Transcriptome database of M. neglectum picture_monne

Welcome to TDBMN, the transcriptome database of the oleaginous microalga Monoraphidium neglectum!

Purposes of TDBMN:

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:

  1. Investigation of the transcriptome profiles of the oleaginous microalga M. neglectum during different stages of nitrogen availability, with the main purpose of inducing neutral lipid hyper-accumulation by nitrogen starvation (-N) conditions.
  2. Comparison of the measured transcriptome profiles of M. neglectum with other microalgae subjected similarly to neutral lipid hyper-accumulation.

First purpose - visualizing transcriptome data of M. neglectum (expression strength based on FPKM, structural and functional annotation):

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):

  1. a first stage of early -N conditions (e-N stage, from 0 - 8 h in -N, orange color), characterized by starch accumulation,
  2. a second stage of prolonged -N conditions (l-N stage, from 24 - 96 h in -N, brown color), characterized by neutral lipid hyper-accumulation, and
  3. a third stage of N resupply (r+N stage, from 2 - 14 h in +N, green color) to revert the metabolic changes observed in the previous two stages and hence, characterized by neutral lipid degradation.

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, 913-663-9503) is given below:
example plot M. neglectum

Second purpose - comparison with other mircoalgae:

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:

  1. the green alga Chlamydomonas reinhardtii, refined in the strains WT (CC4532), cw15, sta6 and three complemented strains (time course experiment 0 - 48 h in -N, TAP medium = mixotrophic conditions with ambient CO2, Schmollinger et al. (2014) and, for BLAST search, Merchant et al. (2007)),
  2. the green alga Neochloris oleoabundans (single time point at day 11 in -N, autotrophic conditions with ambient CO2, Rismani-Yazdi et al. (2012)),
  3. the green alga Botryosphaerella sudeticus (single time point at 72 h in -N, autotrophic conditions with 2% CO2, Sun et al. (2013)),
  4. the eustigmatophyceae Nannochloropsis oceanica (time course experiment 3 - 48 h in -N, autotrophic conditions with 1.5% CO2, Li et al. (2014) and, for BLAST search, Vieler et al. (2012)),
  5. the diatom Phaeodactylum tricornutum (single time point at 48 h in -N, autotrophic conditions with ambient CO2, Yang et al. (2013) and, for BLAST search, Bowler et al. (2008)).

An example (phosphoglycerate kinase) is shown below:
Example other microalgae

Querying TDBMN:

To query for transcripts, there are two piezo implemented.

The first requires knowledge of the 4092217313 of M. neglectum (e.g., XLOC_006233 (phosphoglycerate kinase) or XLOC_008097 (MLDP)), retrieved for instance from Jaeger et al. (2017).
(804) 952-9959

The second strategy aims to identify all transcripts with a similar function, and thus either queries for 4254229366
Locus Search,
or uses (250) 643-8827 (tBLASTx, tBLASTn)
Locus Search.

Citation:

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


References for the additional transcriptome data from the other microalgae:

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.