1.Vicente N, Moreteau J: Statut de Pinna nobilis L. en Mediterranee (mollusque eulamellibranche). Les espèces marines à protéger en Méditerranée 1991:159–168.
2.Zavodnik D, Hrs-Brenko M, Legac M: Synopsis on the fan shell Pinna nobilis L. in the eastern Adriatic Sea. Les espèces marines à protéger en Méditerranée 1991:169–178.
3.Rouanet E, Trigos S, Vicente N: From youth to death of old age: the 50-year story of a Pinna nobilis fan mussel population at Port-Cros Island (Port-Cros National Park, Provence, Mediterranean Sea). Scientific Reports of Port–Cros National Park 2015, 29:209–222.
4.Butler A, Vicente N, De Gaulejac B: Ecology of the pterioid bivalves Pinna bicolor Gmelin and Pinna nobilis L. Marine Life 1993, 3(1–2):37–45.
5.Trigos S, García-March J, Vicente N, Tena J, Torres J: Utilization of muddy detritus as organic matter source by the fan mussel Pinna nobilis. Mediterranean Marine Science 2014, 15(3):667–674.
6.Rabaoui L, Zouari ST, Hassine OKB: Two species of Crustacea (Decapoda) associated with the fan mussel, Pinna nobilis Linnaeus, 1758 (Mollusca, Bivalvia). Crustaceana 2008:433–446.
7.Addis P, Secci M, Brundu G, Manunza A, Corrias S, Cau A: Density, size structure, shell orientation and epibiontic colonization of the fan mussel Pinna nobilis L. 1758 (Mollusca: Bivalvia) in three contrasting habitats in an estuarine area of Sardinia (W Mediterranean). Scientia Marina 2009, 73(1):143–152.
8.Rabaoui L, Tlig-Zouari S, Cosentino A, Hassine OKB: Associated fauna of the fan shell Pinna nobilis (Mollusca: Bivalvia) in the northern and eastern Tunisian coasts. Scientia Marina 2009, 73(1):129–141.
9.Basso L, Vazquez-Luis M, Garcia-March JR, Deudero S, Alvarez E, Vicente N, Duarte CM, Hendriks IE: The pen shell, Pinna nobilis: A review of population status and recommended research priorities in the Mediterranean Sea. Advances in marine biology 2015, 71:109–160.
10.Médioni E. V, N.: Kinetic study of the populations of Pinna nobilis L.1758, on the French Mediterranean coasts. Premier séminaire international sur la grande nacre de Méditerranée 10–12 octobre 2002, Ile des Embiez, France 2002, Mémoires de l’Institut océanographique Paul Ricard:43–48.
11.Vicente N: La grande nacre de Méditerranée Pinna nobilis. Présentation générale. Premier séminaire international sur la grande nacre de Méditerranée 10–12 octobre 2002, Ile des Embiez, France 2002, Mémoires de l’Institut océanographique Paul Ricard:7–16.
12.Siletic T, Peharda M: Population study of the fan shell Pinna nobilis L. in Malo and Veliko Jezero of the Mljet National Park (Adriatic Sea). Scientia Marina 2003, 67(1):91–98.
13.Centoducati G, Tarsitano E, Bottalico A, Marvulli M, Lai OR, Crescenzo G: Monitoring of the endangered Pinna nobilis Linne, 1758 in the Mar Grande of Taranto (Ionian sea, Italy). Environmental Monitoring and Assessment 2007, 131(1–3):339–347.
14.Darriba S: First haplosporidan parasite reported infecting a member of the Superfamily Pinnoidea (Pinna nobilis) during a mortality event in Alicante (Spain, Western Mediterranean). Journal of invertebrate pathology 2017, 148:14–19.
15.Vázquez-Luis M, Álvarez E, Barrajón A, García-March JR, Grau A, Hendriks IE, Jiménez S, Kersting D, Moreno D, Pérez M: SOS Pinna nobilis: a mass mortality event in western Mediterranean Sea. Frontiers in Marine Science 2017, 4:220.
16.Carella F, Aceto S, Pollaro F, Miccio A, Iaria C, Carrasco N, Prado P, De Vico G: A mycobacterial disease is associated with the silent mass mortality of the pen shell Pinna nobilis along the Tyrrhenian coastline of Italy. Scientific reports 2019, 9(1):2725.
17.García-March JR T-MJ, Henandis-Caballero S, Vázquez-Luis M, López D, Téllez C, Prado P, Navas JI, Bernal J, Catanese G, Grau A, López-Sanmartín M, Nebot-Colomer E, Ortega A, Planes S, Kersting D, Jimenez S, Hendriks I, Moreno D, Giménez-Casalduero F, Pérez M, Izquierdo A, Sánchez J, Vicente N, Sanmarti N, Guimerans Mt, Crespo JL, Valencia JM, Torres J, Barrajon A, Álvarez E, Peyran C, Morage T, Deudero S,: Can we save a marine species affected by a highly-infective-highly-lethal-waterborne disease from extinction? Biological Conservation (In review).
18.IUCN: https://www.iucn.org/news/mediterranean/201907/mediterranean-noble-pen-shell-crisis-pinna-nobilis-june–2019-update. 2019.
19.Katsanevakis S, Tsirintanis K, Tsaparis D, Doukas D, Sini M, Athanassopoulou F, Κolygas M, Tontis D, Koutsoubas D, Bakopoulos V: The cryptogenic parasite Haplosporidium pinnae invades the Aegean Sea and causes the collapse of Pinna nobilis populations. Aquatic Invasions 2019, 14(2):150–164.
