Altieri, A. H. et al. Tropical dead zones and mass mortalities on coral reefs. Proc. Natl. Acad. Sci. 114, 3660–3665 (2017).
Google Scholar
Lehrter, J. C., Ko, D. S., Lowe, L. L. & Penta, B. Predicted effects of climate change on northern Gulf of Mexico hypoxia. In Modeling coastal hypoxia 173–214 (Springer, 2017).
Breitburg, D. et al. Declining oxygen in the global ocean and coastal waters. Science 359, eaam7240 (2018).
Google Scholar
Nelson, H. R. & Altieri, A. H. Oxygen: The universal currency on coral reefs. Coral Reefs 38, 177–198 (2019).
Google Scholar
Hughes, D. J. et al. Coral reef survival under accelerating ocean deoxygenation. Nat. Clim. Change 10, 1–12 (2020).
Google Scholar
Murphy, J. W. & Richmond, R. H. Changes to coral health and metabolic activity under oxygen deprivation. PeerJ 4, e1956 (2016).
Google Scholar
Harborne, A. R., Rogers, A., Bozec, Y.-M. & Mumby, P. J. Multiple stressors and the functioning of coral reefs. Ann. Rev. Mar. Sci. 9, 5.1-5.24 (2017).
Google Scholar
Van Oppen, M. J. et al. Shifting paradigms in restoration of the world’s coral reefs. Glob. Change Biol. 23, 3437–3448 (2017).
Google Scholar
Montagna, P. A. & Ritter, C. Direct and indirect effects of hypoxia on benthos in Corpus Christi Bay, Texas, USA. J. Exp. Mar. Biol. Ecol. 330, 119–131 (2006).
Google Scholar
Pollock, M., Clarke, L. & Dubé, M. The effects of hypoxia on fishes: from ecological relevance to physiological effects. Environ. Rev. 15, 1–14 (2007).
Google Scholar
Seitz, R. D., Dauer, D. M., Llansó, R. J. & Long, W. C. Broad-scale effects of hypoxia on benthic community structure in Chesapeake Bay, USA. J. Exp. Mar. Biol. Ecol. 381, S4–S12 (2009).
Google Scholar
Diaz, R. J. & Rosenberg, R. Marine benthic hypoxia: A review of its ecological effects and the behavioural responses of benthic macrofauna. Oceanogr. Mar. Biol. Ann. Rev. 33, 245–203 (1995).
Dean, T. L. & Richardson, J. Responses of seven species of native freshwater fish and a shrimp to low levels of dissolved oxygen. NZ J. Mar. Freshw. Res. 33, 99–106 (1999).
Google Scholar
Wannamaker, C. M. & Rice, J. A. Effects of hypoxia on movements and behavior of selected estuarine organisms from the southeastern United States. J. Exp. Mar. Biol. Ecol. 249, 145–163 (2000).
Google Scholar
Richardson, J., Williams, E. K. & Hickey, C. W. Avoidance behaviour of freshwater fish and shrimp exposed to ammonia and low dissolved oxygen separately and in combination. NZ J. Mar. Freshwat. Res. 35, 625–633 (2001).
Google Scholar
McAllen, R., Davenport, J., Bredendieck, K. & Dunne, D. Seasonal structuring of a benthic community exposed to regular hypoxic events. J. Exp. Mar. Biol. Ecol. 368, 67–74 (2009).
Google Scholar
Ogino, T. & Toyohara, H. Identification of possible hypoxia sensor for behavioral responses in a marine annelid. Capitella teleta. Biol. Open 8, bio37630 (2019).
Lenihan, H. S. & Peterson, C. H. How habitat degradation through fishery disturbance enhances impacts of hypoxia on oyster reefs. Ecol. Appl. 8, 128–140 (1998).
Google Scholar
Li, F.-G., Chen, J., Jiang, X.-Y. & Zou, S.-M. Transcriptome analysis of blunt snout bream (Megalobrama amblycephala) reveals putative differential expression genes related to growth and hypoxia. PLoS ONE 10, e0142801 (2015).
Google Scholar
Sahlmann, A., Wolf, R., Holth, T. F., Titelman, J. & Hylland, K. Baseline and oxidative DNA damage in marine invertebrates. J. Toxicol. Environ. Health A 80, 807–819 (2017).
Google Scholar
Zoccola, D. et al. Structural and functional analysis of coral Hypoxia Inducible Factor. PLoS ONE 12, e0186262 (2017).
