@article{a82954e8281a4763a2dfdb1312a061ef,
title = "Genomic characterization reveals significant divergence within Chlorella sorokiniana (Chlorellales, Trebouxiophyceae)",
abstract = "Selection of highly productive algal strains is crucial for establishing economically viable biomass and bioproduct cultivation systems. Characterization of algal genomes, including understanding strain-specific differences in genome content and architecture is a critical step in this process. Using genomic analyses, we demonstrate significant differences between three strains of Chlorella sorokiniana (strain 1228, UTEX 1230, and DOE1412). We found that unique, strain-specific genes comprise a substantial proportion of each genome, and genomic regions with >80% local nucleotide identity constitute <15% of each genome among the strains, indicating substantial strain specific evolution. Furthermore, cataloging of meiosis and other sex-related genes in C. sorokiniana strains suggests strategic breeding could be utilized to improve biomass and bioproduct yields if a sexual cycle can be characterized. Finally, preliminary investigation of epigenetic machinery suggests the presence of potentially unique transcriptional regulation in each strain. Our data demonstrate that these three C. sorokiniana strains represent significantly different genomic content. Based on these findings, we propose individualized assessment of each strain for potential performance in cultivation systems.",
keywords = "Chlorella sorokiniana, DNA methylation, Genome analysis, Meiosis, Polyketide synthetase (PKS)",
author = "Hovde, {Blake T.} and Hanschen, {Erik R.} and {Steadman Tyler}, {Christina R.} and Lo, {Chien Chi} and Yuliya Kunde and Karen Davenport and Hajnalka Daligault and Joseph Msanne and Stephanie Canny and Eyun, {Seong il} and Riethoven, {Jean Jack M.} and Juergen Polle and Starkenburg, {Shawn R.}",
note = "Funding Information: This work was supported by the Bioenergy Technology Office within the U.S. Department of Energy Office of Energy Efficiency and Renewable Energy through contract DE-NL0029949 . Special thanks to Cheryl Gleasner and Kim McMurry for technical assistance. B.H. performed the genome annotation, global comparative analysis including genome rearrangement and assembly statistics, unique gene analysis, and retrotransposon analysis. E.R.H. performed the global comparative analysis including species phylogeny, ViridiCut2 gene, sex-related gene, and PKS gene annotations. C.R.S. performed the epigenetic analysis. C.L. completed the comparative nucleotide identity analysis. Y.K., K.D., and H.D. contributed to the sequencing and assembly of all three Chlorella genomes. J.M. purified genomic DNA and S.C., S.E., and J.J.R. contributed to the assembly and annotation of the UTEX 1230 genome. J.P. extracted DNA from DOE1412 and conceived the project. S.R.S. designed and conceived of this study, and with B.H. and E.R.H., performed the global comparative analysis. All authors except J.M., S.C., S.E., and J.J.R. contributed to the writing and/or editing of the article. The authors declare no potential financial or other interests that could be perceived to influence the outcomes of the research. No conflicts, informed consent, human or animal rights applicable. All authors declare agreement to authorship and submission of the manuscript for peer review. Publisher Copyright: {\textcopyright} 2018 The Authors",
year = "2018",
month = nov,
doi = "10.1016/j.algal.2018.09.012",
language = "English (US)",
volume = "35",
pages = "449--461",
journal = "Algal Research",
issn = "2211-9264",
publisher = "Elsevier B.V.",
}