Genome browser

 

The genomic browser contains the full annotation of the genome, and the RNA-Seq experiments.

Annotation query

 

This powerful interface allows to retrieve list of genes composing complex queries.

BLAST Search

 

Align multiple sequences against the genome (or genes) of N. gaditana.

 
Blog

New data on lipid accumulation in Nannochloropsis

We have already discussed in a previous post two possible models of cellular metabolism that can account for oil accumulationmicoralgae's oil and that are in agreement with the profile of transcript and protein abundance in Nannochloropsis‘ cultures that accumulate lipids. New experimental data became recently available for the scientific community concerning this issue. Jing Li and coworkers  performed a time course experiment, tracking simultaneously transcript abundance and lipid content of Nannochloropsis cultures grown in N sufficient (+N) and N depleted (-N) media. The data and their analysis were published on Plant Cell (doi: http:/​/​dx.​doi.​org/​10.​1105/​tpc.​113.​121418). Full reference is reported at the end of this post (reference n 1).

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Access to N.gaditana B-31 data through the NCBI

After manual review by the NCBI experts, the genomic data of Nannochloropsis gaditana B-31 are now indexed in the NCBI databases and are accessible through the NCBI web interface and through the NCBI search tools (e.g. blast).

NCBI banner

The genomes of the nucleus and of the organelles and the complete annotation of the genomic sequences are registered as bioproject PRJNA170989 ID: 170989, and can be accessed through the following links:

http://www.ncbi.nlm.nih.gov/bioproject/170989 ;

http://www.ncbi.nlm.nih.gov/nuccore/585113370

The sequencing data used to assembly of the genomes were also submitted to the NCBI SRA database and are available for consulting and download. You can find the data of: a fragment library of Nannochloropsis gaditana B-31 whole genomic DNA (i.e. includes DNA from the nucleus and from the organelles) sequenced using 454FLX Titanium XL  sequencing kit, 2 half plates (http://www.ncbi.nlm.nih.gov/sra/SRX390591); a mate pair library of Nannochloropsis gaditana B-31 whole genomic DNA with an insert size of 1.5-3Kb sequenced using the SOLiD 3 Plus sequencing kit, half plate (http://www.ncbi.nlm.nih.gov/sra/SRX390674); a mate pair library of Nannochloropsis gaditana B-31 whole genomic DNA with an insert size of 3-5Kb sequenced using the SOLiD 3 Plus sequencing kit, half plate (http://www.ncbi.nlm.nih.gov/sra/SRX390681). Note that details about the biosamples and about the experiments are linked o the data.
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New features on the Bibliography section

We added a new feature to the Bibliography: “Altmetric donuts” close to each publication listed in the page.

What are the Article Level metrics (Altmetric) ?

Altmetric donut

Altmetrics give a measure of the digital impact and reach of an article by combining a selection of online indicators (both scholarly and non-scholarly) . They do this by tracking, collecting and measuring large amounts of data collected from all of the places where people talk about science online – for example, blogs, Twitter, Facebook, Google+, message boards and mainstream newspapers and magazines. Altmetric allows authors and publishers to see what people are saying about a scholarly paper and can tell them how much attention a paper is receiving relative to their peers.
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Proteomics and transcriptomics findings on lipids accumulation in Nannochloropsis

Confocal microscopy image of Nannochloropsis cell grown in nitrogen deprivation. Lipid droplets are in yellow and chloroplast is in red. From "Going ultradeep to unravel the secret recipe of biofuel" Elisa Corteggiani Carpienelli

Confocal microscopy image of Nannochloropsis cell grown in nitrogen deprivation. Lipid droplets are in yellow and chloroplast is in red. From “Going ultra deep to unravel the secret recipe of biofuel” by Elisa Corteggiani Carpinelli

What is the mechanism by which Nannochloropsis cells synthesise and accumulate lipids in certain culturing conditions? And moreover is there a key control that we can manipulate to improve lipid yields and overcome the tradeoff between lipid production and growth? This is probably the “holy grail” of Nannochloropsis research. The general feeling is that we do not have an answer yet, but at least we have some clues to start our quest.

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FTP area updated

Misc-Download-iconWe updated our FTP area, now including datasets from other Nannochloropsis species and strains and the list of families of orthologous proteins obtained from the comparison of N. gaditana and N. oceeanica predicted proteins.

