Dual-compartmental transcriptomic + proteomic analysis of a marine endosymbiosis exposed to environmental change

Molecular Ecology

Volumn 25, Issue 23, 2016, Pages 5944-5958

  Mayfield, Anderson B ^a,b   Wang, Yu Bin ^c,d   Chen, Chii Shiarng ^a,e,f,g   Chen, Shu Hwa ^d   Lin, Chung Yen ^c,d,h  

^a NATIONAL MUSEUM OF MARINE BIOLOGY AND AQUARIUM   (Taiwan)

^b Living Oceans Foundation   (United States)

^c NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^d INSTITUTE OF INFORMATION SCIENCE   (Taiwan)

^e Taiwan Coral Research Center   (Taiwan)

^f NATIONAL DONG HWA UNIVERSITY   (Taiwan)

^g NATIONAL SUN YAT SEN UNIVERSITY   (Taiwan)

^h NATIONAL HEALTH RESEARCH INSTITUTES   (Taiwan)

Author keywords

acclimation; coral reef; endosymbiosis; environmental change; gene expression; proteome; transcriptome

Indexed keywords

PROTEOME; TRANSCRIPTOME;

ANIMAL; ANTHOZOA; GENE EXPRESSION REGULATION; GENETICS; SEA; SYMBIOSIS; TEMPERATURE;

ANIMALS; ANTHOZOA; GENE EXPRESSION REGULATION; OCEANS AND SEAS; PROTEOME; SYMBIOSIS; TEMPERATURE; TRANSCRIPTOME;

EID: 84999025077     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.13896     Document Type: Article

References (34)

