. Data, Supplementary table S1 containing the complete list and description of all 488 proteins identified in E. complanata and V. Lienosa nacre matrices by shotgun proteomics has 489 been uploaded as electronic supplementary materials

. Copamox and . Dmp, dentin matrix protein; EGF, epidermal growth factor; 496 FAM20C, family with sequence similarity 20 -member C; FN3, fibronectin 3; IGF-BP, 497 insulin growth factor-binding protein; KU, Kunitz-like domain; LamG, laminin G; MSP, 498 mesenchym-specific protein; MSI60, matrix silk-like insoluble protein 60, p.499

G. B. Author-'s-contribution and S. B. Conception, preparation of the sample, analysis and interpretation of the data

D. Piquemal, F. Marin, Y. Gueguen, and C. Montagnani, 2012 Different secretory repertoires 522 control the biomineralization processes of prism and nacre deposition of the pearl oyster 523 shell, Proc Natl Acad Sci, vol.109, pp.20986-20991

M. Suzuki and H. Nagasawa, 2013 Mollusk shell structures and their formation mechanism, p.527
DOI : 10.1139/cjz-2012-0333

G. Falini, S. Albeck, S. Weiner, and L. Addadi, Control of Aragonite or Calcite Polymorphism by Mollusk Shell Macromolecules, Science, vol.271, issue.5245, pp.67-69
DOI : 10.1126/science.271.5245.67

S. Berland, O. Delattre, S. Borzeix, Y. Catonne, and E. Lopez, Nacre/bone interface changes in durable nacre endosseous implants in sheep, Biomaterials, vol.26, issue.15, pp.2767-2773, 2005.
DOI : 10.1016/j.biomaterials.2004.07.019

URL : https://hal.archives-ouvertes.fr/hal-00131382

F. Marin, G. Luquet, M. B. Medakovic, and D. , Molluscan shell proteins, Comptes Rendus Palevol, vol.3, issue.6-7, pp.209-276, 2008.
DOI : 10.1016/j.crpv.2004.07.009

URL : https://hal.archives-ouvertes.fr/hal-00197133

F. Marin, L. Roy, N. , and M. B. , 2012 The formation and mineralization of mollusc shell, p.537

L. Addadi, D. Joester, F. Nudelman, and S. Weiner, Mollusk shell formation: a source of 539 new concepts for understanding biomineralization processes, Geometrical and crystallographic constrains 541 determine the self-organisation of the shell microstructures in Unionidae, pp.980-987, 2001.

A. Kouchinsky, Shell microstructures in Early Cambrian molluscs, Acta Palaeontol, p.544, 2000.

J. Carter, Skeletal Biomineralization: Patterns, Processes and Evolutionary Trends, p.549, 1990.

C. Liu, S. Li, J. Kong, Y. Liu, T. Wang et al., 2015 In-depth proteomic analysis 554 of shell proteins of Pinctada fucata, pp.17269-555

P. Gao, Z. Liao, X. Wang, L. Bao, M. Fan et al., 2015 Layer-by-layer 556 proteomic analysis of Mytilus galloprovincialis shell, PLoS ONE, vol.10, pp.133913-557

Z. Liao, L. Bao, M. Fan, P. Gao, X. Wang et al., In-depth proteomic analysis of nacre, prism, and myostracum of Mytilus shell, Journal of Proteomics, vol.122, pp.26-40
DOI : 10.1016/j.jprot.2015.03.027

D. Rokshar, C. Montagnani, C. Joubert, D. Piquemal, and B. Degnan, 2010 Parallel evolution 564 of nacre building gene sets in molluscs, Mol Biol Evol, vol.27, pp.591-608

L. Plasseraud, M. Corneillat, G. Alcaraz, J. Kaandorp, and F. Marin, 2012 Novel molluscan 570 biomineralization proteins retrieved from proteomics: a case study with Upsalin

S. Berland, Y. Ma, M. A. Andrieu, J. Bédouet, L. Feng et al., Proteomic and profile 573 analysis of the proteins laced with aragonite and vaterite mussel Hyriopsis cumingii shell 574 biominerals, pp.1170-1180, 2013.

B. Marie, J. Aviralagan, L. Dubost, S. Berland, M. A. Marin et al., Unveiling the Evolution of Bivalve Nacre Proteins by Shell Proteomics of Unionoidae, Key Engineering Materials, vol.672, issue.577, pp.158-167
DOI : 10.4028/www.scientific.net/KEM.672.158

URL : https://hal.archives-ouvertes.fr/hal-01194537

R. Wang, C. Li, J. Stoeckel, G. Moyer, Z. Liu et al., (Bivalvia:Unionidae), using an RNA-seq-based approach, Freshwater Science, vol.31, issue.3, pp.695-708
DOI : 10.1899/11-149.1.s6