20.Panarese R, Tedesco P, Chimienti G, Latrofa MS, Quaglio F, Passantino G, Buonavoglia C, Gustinelli A, Tursi A, Otranto D: Haplosporidium pinnae associated with mass mortality in endangered Pinna nobilis (Linnaeus 1758) fan mussels. Journal of invertebrate pathology 2019, 164:32–37.
21.Miller DJ, Hemmrich G, Ball EE, Hayward DC, Khalturin K, Funayama N, Agata K, Bosch TC: The innate immune repertoire in Cnidaria - ancestral complexity and stochastic gene loss. Genome Biology 2007, 8(4):R59.
22.Ponting CP: The functional repertoires of metazoan genomes. Nature Reviews Genetics 2008, 9(9):689.
23.Gerdol M: Immune-related genes in gastropods and bivalves: a comparative overview. Invertebrate Survival Journal 2017(1):103–118%V 114.
24.Philipp EE, Kraemer L, Melzner F, Poustka AJ, Thieme S, Findeisen U, Schreiber S, Rosenstiel P: Massively parallel RNA sequencing identifies a complex immune gene repertoire in the lophotrochozoan Mytilus edulis. PLoS One 2012, 7(3):e33091.
25.Goldstone JV, Hamdoun A, Cole BJ, Howard-Ashby M, Nebert DW, Scally M, Dean M, Epel D, Hahn ME, Stegeman JJ: The chemical defensome: environmental sensing and response genes in the Strongylocentrotus purpuratus genome. Dev Biol 2006, 300(1):366–384.
26.Du X, Fan G, Jiao Y, Zhang H, Guo X, Huang R, Zheng Z, Bian C, Deng Y, Wang Q: The pearl oyster Pinctada fucata martensii genome and multi-omic analyses provide insights into biomineralization. GigaScience 2017, 6(8):gix059.
27.Murgarella M, Puiu D, Novoa B, Figueras A, Posada D, Canchaya C: A First Insight into the Genome of the Filter-Feeder Mussel Mytilus galloprovincialis. PLoS One 2016, 11(3):e0151561-e0151561.
28.Zhang G, Fang X, Guo X, Li L, Luo R, Xu F, Yang P, Zhang L, Wang X, Qi H: The oyster genome reveals stress adaptation and complexity of shell formation. Nature 2012, 490(7418):49.
29.Gestal C, Roch P, Renault T, Pallavicini A, Paillard C, Novoa B, Oubella R, Venier P, Figueras A: Study of diseases and the immune system of bivalves using molecular biology and genomics. Reviews in Fisheries Science 2008, 16(sup1):133–156.
30.Gerdol M, Venier P: An updated molecular basis for mussel immunity. Fish & shellfish immunology 2015, 46(1):17–38.
31.Venier P, Varotto L, Rosani U, Millino C, Celegato B, Bernante F, Lanfranchi G, Novoa B, Roch P, Figueras A: Insights into the innate immunity of the Mediterranean mussel Mytilus galloprovincialis. BMC genomics 2011, 12(1):69.
32.Watermann B, Herlyn M, Daehne B, Bergmann S, Meemken M, Kolodzey H: Pathology and mass mortality of Pacific oysters, Crassostrea gigas (Thunberg), in 2005 at the East Frisian coast, Germany. Journal of Fish Diseases 2008, 31(8):621–630.
33.Gurevich A, Saveliev V, Vyahhi N, Tesler G: QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013, 29(8):1072–1075.
34.Marçais G, Kingsford C: A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 2011, 27(6):764–770.
35.Kelley DR, Schatz MC, Salzberg SL: Quake: quality-aware detection and correction of sequencing errors. Genome Biology 2010, 11(11):R116.
36.Gregory TR: Animal Genome Size Database. http://www.genomesize.com. 2019.
37.Takeuchi T, Kawashima T, Koyanagi R, Gyoja F, Tanaka M, Ikuta T, Shoguchi E, Fujiwara M, Shinzato C, Hisata K: Draft genome of the pearl oyster Pinctada fucata: a platform for understanding bivalve biology. DNA research 2012, 19(2):117–130.
38.Chikhi R, Medvedev P: Informed and automated k-mer size selection for genome assembly. Bioinformatics 2013, 30(1):31–37.
39.Vurture GW, Sedlazeck FJ, Nattestad M, Underwood CJ, Fang H, Gurtowski J, Schatz MC: GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics 2017, 33(14):2202–2204.
40.http://www.repeatmasker.org.
41.Pickett BD, Miller JB, Ridge PG: Kmer-SSR: a fast and exhaustive SSR search algorithm. Bioinformatics 2017, 33(24):3922–3928.
42.Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M: Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005, 21(18):3674–3676.
43.Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM: BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 2015, 31(19):3210–3212.
44.Waterhouse RM, Seppey M, Simão FA, Manni M, Ioannidis P, Klioutchnikov G, Kriventseva EV, Zdobnov EM: BUSCO applications from quality assessments to gene prediction and phylogenomics. Molecular biology and evolution 2017, 35(3):543–548.
45.Stanke M, Steinkamp R, Waack S, Morgenstern B: AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic acids research 2004, 32(suppl_2):W309-W312.
46.Jones P, Binns D, Chang H-Y, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G et al: InterProScan 5: genome-scale protein function classification. Bioinformatics 2014, 30(9):1236–1240.
