title: High-Resolution Profiling of a Synchronized Diurnal Transcriptome from Chlamydomonas reinhardtii Reveals Continuous Cell and Metabolic Differentiation.
abstract: The green alga Chlamydomonas reinhardtii is a useful model organism for investigating diverse biological processes, such as photosynthesis and chloroplast biogenesis, flagella and basal body structure/function, cell growth and division, and many others. We combined a highly synchronous photobioreactor culture system with frequent temporal sampling to characterize genome-wide diurnal gene expression in Chlamydomonas. Over 80% of the measured transcriptome was expressed with strong periodicity, forming 18 major clusters. Genes associated with complex structures and processes, including cell cycle control, flagella and basal bodies, ribosome biogenesis, and energy metabolism, all had distinct signatures of coexpression with strong predictive value for assigning and temporally ordering function. Importantly, the frequent sampling regime allowed us to discern meaningful fine-scale phase differences between and within subgroups of genes and enabled the identification of a transiently expressed cluster of light stress genes. Coexpression was further used both as a data-mining tool to classify and/or validate genes from other data sets related to the cell cycle and to flagella and basal bodies and to assign isoforms of duplicated enzymes to their cognate pathways of central carbon metabolism. Our diurnal coexpression data capture functional relationships established by dozens of prior studies and are a valuable new resource for investigating a variety of biological processes in Chlamydomonas and other eukaryotes.
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, Missouri 63132 Division of Biological Sciences, University of California San Diego, La Jolla, California 92093.
authors.forename: James Matt
authors.identifier: http://orcid.org/0000-0001-8346-7869
authors.initials: JM
authors.lastname: Zones
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095.
authors.forename: Ian K
authors.identifier: http://orcid.org/0000-0002-1631-3154
authors.initials: IK
authors.lastname: Blaby
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095 Institute of Genomics and Proteomics, University of California, Los Angeles, California 90095.
authors.forename: Sabeeha S
authors.identifier: http://orcid.org/0000-0002-2594-509X
authors.initials: SS
authors.lastname: Merchant
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, Missouri 63132 jumen@danforthcenter.org.
authors.forename: James G
authors.identifier: http://orcid.org/0000-0003-4094-9045
authors.initials: JG
authors.lastname: Umen
mesh_terms: D064652:Basal Bodies / Q000378:metabolism; D002453:Cell Cycle; D002454:Cell Differentiation; D016825:Chlamydomonas reinhardtii / Q000235:genetics* / Q000254:growth & development / Q000502:physiology; D002736:Chloroplasts / Q000378:metabolism; D002940:Circadian Rhythm; D005407:Flagella / Q000378:metabolism; D005786:Gene Expression Regulation; D053858:Metabolic Networks and Pathways; D010788:Photosynthesis; D059467:Transcriptome