Prevalence, evolution, and cis-regulation of diel transcription in Chlamydomonas reinhardtii

Nicholas Panchy, Guangxi Wu, Linsey Newton, Chia Hong Tsai, Jin Chen, Christoph Benning, Eva M. Farré, Shin Han Shiu

Research output: Contribution to journalArticlepeer-review

23 Scopus citations


Endogenous (circadian) and exogenous (e.g., diel) biological rhythms are a prominent feature of many living systems. In green algal species, knowledge of the extent of diel rhythmicity of genome-wide gene expression, its evolution, and its cis-regulatory mechanism is limited. In this study, we identified cyclically expressed genes under diel conditions in Chlamydomonas reinhardtii and found that ~50% of the 17,114 annotated genes exhibited cyclic expression. These cyclic expression patterns indicate a clear succession of biological processes during the course of a day. Among 237 functional categories enriched in cyclically expressed genes, >90% were phase-specific, including photosynthesis, cell division, and motilityrelated processes. By contrasting cyclic expression between C. reinhardtii and Arabidopsis thaliana putative orthologs, we found significant but weak conservation in cyclic gene expression patterns. On the other hand, within C. reinhardtii cyclic expression was preferentially maintained between duplicates, and the evolution of phase between paralogs is limited to relatively minor time shifts. Finally, to better understand the cis regulatory basis of diel expression, putative cis-regulatory elements were identified that could predict the expression phase of a subset of the cyclic transcriptome. Our findings demonstrate both the prevalence of cycling genes as well as the complex regulatory circuitry required to control cyclic expression in a green algal model, highlighting the need to consider diel expression in studying algal molecular networks and in future biotechnological applications.

Original languageEnglish
Pages (from-to)2461-2471
Number of pages11
JournalG3: Genes, Genomes, Genetics
Issue number12
StatePublished - 2014

Bibliographical note

Publisher Copyright:
© 2014 Panchy et al.


  • Cis-regulatory
  • Diel expression
  • Element
  • Evolution
  • Gene regulation
  • Green algae
  • Transcriptomics

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)


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