Characterization of the small RNA transcriptome of the marine coccolithophorid, Emiliania huxleyi

Zhang, Xiaoyu, Gamarra, Jaime, Castro, Steven, Carrasco, Estela, Hernandez, Aaron, Mock, Thomas ORCID: https://orcid.org/0000-0001-9604-0362, Hadaegh, Ahmad R. and Read, Betsy A. (2016) Characterization of the small RNA transcriptome of the marine coccolithophorid, Emiliania huxleyi. PLoS One, 11 (4). ISSN 1932-6203

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Abstract

Small RNAs (smRNAs) control a variety of cellular processes by silencing target genes at the transcriptional or post-transcription level. While extensively studied in plants, relatively little is known about smRNAs and their targets in marine phytoplankton, such as Emiliania huxleyi (E. huxleyi). Deep sequencing was performed of smRNAs extracted at different time points as E. huxleyi cells transition from logarithmic to stationary phase growth in batch culture. Computational analyses predicted 18 E. huxleyi specific miRNAs. The 18 miRNA candidates and their precursors vary in length (18-24 nt and 71-252 nt, respectively), genome copy number (3-1,459), and the number of genes targeted (2-107). Stem-loop real time reverse transcriptase (RT) PCR was used to validate miRNA expression which varied by nearly three orders of magnitude when growth slows and cells enter stationary phase. Stem-loop RT PCR was also used to examine the expression profiles of miRNA in calcifying and non-calcifying cultures, and a small subset was found to be differentially expressed when nutrients become limiting and calcification is enhanced. In addition to miRNAs, endogenous small RNAs such as ra-siRNAs, ta-siRNAs, nat-siRNAs, and piwiRNAs were predicted along with the machinery for the biogenesis and processing of si-RNAs. This study is the first genome-wide investigation smRNAs pathways in E. huxleyi. Results provide new insights into the importance of smRNAs in regulating aspects of physiological growth and adaptation in marine phytoplankton and further challenge the notion that smRNAs evolved with multicellularity, expanding our perspective of these ancient regulatory pathways.

Item Type:	Article
Additional Information:	© 2016 Zhang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Uncontrolled Keywords:	sdg 14 - life below water ,/dk/atira/pure/sustainabledevelopmentgoals/life_below_water
Faculty \ School:	Faculty of Science > School of Environmental Sciences
UEA Research Groups:	Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation Faculty of Science > Research Groups > Centre for Ocean and Atmospheric Sciences Faculty of Science > Research Groups > Environmental Biology
Depositing User:	Pure Connector
Date Deposited:	04 May 2016 15:00
Last Modified:	31 Oct 2023 01:46
URI:	https://ueaeprints.uea.ac.uk/id/eprint/58574
DOI:	10.1371/journal.pone.0154279

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