Google Scholar
Díaz, R. J. & Rosenberg, R. Marine benthic hypoxia: A review of its ecological effects and the behavioural responses of benthic macrofauna. Oceanogr. Mar. Biol. Annu. Rev. 33, 245–303 (1995).
Bodamer, B. L. & Bridgeman, T. B. Experimental dead zones: two designs for creating oxygen gradients in aquatic ecological studies. Limnol. Oceanogr. Methods 12, 441–454 (2014).
Google Scholar
Vaquer-Sunyer, R. & Duarte, C. M. Thresholds of hypoxia for marine biodiversity. Proc. Natl. Acad. Sci. 105, 15452–15457. https://doi.org/10.1073/pnas.0803833105 (2008).
Google Scholar
Branco, P. et al. Potamodromous fish movements under multiple stressors: Connectivity reduction and oxygen depletion. Sci. Total Environ. 572, 520–525 (2016).
Google Scholar
Hayes, D. S., Branco, P., Santos, J. M. & Ferreira, T. Oxygen depletion affects kinematics and shoaling cohesion of cyprinid fish. Water 11, 642 (2019).
Google Scholar
Grimes, C. J., Capps, C., Petersen, L. H. & Schulze, A. Oxygen consumption during and post hypoxia exposure in bearded fireworms (Annelida: Amphinomidae). J. Comp. Physiol. B 190, 681–689 (2020).
Google Scholar
Semenza, G. L. Hypoxia-inducible factor 1 (HIF-1) pathway. Sci. Stke 407, 1–3 (2007).
Taylor, C. T. & McElwain, J. C. Ancient atmospheres and the evolution of oxygen sensing via the hypoxia-inducible factor in metazoans. Physiology 25, 272–279 (2010).
Google Scholar
Wang, G. L., Jiang, B.-H., Rue, E. A. & Semenza, G. L. Hypoxia-inducible factor 1 is a basic-helix-loop-helix-PAS heterodimer regulated by cellular O2 tension. Proc. Natl. Acad. Sci. 92, 5510–5514 (1995).
Google Scholar
Kaelin, W. G. Jr. & Ratcliffe, P. J. Oxygen sensing by metazoans: the central role of the HIF hydroxylase pathway. Mol. Cell 30, 393–402 (2008).
Google Scholar
Marques, I. J. et al. Transcriptome analysis of the response to chronic constant hypoxia in zebrafish hearts. J. Comp. Physiol. B. 178, 77–92 (2008).
Google Scholar
Schulze, A., Grimes, C. J. & Rudek, T. E. Tough, armed and omnivorous: Hermodice carunculata (Annelida: Amphinomidae) is prepared for ecological challenges. J. Mar. Biol. Assoc. UK. 97,1–6 (2017).
Witman, J. D. Effects of predation by the fireworm Hermodice carunculata on milleporid hydrocorals. Bull. Mar. Sci. 42, 446–458 (1988).
Vreeland, H. & Lasker, H. Selective feeding of the polychaete Hermodice carunculata Pallas on Caribbean gorgonians. J. Exp. Mar. Biol. Ecol. 129, 265–277 (1989).
Google Scholar
Vargas-Ángel, B., Thomas, J. D. & Hoke, S. M. High-latitude Acropora cervicornis thickets off Fort Lauderdale, Florida, USA. Coral Reefs 22, 465–473 (2003).
Google Scholar
Miller, M., Marmet, C., Cameron, C. & Williams, D. Prevalence, consequences, and mitigation of fireworm predation on endangered staghorn coral. Mar. Ecol. Prog. Ser. 516, 187–194 (2014).
Google Scholar
Lucey, N. M., Collins, M. & Collin, R. Oxygen‐mediated plasticity confers hypoxia tolerance in a corallivorous polychaete. Ecol. Evol. 10, 1145–1157 (2019).
Grimes, C. J., Paiva, P. C., Petersen, L. H. & Schulze, A. Rapid plastic responses to chronic hypoxia in the bearded fireworm, Hermodice carunculata (Annelida: Amphinomidae). Mar. Biol. https://doi.org/10.1007/s00227-020-03756-0 (2020).
Google Scholar
Yáñez-Rivera, B. & Salazar-Vallejo, S. I. Revision of Hermodice Kinberg, 1857 (Polychaeta: Amphinomidae). Sci. Mar. 75, 251–262 (2011).
