Daszak, P. Emerging infectious diseases of wildlife-threats to biodiversity and human health. Science 287, 443–449 (2000).
Google Scholar
Jones, K. E. et al. Global trends in emerging infectious diseases. Nature 451, 990–993 (2008).
Google Scholar
Altizer, S., Ostfeld, R. S., Johnson, P. T. J., Kutz, S. & Harvell, C. D. Climate change and infectious diseases: From evidence to a predictive framework. Science 1979(341), 514–519 (2013).
Google Scholar
Kilpatrick, A. M., Briggs, C. J. & Daszak, P. The ecology and impact of chytridiomycosis: An emerging disease of amphibians. Trends Ecol. Evol. 25, 109–118 (2010).
Google Scholar
Blehert, D. S. et al. Bat white-nose syndrome: An emerging fungal pathogen?. Science 1979(323), 227–227 (2009).
Google Scholar
Wilfert, L. et al. Deformed wing virus is a recent global epidemic in honeybees driven by Varroa mites. Science 1979(351), 594–597 (2016).
Google Scholar
Garamszegi, L. Z. Climate change increases the risk of malaria in birds. Glob. Change Biol. 17, 1751–1759 (2011).
Google Scholar
Zamora-Vilchis, I., Williams, S. E. & Johnson, C. N. Environmental temperature affects prevalence of blood parasites of birds on an elevation gradient: Implications for disease in a warming climate. PLoS ONE 7, e39208 (2012).
Google Scholar
Harvell, D., Altizer, S., Cattadori, I. M., Harrington, L. & Weil, E. Climate change and wildlife diseases: When does the host matter the most?. Ecology 90, 912–920 (2009).
Google Scholar
Burge, C. A. et al. Climate change influences on marine infectious diseases: Implications for management and society. Ann. Rev. Mar. Sci. 6, 249–277 (2014).
Google Scholar
Tracy, A. M., Pielmeier, M. L., Yoshioka, R. M., Heron, S. F. & Harvell, C. D. Increases and decreases in marine disease reports in an era of global change. Proc. R. Soc. B Biol. Sci. 286, 20191718 (2019).
Google Scholar
Lejeusne, C., Chevaldonné, P., Pergent-Martini, C., Boudouresque, C. F. & Pérez, T. Climate change effects on a miniature ocean: The highly diverse, highly impacted Mediterranean Sea. Trends Ecol. Evol. 25, 250–260 (2010).
Google Scholar
Basso, L. et al. The Pen Shell, Pinna nobilis: A review of population status and recommended research priorities in the Mediterranean Sea. Adv. Mar. Biol. 71, 109–160 (2015).
Google Scholar
Catanese, G. et al. Haplosporidium pinnae sp. nov., a haplosporidan parasite associated with mass mortalities of the fan mussel, Pinna nobilis, in the Western Mediterranean Sea. J. Invertebr. Pathol. 157, 9–24 (2018).
Google Scholar
Vázquez-Luis, M. et al. S.O.S. Pinna nobilis: A mass mortality event in western Mediterranean sea. Front. Mar. Sci. 4, 220 (2017).
Google Scholar
García-March, J. R. et al. Can we save a marine species affected by a highly infective, highly lethal, waterborne disease from extinction?. Biol. Conserv. 243, 108498 (2020).
Google Scholar
Prado, P. et al. Pinna nobilis in suboptimal environments are more tolerant to disease but more vulnerable to severe weather phenomena. Mar. Environ. Res. 163, 105220 (2021).
Google Scholar
Cabanellas-Reboredo, M. et al. Tracking a mass mortality outbreak of pen shell Pinna nobilis populations: A collaborative effort of scientists and citizens. Sci. Rep. 9, 13355 (2019).
Google Scholar
Kersting, D. K. et al. Recruitment disruption and the role of unaffected populations for potential recovery after the Pinna nobilis mass mortality event. Front. Mar. Sci. 7, 1–11 (2020).
Google Scholar
Box, A. et al. Reduced antioxidant response of the fan mussel Pinna nobilis related to the presence of haplosporidium pinnae. Pathogens 9, 1–14 (2020).