R. Cornman, L. Robertson, H. Galbraith, and C. Blakeslee, Transcriptomic Analysis of the Mussel Elliptio complanata Identifies Candidate Stress-Response Genes and an Abundance of Novel or Noncoding Transcripts, PLoS ONE, vol.40, issue.11, pp.112420-584
DOI : 10.1371/journal.pone.0112420.s007

M. Suzuki, A. Iwasima, N. Tsutsui, T. Ohira, T. Kogure et al., 2011 Identification 588 and characterisation of a calcium carbonate-binding protein, blue mussel shell protein 589 (BMSP), from the nacreous layer, ChemBioChem, vol.16, pp.278-287

B. Marie, D. Jackson, P. Ramos-silva, I. Zanella-cléon, N. Guichard et al., reveals both deep conservations and lineage-specific novelties, FEBS Journal, vol.36, issue.1, pp.214-232
DOI : 10.1111/febs.12062

URL : https://hal.archives-ouvertes.fr/hal-00771503

B. Marie, L. Roy, N. Zanella-cléon, I. Becchi, M. Marin et al., 2011 Molecular evolution of 594 mollusc shell proteins: insights from proteomic analysis of the edible mussel Mytilus, p.595

B. Marie, I. Zanella-cléon, N. Guicahrd, M. Becchi, and F. Marin, The calcifying shell 597 matrix of the Pacific oyster Crassostrea gigas: proteomic identification of novel proteins, p.598, 2011.

J. Xiao, V. Tagliabracci, J. Wen, S. Kim, and J. Dixon, Crystal structure of the Golgi casein kinase, Proceedings of the National Academy of Sciences, vol.37, issue.suppl_1, pp.10574-10579
DOI : 10.1093/nar/gkn750

J. Sagert and J. Waite, Hyperunstable matrix protein in the byssus of Mytilus 602 galloprovincialis, J Exp Biol, vol.212, pp.224-2236, 2009.

T. Takahashi, Structures of mollusc shell framework proteins, Nature, vol.387, pp.563-564, 1997.

X. Liu, S. Dong, C. Jin, Z. Bai, G. Wang et al., Silkmapin of Hyriopsis cumingii, a novel silk-like shell matrix protein involved in nacre formation, Gene, vol.555, issue.2, pp.217-222
DOI : 10.1016/j.gene.2014.11.006

N. Yano, K. Nagai, K. Morimoto, and H. Miyamoto, Shematrin: A family of glycine-rich structural proteins in the shell of the pearl oyster Pinctada fucata, Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, vol.144, issue.2, pp.254-262, 2006.
DOI : 10.1016/j.cbpb.2006.03.004

T. Samata, Daily oscillation of gene expression associated with nacreous layer 611 formation, Front Mater Sci China, vol.2, pp.162-166, 2008.

C. Qin, Q. Pan, Q. Qi, M. Fan, J. Sin et al., In-depth proteomic analysis of the byssus from marine mussel Mytilus coruscus, Journal of Proteomics, vol.144, pp.87-98
DOI : 10.1016/j.jprot.2016.06.014

S. Berland, M. A. Duplat, D. Milet, C. Sire, J. Bédouet et al., Coupling Proteomics and Transcriptomics for the Identification of Novel and Variant Forms of Mollusk Shell Proteins: A Study with P. margaritifera, ChemBioChem, vol.270, issue.6, pp.950-961
DOI : 10.1002/cbic.201000667

K. Kawasaki, A. Buchanan, and K. Weiss, Biomineralization in Humans: Making the Hard Choices in Life, Annual Review of Genetics, vol.43, issue.1, pp.119-142, 2009.
DOI : 10.1146/annurev-genet-102108-134242

J. Catesy, C. Hayashi, D. Motruik, J. Woods, and R. Lewis, Conservation and convergence 620 of spider silk fibroin sequences, Science, vol.291, pp.2603-2605, 2001.

B. Marie, C. Joubert, A. Tayale, I. Zanella-cléon, F. Marin et al., MRNP34, a novel methionine-rich protein from the pearl oysters, Amino Acids, vol.622, issue.623, pp.2012-2009
URL : https://hal.archives-ouvertes.fr/hal-00687965

C. Mcdougall, F. Aguilera, and B. Degnan, 2013 Rapid evolution of pearl oyster shell matrix 625 proteins with repetitive, low complexity domains, J R Soc Interface, vol.10, p.626, 20130041.

D. Jackson, L. Macis, J. Reitner, B. Degnan, and G. Wörheide, Sponge paleogenomics 630 reveals an ancient role for carbonic anhydrase in skeletogenesis, Science, vol.216, pp.1893-1895, 2007.

