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

Xu Z, He J, Qi S, Liu J - Genom Data (2015)

Bottom Line: 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.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).

View Article: PubMed Central - PubMed

Affiliation: Ocean College, Zhejiang University, Hangzhou, Zhejiang 310058, China.

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).

No MeSH data available.


Venn diagram of B. braunii 779 ESTs sharing homology to 4 annotated genomes.
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f0005: Venn diagram of B. braunii 779 ESTs sharing homology to 4 annotated genomes.

Mentions: Subsequently, non-redundant ESTs were subjected to sequence homologous comparison analysis against 6 comprehensively annotated algal genomes (i.e., Coccomyxa subellipsoidea C-169 v2, Chlorella variabilis NC64A v1, Chlamydomonas reinhardtii v4, Micromonas pusilla RCC299 v3, Ostreococcus lucimarinus v2 and Thalassiosira pseudonana CCMP 1335) (http://genome.jgi-psf.org) using BLASTX method. Majority of the best-hits were derived from the C. subellipsoidea genome. For simplicity, only 4 well-separated species were shown in Venn diagram (Fig. 1). Based on the cutoff for e-value < 1E-07 and homology percentage > 40%, 12,292 ESTs were found to have a best-hit in the annotated genomes, of which, 8888 (or 72.3%) and 3386 (or 27.5%) were associated with at least one GO function and KEGG ortholog function, respectively.


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

Xu Z, He J, Qi S, Liu J - Genom Data (2015)

Venn diagram of B. braunii 779 ESTs sharing homology to 4 annotated genomes.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664756&req=5

f0005: Venn diagram of B. braunii 779 ESTs sharing homology to 4 annotated genomes.
Mentions: Subsequently, non-redundant ESTs were subjected to sequence homologous comparison analysis against 6 comprehensively annotated algal genomes (i.e., Coccomyxa subellipsoidea C-169 v2, Chlorella variabilis NC64A v1, Chlamydomonas reinhardtii v4, Micromonas pusilla RCC299 v3, Ostreococcus lucimarinus v2 and Thalassiosira pseudonana CCMP 1335) (http://genome.jgi-psf.org) using BLASTX method. Majority of the best-hits were derived from the C. subellipsoidea genome. For simplicity, only 4 well-separated species were shown in Venn diagram (Fig. 1). Based on the cutoff for e-value < 1E-07 and homology percentage > 40%, 12,292 ESTs were found to have a best-hit in the annotated genomes, of which, 8888 (or 72.3%) and 3386 (or 27.5%) were associated with at least one GO function and KEGG ortholog function, respectively.

Bottom Line: 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.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).

View Article: PubMed Central - PubMed

Affiliation: Ocean College, Zhejiang University, Hangzhou, Zhejiang 310058, China.

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).

No MeSH data available.