Genome Sequence of the Oleaginous Green Alga, Chlorella vulgaris UTEX 395
Michael T. Guarnieri1* 
Jennifer Levering2 
Calvin A. Henard1 
Jeffrey L. Boore3 Michael J. Betenbaugh4 Karsten Zengler2 
Eric P. Knoshaug1- 1National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
- 2Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States
- 3Genome Project Solutions, Inc., Hercules, CA, United States
- 4Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States
Introduction
Microalgae have garnered extensive interest as renewable fuel feedstocks due to their high production potential relative to terrestrial crops, and unique cultivation capacity on non-arable lands (Wijffels and Barbosa, 2010; Davis et al., 2011). The oleaginous chlorophyte Chlorella vulgaris represents a promising model microalgal system and production host, due to its ability to synthesize and accumulate large quantities of fuel intermediates in the form of storage lipids (Guarnieri et al., 2011, 2012; Gerken et al., 2013; Griffiths et al., 2014; Zuñiga et al., 2016). Recent omic analyses have identified transcriptional, post-transcriptional and -translational mechanisms governing lipid accumulation in this alga (Guarnieri et al., 2011, 2013), including active protein nitrosylation (Henard et al., 2017). Here we report the draft nuclear genome and annotation of C. vulgaris UTEX 395.
Materials and Methods
Cultivation and Genomic DNA Isolation
For genomic DNA isolation C. vulgaris UTEX 395 was grown photoautotrophically to exponential phase in Bold's Basal Media, under constant illumination (200 μE m−2 s−1 white fluorescent light), and supplemented with 2% CO2/air, as described previously (Guarnieri et al., 2011, 2013). Genomic DNA was extracted following the protocol adapted from Varela-Alvarez et al. (2006).
Genome Sequencing and Assembly
Sequencing was performed using Illumina HiSeq 2000 technology with 108 cycles. 171,758,456 paired-end (SIPES) reads were trimmed to an error rate of <1:100, then trimmed until no ambiguous nucleotides remain; reads shorter than 20 nucleotides were discarded, retaining 168,611,711 reads, of which 165,874,962 remained as pairs. Resultant reads were assembled using a DeBruijn method; 113 scaffolds were generated at ≥1,000x depth of coverage, 24 of which were longer than 100 kb and 566 of which were 20–100 kb, ultimately generating a total assembly size of 37.34 Mb, with a 61.5% GC content. This represents the smallest nuclear genome size and lowest GC content reported to date for a sequenced Chlorella species (Supplemental Table 1).
Genome Annotation
Transcript prediction was conducted using Maker (Cantarel et al., 2008; Campbell et al., 2014). Transcripts were six-frame translated into protein sequences and functionally annotated with EC, GO and InterProScan identifiers using two approaches. First, a bidirectional BLASTp against SwissProt sequences was carried out and paralogs were identified using BLASTclust. Secondly, InterProScan and PRIAM analyses with gene and genome-specific profiles were conducted.
To facilitate refined annotation and comprehensive pathway mapping of C. vulgaris, a draft nuclear genome sequence was generated and integrated with previously acquired de novo transcriptomic datasets (Guarnieri et al., 2011). 7,100 transcripts were predicted from the C. vulgaris genome, resulting in 6,056 annotated gene models. Genomic queries identified complete gene sets encoding fatty acid and triacylglyceride biosynthetic pathways. The nitrogen assimilation inventory includes genes for nitrate/nitrite transporters and reductases. The genome also encodes meiosis-associated DMC1 and Rad51 DNA recombinase homologs (Fanning et al., 2006; Broderick et al., 2010), offering a possibility that sexual mating may occur in this microalga. Genes for the synthesis of the global stress response alarmone, guanine tetraphosphate (ppGpp) (Takahashi et al., 2004; Tozawa and Nomura, 2011), were also identified. Combined, these genetic pathways will enable potential markerless strain-engineering strategies targeting lipid accumulation in the absence of stress induction, ultimately facilitating the development of robust, deployment-viable microalgae for cost-competitive biofuel production.
Direct Link to Deposited Data and Information to Users
This whole-genome project has been deposited at DDBJ/EMBL/GenBank under the accession LDKB00000000. The version described in this paper is version LDKB01000000. Additional details can be found at http://www.nrel.gov/biomass/proj_microalgal_biofuels.html and http://chlorella.genomeprojectsolutions-databases.com.
Author Contributions
The work was designed by EK, MB, KZ, and MG. MG directed wet lab analyses. JB directed genome assembly. JL and CH directed genome annotation and pathway mapping.
Conflict of Interest Statement
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Acknowledgments
This work was supported by National Renewable Energy Laboratory, Laboratory-Directed Research and Development (LDRD) grants 06511103 and 06511301 and by the U.S. Department of Energy, Office of Science, Office of Biological & Environmental Research under Award Number DE-SC-0012658 and Office of Energy Efficiency and Renewable Energy (EERE) under Agreement No. 22000. The views and opinions of the authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof. Neither the United States Government nor any agency thereof, nor any of their employees, makes any warranty, expressed or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. We kindly thank Robert Stiles for assistance in genome assembly.
Supplementary Material
The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fbioe.2018.00037/full#supplementary-material
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Keywords: microalgae, biofuels, lipids, genome, Chlorella vulgaris
Citation: Guarnieri MT, Levering J, Henard CA, Boore JL, Betenbaugh MJ, Zengler K and Knoshaug EP (2018) Genome Sequence of the Oleaginous Green Alga, Chlorella vulgaris UTEX 395. Front. Bioeng. Biotechnol. 6:37. doi: 10.3389/fbioe.2018.00037
Received: 04 October 2017; Accepted: 19 March 2018;
Published: 05 April 2018.
Edited by:
Qiang Wang, Institute of Hydrobiology (Chinese Academy of Sciences), ChinaReviewed by:
Jianhua Fan, East China University of Science and Technology, ChinaYingchun Wang, Chinese Academy of Sciences, China
Copyright © 2018 Guarnieri, Levering, Henard, Boore, Betenbaugh, Zengler and Knoshaug. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Michael T. Guarnieri, michael.guarnieri@nrel.gov