K. Mann, B. Macek, and J. Olsen, Proteomic analysis of the acid-soluble organic matrix of the chicken calcified eggshell layer, PROTEOMICS, vol.15, issue.13, pp.3801-3810, 2006.
DOI : 10.1002/pmic.200600120

K. Nagai, M. Yano, K. Morimoto, and H. Miyamoto, Tyrosinase localization in mollusc shells, Tyrosinase localization in mollusc 634 shells, pp.207-214, 2007.
DOI : 10.1016/j.cbpb.2006.10.105

K. Mann and E. Edsinger, 2014 The Lottia gigantea shell matrix proteome: re-analysis 636 including MaxQaunt iBAQ quantification and phosphoproteome analysis, Proteome Sci, vol.637, issue.28, pp.12-638

C. Oliveri, L. Peric, S. Sforzini, M. Banni, A. Viarengo et al., 2014 Biochemical and 639 proteomic characterisation of haemolymph serum reveals the origin of the alkali-labile 640 phosphate (ALP) in mussel (Mytilus galloprovincialis), Comp Biochem Physiol Part D, p.641

L. Treccani, K. Mann, F. Heinemann, and M. Fritz, Perlwapin, an Abalone Nacre Protein with Three Four-Disulfide Core (Whey Acidic Protein) Domains, Inhibits the Growth of Calcium Carbonate Crystals, Biophysical Journal, vol.91, issue.7, pp.2601-2608, 2006.
DOI : 10.1529/biophysj.106.086108

J. Arivalagan, M. B. Sleight, V. Clark, M. Berland, S. et al., 2016 Shell matrix 652 proteins of the clam, Mya truncata: Roles beyond shell formation through proteomic study 653

. Eggsepins, The chicken and/or the egg dilemma Semin Cell Dev Biol in press

M. Rousseau and E. Lopez, 2010 Voyaging around nacre with the X-ray shuttle: from bio- 664 mineralisation to prosthetics via mollusc phylogeny, Mater Sci Engin A, vol.528, pp.37-51

D. Jackson, K. Mann, V. Häussermann, M. Schilhabel, C. Lüter et al., 2015 The Magellania venosa biomineralizing proteome, p.667
DOI : 10.1093/gbe/evv074

URL : http://doi.org/10.1093/gbe/evv074

S. Yamasaki, K. Endo, and N. Satoh, 2015 The Lingula genome provides insights into 670 brachiopod evolution and the origin of phosphate biomineralization, Nature Comm, vol.6, pp.671-8301

F. Marin, P. Layrolle, D. Groot, K. Westbroek, and P. , The Origin of metazoan skeleton, p.673, 2003.

L. Roy, N. Jackson, D. , M. B. Ramos-silva, P. Marin et al., 2014 The volution of metazoan 676 ?-carbonic anhydrases and their roles in calcium carbonate Antibodies 678 to a fusion protein identify a cDNA clone encoding msp130, a primary mesenchyme- 679 specific cell surface protein of the sea urchin embryo, Frontiers Zool Dev Biol, vol.11, issue.121, pp.29-40, 1987.

K. Mann, F. Wilt, and A. Poustka, 2010 Proteomic analysis of sea urchin (Strongylocentrotus 684 purpuratus) spicule matrix, Proteome Sci, vol.8, issue.33, p.685
DOI : 10.1186/1477-5956-8-33

URL : http://doi.org/10.1186/1477-5956-8-33

R. Szabo, D. Ferrier, S. Wiley, X. Guo, L. Kinch et al., gene structure across Bilateria, Evolution & Development, vol.22, issue.3, pp.195-197
DOI : 10.1111/ede.12122

J. Engel, J. Coon, N. Grishin, L. Pinna, D. Pagliarini et al., 2015 A single Kinase generates 689 the majority of the secreted phosphoproteome, Cell, vol.161, pp.1619-1632

F. Marin, I. Bundeleva, T. Takeuchi, F. Immel, and D. Medakovic, 2016 Organic matrices in 691 metazoan calcium carbonate skeletons: composition, functions, evolution, J Struct Biol
DOI : 10.1016/j.jsb.2016.04.006

B. Marie, P. Ramos-silva, F. Marin, and M. A. , biomineral-associated proteins: How to properly address their analysis, PROTEOMICS, vol.12, issue.21, pp.3109-3116
DOI : 10.1002/pmic.201300162

URL : https://hal.archives-ouvertes.fr/hal-00954233

S. Berland, 2016 Insight from the shell proteome: biomineralization to adaptation, Mol Biol, vol.697

L. Kelley, S. Mezullis, C. Yates, M. Wass, and M. Stengerg, The Phyre2 web portal for protein modeling, prediction and analysis, Nature Protocols, vol.1, issue.6, pp.845-858
DOI : 10.1093/bioinformatics/btl677

H. Xie, Y. Holland, P. Paps, J. Zhu, Y. Wu et al., 2012 The oyster genome reveals stress 702 adaptation and complexity of shell formation, Nature, vol.490, pp.49-54

K. Mann and D. Jackson, Characterization of the pigmented shell-forming proteome of the common grove snail Cepaea nemoralis, BMC Genomics, vol.15, issue.1, p.249
DOI : 10.1101/gr.092759.109