47.De Castro E, Sigrist CJ, Gattiker A, Bulliard V, Langendijk-Genevaux PS, Gasteiger E, Bairoch A, Hulo N: ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic acids research 2006, 34(suppl_2):W362-W365.
48.Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nature Methods 2012, 9:357.
49.Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Subgroup GPDP: The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25(16):2078–2079.
50.Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF: MITOS: improved de novo metazoan mitochondrial genome annotation. Molecular phylogenetics and evolution 2013, 69(2):313–319.
51.http://mitos2.bioinf.uni-leipzig.de.
52.https://www.ncbi.nlm.nih.gov/orffinder/.
53.Rice P, Longden I, Bleasby A: EMBOSS: the European molecular biology open software suite. In.: Elsevier current trends; 2000.
54.Benson G: Tandem repeats finder: a program to analyze DNA sequences. Nucleic acids research 1999, 27(2):573–580.
55.Gong C, Maquat LE: lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements. Nature 2011, 470(7333):284–288.
56.Makałowski W: Genomic scrap yard: how genomes utilize all that junk. Gene 2000, 259(1):61–67.
57.Ponicsan SL, Kugel JF, Goodrich JA: Genomic gems: SINE RNAs regulate mRNA production. Current opinion in genetics & development 2010, 20(2):149–155.
58.Bartolomé C, Maside X, Charlesworth B: On the abundance and distribution of transposable elements in the genome of Drosophila melanogaster. Molecular biology and evolution 2002, 19(6):926–937.
59.Finnegan DJ: Transposable elements. Current Opinion in Genetics & Development 1992, 2(6):861–867.
60.Hollister JD, Gaut BS: Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. Genome Research 2009, 19(8):1419–1428.
61.Sun J, Zhang Y, Xu T, Zhang Y, Mu H, Zhang Y, Lan Y, Fields CJ, Hui JHL, Zhang W: Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes. Nature ecology & evolution 2017, 1(5):0121.
62.Wong YH, Sun J, He LS, Chen LG, Qiu J-W, Qian P-Y: High-throughput transcriptome sequencing of the cold seep mussel Bathymodiolus platifrons. Scientific reports 2015, 5:16597.
63.Xu M, Huang J, Shi Y, Zhang H, He M: Comparative transcriptomic and proteomic analysis of yellow shell and black shell pearl oysters, Pinctada fucata martensii. BMC genomics 2019, 20(1):469.
64.Gerdol M, Manfrin C, De Moro G, Figueras A, Novoa B, Venier P, Pallavicini A: The C1q domain containing proteins of the Mediterranean mussel Mytilus galloprovincialis: A widespread and diverse family of immune-related molecules. Developmental & Comparative Immunology 2011, 35(6):635–643.
65.Toubiana M, Gerdol M, Rosani U, Pallavicini A, Venier P, Roch P: Toll-like receptors and MyD88 adaptors in Mytilus: complete cds and gene expression levels. Developmental & Comparative Immunology 2013, 40(2):158–166.
66.Barral PM, Sarkar D, Su Z-z, Barber GN, DeSalle R, Racaniello VR, Fisher PB: Functions of the cytoplasmic RNA sensors RIG-I and MDA–5: key regulators of innate immunity. Pharmacology & therapeutics 2009, 124(2):219–234.
67.Cao X: New DNA-sensing pathway feeds RIG-I with RNA. Nature immunology 2009, 10(10):1049.
68.Aderem A, Ulevitch RJ: Toll-like receptors in the induction of the innate immune response. Nature 2000, 406(6797):782.
69.Vijay K: Toll-like receptors in immunity and inflammatory diseases: past, present, and future. International immunopharmacology 2018, 59:391–412.
70.Smith LC, Rast JP, Brockton V, Terwilliger DP, Nair SV, Buckley KM, Majeske AJ: The sea urchin immune system. Invertebrate Survival Journal 2006, 3(1):25–39.
71.Tu Q, Cameron RA, Worley KC, Gibbs RA, Davidson EH: Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis. Genome research 2012, 22(10):2079–2087.
72.Mateo DR, Greenwood SJ, Araya MT, Berthe FCJ, Johnson GR, Siah A: Differential gene expression of γ-actin, Toll-like receptor 2 (TLR–2) and interleukin–1 receptor-associated kinase 4 (IRAK–4) in Mya arenaria haemocytes induced by in vivo infections with two Vibrio splendidus strains. Developmental and Comparative Immunology 2010, 34(7):710–714.
73.Qiu L, Song L, Xu W, Ni D, Yu Y: Molecular cloning and expression of a Toll receptor gene homologue from Zhikong Scallop, Chlamys farreri. Fish & Shellfish Immunology 2007, 22(5):451–466.
74.Itoh N, Takahashi KG: A novel peptidoglycan recognition protein containing a goose-type lysozyme domain from the Pacific oyster, Crassostrea gigas. Molecular Immunology 2009, 46(8):1768–1774.
75.Ni D, Song L, Wu L, Chang Y, Yu Y, Qiu L, Wang L: Molecular cloning and mRNA expression of peptidoglycan recognition protein (PGRP) gene in bay scallop (Argopecten irradians, Lamarck 1819). Developmental & Comparative Immunology 2007, 31(6):548–558.
76.Dziarski R: Peptidoglycan recognition proteins (PGRPs). Molecular immunology 2004, 40(12):877–886.
