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

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

doi:10.1371/journal.pgen.1003064

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

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

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

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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 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.

Original language	English
Article number	e1003064
Journal	PLoS Genetics
Volume	8
Issue number	11
Online published	15 Nov 2012
DOIs	https://doi.org/10.1371/journal.pgen.1003064
Publication status	Published - Nov 2012
Externally published	Yes

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This full text is made available under CC-BY 4.0. https://creativecommons.org/licenses/by/4.0/

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This output contributes to the following UN Sustainable Development Goals (SDGs)

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Vieler, A., Wu, G., Tsai, C.-H., Bullard, B., Cornish, A. J., Harvey, C., Reca, I.-B., Thornburg, C., Achawanantakun, R., Buehl, C. J., Campbell, M. S., Cavalier, D., Childs, K. L., Clark, T. J., Deshpande, R., Erickson, E., Armenia Ferguson, A., Handee, W., Kong, Q., ... Benning, C. (2012). Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga Nannochloropsis oceanica CCMP1779. PLoS Genetics, 8(11), Article e1003064. https://doi.org/10.1371/journal.pgen.1003064

@article{6d348db3457c4a2c8b436d64788c678c,

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

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 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. ",

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

year = "2012",

month = nov,

doi = "10.1371/journal.pgen.1003064",

language = "English",

volume = "8",

journal = "PLoS Genetics",

issn = "1553-7390",

publisher = "Public Library of Science (PLoS)",

number = "11",

}

Vieler, A, Wu, G, Tsai, C-H, Bullard, B, Cornish, AJ, Harvey, C, Reca, I-B, Thornburg, C, Achawanantakun, R, Buehl, CJ, Campbell, MS, Cavalier, D, Childs, KL, Clark, TJ, Deshpande, R, Erickson, E, Armenia Ferguson, A, Handee, W, Kong, Q, Li, X, Liu, B, Lundback, S, Peng, C, Roston, RL, Sanjaya, Simpson, JP, TerBush, A, Warakanont, J, Zäuner, S, Farre, EM, Hegg, EL, Jiang, N, Kuo, M-H, Lu, Y, Niyogi, KK, Ohlrogge, J, Osteryoung, KW, Shachar-Hill, Y, Sears, BB, Sun, Y, Takahashi, H, Yandell, M, Shiu, S-H & Benning, C 2012, 'Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga Nannochloropsis oceanica CCMP1779', PLoS Genetics, vol. 8, no. 11, e1003064. https://doi.org/10.1371/journal.pgen.1003064

TY - JOUR

T1 - Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga Nannochloropsis oceanica CCMP1779

AU - Vieler, Astrid

AU - Wu, Guangxi

AU - Tsai, Chia-Hong

AU - Bullard, Blair

AU - Cornish, Adam J.

AU - Harvey, Christopher

AU - Reca, Ida-Barbara

AU - Thornburg, Chelsea

AU - Achawanantakun, Rujira

AU - Buehl, Christopher J.

AU - Campbell, Michael S.

AU - Cavalier, David

AU - Childs, Kevin L.

AU - Clark, Teresa J.

AU - Deshpande, Rahul

AU - Erickson, Erika

AU - Armenia Ferguson, Ann

AU - Handee, Witawas

AU - Kong, Que

AU - Li, Xiaobo

AU - Liu, Bensheng

AU - Lundback, Steven

AU - Peng, Cheng

AU - Roston, Rebecca L.

AU - Sanjaya, null

AU - Simpson, Jeffrey P.

AU - TerBush, Allan

AU - Warakanont, Jaruswan

AU - Zäuner, Simone

AU - Farre, Eva M.

AU - Hegg, Eric L.

AU - Jiang, Ning

AU - Kuo, Min-Hao

AU - Lu, Yan

AU - Niyogi, Krishna K.

AU - Ohlrogge, John

AU - Osteryoung, Katherine W.

AU - Shachar-Hill, Yair

AU - Sears, Barbara B.

AU - Sun, Yanni

AU - Takahashi, Hideki

AU - Yandell, Mark

AU - Shiu, Shin-Han

AU - Benning, Christoph

PY - 2012/11

Y1 - 2012/11

N2 - 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.

AB - 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.

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U2 - 10.1371/journal.pgen.1003064

DO - 10.1371/journal.pgen.1003064

M3 - RGC 21 - Publication in refereed journal

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JO - PLoS Genetics

JF - PLoS Genetics

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

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Erratum: Correction: Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga Nannochloropsis oceanica CCMP1779 (PLoS genetics (2012) 8 11 (e1003064))

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