This website is intended to augment the conclusions drawn in the study described in Jaeger et al. (2017).
Towards this end, this website serves two purposes:
Regarding the first purpose, you can simply query this website to investigate the transcriptional response of the oleaginous green alga M. neglectum to three different stages of nitrogen availability (autotrophic conditions with 3% CO2):
In addition to the quantitative transcriptome data of M. neglectum, qualitative information about the queried transcript locus is displayed, with both, a structural and a functional annotation.
An example (phosphoglycerate kinase, XLOC_006233) is given below:
Regarding the second purpose, you can furthermore query the transcriptional response of other microalgae subjected similarly to -N conditions and hence, neutral lipid hyper-accumulation.
This allows for comparison of transcriptional responses of M. neglectum with other microalgae to differentiate between shared and unique transcriptional responses.
As this additional transcriptome data was taken from previously published datasets, it should be kept in mind that the experimental conditions in all studies varied slightly.
The transcriptome data that was integrated are from:
To query for transcripts, there are two search strategies implemented.
The first requires knowledge of the transcript locus name(s) of M. neglectum (e.g., XLOC_006233 (phosphoglycerate kinase) or XLOC_008097 (MLDP)), retrieved for instance from Jaeger et al. (2017).
The second strategy aims to identify all transcripts with a similar function, and thus either queries for key words such as “phosphoglycerate kinase”, GO terms or EC numbers
or uses Blast search (tBLASTx, tBLASTn)
If you use data or plots from this website in your project, please cite Jaeger et al. (2017)!
Jaeger et al. (2017):
Jaeger D, Winkler A, Mussgnug JH, Kalinowski J, Goesmann A, Kruse O. Time-resolved transcriptome analysis and lipid pathway reconstruction of the oleaginous green microalga Monoraphidium neglectum reveal a model for triacylglycerol and lipid hyperaccumulation. Biotechnol Biofuels. 2017;10:197. Published 2017 Aug 14. doi:10.1186/s13068-017-0882-1
Schmollinger S, Mühlhaus T, Boyle NR, Blaby IK, Casero D, Mettler T, Moseley JL, Kropat J, Sommer F, Strenkert D: Nitrogen-sparing mechanisms in Chlamydomonas affect the transcriptome, the proteome, and photosynthetic metabolism. The Plant Cell Online 2014, 26:1410-1435.
Li J, Han D, Wang D, Ning K, Jia J, Wei L, Jing X, Huang S, Chen J, Li Y: Choreography of Transcriptomes and Lipidomes of Nannochloropsis Reveals the Mechanisms of Oil Synthesis in Microalgae. The Plant Cell Online 2014, 26:1645-1665.
Yang ZK, Niu YF, Ma YH, Xue J, Zhang MH, Yang WD, Liu JS, Lu SH, Guan Y, Li HY: Molecular and cellular mechanisms of neutral lipid accumulation in diatom following nitrogen deprivation. Biotechnol Biofuels 2013, 6:67.
Rismani-Yazdi H, Haznedaroglu BZ, Hsin C, Peccia J: Transcriptomic analysis of the oleaginous microalga Neochloris oleoabundans reveals metabolic insights into triacylglyceride accumulation. Biotechnol Biofuels 2012, 5:74.
Sun D, Zhu J, Fang L, Zhang X, Chow Y, Liu J: De novo transcriptome profiling uncovers a drastic downregulation of photosynthesis upon nitrogen deprivation in the nonmodel green alga Botryosphaerella sudeticus. BMC genomics 2013, 14:715.
Merchant S, Prochnik S, Vallon O, Harris E, Karpowicz S, Witman G, Terry A, Salamov A, Fritz-Laylin L, Marechal-Drouard L, other s: The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 2007, 318.
Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A, Maheswari U, Martens C, Maumus F, Otillar RP: The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 2008, 456:239-244.
Vieler A, Wu G, Tsai C-H, Bullard B, Cornish AJ, Harvey C, Reca I-B, Thornburg C, Achawanantakun R, Buehl CJ: Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779. PLoS genetics 2012, 8:e1003064.