the directive column signifies that the expression is bilateral (both sides of the directive axis), and a red Y indicates that the expression is unilateral. The character state found in the terminal taxon is indicated in the colored boxes. The internal nodes are shaded to indicate the character states found in hypothetical ancestors. For each gene, the spatial expression is depicted on a diagram of the juvenile polyp. In the case of Dlx, anthox6a and anthox1, the expression pattern that is depicted actually occurs earlier, in the larval stage, but it is represented on a diagram of the polyp to facilitate spatial comparisons with the other genes. The polyp is drawn in lateral view with the overlying ectoderm (dark gray) partially peeled away to reveal the underlying endoderm of the body column (light gray) and the lumen of the pharynx (white). The pharynx is drawn as though everted. Only one representative tentacle is shown. The mesoglea, a largely acellular layer of connective tissue that separates the endoderm from the ectoderm, is depicted as a thin black line. Gene expression is depicted as black shading in the endoderm or ectoderm. The major regions along the primary body axis are demarcated with dotted lines: Ph = pharynx; H = head; C = column; F = foot. Cross-sectional views through the body column (at the arrowheads) are shown for Gbx, anthox7, anthox8a, anthox8b, anthox6a, anthox1a, and NVHD065.</p

Figure 4

<p>Developmental Expression of Hox-ParaHox related genes in <i>Nematostella</i>. Gene expression was assayed throughout embryonic and larval development using <i>in situ</i> hybridization. All images are optical sections that permit visualization of the endodermal tissue layer. Panels M and V are transverse sections, but all other images are longitudinal sections with the future oral end of the animal facing left. The blastopore (site of the future mouth) is indicated by an asterisk. Abbreviations are as follows: apical tuft (at); coelenterone (coe); bodywall ectoderm (ecbw); pharyngeal ectoderm (ecph); bodywall endoderm (enbw); pharyngeal endoderm (enph); mesentery (mes); pharynx (pha); tentacle (tn).</p

Figure 7

<p>Hox/ParaHox evolutionary scenarios. The phylogenies drawn here depict six mutually exclusive scenarios regarding the evolution of the Hox and ParaHox genes. Ten distinct Hox and ParaHox lineages are thought to have been present in the ancestral bilaterian (Hox1, Hox2, Hox3, Hox4, Hox5, Hox6–8, Hox9+, Cdx, Gsx, and Xlox). Five distinct Hox/ParaHox lineages are recognized for <i>Nematostella</i>. (<i>Nematostella</i> homeodomains that tend to cluster together in the phylogenetic analyses are grouped together here: anthox1/1a; anthox2/9; anthox6/6a; anthox7/8a/8b.) Assuming no gene loss in the Cnidaria, then the existence of five Hox/ParaHox lineages in <i>Nematostella</i> implies that the cnidarian-bilaterian ancestor (CBA) could have possessed as few as one Hox/ParaHox gene (scenario A) or as many as five (scenario E). There is some indication that a central class Hox gene was lost in the Cnidaria <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000153#pone.0000153-Kourakis1" target="_blank">[47]</a>, and that the CBA may have possessed six distinct Hox/ParaHox genes (scenario F). The ancestral Hox/ParaHox genes present in the CBA are indicated by solid squares. If a particular hypothetical clade is recovered on one or more of the phylogenetic analyses presented here, this is indicated above the relevant branch (NJ = neighbor-joining, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000153#pone-0000153-g002" target="_blank">Figure 2</a>; Ba = Bayesian inference, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000153#pone.0000153.s001" target="_blank">Figure S1</a>; ML = maximum- likelihood, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000153#pone.0000153.s002" target="_blank">Figure S2</a>; φ = none). Below each branch, the average statistical support is indicated (NJ-bootstrap proportion+Bayes-posterior probability+ML-boostrap proportion/3). Each scenario implies a different number of lineage-specific gene losses.</p