Google Scholar
Ahrens, J. B. et al. The curious case of Hermodice carunculata (Annelida: Amphinomidae): Evidence for genetic homogeneity throughout the Atlantic Ocean and adjacent basins. Mol. Ecol. 22, 2280–2291 (2013).
Google Scholar
Gorr, T. A., Cahn, J. D., Yamagata, H. & Bunn, H. F. Hypoxia-induced synthesis of hemoglobin in the crustacean Daphnia magna is hypoxia-inducible factor-dependent. J. Biol. Chem. 279, 36038–36047 (2004).
Google Scholar
Li, T. & Brouwer, M. Hypoxia-inducible factor, gsHIF, of the grass shrimp Palaemonetes pugio: Molecular characterization and response to hypoxia. Comp. Biochem. Physiol. B: Biochem. Mol. Biol. 147, 11–19 (2007).
Google Scholar
Soñanez-Organis, J. G. et al. Molecular characterization of hypoxia inducible factor-1 (HIF-1) from the white shrimp Litopenaeus vannamei and tissue-specific expression under hypoxia. Comp. Biochem. Physiol. C: Toxicol. Pharmacol. 150, 395–405 (2009).
Wei, L. et al. Comparative studies of hemolymph physiology response and HIF-1 expression in different strains of Litopenaeus vannamei under acute hypoxia. Chemosphere 153, 198–204 (2016).
Google Scholar
Giannetto, A. et al. Hypoxia-inducible factor α and Hif-prolyl hydroxylase characterization and gene expression in short-time air-exposed Mytilus galloprovincialis. Mar. Biotechnol. 17, 768–781 (2015).
Google Scholar
Philipp, E. E. et al. Gene expression and physiological changes of different populations of the long-lived bivalve Arctica islandica under low oxygen conditions. PLoS ONE 7, e44621 (2012).
Google Scholar
Sussarellu, R., Fabioux, C., Le Moullac, G., Fleury, E. & Moraga, D. Transcriptomic response of the Pacific oyster Crassostrea gigas to hypoxia. Mar. Genom. 3, 133–143 (2010).
Google Scholar
Woo, S. et al. Expressions of oxidative stress-related genes and antioxidant enzyme activities in Mytilus galloprovincialis (Bivalvia, Mollusca) exposed to hypoxia. Zool. Stud. 52, 15 (2013).
Google Scholar
Burgeot, T. et al. Oyster summer morality risks associated with environmental stress. Summer Mortality of Pacific Oyster Crassostrea Gigas. The Morest Project. Éd. Ifremer/Quæ, 107–151 (2008).
David, E., Tanguy, A., Pichavant, K. & Moraga, D. Response of the Pacific oyster Crassostrea gigas to hypoxia exposure under experimental conditions. FEBS J. 272, 5635–5652 (2005).
Google Scholar
Hourdez, S. et al. Gas transfer system in Alvinella pompejana (Annelida polychaeta, Terebellida): Functional properties of intracellular and extracellular hemoglobins. Physiol. Biochem. Zool. 73, 365–373 (2000).
Google Scholar
Boutet, I., Jollivet, D., Shillito, B., Moraga, D. & Tanguy, A. Molecular identification of differentially regulated genes in the hydrothermal-vent species Bathymodiolus thermophilus and Paralvinella pandorae in response to temperature. BMC Genom. 10, 222 (2009).
Google Scholar
Eyre, B. D., Andersson, A. J. & Cyronak, T. Benthic coral reef calcium carbonate dissolution in an acidifying ocean. Nat. Clim. Change 4, 969–976 (2014).
Google Scholar
Huggett, J. & Griffiths, C. Some relationships between elevation, physico-chemical variables and biota of intertidal rock pools. Mar. Ecol. Prog. Ser. 29, 189–197 (1986).
Google Scholar
Kinsey, D. & Kinsey, E. Diurnal changes in oxygen content of the water over the coral reef platform at Heron I. Mar. Freshw. Res. 18, 23–34 (1967).
Google Scholar
Helly, J. J. & Levin, L. A. Global distribution of naturally occurring marine hypoxia on continental margins. Deep Sea Res. Part I 51, 1159–1168 (2004).
Google Scholar
Levin, L. A., Gage, J. D., Martin, C. & Lamont, P. A. Macrobenthic community structure within and beneath the oxygen minimum zone, NW Arabian Sea. Deep Sea Res. Part II 47, 189–226 (2000).
