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The small RNA locus map for Chlamydomonas reinhardtii.

Published version
Peer-reviewed

Type

Article

Change log

Authors

Müller, Sebastian Y  ORCID logo  https://orcid.org/0000-0002-0148-7020
Matthews, Nicholas E  ORCID logo  https://orcid.org/0000-0002-8979-3531
Valli, Adrian A 
Baulcombe, David C 

Abstract

Small (s)RNAs play crucial roles in the regulation of gene expression and genome stability across eukaryotes where they direct epigenetic modifications, post-transcriptional gene silencing, and defense against both endogenous and exogenous viruses. It is known that Chlamydomonas reinhardtii, a well-studied unicellular green algae species, possesses sRNA-based mechanisms that are distinct from those of land plants. However, definition of sRNA loci and further systematic classification is not yet available for this or any other algae. Here, using data-driven machine learning approaches including Multiple Correspondence Analysis (MCA) and clustering, we have generated a comprehensively annotated and classified sRNA locus map for C. reinhardtii. This map shows some common characteristics with higher plants and animals, but it also reveals distinct features. These results are consistent with the idea that there was diversification in sRNA mechanisms after the evolutionary divergence of algae from higher plant lineages.

Description

Keywords

Base Composition, Chlamydomonas reinhardtii, Cluster Analysis, DNA Methylation, Evolution, Molecular, Gene Expression Regulation, Plant, Gene Library, Genetic Loci, Machine Learning, Molecular Sequence Annotation, RNA, Antisense, RNA, Plant

Journal Title

PLoS One

Conference Name

Journal ISSN

1932-6203
1932-6203

Volume Title

15

Publisher

Public Library of Science (PLoS)
Sponsorship
Royal Society (RP170001)
European Research Council (340642)
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