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| Status |
Public on Apr 04, 2012 |
| Title |
Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga Nannochloropsis oceanica CCMP1779 |
| Organism |
Nannochloropsis oceanica |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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 makes Nannochloropsis species attractive models to investigate the cell and molecular biology and biochemistry of this fascinating organism group. (Principle findings) Here we present the assembly of the 28.7 Mb genome of Nannochloropsis oceanica CCMP1779. RNA sequencing data from N-replete and N-depleted growth conditions support a total of 11,973 genes, which in addition to automatic annotation 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. In addition, we provide protocols for the transformation of the sequenced strain. (Significance) 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 phylogenetic comparison of Nannochloropsis species by a growing academic community focused on this genus.
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| Overall design |
one sample each of nitrogen-replete and nitrogen-depleted conditions
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| Contributor(s) |
Benning C, Vieler A, Wu G |
| Citation(s) |
23166516 |
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| Submission date |
Mar 30, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Guangxi Wu |
| E-mail(s) |
wuguangx@msu.edu
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| Organization name |
Michigan State University
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| Street address |
S308 Plant Bio Bld
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| City |
East Lansing |
| State/province |
MI |
| ZIP/Postal code |
48824 |
| Country |
USA |
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| Platforms (1) |
| GPL15388 |
Illumina Genome Analyzer II (Nannochloropsis oceanica) |
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| Samples (2) |
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| Relations |
| SRA |
SRP012017 |
| BioProject |
PRJNA157867 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE36959_RAW.tar |
2.1 Mb |
(http)(custom) |
TAR (of GTF) |
| GSE36959_all_gene.gff.gz |
11.4 Mb |
(ftp)(http) |
GFF |
| GSE36959_gene_exp_diff.txt.gz |
499.7 Kb |
(ftp)(http) |
TXT |
| GSE36959_nanno_assembly.fasta.gz |
9.4 Mb |
(ftp)(http) |
FASTA |
| GSE36959_old_new_list.txt.gz |
89.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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