1. Barshis DJ, Ladner JT, Oliver TA et al. (2013) Genomic basis for coral resilience to climate change. Proceedings of the National Academy of Sciences of the United States of America, 110, 1387–1392.
2. Chen WNU, Kang HJ, Weis VM, Mayfield AB, Fang LS, Chen CS (2012) Diel rhythmicity of lipid body formation in a coral-Symbiodinium endosymbiosis. Coral Reefs, 31, 521–534.
3. Chen HK, Song SN, Wang LH et al. (2015) A compartmental comparison of major lipid species in a coral-Symbiodinium endosymbiosis: evidence that the coral host regulates lipogenesis of its cytosolic lipid bodies. PLoS One, e0132519.
4. Cox MP, Peterson DA, Biggs PJ (2010) SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics, 11, 485.
5. Fagerberg L, Hallstrom BM, Oksvold P et al. (2014) Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Molecular and Cellular Proteomics, 13, 397–406.
6. Grabherr MG, Haas BJ, Yassour M et al. (2011) Full-length transcriptome assembly from RNA- Seq data without a reference genome. Nature Biotechnology, 29, 644–652.
7. Greensbaum D, Colangelo C, Williams K, Gerstein M (2003) Comparing protein abundance and mRNA expression on a genomic scale. Genome Biology, 4, 117.
8. Hoegh-Guldberg O, Mumby PJ, Hooten AJ et al. (2007) Coral reefs under rapid climate change and ocean acidification. Science, 318, 1737–1742.
9. Huang YCA, Hsieh HJ, Meng PJ et al. (2011) Nutrient enrichment caused by marine cage culture and its influence on subtropical coral communities in turbid waters. Marine Ecology Progress Series, 423, 83–93.
10. Jan S, Chen CTA (2008) Potential biogeochemical effects from vigorous internal tides generated in Luzon Strait: a case study at the southernmost coast of Taiwan. Journal of Geophysical Research, 114, 1–14.
11. Kim S, Pevzner PA (2014) MS-GF+ makes progress towards a universal database search tool for proteomics. Nature Communications, 5, 5277.
12. Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics, 12, 323.
13. Lin S, Cheng S, Song B et al. (2015) The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis. Science, 350, 691–694.
14. Loya Y, Sakai K, Yamazato K, Nakano Y, Sambali H, van Woesik R (2001) Coral bleaching: the winners and the losers. Ecology Letters, 4, 122–131.
15. Lu P, Vogel C, Wang R, Yao X, Marcotte EM (2007) Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nature Biotechnology, 25, 117–124.
16. Mayfield AB, Gates RD (2007) Osmoregulation in anthozoan-dinoflagellate symbiosis. Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology, 147A, 1–10.
17. Mayfield AB, Hsiao YY, Fan TY, Chen CS, Gates RD (2010) Evaluating the temporal stability of stress-activated protein kinase and cytoskeleton gene expression in the Pacific corals Pocillopora damicornis and Seriatopora hystrix. Journal of Experimental Marine Biology and Ecology, 395, 215–222.
18. Mayfield AB, Wang LH, Tang PC et al. (2011) Assessing the impacts of experimentally elevated temperature on the biological composition and molecular chaperone gene expression of a reef coral. PLoS One, e26529.
19. Mayfield AB, Chan PS, Putnam HM, Chen CS, Fan TY (2012a) The effects of a variable temperature regime on the physiology of the reef-building coral Seriatopora hystrix: results from a laboratory-based reciprocal transplant. The Journal of Experimental Biology, 215, 4183–4195.
20. Mayfield AB, Hsiao YY, Fan TY, Chen CS (2012b) Temporal variation in RNA/DNA and protein/DNA ratios in four anthozoan-dinoflagellate endosymbioses of the Indo-Pacific: implications for molecular diagnostics. Platax, 9, 1–24.
21. Mayfield AB, Chen M, Meng PJ et al. (2013a) The physiological response of the reef coral Pocillopora damicornis to elevated temperature: results from coral reef mesocosm experiments in Southern Taiwan. Marine Environmental Research, 86, 1–11.
22. Mayfield AB, Fan TY, Chen CS (2013b) Physiological acclimation to elevated temperature in a reef-building coral from an upwelling environment. Coral Reefs, 32, 909–921.
23. Mayfield AB, Fan TY, Chen CS (2013c) The physiological impact of ex situ transplantation on the Taiwanese reef-building coral Seriatopora hystrix. Journal of Marine Biology, Article ID 569369.
24. Mayfield AB, Fan TY, Chen CS (2013d) Real-time PCR-based gene expression analysis in the model reef-building coral Pocillopora damicornis: insight from a salinity stress study. Platax, 10, 1–29.
25. Mayfield AB, Chen CS, Liu PJ (2014a) Decreased green fluorescent protein-like chromoprotein gene expression in specimens of the reef-building coral Pocillopora damicornis undergoing high temperature-induced bleaching. Platax, 11, 1–23.
26. Mayfield AB, Chen YH, Dai CF, Chen CS (2014b) The effects of temperature on gene expression in the Indo-Pacific reef-building coral Seriatopora hystrix: insight from aquarium studies in Southern Taiwan. International Journal of Marine Science, 4, 1–23.
27. Mayfield AB, Hsiao YY, Chen HK, Chen CS (2014c) Rubisco expression in the dinoflagellate Symbiodinium sp. is influenced by both photoperiod and endosymbiotic lifestyle. Marine Biotechnology, 16, 371–384.
28. Mayfield AB, Wang YB, Chen CS, Chen SH, Lin CY (2014d) Compartment-specific transcriptomics in a reef-building coral exposed to elevated temperatures. Molecular Ecology, 23, 5816–5830.
29. Mayfield AB, Bruckner AW, Chen CH, Chen CS (2015) A survey of pocilloporids and their endosymbiotic dinoflagellate communities in the Austral and Cook Islands of the South Pacific. Platax, 12, 1–17.
30. Mayfield AB, Chen YJ, Lu CY, Chen CS (2016) Proteins involved in acclimation to variable temperature in the reef-building coral Seriatopora hystrix. In: Coral Reefs: Ecosystems, Environmental Impact and Current Threats (ed. Ortiz S), pp. 1–72. NOVA Publishing, New York.
31. Palumbi SR, Barshis DJ, Traylor-Knowles N, Bay RA (2014) Mechanisms of reef coral resistance to future climate change. Science, 334, 895–898.
32. Peng SE, Chen WNU, Chen HK et al. (2011) Lipid bodies in coral-dinoflagellate endosymbiosis: ultrastructural and proteomic analyses. Proteomics, 17, 3540–3555.
33. Putnam HM, Mayfield AB, Fan TY, Chen CS, Gates RD (2013) The physiological and molecular responses of larvae from the reef-building coral Pocillopora damicornis exposed to near-future increases in temperature and pCO2. Marine Biology, 160, 2157–2173.
34. Shinzato C, Shoguci E, Kawashima T et al. (2011) Using the Acropora digitifera genome to understand coral responses to environmental change. Nature, 476, 320–323.