The Trichoplax genome and the nature of placozoans

Srivastava, Mansi; Begović, Emina; Chapman, Jarrod; Putnam, Nicholas H.; Hellsten, Uffe; Kawashima, Takeshi; Kuo, Alan; Mitros, Therese; Salamov, Asaf; Carpenter, Meredith L.; Signorovitch, Ana Y.; Moreno, Marlene Aparecida; Kamm, Kai; Grimwood, Jane; Schmutz, Jeremy; Shapiro, Harris; Grigoriev, Igor V.; Buss, Leo W.; Schierwater, Bernd; Dellaporta, Stephen L.; Rokhsar, Daniel S.

doi:10.1038/nature07191

Cited by 832 publications

(906 citation statements)

References 49 publications

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“…The present paper considers further ctenophore and sponge EST data, as well as Trichoplax genome data (Srivastava et al 2008), and still gets the same result in analyses of the 1487-, 844-and 330-gene matrices (figure 2). Since the completion of the analyses presented here, an EST study with sampling from all major groups of sponges has been published (Philippe et al 2009).…”

Section: Discussion (A) Acoelomorpha As Sister Group To Other Bilateriamentioning

confidence: 91%

Assessing the root of bilaterian animals with scalable phylogenomic methods

et al. 2009

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A clear picture of animal relationships is a prerequisite to understand how the morphological and ecological diversity of animals evolved over time. Among others, the placement of the acoelomorph flatworms, Acoela and Nemertodermatida, has fundamental implications for the origin and evolution of various animal organ systems. Their position, however, has been inconsistent in phylogenetic studies using one or several genes. Furthermore, Acoela has been among the least stable taxa in recent animal phylogenomic analyses, which simultaneously examine many genes from many species, while Nemertodermatida has not been sampled in any phylogenomic study. New sequence data are presented here from organisms targeted for their instability or lack of representation in prior analyses, and are analysed in combination with other publicly available data. We also designed new automated explicit methods for identifying and selecting common genes across different species, and developed highly optimized supercomputing tools to reconstruct relationships from gene sequences. The results of the work corroborate several recently established findings about animal relationships and provide new support for the placement of other groups. These new data and methods strongly uphold previous suggestions that Acoelomorpha is sister clade to all other bilaterian animals, find diminishing evidence for the placement of the enigmatic Xenoturbella within Deuterostomia, and place Cycliophora with Entoprocta and Ectoprocta. The work highlights the implications that these arrangements have for metazoan evolution and permits a clearer picture of ancestral morphologies and life histories in the deep past.

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Section: Discussion (A) Acoelomorpha As Sister Group To Other Bilateriamentioning

confidence: 91%

Assessing the root of bilaterian animals with scalable phylogenomic methods

et al. 2009

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“…The simplest hypothesis that explains all available data is summarized. I have assumed a basal phylogenetic position for placozoans, as described by Srivastava et al (2008), and, for protostomes, the ecdysozoa/ lophotrochozoa split. Arrows indicate appearances and rectangles indicate losses.…”

Section: Paramecium Tetraureliamentioning

confidence: 99%

“…The recent sequencing of the genomes of two key organisms, the placozoan Trichoplax adhaerens and the cnidarian Nematostella vectensis (Putnam et al 2007;Srivastava et al 2008), which belong to basal branches of the animal tree, allow us to address three of the questions that remained to be answered regarding the evolution of the RBR family in animals. A first significant question is to determine when the animal-specific subfamilies emerged.…”

Section: Introductionmentioning

confidence: 99%

RBR Ubiquitin Ligases: Diversification and Streamlining in Animal Lineages

Marı́n

2009

J Mol Evol

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The patterns of emergence and disappearance in animal species of genes encoding RBR ubiquitin ligases are described. RBR genes can be classified into subfamilies (Parkin, Ariadne, Dorfin, ARA54, etc.) according to sequence and structural data. Here, I show that most animal-specific RBR subfamilies emerged early in animal evolution, and that ancient animals, before the cnidarian/ bilaterian split, had a set of RBR genes, which was as complex as the one currently found in mammals. However, some lineages (nematodes, dipteran insects) have recently suffered multiple losses, leading to a highly simplified set of RBR genes. Genes of a particular RBR subfamily, characterized by containing a helicase domain and so far found only in plants, are present also in some animal species. The meaning of these patterns of diversification and streamlining are discussed at the light of functional data. Extreme evolutionary conservation may be related to gene products having housekeeping functions.

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“…An essential component of the basal lamina is type IV collagen. Although T. adhaerens [42] and some sponges [57] express portions of this protein, they either lack the enzyme peroxidasin, which in eumetazoans converts certain amino acid residues of type IV collagen into sulfilimine cross-links, or their type IV-like collagen domains lack the residues themselves [58]. Recent work indicates that the evolutionary confluence of the enzyme and its protein substrates, which produced a mechanically stable planar scaffold, was a key step in the innovation of true epithelia and diploblasty, and essential to organogenesis [58].…”

Section: Extracellular Matrices Diploblasty and Triploblastymentioning

confidence: 99%

“…Once the full pathway was assembled in the ancestors of sponges (Delta is present in all metazoans including the placozoan [42]), it enabled (by enforcing alternative gene expression states in adjoining cells with a common genome), the regulated coexistence of multiple cell types within a common tissue mass. These states potentially include adhesive differences, which even though established in a local fine-grained fashion by the Notch-DSL lateral inhibition mechanism, will lead to sorting out into distinct tissue layers by virtue of the biogeneric liquid behaviours described above.…”

Section: 'Liquid Tissues' and The First Animalsmentioning

confidence: 99%

‘Biogeneric’ developmental processes: drivers of major transitions in animal evolution

Newman

2016

Phil. Trans. R. Soc. B

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One contribution of 13 to a theme issue 'The major synthetic evolutionary transitions'. Using three examples drawn from animal systems, I advance the hypothesis that major transitions in multicellular evolution often involved the constitution of new cell-based materials with unprecedented morphogenetic capabilities. I term the materials and formative processes that arise when highly evolved cells are incorporated into mesoscale matter 'biogeneric', to reflect their commonality with, and distinctiveness from, the organizational properties of non-living materials. The first transition arose by the innovation of classical cell-adhesive cadherins with transmembrane linkage to the cytoskeleton and the appearance of the morphogen Wnt, transforming some ancestral unicellular holozoans into 'liquid tissues', and thereby originating the metazoans. The second transition involved the new capabilities, within a basal metazoan population, of producing a mechanically stable basal lamina, and of planar cell polarization. This gave rise to the eumetazoans, initially diploblastic (twolayered) forms, and then with the addition of extracellular matrices promoting epithelial-mesenchymal transformation, three-layered triploblasts. The last example is the fin-to-limb transition. Here, the components of a molecular network that promoted the development of species-idiosyncratic endoskeletal elements in gnathostome ancestors are proposed to have evolved to a dynamical regime in which they constituted a Turing-type reaction-diffusion system capable of organizing the stereotypical arrays of elements of lobe-finned fish and tetrapods. The contrasting implications of the biogeneric materialsbased and neo-Darwinian perspectives for understanding major evolutionary transitions are discussed.This article is part of the themed issue 'The major synthetic evolutionary transitions'.

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The Trichoplax genome and the nature of placozoans

Cited by 832 publications

References 49 publications

Assessing the root of bilaterian animals with scalable phylogenomic methods

Assessing the root of bilaterian animals with scalable phylogenomic methods

RBR Ubiquitin Ligases: Diversification and Streamlining in Animal Lineages

‘Biogeneric’ developmental processes: drivers of major transitions in animal evolution

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