Natural genetic variation reveals divergent transcriptomic responses to hyperoxia in two Chlamydomonas reinhardtii ecotypes

Temple, J. A.; Neofotis, P. G.; Lucker, B. F.; Bibik, J. D.; Kramer, D. M.; Strenkert, D.

doi:10.64898/2026.07.09.737578

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bioRxiv · 10.64898/2026.07.09.737578

Natural genetic variation reveals divergent transcriptomic responses to hyperoxia in two Chlamydomonas reinhardtii ecotypes

Temple, J. A.·Neofotis, P. G.·Lucker, B. F.·Bibik, J. D.·Kramer, D. M.·Strenkert, D.

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Abstract

Green algae must continuously balance resource availability to maintain photosynthetic performance. The O2:CO2 ratio is a key determinant of their metabolic mode. Under hyperoxia or low CO2, many algae induce a carbon concentrating mechanism (CCM). In the model green alga Chlamydomonas reinhardtii, the CCM relies on a pyrenoid, a specialized microcompartment that elevates CO2 around rubisco. While ambient CO2 acclimation is well-studied, responses to hyperoxia remain poorly understood, despite its frequent occurrence in nature under high light. Using controlled bioreactors, we exposed two diverse Chlamydomonas ecotypes, CC1009 and CC2343, to 95% oxygen to analyze time-dependent, genome-wide transcriptomic and phenotypic changes. Both ecotypes induced CCM genes, but they exhibited distinct molecular and physiological phenotypes. The tolerant ecotype (CC1009) successfully adapted, developing a functional CCM with a structured starch sheath. Conversely, the sensitive ecotype (CC2343) suffered growth arrest and formed malformed pyrenoids. Transcriptomics revealed that CC1009 initiated a rapid initial response, upregulating chloroplast proteostasis and downregulating nucleotide metabolism. CC2343 showed a massive, delayed transcriptional response, downregulating genes coding for photosystems and tetrapyrrole biosynthesis. This unbiased transcriptomic approach identifies key candidate genes driving algal acclimation to hyperoxic stress in natural, high-light environments.

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Temple, J. A., Neofotis, P. G., Lucker, B. F., Bibik, J. D., Kramer, D. M., Strenkert, D.. 2026-07-15. Natural genetic variation reveals divergent transcriptomic responses to hyperoxia in two Chlamydomonas reinhardtii ecotypes. https://doi.org/10.64898/2026.07.09.737578

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