Szabó R and Ferrier DEK (2018), Two more Posterior Hox genes and Hox cluster di...

ECB-ART-46849

BMC Evol Biol 2018 Dec 27;181:203. doi: 10.1186/s12862-018-1307-x.

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Two more Posterior Hox genes and Hox cluster dispersal in echinoderms.

Szabó R , Ferrier DEK .

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BACKGROUND: Hox genes are key elements in patterning animal development. They are renowned for their, often, clustered organisation in the genome, with supposed mechanistic links between the organisation of the genes and their expression. The widespread distribution and comparable functions of Hox genes across the animals has led to them being a major study system for comparing the molecular bases for construction and divergence of animal morphologies. Echinoderms (including sea urchins, sea stars, sea cucumbers, feather stars and brittle stars) possess one of the most unusual body plans in the animal kingdom with pronounced pentameral symmetry in the adults. Consequently, much interest has focused on their development, evolution and the role of the Hox genes in these processes. In this context, the organisation of echinoderm Hox gene clusters is distinctive. Within the classificatory system of Duboule, echinoderms constitute one of the clearest examples of Disorganized (D) clusters (i.e. intact clusters but with a gene order or orientation rearranged relative to the ancestral state). RESULTS: Here we describe two Hox genes (Hox11/13d and e) that have been overlooked in most previous work and have not been considered in reconstructions of echinoderm Hox complements and cluster organisation. The two genes are related to Posterior Hox genes and are present in all classes of echinoderm. Importantly, they do not reside in the Hox cluster of any species for which genomic linkage data is available. CONCLUSION: Incorporating the two neglected Posterior Hox genes into assessments of echinoderm Hox gene complements and organisation shows that these animals in fact have Split (S) Hox clusters rather than simply Disorganized (D) clusters within the Duboule classification scheme. This then has implications for how these genes are likely regulated, with them no longer covered by any potential long-range Hox cluster-wide, or multigenic sub-cluster, regulatory mechanisms.

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Genes referenced: Hbox7 hoxb6 LOC100887844 LOC105446078

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	Fig. 1. Schematic phylogenetic tree of Ambulacraria with chordates shown as the outgroup. Species used in this study are indicated in brackets next to their respective clades. Species abbreviations: Acpl, Acanthaster planci, Anja, Anneissia japonica, Apja, Apostichopus japonicus, Basi, Balanoglossus simodensis, Brfl, Branchiostoma floridae, Cami, Callorhinchus milii, Lame, Latimeria menadoensis, Lyva, Lytechinus variegatus, Mero, Metacrinus rotundus, Opsp, Ophiothrix spiculata, Pami, Patiria miniata, Papa, Parastichopus parvimensis, Peja, Peronella japonica, Ptfl, Ptychodera flava, Sako, Saccoglossus kowalevskii, Stpu, Strongylocentrotus purpuratus. Tree topology follows [61]
	Fig. 2. Alignment of echinoderm Hox11/13b+ homeodomains and flanking sequences. Identities to S. purpuratus are marked with dots. Potentially diagnostic residues within the homeodomain are highlighted in grey. Flanking sequences (N- and C-peptides) are separated from the homeodomain by a space. The misidentified “Hox11/13c” sequence from ref. [30] is boxed. Species abbreviations: Anja = Anneissia japonica, Mero = Metacrinus rotundus, Opsp = Ophiothrix spiculata, Pami = Patiria miniata, Papa = Parastichopus parvimensis, Peja = Peronella japonica, Stpu = Strongylocentrotus purpuratus
	Fig. 3. Bayesian tree of ANTP class homeodomains from amphioxus, beetle and sea urchin. The dark grey box indicates the Hox/ParaHox clade; Posterior Hox genes are highlighted in light grey and Hox11/13d and e are bolded and boxed. Support values above 50% from the Bayesian, maximum likelihood and NJ analyses are indicated next to the branches. Species abbreviations as before; Trca = Tribolium castaneum
	Fig. 4. Bayesian tree of selected deuterostome Posterior Hox homeodomains and flanking sequences. Grey highlights indicate Hox11/13d and e, and the box shows the position of “Hox11/13c” from P. japonica within our Hox11/13d clade
	Fig. 5. Non-Hox neighbours of Hox11/13d-e. a. Genomic scaffolds containing Hox11/13d. b. Genomic scaffolds containing Hox11/13e. Scale is indicated by the rulers on each scaffold. Scaffolds with reversed rulers have been flipped so that all Hox genes are shown in the same orientation. For sea cucumbers, the species with the most conserved neighbours is shown. The neighbourhood shown for Opsp-Hox11/13d is a composite of two overlapping scaffolds. Gene names prefixed with two-letter species abbreviations are taken directly from Echinobase annotations. Other gene names are based on Genbank annotations, BLAST hits and conserved domain content
	Fig. 6. Potential diagnostic motifs from the non-homeodomain exons of echinoderm Hox11/13b-d. a. Motifs specific to Hox11/13b. b. Motif specific to Hox11/13c. c. Motifs specific to Hox11/13d. Logos were constructed from curated alignments of all echinoderm examples of each motif. For more information see Results and Additional files 3 and 4

References [+] :

Arenas-Mena, Expression of the Hox gene complex in the indirect development of a sea urchin. 1998, Pubmed, Echinobase