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

Research output: Journal Publications and ReviewsRGC 21 - Publication in refereed journalpeer-review

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Author(s)

  • 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
  • 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
  • Hideki Takahashi
  • Mark Yandell
  • Shin-Han Shiu
  • Christoph Benning

Detail(s)

Original languageEnglish
Article numbere1003064
Journal / PublicationPLoS Genetics
Volume8
Issue number11
Online published15 Nov 2012
Publication statusPublished - Nov 2012
Externally publishedYes

Link(s)

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. 

Research Area(s)

Citation Format(s)

Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga Nannochloropsis oceanica CCMP1779. / Vieler, Astrid; Wu, Guangxi; Tsai, Chia-Hong et al.
In: PLoS Genetics, Vol. 8, No. 11, e1003064, 11.2012.

Research output: Journal Publications and ReviewsRGC 21 - Publication in refereed journalpeer-review

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