Google Scholar
Peyran, C., Morage, T., Nebot-Colomer, E., Iwankow, G. & Planes, S. Unexpected residual habitats raise hope for the survival of the fan mussel Pinna nobilis along the Occitan coast (Northwest Mediterranean Sea). Endanger Species Res. 48, 123–137 (2022).
Google Scholar
Rosa, R. D. et al. A hemocyte gene expression signature correlated with predictive capacity of oysters to survive Vibrio infections. BMC Genomics 13, 1–12 (2012).
Google Scholar
van de Vijver, M. J. et al. A gene-expression signature as a predictor of survival in breast cancer. N. Engl. J. Med. 347, 1999–2009 (2002).
Google Scholar
Seppey, M., Manni, M. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness. In Methods in Molecular Biology 227–245 https://doi.org/10.1007/978-1-4939-9173-0_14 (2019).
Smith-Unna, R., Boursnell, C., Patro, R., Hibberd, J. M. & Kelly, S. TransRate: Reference-free quality assessment of de novo transcriptome assemblies. Genome Res. 26, 1134–1144 (2016).
Google Scholar
Guo, X. & Ford, S. E. Infectious diseases of marine mollusks and host responses as revealed by genomic tools. Philos. Trans. R. Soc. B Biol. Sci. https://doi.org/10.1098/rstb.2015.0206 (2016).
Google Scholar
Pauletto, M. et al. Deep transcriptome sequencing of Pecten maximus hemocytes: A genomic resource for bivalve immunology. Fish Shellfish Immunol. 37, 154–165 (2014).
Google Scholar
Caurcel, C. et al. MolluscDB: A genome and transcriptome database for molluscs. Philos. Trans. R. Soc. Lond. B Biol. Sci. 376, 20200157 (2021).
Google Scholar
de Oliveira, A. L. et al. Comparative transcriptomics enlarges the toolkit of known developmental genes in mollusks. BMC Genomics 17, 1–23 (2016).
Google Scholar
Richardson, M. F. & De Sherman, C. D. H. De novo assembly and characterization of the invasive Northern Pacific Seastar transcriptome. PLoS ONE 10, e0142003 (2015).
Google Scholar
Zhang, D., Wang, F., Dong, S. & Lu, Y. D. De novo assembly and transcriptome analysis of osmoregulation in Litopenaeus vannamei under three cultivated conditions with different salinities. Gene 578, 185–193 (2016).
Google Scholar
Werner, G. D. A., Gemmell, P., Grosser, S., Hamer, R. & Shimeld, S. M. Analysis of a deep transcriptome from the mantle tissue of Patella vulgata Linnaeus (Mollusca: Gastropoda: Patellidae) reveals candidate biomineralising genes. Mar. Biotechnol. 15, 230–243 (2013).
Google Scholar
Ding, J. et al. Transcriptome sequencing and characterization of Japanese scallop Patinopecten yessoensis from different shell color lines. PLoS ONE 10, e0116406 (2015).
Google Scholar
Harney, E. et al. De novo assembly and annotation of the European abalone Haliotis tuberculata transcriptome. Mar Genomics 28, 11–16 (2016).
Google Scholar
Khalturin, K., Hemmrich, G., Fraune, S., Augustin, R. & Bosch, T. C. G. More than just orphans: Are taxonomically-restricted genes important in evolution?. Trends Genet. 25, 404–413. https://doi.org/10.1016/j.tig.2009.07.006 (2009).
Google Scholar
Gibson, A. K., Smith, Z., Fuqua, C., Clay, K. & Colbourne, J. K. Why so many unknown genes? Partitioning orphans from a representative transcriptome of the lone star tick Amblyomma americanum. BMC Genomics 14, 135 (2013).
Google Scholar
Albertin, C. B. et al. The octopus genome and the evolution of cephalopod neural and morphological novelties. Nature 524, 220–224 (2015).
