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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.

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [1]; ORCiD logo [2];  [3]; ORCiD logo [4];  [5];  [6];  [1]
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  2. Univ. of Nebraska, Lincoln, NE (United States). Center for Plant Science Innovation. School of Natural Resources
  3. Univ. of Nebraska, Lincoln, NE (United States). Center for Biotechnology
  4. Chung-Ang Univ., Seoul (Korea, Republic of). Dept. of Life Science
  5. Univ. of Nebraska, Lincoln, NE (United States). Center for Biotechnology. School of Biological Sciences
  6. CUNY Brooklyn College, New York, NY (United States)
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE Office of Energy Efficiency and Renewable Energy (EERE), Bioenergy Technologies Office (EE-3B)
OSTI Identifier:
1479995
Report Number(s):
LA-UR-18-24143
Journal ID: ISSN 2211-9264
Grant/Contract Number:  
AC52-06NA25396
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Algal Research
Additional Journal Information:
Journal Volume: 35; Journal ID: ISSN 2211-9264
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; 59 BASIC BIOLOGICAL SCIENCES; Chlorella sorokiniana Genome analysis Meiosis DNA methylation Polyketide synthetase (PKS)

Citation Formats

Hovde, Blake T., Hanschen, Erik R., Steadman Tyler, Christina R., Lo, Chien-Chi, Kunde, Yuliya, Davenport, Karen, Daligault, Hajnalka, Msanne, Joseph, Canny, Stephanie, Eyun, Seong-il, Riethoven, Jean-Jack M., Polle, Juergen, and Starkenburg, Shawn R. Genomic characterization reveals significant divergence within Chlorella sorokiniana (Chlorellales, Trebouxiophyceae). United States: N. p., 2018. Web. doi:10.1016/j.algal.2018.09.012.
Hovde, Blake T., Hanschen, Erik R., Steadman Tyler, Christina R., Lo, Chien-Chi, Kunde, Yuliya, Davenport, Karen, Daligault, Hajnalka, Msanne, Joseph, Canny, Stephanie, Eyun, Seong-il, Riethoven, Jean-Jack M., Polle, Juergen, & Starkenburg, Shawn R. Genomic characterization reveals significant divergence within Chlorella sorokiniana (Chlorellales, Trebouxiophyceae). United States. doi:10.1016/j.algal.2018.09.012.
Hovde, Blake T., Hanschen, Erik R., Steadman Tyler, Christina R., Lo, Chien-Chi, Kunde, Yuliya, Davenport, Karen, Daligault, Hajnalka, Msanne, Joseph, Canny, Stephanie, Eyun, Seong-il, Riethoven, Jean-Jack M., Polle, Juergen, and Starkenburg, Shawn R. Mon . "Genomic characterization reveals significant divergence within Chlorella sorokiniana (Chlorellales, Trebouxiophyceae)". United States. doi:10.1016/j.algal.2018.09.012. https://www.osti.gov/servlets/purl/1479995.
@article{osti_1479995,
title = {Genomic characterization reveals significant divergence within Chlorella sorokiniana (Chlorellales, Trebouxiophyceae)},
author = {Hovde, Blake T. and Hanschen, Erik R. and Steadman Tyler, Christina R. and Lo, Chien-Chi and Kunde, Yuliya and Davenport, Karen and Daligault, Hajnalka and Msanne, Joseph and Canny, Stephanie and Eyun, Seong-il and Riethoven, Jean-Jack M. and Polle, Juergen and Starkenburg, Shawn R.},
abstractNote = {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.},
doi = {10.1016/j.algal.2018.09.012},
journal = {Algal Research},
issn = {2211-9264},
number = ,
volume = 35,
place = {United States},
year = {2018},
month = {10}
}

Journal Article:
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Figures / Tables:

Fig. 1. Fig. 1. : Phylogenetic analysis of Chlorellales based on 27 concatenated chloroplast proteins (Supplementary Table 1). Species sequenced here are emphasized with larger font (center). Independent Bayesian and maximum likelihood (ML) analyses estimated the same tree topology. Numbers indicate ML bootstrap values and Bayesian posterior probabilities respectively. Branch lengths shownmore » are from the ML estimation. The tree is rooted following Sun et al. [57].« less

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