Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-seq of Chlamydomonas reinhardtii under diel conditions to identify cycling genes

ABSTRACT: Biological rhythms in response to both endogenous (circadian) and exogenous (e.g. diel) cycles, with a period of ~24 hours, are a prominent feature of many living systems. In green algal species, knowledge on 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. The 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 motility 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, particularly amongst older duplicates, and the evolution of phase between paralogs is limited to relatively minor shifts in time. 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 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. Total RNA sequences extracted every 3 hours between ZT (Zeitgeber Time, hours since last doawn) 0 and ZT21 from two biological replicates of C. reinhardtiis dw15.1

ORGANISM(S): Chlamydomonas reinhardtii

SUBMITTER: Nicholas Panchy

PROVIDER: E-GEOD-62671 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

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

Panchy Nicholas N Wu Guangxi G Newton Linsey L Tsai Chia-Hong CH Chen Jin J Benning Christoph C Farré Eva M EM Shiu Shin-Han SH

G3 (Bethesda, Md.) 20141028 12

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 indi ...[more]

PMID: 25354782

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Project description:Chemostat experiments: Predator-prey dynamics were followed in four replicate chemostats (continuous-flow aquatic culture vessels) supplied with nitrogen-limited sterile medium that was otherwise sufficient in all nutrient constituents (Yoshida et al. 2003; Becks et al. 2010). Three chemostats contained 380 mL of medium, while the fourth, used for our algal gene expression study, contained 3000 mL so as to provide sufficient material for genetic analysis. Brachionus calyciflorus was isolated originally from Milwaukee harbor, Wisconsin, and provided by M. Boraas. Chlamydomonas reinhardtii was obtained from the University of Texas algal culture collection (UTEX 89). Both species reproduced asexually in our chemostat system. Though B. calyciflorus is naturally cyclically parthenogenetic, the rotifers in our stock culture have evolved not to produce males because the bubbling in our chemostats prevents mating; we used only one mating type of Chlamydomonas. Absence of sexual reproduction does not preclude the processes of microevolution (Bell 2009) that we study, and it is commonly accepted that asexual species can evolve (Lenski et al. 1991; Barrett et al. 2005). We used a Chlamydomonas lineage, founded from our original Chlamydomonas stock and then exposed continuously to Brachionus predation for six months in chemostat culture prior to this study during which Chlamydomonas evolved to form clumps (the 'grazed Chlamydomonas' lineage in Becks et al. 2010). We tracked changes in Chlamydomonas gene expression throughout two complete cycles of algal and rotifer abundance and concurrent cycles in algal defense. Algal samples were taken from one chemostat at intervals of approximately every ten days (8 dates total), chosen to capture critical transitions in cell clumping. A sample taken at the start of the experiment from the culture that was used to inoculate the chemostat was the standard against which algae from later samples were compared (i.e., the M-^Sgrazed ChlamydomonasM-^T). To obtain sufficient material for microarray analysis, ca. 1 - 1.5 L algal samples were collected and filtered through a 10-um mesh to exclude rotifers and rotifer eggs. The algal samples of ca. 100 ml of chemostat medium were concentrated by centrifugation and frozen. Samples were shock frozen in liquid nitrogen and transferred to -80C.

Dataset Information

RNA-seq of Chlamydomonas reinhardtii under diel conditions to identify cycling genes

Publications

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

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