Google Scholar
Vogeler, S., Galloway, T. S., Lyons, B. P. & Bean, T. P. The nuclear receptor gene family in the Pacific oyster, Crassostrea gigas, contains a novel subfamily group. BMC Genomics 15, 369 (2014).
Google Scholar
Allam, B. & Raftos, D. Immune responses to infectious diseases in bivalves. J. Invertebr. Pathol. 131, 121–136. https://doi.org/10.1016/j.jip.2015.05.005 (2015).
Google Scholar
Allam, B. & Pales Espinosa, E. Bivalve immunity and response to infections: Are we looking at the right place?. Fish Shellfish Immunol. 53, 4–12. https://doi.org/10.1016/j.fsi.2016.03.037 (2016).
Google Scholar
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 Immunol. 22, 451–466 (2007).
Google Scholar
Zhang, L., Li, L., Zhu, Y., Zhang, G. & Guo, X. Transcriptome analysis reveals a rich gene set related to innate immunity in the eastern oyster (Crassostrea virginica). Mar. Biotechnol. 16, 17–33 (2014).
Google Scholar
Moreira, R. et al. Transcriptomics of in vitro immune-stimulated hemocytes from the Manila clam Ruditapes philippinarum using high-throughput sequencing. PLoS ONE 7, e35009 (2012).
Google Scholar
Toubiana, M. et al. Toll-like receptors and MyD88 adaptors in Mytilus: Complete cds and gene expression levels. Dev. Comp. Immunol. 40, 158–166 (2013).
Google Scholar
He, Y. et al. Transcriptome analysis reveals strong and complex antiviral response in a mollusc. Fish Shellfish Immunol. 46, 131–144 (2015).
Google Scholar
Zhang, L. et al. Massive expansion and functional divergence of innate immune genes in a protostome. Sci. Rep. 5, 8693 (2015).
Google Scholar
Casadevall, A. & Pirofski, L. A. Host–pathogen interactions: The attributes of virulence. J. Infect. Dis. 184, 337–344. https://doi.org/10.1086/322044 (2001).
Google Scholar
Jones, B., Pascopella, L. & Falkow, S. Entry of microbes into the host: Using M cells to break the mucosal barrier. Curr. Opin. Immunol. 7, 474–478 (1995).
Google Scholar
Liévin-Le Moal, V. & Servin, A. L. The front line of enteric host defense against unwelcome intrusion of harmful microorganisms: Mucins, antimicrobial peptides, and microbiota. Clin. Microbiol. Rev. 19, 315–337. https://doi.org/10.1128/CMR.19.2.315-337.2006 (2006).
Google Scholar
Trigos, S., Vicente, N., Prado, P. & Espinós, F. J. Adult spawning and early larval development of the endangered bivalve Pinna nobilis. Aquaculture 483, 102–110 (2018).
Google Scholar
Vázquez-Luis, M., Nebot-Colomer, E., Deudero, S., Planes, S. & Boissin, E. Natural hybridization between pen shell species: Pinna rudis and the critically endangered Pinna nobilis may explain parasite resistance in P. nobilis. Mol. Biol. Rep. https://doi.org/10.1007/s11033-020-06063-5 (2021).
Google Scholar
Katsares, V., Tsiora, A., Galinou-Mitsoudi, S. & Imsiridou, A. Genetic structure of the endangered species Pinna nobilis (Mollusca: Bivalvia) inferred from mtDNA sequences. Biologia 63, 412–417 (2008).
Google Scholar
Gonzalez-Wanguemert, M. et al. Highly polymorphic microsatellite markers for the Mediterranean endemic fan mussel Pinna nobilis. Mediterr. Mar. Sci. 16, 31 (2014).
Google Scholar
Peyran, C., Planes, S., Tolou, N., Iwankow, G. & Boissin, E. Development of 26 highly polymorphic microsatellite markers for the highly endangered fan mussel Pinna nobilis and cross-species amplification. Mol. Biol. Rep. 47, 2551–2559 (2020).
Google Scholar
Peakall, R. & Smouse, P. E. GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics 28, 2537–2539 (2012).
Google Scholar
Source: Ecology - nature.com