publication . Article . Other literature type . 2015

Metatranscriptome analysis of the reef-building coral Orbicella faveolata indicates holobiont response to coral disease

Lauren K. Yum; Craig T. Michell; Camille Daniels; Cornelia Roder; Ernesto Weil; Sebastian Baumgarten; Chatchanit Arif; Christian R. Voolstra; Till Bayer;
Open Access
  • Published: 11 Sep 2015
  • Publisher: Frontiers
  • Country: Germany
Abstract
White Plague Disease (WPD) is implicated in coral reef decline in the Caribbean and is characterized by microbial community shifts in coral mucus and tissue. Studies thus far have focused on assessing microbial communities or the identification of specific pathogens, yet few have addressed holobiont response across metaorganism compartments in coral disease. Here, we report on the first metatranscriptomic assessment of the coral host, algal symbiont, and microbial compartment in order to survey holobiont structure and function in healthy and diseased samples from Orbicella faveolata collected at reef sites off Puerto Rico. Our data indicate holobiont-wide as wel...
Subjects
Medical Subject Headings: fungibiochemical phenomena, metabolism, and nutritiongeographic locations
free text keywords: coral reef, coral disease, metatranscriptomics, Symbiodinium, metaorganism, metatranscriptomics, coral disease, metaorganism, Science, Q, General. Including nature conservation, geographical distribution, QH1-199.5, Marine Science, ddc:570, Reef, geography.geographical_feature_category, geography, Coral, Holobiont, Coral reef, Innate immune system, Ecology, Chemical defense, Biology, Orbicella faveolata, Symbiodinium, biology.organism_classification
68 references, page 1 of 5

Altschul S. F. Gish W. Miller W. Myers E. W. Lipman D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403–410. 10.1016/S0022-2836(05)80360-2 2231712 [OpenAIRE] [PubMed] [DOI]

Arif C. Daniels C. Bayer T. Ba nguera-Hinestroza E. Barbrook A. Howe C. J. . (2014). Assessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region. Mol. Ecol. 23, 4418–4433. 10.1111/mec.12869 25052021 [OpenAIRE] [PubMed] [DOI]

Barash Y. Sulam R. Loya Y. Rosenberg E. (2005). Bacterial Strain BA-3 and a filterable factor cause a White Plague-like disease in corals from the Eilat coral reef. Aquat. Microb. Ecol. 40, 183–189. 10.3354/ame040183 [OpenAIRE] [DOI]

Barr J. J. Auro R. Furlan M. Whiteson K. L. Erb M. L. Pogliano J. . (2013). Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc. Natl. Acad. Sci. U.S.A. 110, 10771–10776. 10.1073/pnas.1305923110 23690590 [OpenAIRE] [PubMed] [DOI]

Barshis D. J. Ladner J. T. Oliver T. A. Palumbi S. R. (2014). Lineage-specific transcriptional profiles of Symbiodinium spp. unaltered by heat stress in a coral host. Mol. Biol. Evol. 31, 1343–1352. 10.1093/molbev/msu107 24651035 [OpenAIRE] [PubMed] [DOI]

Barshis D. J. Ladner J. T. Oliver T. A. Seneca F. O. Traylor-Knowles N. Palumbi S. R. (2013). Genomic basis for coral resilience to climate change. Proc. Natl. Acad. Sci. U.S.A. 110, 1387–1392. 10.1073/pnas.1210224110 23297204 [OpenAIRE] [PubMed] [DOI]

Baumgarten S. Bayer T. Aranda M. Liew Y. J. Carr A. Micklem G. . (2013). Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals. BMC Genomics 14:704. 10.1186/1471-2164-14-704 24119094 [OpenAIRE] [PubMed] [DOI]

Bayer T. Aranda M. Sunagawa S. Yum L. K. Desalvo M. K. Lindquist E. . (2012). Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals. PLoS ONE 7:e35269. 10.1371/journal.pone.0035269 22529998 [OpenAIRE] [PubMed] [DOI]

Benjamini Y. Hochberg Y. (1995). Controlling the false discovery rate - a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Methodol. 57, 289–300.

Boeckmann B. Bairoch A. Apweiler R. Blatter M. C. Estreicher A. Gasteiger E. . (2003). The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31, 365–370. 10.1093/nar/gkg095 12520024 [OpenAIRE] [PubMed] [DOI]

Bolger A. M. Lohse M. Usadel B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120. 10.1093/bioinformatics/btu170 24695404 [OpenAIRE] [PubMed] [DOI]

Budd A. F. Fukami H. Smith N. D. Knowlton N. (2012). Taxonomic classification of the reef coral family Mussidae (Cnidaria: Anthozoa: Scleractinia). Zool. J. Linn. Soc. 166, 465–529. 10.1111/j.1096-3642.2012.00855.x [OpenAIRE] [DOI]

Burge C. A. Mouchka M. E. Harvell C. D. Roberts S. (2013). Immune response of the Caribbean sea fan, Gorgonia ventalina, exposed to an Aplanochytrium parasite as revealed by transcriptome sequencing. Front. Physiol. 4:180. 10.3389/fphys.2013.00180 23898300 [OpenAIRE] [PubMed] [DOI]

Cárdenas A. Rodriguez-R L. M. Pizarro V. Cadavid L. F. Arévalo-Ferro C. (2012). Shifts in bacterial communities of two caribbean reef-building coral species affected by White Plague Disease. ISME J. 6, 502–512. 10.1038/ismej.2011.123 21955993 [OpenAIRE] [PubMed] [DOI]

