Nucleomorph small RNAs in cryptophyte and chlorarachniophyte algae

Anna K.M. Asman, Bruce A. Curtis, John M. Archibald

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Resumen

The regulation of gene expression and RNA maturation underlies fundamental processes such as cell homeostasis, development, and stress acclimation. The biogenesis and modification of RNA is tightly controlled by an array of regulatory RNAs and nucleic acid-binding proteins. While the role of small RNAs (sRNAs) in gene expression has been studied in-depth in select model organisms, little is known about sRNA biology across the eukaryotic tree of life. We used deep sequencing to explore the repertoires of sRNAs encoded by the miniaturized, endosymbiotically derived "nucleomorph" genomes of two single-celled algae, the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. A total of 32.3 and 35.3 million reads were generated from G. theta and B. natans, respectively. In G. theta, we identified nucleomorph U1, U2, and U4 spliceosomal small nuclear RNAs (snRNAs) as well as 11 C/D box small nucleolar RNAs (snoRNAs), five of which have potential plant and animal homologs. The snoRNAs are predicted to perform20-O methylation of rRNA (but not snRNA). In B. natans, we found the previously undetected 5S rRNA aswell as six orphan sRNAs. Analysis of chlorarachniophyte snRNAs shed light on the removal of theminiature 18-21 nt introns found in B. natans nucleomorph genes. Neither of the nucleomorph genomes appears to encode RNA pseudouridylation machinery, and U5 snRNA cannot be found in the cryptophyte G. theta. Considering the central roles of U5 snRNA and RNA modifications in other organisms, cytoplasm-to-nucleomorph RNA shuttling in cryptophyte algae is a distinct possibility.

Idioma originalEnglish
Páginas (desde-hasta)1117-1134
Número de páginas18
PublicaciónGenome Biology and Evolution
Volumen11
N.º4
DOI
EstadoPublished - abr. 1 2019

Nota bibliográfica

Funding Information:
This research was supported by a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada awarded to J.M.A. (RGPIN-2014-05871). We thank Scott Roy for helpful comments on an earlier version of this article.

Publisher Copyright:
© 2019 The Author(s). Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

ASJC Scopus Subject Areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

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