77.Thörnqvist P-O, Johansson MW, Söderhäll K: Opsonic activity of cell adhesion proteins and β–1, 3-glucan binding proteins from two crustaceans. Developmental & Comparative Immunology 1994, 18(1):3–12.
78.Li X, Wang S, Qi J, Echtenkamp SF, Chatterjee R, Wang M, Boons G-J, Dziarski R, Gupta D: Zebrafish peptidoglycan recognition proteins are bactericidal amidases essential for defense against bacterial infections. Immunity 2007, 27(3):518–529.
79.Royet J, Dziarski R: Peptidoglycan recognition proteins: pleiotropic sensors and effectors of antimicrobial defences. Nature Reviews Microbiology 2007, 5(4):264–277.
80.Vargas-Albores F, Yepiz-Plascencia G: Beta glucan binding protein and its role in shrimp immune response. Aquaculture 2000, 191(1–3):13–21.
81.Taylor ME, Drickamer K: Structure–function analysis of C-type animal lectins. In: Methods in enzymology. vol. 363: Elsevier; 2003: 3–16.
82.McGreal EP, Martinez-Pomares L, Gordon S: Divergent roles for C-type lectins expressed by cells of the innate immune system. Molecular Immunology 2004, 41(11):1109–1121.
83.www.imperial.ac.uk/research/animallectins/ctld/lectins.html.
84.Iordache F, Ionita M, Mitrea LI, Fafaneata C, Pop A: Antimicrobial and antiparasitic activity of lectins. Current pharmaceutical biotechnology 2015, 16(2):152–161.
85.Fujita T, Matsushita M, Endo Y: The lectin‐complement pathway–its role in innate immunity and evolution. Immunological reviews 2004, 198(1):185–202.
86.Elumalai P, Rubeena AS, Arockiaraj J, Wongpanya R, Cammarata M, Ringø E, Vaseeharan B: The Role of Lectins in Finfish: A Review. Reviews in Fisheries Science & Aquaculture 2019, 27(2):152–169.
87.Aumailley M: The laminin family. Cell adhesion & migration 2013, 7(1):48–55.
88.Ekblom P, Lonai P, Talts JF: Expression and biological role of laminin–1. Matrix Biology 2003, 22(1):35–47.
89.Kleinman HK, Cannon FB, Laurie GW, Hassell JR, Aumailley M, Terranova VP, Martin GR, DuBois‐Dalcq M: Biological activities of laminin. Journal of Cellular Biochemistry $V 27 1985(4):317–325.
90.Mercurio AM: Laminin receptors: achieving specificity through cooperation. Trends in Cell Biology 1995, 5(11):419–423.
91.Simon T, Bromberg JS: Regulation of the immune system by laminins. Trends in immunology 2017, 38(11):858–871.
92.Nde PN, Simmons KJ, Kleshchenko YY, Pratap S, Lima MF, Villalta F: Silencing of the Laminin γ–1 Gene Blocks <em>Trypanosoma cruzi</em> Infection. Infection and Immunity 2006, 74(3):1643–1648.
93.Van Wijk XM, Döhrmann S, Hallström BM, Li S, Voldborg BG, Meng BX, McKee KK, Van Kuppevelt TH, Yurchenco PD, Palsson BO: Whole-genome sequencing of invasion-resistant cells identifies laminin α2 as a host factor for bacterial invasion. MBio 2017, 8(1):e02128–02116.
94.Warburg A, Shtern A, Cohen N, Dahan N: Laminin and a Plasmodium ookinete surface protein inhibit melanotic encapsulation of Sephadex beads in the hemocoel of mosquitoes. Microbes and infection 2007, 9(2):192–199.
95.Vasta GR: Roles of galectins in infection. Nature Reviews Microbiology 2009, 7(6):424.
96.Catanese G, Grau A, Valencia JM, Garcia-March JR, Vázquez-Luis M, Alvarez E, Deudero S, Darriba S, Carballal MJ, Villalba A: Haplosporidium pinnae sp. nov., a haplosporidan parasite associated with mass mortalities of the fan mussel, Pinna nobilis, in the Western Mediterranean Sea. Journal of invertebrate pathology 2018, 157:9–24.
97.Li F, Huang S, Wang L, Yang J, Zhang H, Qiu L, Li L, Song L: A macrophage migration inhibitory factor like gene from scallop Chlamys farreri: Involvement in immune response and wound healing. Developmental & Comparative Immunology 2011, 35(1):62–71.
98.Parisi M-G, Toubiana M, Mangano V, Parrinello N, Cammarata M, Roch P: MIF from mussel: coding sequence, phylogeny, polymorphism, 3D model and regulation of expression. Developmental & Comparative Immunology 2012, 36(4):688–696.
99.Wang B, Zhang Z, Wang Y, Zou Z, Wang G, Wang S, Jia X, Lin P: Molecular cloning and characterization of macrophage migration inhibitory factor from small abalone Haliotis diversicolor supertexta. Fish & Shellfish Immunology 2009, 27(1):57–64.
100.Rosani U, Varotto L, Gerdol M, Pallavicini A, Venier P: IL–17 signaling components in bivalves: comparative sequence analysis and involvement in the immune responses. Developmental & Comparative Immunology 2015, 52(2):255–268.
101.Roberts S, Gueguen Y, de Lorgeril J, Goetz F: Rapid accumulation of an interleukin 17 homolog transcript in Crassostrea gigas hemocytes following bacterial exposure. Developmental & Comparative Immunology 2008, 32(9):1099–1104.
