Mollusca evolutionary success can be attributed partly to their efficiency to sustain and protect their soft body with an external biomineralized structure, the shell. Current knowledge of the protein set responsible for the formation of the shell microstructural polymorphism and unique properties remains largely patchy. In Pinctada margaritifera and Pinctada maxima, we identified 80 shell matrix proteins, among which 66 are entirely unique. This is the only description of the whole "biomineralization toolkit" of the matrices that, at least in part, is thought to regulate the formation of the prismatic and nacreous shell layers in the pearl oysters. We unambiguously demonstrate that prisms and nacre are assembled from very different protein repertoires. This suggests that these layers do not derive from each other.mantle | mollusk shell matrix proteins | proteome | transcriptome | evolution

The last decade highlighted polyploidy as a rampant evolutionary process that triggers drastic genome reorganization, but much remains to be understood about their causes and consequences in both autopolyploids and allopolyploids. Here, we provide an overview of the current knowledge on the pathways leading to different types of polyploids and patterns of polyploidy-induced genome restructuring and functional changes in plants. Available evidence leads to a tentative ‘diverge, merge and diverge' model supporting polyploid speciation and stressing patterns of divergence between diploid progenitors as a suitable predictor of polyploid genome reorganization. The merging of genomes at the origin of a polyploid lineage may indeed reveal different kinds of incompatibilities (chromosomal, genic and transposable elements) that have accumulated in diverging progenitors and reduce the fitness of nascent polyploids. Accordingly, successful polyploids have to overcome these incompatibilities through non-Mendelian mechanisms, fostering polyploid genome reorganization in association with the establishment of new lineages. See also sister article focusing on animals by Collares-Pereira et al., in this themed issue.

-Producing high quality cultured black pearls from Pinctada margaritifera is one of the major challenges for the "pearl oyster" industry in French Polynesia. In order to assess donor effect on cultured pearl quality, wild Pinctada margaritifera originating from the Tuamotu Archipelago were used in a duplicated grafting experiment. After 12 months of culture, nucleus retention was assessed and seven pearl quality traits recorded on the 454 cultured pearls harvested from the experiment. The traits scored were nacre thickness and pearl weight, surface defects, lustre, grade, and the colour components: 1) darkness of cultured pearl colour, and 2) visual perception of colour class (bodycolor and/or overtone). Our results demonstrate for the first time that individual wild donors of implanted mantle grafts significantly affect these seven quality traits in P. margaritifera cultured pearls. This finding was repeated in two series of grafts made by different professional grafters. The wild donors could be ranked from "best" (e.g., the donor whose grafts produced the cultured pearl with the maximum lustre) to the "worst". Moreover, we showed strong correlations between: 1) cultured pearl nacre thickness and grade, with grade A showing the greatest nacre thickness on average compared with grade D and rejects; and 2) nacre thickness/cultured pearl weight and colour components (darkness and visual "colour categories"), with the palest cultured pearls (i.e. white cultured pearls) being the smallest (lowest nacre thickness and weight). Thus, one way of enhancing P. margaritifera foundation stocks for a selective breeding program could be to select the "best" donors, using appropriate molecular tools. Generation of selected donor lines from these stocks through hatchery production would be one way to increase the quality of cultured pearl farming of P. margaritifera in French Polynesia.

The shell of pearl oysters is organized in multiple layers of CaCO(3) crystallites packed together in an organic matrix. Relationships between the components of the organic matrix and mechanisms of nacre formation currently constitute the main focus of research into biomineralization. In this study, we characterized the pearlin protein from the oyster Pinctada margaritifera (Pmarg); this shares structural features with other members of a matrix protein family, N14/N16/pearlin. Pmarg pearlin exhibits calcium- and chitin-binding properties. Pmarg pearlin transcripts are distinctively localized in the mineralizing tissue responsible for nacre formation. More specifically, we demonstrate that Pmarg pearlin is localized within the interlamellar matrix of nacre aragonite tablets. Our results support recent models for multidomain matrix protein involvement in nacreous layer formation. We provide evidence here for the existence of a conserved family of nacre-associated proteins in Pteriidae, and reassess the evolutionarily conserved set of biomineralization genes related to nacre formation in this taxa.

SUMMARYLong terminal repeat retrotransposons (LTR-RTs) represent a major fraction of plant genomes, but processes leading to transposition bursts remain elusive. Polyploidy expectedly leads to LTR-RT proliferation, as the merging of divergent diploids provokes a genome shock activating LTR-RTs and/or genetic redundancy supports the accumulation of active LTR-RTs through relaxation of selective constraints. Available evidence supports interspecific hybridization as the main trigger of genome dynamics, but few studies have addressed the consequences of intraspecific polyploidy (i.e. autopolyploidy), where the genome shock is expectedly minimized. The dynamics of LTR-RTs was thus here evaluated through low coverage 454 sequencing of three closely related diploid progenitors and three independent autotetraploids from the young Biscutella laevigata species complex. Genomes from this early diverging Brassicaceae lineage presented a minimum of 40% repeats and a large diversity of transposable elements. Differential abundances and patterns of sequence divergence among genomes for 37 LTR-RT families revealed contrasted dynamics during species diversification. Quiescent LTR-RT families with limited genetic variation among genomes were distinguished from active families (37.8%) having proliferated in specific taxa. Specific families proliferated in autopolyploids only, but most transpositionally active families in polyploids were also differentiated among diploids. Low expression levels of transpositionally active LTR-RT families in autopolyploids further supported that genome shock and redundancy are non-mutually exclusive triggers of LTR-RT proliferation. Although reputed stable, autopolyploid genomes show LTR-RT fractions presenting analogies with polyploids between widely divergent genomes.

Nacre of the Pinctada pearl oyster shells is composed of 98% CaCO3 and 2% organic matrix. The relationship between the organic matrix and the mechanism of nacre formation currently constitutes the main focus regarding the biomineralization process. In this study, we isolated a new nacre matrix protein in P. margaritifera and P. maxima, we called Pmarg- and Pmax-MRNP34 (methionine-rich nacre protein). MRNP34 is a secreted hydrophobic protein, which is remarkably rich in methionine, and which is specifically localised in mineralizing the epithelium cells of the mantle and in the nacre matrix. The structure of this protein is drastically different from those of the other nacre proteins already described. This unusual methionine-rich protein is a new member in the growing list of low complexity domain containing proteins that are associated with biocalcifications. These observations offer new insights to the molecular mechanisms of biomineralization.