Chromochloris zofingiensis SWITCh project
Project Overview: Systems biology With Increased TAG in Chromochloris (SWITCh)
Chromochloris zofingiensis is a unicellular green alga in the class Chlorophyceae, and is closely related to the model alga Chlamydomonas reinhardtii. Interest in C. zofingiensis derives in part from its ability to accumulate large amounts of triacylglycerols in cytoplasmic lipid bodies, which gives it promising commercial potential as a biofuel feedstock. Additionally, C. zofingiensis is capable of producing large quantities of high-value molecules such as the carotenoid astaxanthin, which is an antioxidant and anti-inflammatory nutraceutical beneficial to human health. Research on C. zofingiensis provides insight into the green lineage, regulation of metabolism, and the biosynthesis of astaxanthin. Previously, C. zofingiensis was placed in genera Chlorella, Muriella, and Mychonastes.
Genome Statistics
Genome bulk data (v5.2.3.2) available for download on Phytozome
Gene models used in Foflonker, Fatima, and Crysten E. Blaby-Haas. "Co-locality to co-functionality: Eukaryotic gene neighborhoods as a resource for function discovery." Molecular Biology and Evolution (2020) in press are available HERE.
Publications
Gallaher, SD, Craig, RJ, Ganesan, I, Purvine, SO, McCorkle, SR, Grimwood, J, Strenkert, D, Davidi, L, Roth, MS, Jeffers, TL, Lipton, MS, Niyogi, KK, Schmutz, J, Theg, SM, Blaby-Haas, CE, Merchant, SS. 2021. Widespread polycistronic gene expression in green algae. Proceedings of the National Academy of Sciences USA 118 (7): e2017714118.
Jeffers, TL and Roth, MS. 2021. Revealing mechanisms of algal astaxanthin production and bioengineering potential using multi-omics. In Ravishankar, GA and Ambati, RR (Eds.). Global perspective of astaxanthin: From industrial production to food, health and pharmaceutical applications. Academic Press, USA. Pp 181-208.
Metcalf, AJ, Nagygyor, A, Boyle, NR. 2020. Rapid Annotation of Photosynthetic Systems (RAPS): Automated algorithm to generate genome-scale metabolic networks from algal genomes. Algal Research, 50, 101967.
Foflonker, F and Blaby-Haas, CE, 2020. Colocality to cofunctionality: Eukaryotic gene neighborhoods as a resource for function discovery. Molecular Biology and Evolution, 38 (2), pp.650-662.
Roth, MS, Westcott, DJ, Iwai, M, Niyogi, KK, 2019. Hexokinase is necessary for glucose-mediated photosynthesis repression and lipid accumulation in a green alga. Communications Biology, 2, 347.
Blaby-Haas, CE and Merchant, SS, 2019. Comparative and Functional Algal Genomics. Annual Review of Plant Biology, 70, pp.605-638.
Roth, MS, Gallaher, SD, Westcott, DJ, Iwai, M, Louie, KB, Mueller, M, Walter, A, Foflonker, F, Bowen, BP, Ataii, NN, Song, J, Chen, J-H, Blaby-Haas, C, Larabell, C, Auer, M, Northen, T, Merchant, SS, Niyogi, KK. 2019. Regulation of oxygenic photosynthesis during trophic transitions in the green alga Chromochloris zofingiensis. The Plant Cell, 31(3), pp.579-601.
Iwai, M, Roth, MS, Niyogi, KK, 2018. Subdiffraction‐resolution live‐cell imaging for visualizing thylakoid membranes. The Plant Journal, 96(1), pp.233-243.
Gallaher, SD and Roth, MS. 2018. RNA purification from the unicellular green alga, Chromochloris zofingiensis. Bio-protocol 8, e2793. DOI: 10.21769/BioProtoc.2793
Roth, MS, Cokus, SJ, Gallaher, SD, Walter, A, Lopez, D, Erickson, E, Endelman, B, Westcott, D, Larabell, CA, Merchant, SS, Pellegrini, M, Niyogi, KK.. 2017. Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production. Proceedings of the National Academy of Sciences, 114(21), pp.E4296-E4305.
Patents
Roth, MS, Niyogi, KK, Gallaher, SD, Merchant, S. 2021. Genes involved in astaxanthin biosynthesis (US Patent Number 11,124,819). United States Patent and Trademark Office URL
Funding
