Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga Nannochloropsis oceanica CCMP1779

被引：324

作者：

Vieler, Astrid ^{[1
]}

Wu, Guangxi ^{[2
]}

Tsai, Chia-Hong ^{[3
,4
]}

Bullard, Blair ^{[1
]}

Cornish, Adam J. ^{[1
]}

Harvey, Christopher ^{[1
]}

Reca, Ida-Barbara ^{[4
]}

Thornburg, Chelsea ^{[1
]}

Achawanantakun, Rujira ^{[5
]}

Buehl, Christopher J. ^{[1
,2
]}

Campbell, Michael S. ^{[6
]}

Cavalier, David ^{[4
]}

Childs, Kevin L. ^{[3
]}

Clark, Teresa J. ^{[7
]}

Deshpande, Rahul ^{[3
]}

Erickson, Erika ^{[8
,9
]}

Ferguson, Ann Armenia ^{[10
]}

Handee, Witawas ^{[2
]}

Kong, Que ^{[1
]}

Li, Xiaobo ^{[3
,4
]}

Liu, Bensheng ^{[1
]}

Lundback, Steven ^{[1
]}

Peng, Cheng ^{[3
,4
]}

Roston, Rebecca L. ^{[1
]}

Sanjaya ^{[1
]}

Simpson, Jeffrey P. ^{[3
]}

TerBush, Allan ^{[1
,3
]}

Warakanont, Jaruswan ^{[3
]}

Zaeuner, Simone ^{[1
]}

Farre, Eva M. ^{[3
]}

Hegg, Eric L. ^{[1
]}

Jiang, Ning ^{[10
]}

Kuo, Min-Hao ^{[1
]}

Lu, Yan ^{[7
]}

Niyogi, Krishna K. ^{[8
,9
]}

Ohlrogge, John ^{[3
]}

Osteryoung, Katherine W. ^{[3
]}

Shachar-Hill, Yair ^{[3
]}

Sears, Barbara B. ^{[3
]}

Sun, Yanni ^{[5
]}

Takahashi, Hideki ^{[1
]}

Yandell, Mark ^{[6
]}

Shiu, Shin-Han ^{[2
,3
]}

Benning, Christoph ^{[1
]}

机构：

[1] Michigan State Univ, Dept Biochem & Mol Biol, E Lansing, MI 48824 USA

[2] Michigan State Univ, Cell & Mol Biol Program, E Lansing, MI 48824 USA

[3] Michigan State Univ, Dept Plant Biol, E Lansing, MI 48824 USA

[4] Michigan State Univ, DOE Plant Res Lab, E Lansing, MI 48824 USA

[5] Michigan State Univ, Deptartment Comp Sci & Engn, E Lansing, MI 48824 USA

[6] Univ Utah, Dept Human Genet, Salt Lake City, UT USA

[7] Western Michigan Univ, Dept Biol Sci, Kalamazoo, MI 49008 USA

[8] Univ Calif Berkeley, Howard Hughes Med Inst, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA

[9] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA

[10] Michigan State Univ, Dept Hort, E Lansing, MI 48824 USA

来源：

PLOS GENETICS | 2012年 / 8卷 / 11期

基金：

美国国家科学基金会;

关键词：

FATTY-ACID-COMPOSITION; DIATOM THALASSIOSIRA-PSEUDONANA; DIOXIDE CONCENTRATING MECHANISM; A/B-BINDING-PROTEINS; TRANSCRIPTION FACTORS; HIGH LIGHT; OCULATA EUSTIGMATOPHYCEAE; XANTHOPHYLL CYCLE; PLASTID DIVISION; LIPID-SYNTHESIS;

D O I：

10.1371/journal.pgen.1003064

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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 nitrogen-depleted 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.

引用

页数：25

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