Characterization of the Small RNA Transcriptome of the Marine Coccolithophorid, Emiliania huxleyi.
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.
Department of Computer Science and Information Systems, California State University, San Marcos, CA, 92096, United States of America.
Xiaoyu
X
Zhang
Department of Computer Science and Information Systems, California State University, San Marcos, CA, 92096, United States of America.
Jaime
J
Gamarra
Department of Biological Sciences, California State University, San Marcos, CA, 92096, United States of America.
Steven
S
Castro
Department of Biological Sciences, California State University, San Marcos, CA, 92096, United States of America.
Estela
E
Carrasco
Department of Biological Sciences, California State University, San Marcos, CA, 92096, United States of America.
Aaron
A
Hernandez
School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, United Kingdom.
Thomas
T
Mock
Department of Computer Science and Information Systems, California State University, San Marcos, CA, 92096, United States of America.
Ahmad R
AR
Hadaegh
Department of Biological Sciences, California State University, San Marcos, CA, 92096, United States of America.
Betsy A
BA
Read
D020418:Algal Proteins / Q000235:genetics / Q000378:metabolism; D000595:Amino Acid Sequence; D060565:Argonaute Proteins / Q000235:genetics / Q000378:metabolism; D061249:Batch Cell Culture Techniques; D020869:Gene Expression Profiling; D016678:Genome; D058087:Haptophyta / Q000235:genetics* / Q000378:metabolism; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D010839:Phytoplankton / Q000235:genetics* / Q000378:metabolism; D034741:RNA, Small Interfering / Q000235:genetics* / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D059467:Transcriptome
D020418:Algal Proteins; D060565:Argonaute Proteins; D035683:MicroRNAs; D034741:RNA, Small Interfering