Biochemistry, Department of

 

Authors

Astrid Vieler, Michigan State University
Guangxi Wu, Michigan State University
Chia-Hong Tsai, Michigan State University
Blair Bullard, Michigan State University
Adam J. Cornish, Michigan State University
Christopher Harvey, Michigan State University
Ida-Barbara Reca, Michigan State University
Chelsea Thornburg, Michigan State University
Rujira Achawanantakun, Michigan State University
Christopher J. Buehl, Michigan State University
Michael S. Campbell, University of Utah
David Cavalier, Michigan State University
Kevin L. Childs, Michigan State UniversityFollow
Teresa J. Clark, Western Michigan University
Rahul Deshpande, Michigan State University
Erika Erickson, University of California - Berkeley
Ann Armenia Ferguson, Michigan State University
Witawas Handee, Michigan State University
Que Kong, Michigan State University
Xiaobo Li, Michigan State University
Bensheng Liu, Michigan State University
Steven Lundback, Michigan State University
Cheng Peng, Michigan State University
Rebecca Roston, University of Nebraska- LincolnFollow
Michigan State University, Michigan State University
Jeffrey P. Simpson, Michigan State University
Allan TerBush, Michigan State University
Jaruswan Warakanont, Michigan State University
Simone Zäuner, Michigan State University
Eva M. Farre, Michigan State University
Eric L. Hegg, Michigan State University
Ning Jiang, Michigan State University
Min-Hao Kuo, Michigan State University
Yan Lu, Western Michigan University
Krishna K. Niyogi, University of California Berkeley
John Ohlrogge, Michigan State University
Katherine W. Osteryoung, Michigan State University
Yair Shachar-Hill, Michigan State University
Barbara B. Sears, Michigan State University
Yanni Sun, Michigan State University
Hideki Takahashi, Michigan State University
Mark Yandell, University of Utah
Shin-Han Shiu, Michigan State University
Christoph Benning, Michigan State University

Document Type

Article

Date of this Version

2012

Citation

Vieler A, Wu G, Tsai C-H, Bullard B, Cornish AJ, et al. (2012) Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga Nannochloropsis oceanica CCMP1779. PLoS Genet 8(11): e1003064.

Comments

Copyright 2012 Vieler et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License.

Abstract

Unicellular marine algae have promise for providing sustainable and scalable biofuel feedstocks, although no single species has emerged as a preferred organism. Moreover, adequate molecular and genetic resources prerequisite for the rational engineering of marine algal feedstocks are lacking for most candidate species. Heterokonts of the genus Nannochloropsis naturally have high cellular oil content and are already in use for industrial production of high-value lipid products. First success in applying reverse genetics by targeted gene replacement makes Nannochloropsis oceanica an attractive model to investigate the cell and molecular biology and biochemistry of this fascinating organism group. Here we present the assembly of the 28.7 Mb genome of N. oceanica CCMP1779. RNA sequencing data from nitrogen-replete and nitrogendepleted growth conditions support a total of 11,973 genes, of which in addition to automatic annotation some were manually inspected to predict the biochemical repertoire for this organism. Among others, more than 100 genes putatively related to lipid metabolism, 114 predicted transcription factors, and 109 transcriptional regulators were annotated. Comparison of the N. oceanica CCMP1779 gene repertoire with the recently published N. gaditana genome identified 2,649 genes likely specific to N. oceanica CCMP1779. Many of these N. oceanica–specific genes have putative orthologs in other species or are supported by transcriptional evidence. However, because similarity-based annotations are limited, functions of most of these species-specific genes remain unknown. Aside from the genome sequence and its analysis, protocols for the transformation of N. oceanica CCMP1779 are provided. The availability of genomic and transcriptomic data for Nannochloropsis oceanica CCMP1779, along with efficient transformation protocols, provides a blueprint for future detailed gene functional analysis and genetic engineering of Nannochloropsis species by a growing academic community focused on this genus.

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