Dataset Information

Nitrogen deprivation-induced de novo transcriptomic profiling of the oleaginous green alga Botryococcus braunii 779.

ABSTRACT: To assess the effect of nitrogen deprivation (ND), a moderately growing A-race Botryococcus braunii subisolate 779 was subjected to nitrogen deprivation for 3 days. De novo transcriptome was assembled and annotated by using Trinity software and Basic Local Alignment Search Tools (BLAST), respectively. Comparative analysis indicates that transcriptomes of A-races differ from those of B-races. Furthermore, majority of the homologous ESTs in A-race but not B-race transcriptomes were unknown sequences. Upon ND, level of photosynthetic transcripts, but not photosynthetic efficiency was downregulated. Unlike hydrocarbon contents, ESTs involved in hydrocarbon biosynthesis were not upregulated. Taken together, our results imply that A- and B-races belong to different B. braunii subspecies. Upon ND, excess photosynthetic transcripts are recycled for nitrogen; and hydrocarbon accumulation is not via de novo biosynthesis. Here we describe in details the data contents and analytic methodologies associated with the data uploaded to Gene Expression Omnibus (accession number GSE71296).

SUBMITTER: Xu Z

PROVIDER: S-EPMC4664756 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Nitrogen deprivation-induced de novo transcriptomic profiling of the oleaginous green alga Botryococcus braunii 779.

Xu Zhenyu Z He Jing J Qi Shuyuan S Liu Jianhua J

Genomics data 20151024

To assess the effect of nitrogen deprivation (ND), a moderately growing A-race Botryococcus braunii subisolate 779 was subjected to nitrogen deprivation for 3 days. De novo transcriptome was assembled and annotated by using Trinity software and Basic Local Alignment Search Tools (BLAST), respectively. Comparative analysis indicates that transcriptomes of A-races differ from those of B-races. Furthermore, majority of the homologous ESTs in A-race but not B-race transcriptomes were unknown sequenc ...[more]

PMID: 26697382

Similar Datasets

Project description:BackgroundThe colonial microalga Botryococcus braunii has been brought to people's attention for its conspicuous ability to accumulate a variety of lipids including hydrocarbons. B. braunii strains are classified into 3 races based on the types of hydrocarbons. A and B races are known to accumulate high level of lipids. However, their extreme slow growth rate has impeded its application for renewable biofuel production.ResultsIn this study, we report the transcriptomic response of a moderately growing subisolate from the culture of Botryococcus sp. CCALA-779 upon nitrogen deprivation (ND). We show that the subisolate has an average growth rate of 0.52 g l(-1) day(-1) under photoautotrophic growth conditions and lipid content is enhanced to 75 % of CDW upon ND. Both rDNA sequence and hydrocarbon composition analyses indicate that the subisolate belongs to A race B. braunii. Hence, it is designated as B. braunii 779. We show that B. braunii 779 transcriptome shares homology to majority of the A race but not B race B. braunii ESTs, suggesting that transcriptomes of A race differ from that of B race. We found that many homologous ESTs between A races 779 and Bot-88 are unknown sequences, implying that A race contains many unknown genes. Pathway-based transcriptomic analysis indicates that energy metabolisms are among the top expressed functions in log-phase cells, indicating that the slow growth rate is a result that energy flow is directed to lipid biosynthesis but not population growth. Upon ND, reconfiguration of metabolisms for reducing power is apparent, suggesting that B. braunii 779 is rapidly adapting under ND condition by transcriptomic reprogramming.ConclusionsTaken together, our result shows that the subisolate B. braunii 779, similar to the Gottingen strain, is useful for biofuel production. Difference between transcriptomes of A and B races implies that different races of B. braunii strains belong to different sub-species. Furthermore, there are many novel genes that are unique to A race, suggesting that sequences of many enzymes involved in hydrocarbon biosynthesis are not currently known. We propose that B. braunii transcriptomes provide a rich source for discovery of novel genes involved in hydrocarbon biosynthesis.

Project description:BackgroundNeutral lipid storage is enhanced by nitrogen deprivation (ND) in numbers of green microalgal species. However, little is known about the metabolic pathways whose transcription levels are most significantly altered following ND in green microalgae, especially the nonmodel species.ResultsTo start gaining knowledge on this, we performed transcriptome profiling of the nonmodel green microalga Botryosphaerella sudeticus cells in response to ND. Transcriptome of B. sudeticus is de novo assembled based on millions of HiSEQ short sequence reads using CLC Genomics Workbench software. The resulting non-redundant ESTs are annotated based on the best hits generated from the BLASTX homology comparison against the "best" proteins in the model microalgae Chlamydomonas reinhardtii and Chlorella variabilis. By using a pathway-based approach according to KEGG databases, we show that ESTs encoding ribosomal proteins and photosynthetic functions are the most abundantly expressed ESTs in the rapidly growing B. sudeticus cells. We find that ESTs encoding photosynthetic function but not the ribosomal proteins are most drastically downregulated upon ND. Notably, ESTs encoding lipid metabolic pathways are not significantly upregulated. Further analyses indicate that chlorophyll content is markedly decreased by 3-fold and total lipid content is only slightly increased by 50%, consistent with the transcriptional profiling. On the other hand, carbon content and photosynthesis efficiency are only marginally decreased by 7% and 20%, respectively, indicating that photosynthesis is only slightly reduced upon drastic downregulation of photosynthetic ESTs and chlorophyll content upon ND. In addition, TAG content is found to be greatly increased by 50-fold, though total lipid content is only slightly increased by 1.5-fold.ConclusionsTaken together, our results suggest that light-harvesting proteins and chlorophylls are in excess in B. sudeticus. Degradation of excess photosynthesis proteins is most likely a mechanism for recycling of nitrogen-rich molecules to synthesize new proteins for preparation of gametogenesis and zygospore formation in adaptation and survival upon ND. Furthermore, our analyses indicate that TAG accumulation is largely attributed to the modification of other pre-existing lipid molecules, rather than de novo synthesis. We propose that this is likely an evolutionarily conserved mechanism in many green microalgae species.

Dataset Information

Nitrogen deprivation-induced de novo transcriptomic profiling of the oleaginous green alga Botryococcus braunii 779.

Publications

Nitrogen deprivation-induced de novo transcriptomic profiling of the oleaginous green alga Botryococcus braunii 779.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets