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

Salomé, Patrice A.; Merchant, Sabeeha S.

doi:10.1093/plcell/koab042

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

Journal Article · Tue Feb 02 00:00:00 EST 2021 · The Plant Cell

DOI:https://doi.org/10.1093/plcell/koab042· OSTI ID:1814429

Salomé, Patrice A. ^[1];

^[2]

Univ. of California, Los Angeles, CA (United States)
Univ. of California, Los Angeles, CA (United States); Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

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.

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Research Organization:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; FC02-02ER63421; SC0018301

OSTI ID:: 1814429

Journal Information:: The Plant Cell, Vol. 33, Issue 4; ISSN 1040-4651

Publisher:: American Society of Plant BiologistsCopyright Statement

Country of Publication:: United States

Language:: English

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Co-expression networks in Chlamydomonas reveal significant rhythmicity in batch cultures and empower gene function discovery Salomé, Patrice; Merchant, Sabeeha Dryad https://doi.org/10.5068/d1wd55	dataset	January 2021

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