Abstract
To understand the physiological responses of the brown macroalga Macrocystis integrifolia during the marine tidal cycle, two RNA libraries were prepared from algal frond samples collected in the intertidal zone (0 m depth) and subtidal zone (10 m depth). Samples collected from intertidal zone during low tide was considered as abiotic stressed (MI0), while samples collected from subtidal zone was considered as control (MI10). Both RNA libraries were sequenced on Illumina NextSeq 500 which generated approx. 46.9 million and 47.7 million raw paired-end reads for MI0 and MI10, respectively. Among the representative transcripts (RTs), a total of 16,398 RTs (39.20%) from MI0 and 21,646 RTs (39.24%) from MI10 were successfully annotated. A total of 535 unigenes (271 upregulated and 264 downregulated) showed significantly altered expression between MI0 and MI10. In abiotic-stressed condition (MI0), the relative expression levels of genes associated with antioxidant defenses (vanadium-dependent bromoperoxidase, glutathione S-transferase, lipoxygenase, serine/threonine-protein kinase, aspartate Aminotransferase, HSPs), water transport (aquaporin), photosynthesis (light-harvesting complex) protein were significantly upregulated, while in control condition (MI10) most of the genes predominantly involved in energy metabolism (NADH-ubiquinone oxidoreductase/NADH dehydrogenase, NAD(P)H-Nitrate reductase, long-chain acyl-CoA synthetase, udp-n-acetylglucosamine pyrophosphorylase) were overexpressed.
This is a preview of subscription content, log in via an institution to check access.
References
Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215:403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
Alveal K (1995) Manejo de algas marinas. In: Alveal K, Ferrario M, Oliveira E, Sar E (eds) Manual de métodos ficológicos. Ediciones Universidad de Concepción, Concepción, pp 825–863
Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11:R106. https://doi.org/10.1186/gb-2010-11-10-r106
Andrews S (2010) FastQC: A quality control tool for high throughput sequence data. http://www.Bioinformatics.Babraham.Ac.Uk/Projects/Fastqc/
Bixler HJ, Porse H (2011) A decade of change in the seaweed hydrocolloids industry. J Appl Phycol 23:321–335. https://doi.org/10.1007/s10811-010-9529-3
Chapman AS, Stévant P, Larssen WE (2015) Food or fad? challenges and opportunities for including seaweeds in a Nordic diet. Bot Mar 58:423–433. https://doi.org/10.1515/bot-2015-0044
Fleurence J (2016) Seaweeds as food: seaweed in health and disease prevention. Academic Press, Cambridge, pp 149–167
Grabherr MG, Haas BJ, Yassour M et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652. https://doi.org/10.1038/nbt.1883
Hafting JT, Critchley AT, Cornish ML et al (2012) On-land cultivation of functional seaweed products for human usage. J Appl Phycol 24:385–392. https://doi.org/10.1007/s10811-011-9720-1
Jensen A (1993) Present and future needs for algae and algal products. Hydrobiologia 260–261:15–23. https://doi.org/10.1007/BF00048998
Kupper FC, Carpenter LJ, McFiggans GB et al (2008) Iodide accumulation provides kelp with an inorganic antioxidant impacting atmospheric chemistry. Proc Natl Acad Sci 105:6954–6958. https://doi.org/10.1073/pnas.0709959105
Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658–1659. https://doi.org/10.1093/bioinformatics/btl158
López-Cristoffanini C, Tellier F, Otaíza R et al (2013) Tolerance to air exposure: A feature driving the latitudinal distribution of two sibling kelp species. Bot Mar 56:431–440. https://doi.org/10.1515/bot-2013-0042
McHugh DJ (2003) A Guide to the Seaweed Industry. FAO Fisheries Technical Paper. ISBN 92-5-104958-0
Synytsya A, Copiková J, Kim WJ, Park YI (2015) Cell wall polysaccharides of marine algae. Springer handbook of marine biotechnology. Springer, Berlin, pp 543–590
Tønnesen HH, Karlsen J (2002) Alginate in drug delivery systems. Drug Dev Ind Pharm 28:621–630. https://doi.org/10.1081/DDC-120003853
Vo TS, Ngo DH, Kim SK (2012) Marine algae as a potential pharmaceutical source for anti-allergic therapeutics. Process Biochem 47:386–394
Acknowledgements
This work was supported by the Grant no 352-PNICP-PIBA-2014 from Programa Nacional de Innovación para la Competitividad y Productividad (INNOVATE PERU), Ministry of Production of Peru. Erika Salavarría was funded by scholarship program “Academia 2010”. SENESCYT. Ecuador. We acknowledge Peruvian Seaweeds S.R.L. and Gunter Villena for logistic facilitated for the sampling. We acknowledge Genotypic Technology Pvt. Ltd Bengaluru, India for additional analysis. We want to thank Dr. Marcel Gutiérrez-Correa (RIP) for his extraordinary support and useful advice during the development of this work.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they don’t have any conflict of interest.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Salavarría, E., Paul, S., Gil-Kodaka, P. et al. First global transcriptome analysis of brown algae Macrocystis integrifolia (Phaeophyceae) under marine intertidal conditions. 3 Biotech 8, 185 (2018). https://doi.org/10.1007/s13205-018-1204-4
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s13205-018-1204-4