Global discovery and characterization of small non-coding RNAs in marine microalgae

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• 作者：Sara Lopez-Gomollon (5) (9)
  Matthew Beckers (6)
  Tina Rathjen (10) (5)
  Simon Moxon (11) (6)
  Florian Maumus (7)
  Irina Mohorianu (5)
  Vincent Moulton (6)
  Tamas Dalmay (5)
  Thomas Mock (8)
  
  5. School of Biological Sciences ; University of East Anglia ; Norwich ; NR4 7TJ ; UK
  9. Estaci贸n Experimental Aula Dei ; CSIC (Consejo Superior de Investigaciones Cient铆ficas) ; 50059 ; Zaragoza ; Spain
  6. School of Computing Sciences ; University of East Anglia ; Norwich ; NR4 7TJ ; UK
  10. Commonwealth Scientific and Industrial Research Organization Plant Industry ; Canberra ; Australian Capital Territory ; 2601 ; Australia
  11. The Genome Analysis Centre ; Norwich ; NR4 7UH ; UK
  7. UR1164 URGI-Research Unit in Genomics-Info ; INRA de Versailles-Grignon ; Route de Saint-Cyr ; Versailles ; 78026 ; France
  8. School of Environmental Sciences ; University of East Anglia ; Norwich ; NR4 7TJ ; UK
  
• 关键词：Coccolithophores ; Diatoms ; Growth ; Marine phytoplankton ; MicroRNA ; Non ; coding RNAs ; Small RNA ; Stress ; tRNA
• 刊名：BMC Genomics
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：15
• 期：1
• 全文大小：3,374 KB
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• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

Background Marine phytoplankton are responsible for 50% of the CO2 that is fixed annually worldwide and contribute massively to other biogeochemical cycles in the oceans. Diatoms and coccolithophores play a significant role as the base of the marine food web and they sequester carbon due to their ability to form blooms and to biomineralise. To discover the presence and regulation of short non-coding RNAs (sRNAs) in these two important phytoplankton groups, we sequenced short RNA transcriptomes of two diatom species (Thalassiosira pseudonana, Fragilariopsis cylindrus) and validated them by Northern blots along with the coccolithophore Emiliania huxleyi. Results Despite an exhaustive search, we did not find canonical miRNAs in diatoms. The most prominent classes of sRNAs in diatoms were repeat-associated sRNAs and tRNA-derived sRNAs. The latter were also present in E. huxleyi. tRNA-derived sRNAs in diatoms were induced under important environmental stress conditions (iron and silicate limitation, oxidative stress, alkaline pH), and they were very abundant especially in the polar diatom F. cylindrus (20.7% of all sRNAs) even under optimal growth conditions. Conclusions This study provides first experimental evidence for the existence of short non-coding RNAs in marine microalgae. Our data suggest that canonical miRNAs are absent from diatoms. However, the group of tRNA-derived sRNAs seems to be very prominent in diatoms and coccolithophores and maybe used for acclimation to environmental conditions.