102.Betti M, Ciacci C, Lorusso LC, Canonico B, Falcioni T, Gallo G, Canesi L: Effects of tumour necrosis factor α (TNFα) on Mytilus haemocytes: role of stress‐activated mitogen‐activated protein kinases (MAPKs). Biology of the Cell 2006, 98(4):233–244.
103.Lacoste A, Jalabert F, Malham SK, Cueff A, Poulet SA: Stress and stress-induced neuroendocrine changes increase the susceptibility of juvenile oysters (Crassostrea gigas) to Vibrio splendidus. Appl Environ Microbiol 2001, 67(5):2304–2309.
104.Liu Z, Li M, Yi Q, Wang L, Song L: The Neuroendocrine-Immune Regulation in Response to Environmental Stress in Marine Bivalves. Frontiers in Physiology 2018, 9(1456).
105.Shaliapina V: The functional swings in the neuroendocrine regulation of stress. Fiziologicheskii zhurnal imeni IM Sechenova 1996, 82(4):9–14.
106.Wang L, Song X, Song L: The oyster immunity. Developmental & Comparative Immunology 2018, 80:99–118.
107.Janeway Jr CA, Travers P, Walport M, Shlomchik MJ: The complement system and innate immunity. In: Immunobiology: The Immune System in Health and Disease 5th edition. Garland Science; 2001.
108.Gasque P: Complement: a unique innate immune sensor for danger signals. Molecular Immunology 2004, 41(11):1089–1098.
109.Ward PA: Role of Complement, Chemokines, & Regulatory Cytokines in Acute Lung Injury. 1996.
110.Nonaka M: The complement C3 protein family in invertebrates. Invertebrate Survival Journal 2011, 8(1):21–32.
111.Vizioli J, Salzet M: Antimicrobial peptides from animals: focus on invertebrates. Trends in pharmacological sciences 2002, 23(11):494–496.
112.Brogden KA: Antimicrobial peptides: pore formers or metabolic inhibitors in bacteria? Nature reviews microbiology 2005, 3(3):238.
113.Sitaram N, Nagaraj R: Host-defense antimicrobial peptides: importance of structure for activity. Current pharmaceutical design 2002, 8(9):727–742.
114.Gerdol M, De Moro G, Manfrin C, Venier P, Pallavicini A: Big defensins and mytimacins, new AMP families of the Mediterranean mussel Mytilus galloprovincialis. Developmental & Comparative Immunology 2012, 36(2):390–399.
115.Padhi A, Verghese B: Molecular diversity and evolution of myticin-C antimicrobial peptide variants in the Mediterranean mussel, Mytilus galloprovincialis. Peptides 2008, 29(7):1094–1101.
116.Sonthi M, Toubiana M, Pallavicini A, Venier P, Roch P: Diversity of coding sequences and gene structures of the antifungal peptide mytimycin (MytM) from the Mediterranean mussel, Mytilus galloprovincialis. Marine biotechnology 2011, 13(5):857–867.
117.Charlet M, Chernysh S, Philippe H, Hetru C, Hoffmann JA, Bulet P: Innate immunity isolation of several cysteine-rich antimicrobial peptides from the blood of a mollusc, Mytilus edulis. Journal of Biological Chemistry 1996, 271(36):21808–21813.
118.Furukawa R, Matsumoto M, Kaneko H: Characterization of a scavenger receptor cysteine-rich-domain-containing protein of the starfish, Asterina pectinifera: ApSRCR1 acts as an opsonin in the larval and adult innate immune systems. Developmental & Comparative Immunology 2012, 36(1):51–61.
119.Liu Z, Dong S, Xu J, Zeng M, Song H, Zhao Y: Production of cysteine-rich antimicrobial peptide by digestion of oyster (Crassostrea gigas) with alcalase and bromelin. Food Control 2008, 19(3):231–235.
120.Sarrias MR, Gronlund J, Padilla O, Madsen J, Holmskov U, Lozano F: The Scavenger Receptor Cysteine-Rich (SRCR) domain: an ancient and highly conserved protein module of the innate immune system. Critical Reviews™ in Immunology 2004, 24(1).
121.Everett H, McFadden G: Apoptosis: an innate immune response to virus infection. Trends in Microbiology 1999, 7(4):160–165.
122.Miao EA, Leaf IA, Treuting PM, Mao DP, Dors M, Sarkar A, Warren SE, Wewers MD, Aderem A: Caspase–1-induced pyroptosis is an innate immune effector mechanism against intracellular bacteria. Nature Immunology 2010, 11:1136.
123.Sokolova I: Apoptosis in molluscan immune defense. Invertebrate Survival Journal 2009, 6(1):49–58.
124.Kültz D: MOLECULAR AND EVOLUTIONARY BASIS OF THE CELLULAR STRESS RESPONSE. Annual Review of Physiology 2005, 67(1):225–257.
125.Goldstone JV: Environmental sensing and response genes in cnidaria: the chemical defensome in the sea anemone Nematostella vectensis. Cell biology and toxicology 2008, 24(6):483–502.
126.Werck-Reichhart D, Feyereisen R: Cytochromes P450: a success story. Genome biology 2000, 1(6):reviews3003. 3001.
127.Nelson DR: Cytochrome P450 Nomenclature, 2004. In: Cytochrome P450 protocols. Springer; 2006: 1–10.
