References
Andrews, S. (2010). FastQC: a quality control tool for high throughput sequence data. In: Babraham Bioinformatics, Babraham Institute, Cambridge, United Kingdom.
Ardi, V. C., Van den Steen, P. E., Opdenakker, G., Schweighofer, B., Deryugina, E. I., & Quigley, J. P. (2009). Neutrophil MMP-9 proenzyme, unencumbered by TIMP-1, undergoes efficient activation in vivo and catalytically induces angiogenesis via a basic fibroblast growth factor (FGF-2)/FGFR-2 pathway. Journal of Biological Chemistry, 284 (38), 25854-25866.
Bader, M., & Steller, H. (2009). Regulation of cell death by the ubiquitin–proteasome system. Current opinion in cell biology, 21 (6), 878-884.
Birkedal-Hansen, H., Moore, W., Bodden, M., Windsor, L., Birkedal-Hansen, B., DeCarlo, A., & Engler, J. (1993). Matrix metalloproteinases: a review. Critical Reviews in Oral Biology & Medicine, 4 (2), 197-250.
Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30 (15), 2114-2120.
Capel, K. C. C., Migotto, A., Zilberberg, C., & Kitahara, M. V. (2014). Another tool towards invasion? Polyp “bail-out” in Tubastraeacoccinea.Coral reefs, 33 (4), 1165-1165.
Chen, Y.-S., & Qiu, X.-B. (2013). Ubiquitin at the crossroad of cell death and survival. Chinese journal of cancer, 32 (12), 640.
Chomczynski, P. (1993). A reagent for the single-step simultaneous isolation of RNA, DNA and proteins from cell and tissue samples.Biotechniques, 15 (3), 532-534, 536-537.
Cunning, R., Bay, R., Gillette, P., Baker, A., & Traylor-Knowles, N. (2018). Comparative analysis of the Pocillopora damicornis genome highlights role of immune system in coral evolution. Scientific reports, 8 (1), 16134.
Deveraux, Q. L., Takahashi, R., Salvesen, G. S., & Reed, J. C. (1997). X-linked IAP is a direct inhibitor of cell-death proteases.Nature, 388 (6639), 300-304.
Domart-Coulon, I., Tambutté, S., Tambutté, E., & Allemand, D. (2004). Short term viability of soft tissue detached from the skeleton of reef-building corals. Journal of Experimental Marine Biology and Ecology, 309 (2), 199-217.
Fordyce, A. J., Camp, E. F., & Ainsworth, T. D. (2017). Polyp bailout in Pocillopora damicornis following thermal stress. F1000Research, 6 .
Gavish, A. R., Shapiro, O. H., Kramarsky-Winter, E., & Vardi, A. (2018). Microscale tracking of coral disease reveals timeline of infection and heterogeneity of polyp fate. bioRxiv , 302778.
Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., . . . Zeng, Q. (2011). Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data.Nature biotechnology, 29 (7), 644.
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2008). Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic acids research, 37 (1), 1-13.
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature protocols, 4 (1), 44.
Johnston, E. C., Forsman, Z. H., Flot, J.-F., Schmidt-Roach, S., Pinzón, J. H., Knapp, I. S., & Toonen, R. J. (2017). A genomic glance through the fog of plasticity and diversification in Pocillopora.Scientific reports, 7 (1), 5991.
Karin, M., & Lin, A. (2002). NF-κB at the crossroads of life and death.Nature immunology, 3 (3), 221.
Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., & Salzberg, S. L. (2013). TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome biology, 14 (4), R36.
Kojima, S.-i., Itoh, Y., Matsumoto, S.-i., Masuho, Y., & Seiki, M. (2000). Membrane‐type 6 matrix metalloproteinase (MT6‐MMP, MMP‐25) is the second glycosyl‐phosphatidyl inositol (GPI)‐anchored MMP. FEBS letters, 480 (2-3), 142-146.
Kvitt, H., Kramarsky-Winter, E., Maor-Landaw, K., Zandbank, K., Kushmaro, A., Rosenfeld, H., . . . Tchernov, D. (2015). Breakdown of coral colonial form under reduced pH conditions is initiated in polyps and mediated through apoptosis. Proceedings of the national academy of sciences, 112 (7), 2082-2086.
Kvitt, H., Rosenfeld, H., Zandbank, K., & Tchernov, D. (2011). Regulation of apoptotic pathways by Stylophora pistillata (Anthozoa, Pocilloporidae) to survive thermal stress and bleaching. PloS one, 6 (12), e28665.
Li, B., & Dewey, C. N. (2011). RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC bioinformatics, 12 (1), 323.
Littman, R., Willis, B. L., & Bourne, D. G. (2011). Metagenomic analysis of the coral holobiont during a natural bleaching event on the Great Barrier Reef. Environmental Microbiology Reports, 3 (6), 651-660.
Lu, M., Lin, S.-C., Huang, Y., Kang, Y. J., Rich, R., Lo, Y.-C., . . . Wu, H. (2007). XIAP induces NF-κB activation via the BIR1/TAB1 interaction and BIR1 dimerization. Molecular cell, 26 (5), 689-702.
Nakano, H. (2004). Signaling crosstalk between NF-κB and JNK.Trends in immunology, 25 (8), 402-405.