Google Scholar
Gallardo, V. et al. Macrobenthic zonation caused by the oxygen minimum zone on the shelf and slope off central Chile. Deep Sea Res. Part II 51, 2475–2490 (2004).
Google Scholar
Gooday, A. et al. Faunal responses to oxygen gradients on the Pakistan margin: a comparison of foraminiferans, macrofauna and megafauna. Deep Sea Res. Part II 56, 488–502 (2009).
Google Scholar
Prabhakar, N. R. & Semenza, G. L. Adaptive and maladaptive cardiorespiratory responses to continuous and intermittent hypoxia mediated by hypoxia-inducible factors 1 and 2. Physiol. Rev. 92, 967–1003 (2012).
Google Scholar
Du, S. N., Mahalingam, S., Borowiec, B. G. & Scott, G. R. Mitochondrial physiology and reactive oxygen species production are altered by hypoxia acclimation in killifish (Fundulus heteroclitus). J. Exp. Biol. 219, 1130–1138 (2016).
Google Scholar
Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644 (2011).
Google Scholar
Bryant, D. M. et al. A tissue-mapped axolotl de novo transcriptome enables identification of limb regeneration factors. Cell Rep. 18, 762–776 (2017).
Google Scholar
Haas, B. J. et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat. Protoc. 8, 1494–1512 (2013).
Google Scholar
Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34, 525 (2016).
Google Scholar
Soneson, C., Love, M. I. & Robinson, M. D. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Research 4, 1–19 (2015).
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).
Google Scholar
Conesa, A., Nueda, M. J., Ferrer, A. & Talón, M. maSigPro: A method to identify significantly differential expression profiles in time-course microarray experiments. Bioinformatics 22, 1096–1102 (2006).
Google Scholar
Nueda, M.J., Tarazona, S., & Conesa, A. Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series. Bioinformatics, 30, 2598–2602. https://doi.org/10.1093/bioinformatics/btu333 (2014).
Google Scholar
OmicsBox. Bioinformatics Made Easy, BioBam Bioinformatics. https://www.biobam.com/omicsbox (2019).
Costa-Paiva, E. M., Schrago, C. G., Coates, C. J. & Halanych, K. M. Discovery of novel hemocyanin-like genes in Metazoans. Biol. Bull. 235, 134–151 (2018).
Google Scholar
Kanaoka, Y. & Urade, Y. Hematopoietic prostaglandin D synthase. Prostaglandins Leukot. Essent. Fatty Acids 69, 163–167 (2003).
Google Scholar
Altun, M. et al. Ubiquitin-specific protease 19 (USP19) regulates hypoxia-inducible factor 1α (HIF-1α) during hypoxia. J. Biol. Chem. 287, 1962–1969 (2012).
Google Scholar
Ogawa, M. et al. 17β-estradiol represses myogenic differentiation by increasing ubiquitin-specific peptidase 19 through estrogen receptor α. J. Biol. Chem. 286, 41455–41465 (2011).
Google Scholar
Isaacs, J. S. et al. Hsp90 regulates a von Hippel Lindau-independent hypoxia-inducible factor-1α-degradative pathway. J. Biol. Chem. 277, 29936–29944 (2002).
Google Scholar
Nallapalli, R. K. et al. Targeting filamin A reduces K-RAS–induced lung adenocarcinomas and endothelial response to tumor growth in mice. Mol. Cancer 11, 1–11 (2012).
Google Scholar
Feng, Y. et al. Filamin A (FLNA) is required for cell–cell contact in vascular development and cardiac morphogenesis. Proc. Natl. Acad. Sci. 103, 19836–19841 (2006).
Google Scholar
Muñoz-Chápuli, R. Evolution of angiogenesis. Int. J. Dev. Biol. 55, 345–351 (2011).
Google Scholar
Kim, S., Lee, M. & Choi, Y. K. The role of a neurovascular signaling pathway involving hypoxia-inducible factor and notch in the function of the central nervous system. Biomol. Ther. 28, 45 (2020).
Google Scholar
Nie, H., Wang, H., Jiang, K. & Yan, X. Transcriptome analysis reveals differential immune related genes expression in Ruditapes philippinarum under hypoxia stress: potential HIF and NF-κB crosstalk in immune responses in clam. BMC Genom. 21, 1–16 (2020).
Google Scholar
Source: Ecology - nature.com