128.Zanette J, Goldstone JV, Bainy AC, Stegeman JJ: Identification of CYP genes in Mytilus (mussel) and Crassostrea (oyster) species: first approach to the full complement of cytochrome P450 genes in bivalves. Marine environmental research 2010, 69:S1-S3.
129.Goldstone JV, Sundaramoorthy M, Zhao B, Waterman MR, Stegeman JJ, Lamb DC: Genetic and structural analyses of cytochrome P450 hydroxylases in sex hormone biosynthesis: Sequential origin and subsequent coevolution. Molecular Phylogenetics and Evolution 2016, 94:676–687.
130.Hallmann A, Konieczna L, Swiezak J, Milczarek R, Smolarz K: Aromatisation of steroids in the bivalve Mytilus trossulus. PeerJ 2019, 7:e6953.
131.Blanchard RL, Freimuth RR, Buck J, Weinshilboum RM, Coughtrie MW: A proposed nomenclature system for the cytosolic sulfotransferase (SULT) superfamily. Pharmacogenetics and Genomics 2004, 14(3):199–211.
132.Coughtrie MW: Function and organization of the human cytosolic sulfotransferase (SULT) family. Chemico-biological interactions 2016, 259:2–7.
133.Bojarová P, Williams SJ: Sulfotransferases, sulfatases and formylglycine-generating enzymes: a sulfation fascination. Current opinion in chemical biology 2008, 12(5):573–581.
134.Bundgaard JR, Rehfeld JF: Chapter 250 - Tyrosylprotein sulfotransferases. In: Handbook of Biologically Active Peptides (Second Edition). Edited by Kastin AJ. Boston: Academic Press; 2013: 1829–1834.
135.Li Y, Sun X, Hu X, Xun X, Zhang J, Guo X, Jiao W, Zhang L, Liu W, Wang J et al: Scallop genome reveals molecular adaptations to semi-sessile life and neurotoxins. Nature Communications 2017, 8(1):1721.
136.Frova C: Glutathione transferases in the genomics era: New insights and perspectives. Biomolecular Engineering 2006, 23(4):149–169.
137.Hayes JD, Flanagan JU, Jowsey IR: GLUTATHIONE TRANSFERASES. Annual Review of Pharmacology and Toxicology 2005, 45(1):51–88.
138.Ranson H, Hemingway J: Mosquito glutathione transferases. Methods in enzymology 2005, 401:226–241.
139.Sheehan D, Meade G, Foley VM: Structure, function and evolution of glutathione transferases: implications for classification of non-mammalian members of an ancient enzyme superfamily. Biochemical Journal 2001, 360(1):1–16.
140.Che-Mendoza A, Penilla RP, Rodríguez DA: Insecticide resistance and glutathione S-transferases in mosquitoes: a review. African Journal of Biotechnology 2009, 8(8).
141.Sandamalika WG, Priyathilaka TT, Lee S, Yang H, Lee J: Immune and xenobiotic responses of glutathione S-Transferase theta (GST-θ) from marine invertebrate disk abalone (Haliotis discus discus): With molecular characterization and functional analysis. Fish & shellfish immunology 2019, 91:159–171.
142.Board PG, Menon D: Glutathione transferases, regulators of cellular metabolism and physiology. Biochimica et biophysica acta (bba)-general subjects 2013, 1830(5):3267–3288.
143.Holm PJ, Bhakat P, Jegerschöld C, Gyobu N, Mitsuoka K, Fujiyoshi Y, Morgenstern R, Hebert H: Structural basis for detoxification and oxidative stress protection in membranes. Journal of molecular biology 2006, 360(5):934–945.
144.Molina DM, Wetterholm A, Kohl A, McCarthy AA, Niegowski D, Ohlson E, Hammarberg T, Eshaghi S, Haeggström JZ, Nordlund P: Structural basis for synthesis of inflammatory mediators by human leukotriene C 4 synthase. Nature 2007, 448(7153):613.
145.Best JH, Pflugmacher S, Wiegand C, Eddy FB, Metcalf JS, Codd GA: Effects of enteric bacterial and cyanobacterial lipopolysaccharides, and of microcystin-LR, on glutathione S-transferase activities in zebra fish (Danio rerio). Aquatic toxicology 2002, 60(3–4):223–231.
146.Sundberg K, Widersten M, Seidel A, Mannervik B, Jernström B: Glutathione conjugation of bay-and fjord-region diol epoxides of polycyclic aromatic hydrocarbons by glutathione transferases M1–1 and P1–1. Chemical research in toxicology 1997, 10(11):1221–1227.
147.Blackburn AC, Matthaei KI, Lim C, Taylor MC, Cappello JY, Hayes JD, Anders M, Board PG: Deficiency of glutathione transferase zeta causes oxidative stress and activation of antioxidant response pathways. Molecular pharmacology 2006, 69(2):650–657.
148.Enayati AA, Ranson H, Hemingway J: Insect glutathione transferases and insecticide resistance. Insect Molecular Biology 2005, 14(1):3–8.
149.McLellan LI, Wolf CR: Glutathione and glutathione-dependent enzymes in cancer drug resistance. Drug Resistance Updates 1999, 2(3):153–164.
150.Revathy KS, Umasuthan N, Lee Y, Choi CY, Whang I, Lee J: First molluscan theta-class Glutathione S-Transferase: Identification, cloning, characterization and transcriptional analysis post immune challenges. Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology 2012, 162(1–3):10–23.