Pintucci, G., Yu, P. J., Sharony, R., Baumann, F. G., Saponara, F., Frasca, A., . . . Mignatti, P. (2003). Induction of stromelysin‐1 (MMP‐3) by fibroblast growth factor‐2 (FGF‐2) in FGF‐2−/− microvascular endothelial cells requires prolonged activation of extracellular signal‐regulated kinases‐1 and‐2 (ERK‐1/2). Journal of cellular biochemistry, 90 (5), 1015-1025.
Pinzon, J. H., & LaJeunesse, T. C. (2011). Species delimitation of common reef corals in the genus Pocillopora using nucleotide sequence phylogenies, population genetics and symbiosis ecology. Molecular ecology, 20 (2), 311-325.
Poquita-Du, R. C., Quek, Z. B. R., Jain, S. S., Schmidt-Roach, S., Tun, K., Heery, E. C., . . . Huang, D. (2019). Last species standing: loss of Pocilloporidae corals associated with coastal urbanization in a tropical city state. Marine Biodiversity , 1-15.
Puverel, S., Tambutte, E., Zoccola, D., Domart-Coulon, I., Bouchot, A., Lotto, S., . . . Tambutte, S. (2005). Antibodies against the organic matrix in scleractinians: a new tool to study coral biomineralization.Coral reefs, 24 (1), 149-156.
Quistad, S. D., Stotland, A., Barott, K. L., Smurthwaite, C. A., Hilton, B. J., Grasis, J. A., . . . Rohwer, F. L. (2014). Evolution of TNF-induced apoptosis reveals 550 My of functional conservation.Proceedings of the national academy of sciences , 201405912.
Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26 (1), 139-140.
Roulston, A., Reinhard, C., Amiri, P., & Williams, L. T. (1998). Early activation of c-Jun N-terminal kinase and p38 kinase regulate cell survival in response to tumor necrosis factor α. Journal of Biological Chemistry, 273 (17), 10232-10239.
Sammarco, P. W. (1982). Polyp bail-out: an escape response to environmental stress and a new means of reproduction in corals.Marine ecology progress series. Oldendorf, 10 (1), 57-65.
Schmidt-Roach, S., Miller, K. J., Lundgren, P., & Andreakis, N. (2014). With eyes wide open: a revision of species within and closely related to the Pocillopora damicornis species complex (Scleractinia; Pocilloporidae) using morphology and genetics. Zoological Journal of the Linnean Society, 170 (1), 1-33.
Serrano, E., Coma, R., Inostroza, K., & Serrano, O. (2018). Polyp bail-out by the coral Astroides calycularis (Scleractinia, Dendrophylliidae). Marine Biodiversity, 48 (3), 1661-1665.
Shapiro, O. H., Kramarsky-Winter, E., Gavish, A. R., Stocker, R., & Vardi, A. (2016). A coral-on-a-chip microfluidic platform enabling live-imaging microscopy of reef-building corals. Nature communications, 7 , 10860.
Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., & Zdobnov, E. M. (2015). BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31 (19), 3210-3212.
Tang, G., Minemoto, Y., Dibling, B., Purcell, N. H., Li, Z., Karin, M., & Lin, A. (2001). Inhibition of JNK activation through NF-κ B target genes. Nature, 414 (6861), 313-317.
Traylor-Knowles, N., Granger, B. R., Lubinski, T. J., Parikh, J. R., Garamszegi, S., Xia, Y., . . . Finnerty, J. R. (2011). Production of a reference transcriptome and transcriptomic database (PocilloporaBase) for the cauliflower coral, Pocillopora damicornis. BMC genomics, 12 (1), 585.
Van Antwerp, D. J., Martin, S. J., Kafri, T., Green, D. R., & Verma, I. M. (1996). Suppression of TNF-α-induced apoptosis by NF-κB.science, 274 (5288), 787-789.
Voolstra, C. R., Li, Y., Liew, Y. J., Baumgarten, S., Zoccola, D., Flot, J.-F., . . . Aranda, M. (2017). Comparative analysis of the genomes ofStylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals.Scientific reports, 7 (1), 17583.
Webster, N., Negri, A., Flores, F., Humphrey, C., Soo, R., Botté, E., . . . Uthicke, S. (2013). Near‐future ocean acidification causes differences in microbial associations within diverse coral reef taxa.Environmental Microbiology Reports, 5 (2), 243-251.
Wecker, P., Lecellier, G., Guibert, I., Zhou, Y., Bonnard, I., & Berteaux-Lecellier, V. (2018). Exposure to the environmentally-persistent insecticide chlordecone induces detoxification genes and causes polyp bail-out in the coral P. damicornis. Chemosphere, 195 , 190-200.
Whitelock, J. M., Murdoch, A. D., Iozzo, R. V., & Underwood, P. A. (1996). The degradation of human endothelial cell-derived perlecan and release of bound basic fibroblast growth factor by stromelysin, collagenase, plasmin, and heparanases. Journal of Biological Chemistry, 271 (17), 10079-10086.
Wild, C., Rixen, T., Sanchez-Noguera, C., Stuhldreier, I., Jimenez, C., & Merico, A. (2014). Massive coral tissue ablations in reefs of Pacific Costa Rica. Galaxea, Journal of Coral Reef Studies, 16 (1), 13-14.