Co-expression networks in Chlamydomonas reveal significant rhythmicity in batch cultures and empower gene function discovery

The unicellular green alga Chlamydomonas reinhardtii is a choice reference system for the study of photosynthesis and chloroplast metabolism, cilium assembly and function, lipid and starch metabolism, and metal homeostasis. Despite decades of research, the functions of thousands of genes remain larg...

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Bibliographic Details
Published in:The Plant cell 2021-05, Vol.33 (4), p.1058-1082
Main Authors: Salomé, Patrice A, Merchant, Sabeeha S
Format: Article
Language:English
Subjects:
Arabidopsis - genetics
BASIC BIOLOGICAL SCIENCES
Batch Cell Culture Techniques
Cell Nucleus - genetics
Cell Nucleus - metabolism
Chlamydomonas reinhardtii - cytology
Chlamydomonas reinhardtii - genetics
Cilia - genetics
Circadian Rhythm - genetics
Focus on the Biology of Plant Genomes
Gene Expression Regulation, Plant
Gene Regulatory Networks
Genes, Plant
Histones - genetics
Photosynthesis - genetics
Ribosomal Proteins - genetics
Volvox - genetics
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Summary:The unicellular green alga Chlamydomonas reinhardtii is a choice reference system for the study of photosynthesis and chloroplast metabolism, cilium assembly and function, lipid and starch metabolism, and metal homeostasis. Despite decades of research, the functions of thousands of genes remain largely unknown, and new approaches are needed to categorically assign genes to cellular pathways. Growing collections of transcriptome and proteome data now allow a systematic approach based on integrative co-expression analysis. We used a dataset comprising 518 deep transcriptome samples derived from 58 independent experiments to identify potential co-expression relationships between genes. We visualized co-expression potential with the R package corrplot, to easily assess co-expression and anti-correlation between genes. We extracted several hundred high-confidence genes at the intersection of multiple curated lists involved in cilia, cell division, and photosynthesis, illustrating the power of our method. Surprisingly, Chlamydomonas experiments retained a significant rhythmic component across the transcriptome, suggesting an underappreciated variable during sample collection, even in samples collected in constant light. Our results therefore document substantial residual synchronization in batch cultures, contrary to assumptions of asynchrony. We provide step-by-step protocols for the analysis of co-expression across transcriptome data sets from Chlamydomonas and other species to help foster gene function discovery.
ISSN:1040-4651
1532-298X
1532-298X
DOI:10.1093/plcell/koab042