151.Roncalli V, Cieslak MC, Passamaneck Y, Christie AE, Lenz PH: Glutathione S-transferase (GST) gene diversity in the crustacean Calanus finmarchicus–contributors to cellular detoxification. PLoS One 2015, 10(5):e0123322.
152.Dean M, Hamon Y, Chimini G: The human ATP-binding cassette (ABC) transporter superfamily. Journal of lipid research 2001, 42(7):1007–1017.
153.Della Torre C, Bocci E, Focardi SE, Corsi I: Differential ABCB and ABCC gene expression and efflux activities in gills and hemocytes of Mytilus galloprovincialis and their involvement in cadmium response. Marine environmental research 2014, 93:56–63.
154.Huang L, Liu S-L, Zheng J-W, Li H-Y, Liu J-S, Yang W-D: P-glycoprotein and its inducible expression in three bivalve species after exposure to Prorocentrum lima. Aquatic Toxicology 2015, 169:123–132.
155.Kingtong S, Chitramvong Y, Janvilisri T: ATP-binding cassette multidrug transporters in Indian-rock oyster Saccostrea forskali and their role in the export of an environmental organic pollutant tributyltin. Aquatic Toxicology 2007, 85(2):124–132.
156.Leslie EM, Deeley RG, Cole SPC: Multidrug resistance proteins: role of P-glycoprotein, MRP1, MRP2, and BCRP (ABCG2) in tissue defense. Toxicology and Applied Pharmacology $V 204 2005(3):216–237.
157.Popovic M, Zaja R, Loncar J, Smital T: A novel ABC transporter: the first insight into zebrafish (Danio rerio) ABCH1. Marine environmental research 2010, 69:S11-S13.
158.Achard M, Baudrimont M, Boudou A, Bourdineaud J: Induction of a multixenobiotic resistance protein (MXR) in the Asiatic clam Corbicula fluminea after heavy metals exposure. Aquatic toxicology 2004, 67(4):347–357.
159.Acs A, Imre K, Kiss G, Csaba J, Gyori J, Vehovszky A, Farkas A: Evaluation of multixenobiotic resistance in dreissenid mussels as a screening tool for toxicity in freshwater sediments. Arch Environ Contam Toxicol 2015, 68(4):707–717.
160.Bonnafé E, Sroda S, Budzinski H, Valière A, Pedelluc J, Marty P, Geret F: Responses of cytochrome P450, GST, and MXR in the mollusk Corbicula fluminea to the exposure to hospital wastewater effluents. Environmental Science and Pollution Research 2015, 22(14):11033–11046.
161.Deeley RG, Westlake C, Cole SP: Transmembrane transport of endo-and xenobiotics by mammalian ATP-binding cassette multidrug resistance proteins. Physiological reviews 2006, 86(3):849–899.
162.Dean M, Annilo T: Evolution of the ATP-binding cassette (ABC) transporter superfamily in vertebrates. Annu Rev Genomics Hum Genet 2005, 6:123–142.
163.Jeong C-B, Kim B-M, Lee J-S, Rhee J-S: Genome-wide identification of whole ATP-binding cassette (ABC) transporters in the intertidal copepod Tigriopus japonicus. BMC Genomics 2014, 15(1):651.
164.Manduzio H, Rocher B, Durand F, Galap C, Leboulenger F: The point about oxidative stress in molluscs. Invertebrate Survival Journal 2005(2):91–104%V 102.
165.Sies H: Oxidative stress: oxidants and antioxidants. Experimental Physiology: Translation and Integration 1997, 82(2):291–295.
166.Valavanidis A, Vlahogianni T, Dassenakis M, Scoullos M: Molecular biomarkers of oxidative stress in aquatic organisms in relation to toxic environmental pollutants. Ecotoxicology and environmental safety 2006, 64(2):178–189.
167.Abebe AT, Devoid SJ, Sugumaran M, Etter R, Robinson WE: Identification and quantification of histidine-rich glycoprotein (HRG) in the blood plasma of six marine bivalves. Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology 2007, 147(1):74–81.
168.Devoid SJ, Etter R, Sugumaran M, Wallace GT, Robinson WE: Histidine‐rich glycoprotein from the hemolymph of the marine mussel Mytilus edulis L. binds Class A, Class B, and borderline metals. Environmental Toxicology and Chemistry: An International Journal 2007, 26(5):872–877.
169.Feder ME, Hofmann GE: HEAT-SHOCK PROTEINS, MOLECULAR CHAPERONES, AND THE STRESS RESPONSE: Evolutionary and Ecological Physiology. Annual Review of Physiology 1999, 61(1):243–282.
170.Kim HP, Morse D, Choi AM: Heat-shock proteins: new keys to the development of cytoprotective therapies. Expert opinion on therapeutic targets 2006, 10(5):759–769.
171.Place SP, Zippay ML, Hofmann GE: Constitutive roles for inducible genes: evidence for the alteration in expression of the inducible hsp70 gene in Antarctic notothenioid fishes. American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 2004, 287(2):R429-R436.
172.Acharya P, Kumar R, Tatu U: Chaperoning a cellular upheaval in malaria: heat shock proteins in Plasmodium falciparum. Molecular and biochemical parasitology 2007, 153(2):85–94.
173.Sahi C, Kominek J, Ziegelhoffer T, Yu HY, Baranowski M, Marszalek J, Craig EA: Sequential duplications of an ancient member of the DnaJ-family expanded the functional chaperone network in the eukaryotic cytosol. Molecular biology and evolution 2013, 30(5):985–998.