Chen D. Toone W. M. Mata J. Lyne R. Burns G. Kivinen K. . (2003). Global transcriptional responses of fission yeast to environmental stress. Mol. Biol. Cell 14, 214–229. 10.1091/mbc.E02-08-0499 12529438 [OpenAIRE] [PubMed] [DOI]

68 references, page 1 of 5
Abstract
White Plague Disease (WPD) is implicated in coral reef decline in the Caribbean and is characterized by microbial community shifts in coral mucus and tissue. Studies thus far have focused on assessing microbial communities or the identification of specific pathogens, yet few have addressed holobiont response across metaorganism compartments in coral disease. Here, we report on the first metatranscriptomic assessment of the coral host, algal symbiont, and microbial compartment in order to survey holobiont structure and function in healthy and diseased samples from Orbicella faveolata collected at reef sites off Puerto Rico. Our data indicate holobiont-wide as wel...
Subjects
Medical Subject Headings: fungibiochemical phenomena, metabolism, and nutritiongeographic locations
free text keywords: coral reef, coral disease, metatranscriptomics, Symbiodinium, metaorganism, metatranscriptomics, coral disease, metaorganism, Science, Q, General. Including nature conservation, geographical distribution, QH1-199.5, Marine Science, ddc:570, Reef, geography.geographical_feature_category, geography, Coral, Holobiont, Coral reef, Innate immune system, Ecology, Chemical defense, Biology, Orbicella faveolata, Symbiodinium, biology.organism_classification
68 references, page 1 of 5

Altschul S. F. Gish W. Miller W. Myers E. W. Lipman D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403–410. 10.1016/S0022-2836(05)80360-2 2231712 [OpenAIRE] [PubMed] [DOI]

Arif C. Daniels C. Bayer T. Ba nguera-Hinestroza E. Barbrook A. Howe C. J. . (2014). Assessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region. Mol. Ecol. 23, 4418–4433. 10.1111/mec.12869 25052021 [OpenAIRE] [PubMed] [DOI]

Barash Y. Sulam R. Loya Y. Rosenberg E. (2005). Bacterial Strain BA-3 and a filterable factor cause a White Plague-like disease in corals from the Eilat coral reef. Aquat. Microb. Ecol. 40, 183–189. 10.3354/ame040183 [OpenAIRE] [DOI]

Barr J. J. Auro R. Furlan M. Whiteson K. L. Erb M. L. Pogliano J. . (2013). Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc. Natl. Acad. Sci. U.S.A. 110, 10771–10776. 10.1073/pnas.1305923110 23690590 [OpenAIRE] [PubMed] [DOI]

Barshis D. J. Ladner J. T. Oliver T. A. Palumbi S. R. (2014). Lineage-specific transcriptional profiles of Symbiodinium spp. unaltered by heat stress in a coral host. Mol. Biol. Evol. 31, 1343–1352. 10.1093/molbev/msu107 24651035 [OpenAIRE] [PubMed] [DOI]

Barshis D. J. Ladner J. T. Oliver T. A. Seneca F. O. Traylor-Knowles N. Palumbi S. R. (2013). Genomic basis for coral resilience to climate change. Proc. Natl. Acad. Sci. U.S.A. 110, 1387–1392. 10.1073/pnas.1210224110 23297204 [OpenAIRE] [PubMed] [DOI]

Baumgarten S. Bayer T. Aranda M. Liew Y. J. Carr A. Micklem G. . (2013). Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals. BMC Genomics 14:704. 10.1186/1471-2164-14-704 24119094 [OpenAIRE] [PubMed] [DOI]

Bayer T. Aranda M. Sunagawa S. Yum L. K. Desalvo M. K. Lindquist E. . (2012). Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals. PLoS ONE 7:e35269. 10.1371/journal.pone.0035269 22529998 [OpenAIRE] [PubMed] [DOI]

Benjamini Y. Hochberg Y. (1995). Controlling the false discovery rate - a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Methodol. 57, 289–300.

Boeckmann B. Bairoch A. Apweiler R. Blatter M. C. Estreicher A. Gasteiger E. . (2003). The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31, 365–370. 10.1093/nar/gkg095 12520024 [OpenAIRE] [PubMed] [DOI]

Bolger A. M. Lohse M. Usadel B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120. 10.1093/bioinformatics/btu170 24695404 [OpenAIRE] [PubMed] [DOI]

Budd A. F. Fukami H. Smith N. D. Knowlton N. (2012). Taxonomic classification of the reef coral family Mussidae (Cnidaria: Anthozoa: Scleractinia). Zool. J. Linn. Soc. 166, 465–529. 10.1111/j.1096-3642.2012.00855.x [OpenAIRE] [DOI]

Burge C. A. Mouchka M. E. Harvell C. D. Roberts S. (2013). Immune response of the Caribbean sea fan, Gorgonia ventalina, exposed to an Aplanochytrium parasite as revealed by transcriptome sequencing. Front. Physiol. 4:180. 10.3389/fphys.2013.00180 23898300 [OpenAIRE] [PubMed] [DOI]

Cárdenas A. Rodriguez-R L. M. Pizarro V. Cadavid L. F. Arévalo-Ferro C. (2012). Shifts in bacterial communities of two caribbean reef-building coral species affected by White Plague Disease. ISME J. 6, 502–512. 10.1038/ismej.2011.123 21955993 [OpenAIRE] [PubMed] [DOI]

Chen D. Toone W. M. Mata J. Lyne R. Burns G. Kivinen K. . (2003). Global transcriptional responses of fission yeast to environmental stress. Mol. Biol. Cell 14, 214–229. 10.1091/mbc.E02-08-0499 12529438 [OpenAIRE] [PubMed] [DOI]

68 references, page 1 of 5
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