Diversification of spatiotemporal expression and copy number variation of the echinoid hbox12/pmar1/micro1 multigene family.

Michael Schubert,Vincenzo Cavalieri,Giovanni Spinelli,Fabiana Geraci

doi:10.1371/journal.pone.0174404

Abstract

Changes occurring during evolution in the cis-regulatory landscapes of individual members of multigene families might impart diversification in their spatiotemporal expression and function. The archetypal member of the echinoid hbox12/pmar1/micro1 family is hbox12-a, a homeobox-containing gene expressed exclusively by dorsal blastomeres, where it governs the dorsal/ventral gene regulatory network during embryogenesis of the sea urchin Paracentrotus lividus. Here we describe the inventory of the hbox12/pmar1/micro1 genes in P. lividus, highlighting that gene copy number variation occurs across individual sea urchins of the same species. We show that the various hbox12/pmar1/micro1 genes group into three subfamilies according to their spatiotemporal expression, which ranges from broad transcription throughout development to transient expression in either the animal hemisphere or micromeres of the early embryo. Interestingly, the promoter regions of those genes showing comparable expression patterns are highly similar, while differing from those of the other subfamilies. Strikingly, phylogenetic analysis suggests that the hbox12/pmar1/micro1 genes are species-specific, exhibiting extensive divergence in their noncoding, but not in their coding, sequences across three distinct sea urchin species. In spite of this, two micromere-specific genes of P. lividus possess a TCF/LEF-binding motif in a similar position, and their transcription relies on Wnt/β-catenin signaling, similar to the pmar1 and micro1 genes, which in other sea urchin species are involved in micromere specification. Altogether, our findings suggest that the hbox12/pmar1/micro1 gene family evolved rather rapidly, generating paralogs whose cis-regulatory sequences diverged following multiple rounds of duplication from a common ancestor.

Highlights

The last two decades of research in the field of molecular embryology have provided a detailed mechanistic explanation of how fates of different cell types are encoded in the genome and sculpted through the sequential progression of transcriptional states of defined regulatory genes [1,2,3,4]
The fact that the Hbox12-a and Pmar1/Micro1 regulators display high sequence similarity across species but serve different functions poses the question of whether diversification of their cisregulatory sequences has arisen during evolution by duplication of a common ancestor. We address this question by describing the inventory of the hbox12/ pmar1/micro1 genes present in P. lividus, and highlighting that gene copy number variation occurs across the genome of distinct individual sea urchins of the same species
Members of multigene families expanded rapidly as tandem duplicates displaying a multitude of highly diverse tissue-specific expression during embryogenesis of drosophilids [58,59,60]

Summary

Introduction

The last two decades of research in the field of molecular embryology have provided a detailed mechanistic explanation of how fates of different cell types are encoded in the genome and sculpted through the sequential progression of transcriptional states of defined regulatory genes [1,2,3,4]. Much less is known about the driving forces underlying dynamic rewiring of gene regulatory network circuitries during evolution [5,6,7,8,9]. The echinoid hbox12/pmar1/micro multigene family commonly accepted that gene duplication provides a major source of both evolutionary novelty and species diversification. By transient inactivation of p38-MAP kinase activity during very early cleavage, Hbox12-a defines the future dorsal side of the embryo, allowing the expression of the TGF-β superfamily member Nodal on the opposite side [14,15,16]. Afterwards, Nodal-dependent signaling imposes the dorsal-ventral polarity in the developing embryo [17,18,19,20]

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Results

Conclusion