174.Vos MJ, Hageman J, Carra S, Kampinga HH: Structural and functional diversities between members of the human HSPB, HSPH, HSPA, and DNAJ chaperone families. Biochemistry 2008, 47(27):7001–7011.
175.Cheetham ME, Caplan AJ: Structure, function and evolution of DnaJ: conservation and adaptation of chaperone function. Cell stress & chaperones 1998, 3(1):28.
176.Qiu X-B, Shao Y-M, Miao S, Wang L: The diversity of the DnaJ/Hsp40 family, the crucial partners for Hsp70 chaperones. Cellular and Molecular Life Sciences CMLS 2006, 63(22):2560–2570.
177.Mangelsdorf DJ, Thummel C, Beato M, Herrlich P, Schütz G, Umesono K, Blumberg B, Kastner P, Mark M, Chambon P et al: The nuclear receptor superfamily: the second decade. Cell 1995, 83(6):835–839.
178.Sluder AE, Maina CV: Nuclear receptors in nematodes: themes and variations. TRENDS in Genetics 2001, 17(4):206–213.
179.Laudet V, Gronemeyer H: The nuclear receptor factsbook: Gulf Professional Publishing; 2002.
180.Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF: The genome sequence of Drosophila melanogaster. Science 2000, 287(5461):2185–2195.
181.Hwang D-S, Lee B-Y, Kim H-S, Lee MC, Kyung D-H, Om A-S, Rhee J-S, Lee J-S: Genome-wide identification of nuclear receptor (NR) superfamily genes in the copepod Tigriopus japonicus. BMC genomics 2014, 15(1):993.
182.Kaur S, Jobling S, Jones CS, Noble LR, Routledge EJ, Lockyer AE: The nuclear receptors of Biomphalaria glabrata and Lottia gigantea: implications for developing new model organisms. PLoS One 2015, 10(4):e0121259-e0121259.
183.Vogeler S, Galloway TS, Lyons BP, Bean TP: The nuclear receptor gene family in the Pacific oyster, Crassostrea gigas, contains a novel subfamily group. BMC genomics 2014, 15(1):369.
184.Robinson-Rechavi M, Carpentier A-S, Duffraisse M, Laudet V: How many nuclear hormone receptors are there in the human genome? TRENDS in Genetics 2001, 17(10):554–556.
185.Cruzeiro C, Lopes-Marques M, Ruivo R, Rodrigues-Oliveira N, Santos MM, Rocha MJ, Rocha E, Castro LFC: A mollusk VDR/PXR/CAR-like (NR1J) nuclear receptor provides insight into ancient detoxification mechanisms. Aquatic Toxicology 2016, 174:61–69.
186.Janošek J, Hilscherová K, Bláha L, Holoubek I: Environmental xenobiotics and nuclear receptors—Interactions, effects and in vitro assessment. Toxicology in Vitro 2006, 20(1):18–37.
187.Kewley RJ, Whitelaw ML, Chapman-Smith A: The mammalian basic helix–loop–helix/PAS family of transcriptional regulators. The International Journal of Biochemistry & Cell Biology 2004, 36(2):189–204.
188.Murphy BJ, Sato BG, Dalton TP, Laderoute KR: The metal-responsive transcription factor–1 contributes to HIF–1 activation during hypoxic stress. Biochemical and Biophysical Research Communications $V 337 2005(3):860–867.
189.Igarashi K, Sun J: The heme-Bach1 pathway in the regulation of oxidative stress response and erythroid differentiation. Antioxidants & redox signaling 2006, 8(1–2):107–118.
190.Yan J-k, Wu B, Yang A-g, Zhou L-q, Liu Z-h: The complete mitochondrial genome of the pen shell Atrina pectinata (Mollusca: Bivalvia: Pinnidae): The first representative from the family Pinnidae. Mitochondrial DNA 2013, 24(4):368–369.
191.Lubośny M, Przyłucka A, Śmietanka B, Breton S, Burzyński A: Actively transcribed and expressed atp8 gene in Mytilus edulis mussels. PeerJ 2018, 6:e4897-e4897.
192.Sanna D, Cossu P, Dedola GL, Scarpa F, Maltagliati F, Castelli A, Franzoi P, Lai T, Cristo B, Curini-Galletti M: Mitochondrial DNA reveals genetic structuring of Pinna nobilis across the Mediterranean Sea. PLoS One 2013, 8(6):e67372.
193.Wesselmann M, González-Wangüemert M, Serrão EA, Engelen AH, Renault L, García-March JR, Duarte CM, Hendriks IE: Genetic and oceanographic tools reveal high population connectivity and diversity in the endangered pen shell Pinna nobilis. Scientific reports 2018, 8(1):4770.
194.http://wolfe.ucd.ie/GenomeVx/.
195.Adamo SA: The effects of the stress response on immune function in invertebrates: an evolutionary perspective on an ancient connection. Hormones and behavior 2012, 62(3):324–330.
196.GIRON PEREZ MI: Relationships between innate immunity in bivalve molluscs and environmental pollution. CONACYT 2010.
197.Malagoli D, Casarini L, Sacchi S, Ottaviani E: Stress and immune response in the mussel Mytilus galloprovincialis. Fish & Shellfish Immunology 2007, 23(1):171–177.
198.Mydlarz LD, Jones LE, Harvell CD: Innate Immunity, Environmental Drivers, and Disease Ecology of Marine and Freshwater Invertebrates. Annual Review of Ecology, Evolution, and Systematics 2006, 37(1):251–288.