 

Families of orthologous proteins: file type

venn_protein_clusters
Comparing the protein families of N. gaditana and N. oceanica, we produced the lists of exclusive proteins of each species. These lists are available for download in our FTP area.
Each file is a list of families of orthologous proteins. All the families of each file are populated only by proteins belonging to one species of Nannochloropsis. The families may contain proteins of one or more strains of the same Nannochloropsis species.
In the .txt files there is one family per line, described by the name of the organism (species and strain), then a “|”, the list of the proteins of that organism (indicated by the protein ID) the name of the following organism, another “|”, the proteins of the following organism and finally the annotation of the listed proteins.
 
example:
N.gaditanaB-31|Naga_100019g47.1 N.gaditanaCCMP526|Nga20827 nudix hydrolase;

Even though the differences and the imprecisions of the various gene predictions probably play a major role in the determination of the differences among the two species, a close look at the lists of proteins that are putatively assigned as characteristic of each species my reserve interesting surprises!

References

  1. Corteggiani Carpinelli, E. et al. “Chromosome scale genome assembly and transcriptome profiling of Nannochloropsis gaditana in nitrogen depletion.Molecular Plant (2014) 7 (2): 323-335.doi: 10.1093/mp/sst120
 

We’re looking for new authors and contributors

BloggerBirdStackBooksAre you an expert about Nannochloropsis? Is your research focused on this organism?

Consider becoming a new author of this blog and contributing to the scientific discussion!

Why don’t you start with advertising your recent publication or commenting on the posts of this blog?

Is there any hot topic that you would like to discuss or any suggestion that you would like to ask to this scientific community?

Fill this form and we will be happy to consider you application as new author

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Proteomics and transcriptomics findings on Nitrogen stress respons in Nannochloropsis

Nannochloropsis cultivated in normal growth condition and deprived of a nitrogen source continues growing for at least 4–5 days.

Analyses of the gene expression and of the protein abundance in nitrogen scarcity, reveal that Nannochloropsis activates mechanisms for nitrogen assimilation and redistribution to allow survival through a partial reorganisation of the cellular metabolism.

Model of Nannochloropsis response to nitrogen deprivation

This figure reports the model of the response to nitrogen deprivation elaborated by Corteggiani Carpinelli et al. (2013).

DEGRADATIVE PROCESSES

Various genes involved in controlled degradation of proteins are over-expressed in the cells grown in nitrogen deprivation, including: cullin (Naga_100070g1), which is responsible for protein ubiquitination; ubiquitin-specific protease (Naga_100587g2); proteases (Naga_100611g3, Naga_100098g23, Naga_100015g80.1); endopeptidase Naga_101780g1); aminopeptidase (Naga_100024g51) and two autophagy-related proteins (Naga_101823g1 and Naga_100732g4), which are likely involved in the formation of cytosolic sequestering vesicles used for degradation and recycling of cellular components.

The proteomic study shows that the relative abundance of one subunit of the protein degrading complex (Proteasome subunit alpha) increases in nitrogen starvation supporting the evidence that processes of protein degradation are activated in response to nitrogen starvation. The analysis of protein abundance also suggests that in nitrogen starvation autophagy is induced. Indeed the abundance of a receptor-mediated endocytosis protein slightly increases and also that of two vacuolar proton pump subunits. These data, together with morfological observations, support the hypothesis that upon nitrogen deprivation the organelles are degraded in the vacuoles through a process of controlled autophagy.

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Nannochloropsis genomes, what have we learnt?

Nannochloropsis

Schematic representation of Nannochloropsis cell by Andrea Telatin

Thanks to the sequencing of the genomes of two strains of  Nannochloropsis gaditana [1][2] and two strains of Nannochloropsis oceanica [3][4] we now have the reference sequences to design molecular biology experiments on this microorganism. Moreover we have learnt a great deal of information, opened up new interrogatives .. and more will come analysing the data available though this portal and through the other web resources: N. gaditana CCMP526 genome and N. oceanica CCMP1779 genome.

Nannochloropsis genome is small, about 28-29 Mega bases, and very compact: there is on average 1 gene each 2.7 kilo bases in N. gaditana B-31, the genes are long on average 1.2 kilo bases and they contain very few introns.

The proteins predicted in the two species are in large part similar, about 80% of the proteins of each species are found in clusters of homologous proteins, ~60% of which accomodate proteins common to the two species. Further studies will help ruling out the limits and the  inaccuracies of the gene predictions allowing to focus on the actual differences between the two species.

The pathways leading to the synthesis of cellulose and sulfated fucans and to the remodelling of cellulose in the cell wall have been identified both in N. gaditana and in N. oceanica, casting a light on the molecular composition of the cell wall and suggesting possible targets of genetic modification.

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Thank you!

We currently have more than 1.000 unique visitors per month, accounting for roughly 18,000 pageviews per month. Visitors are spread across the four continents…  Thank you for keeping alive Nannochloropsis.org. We are doing our best to update this site and we are also preparing new resources (to be released soon).

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