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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.


Comparative analysis of B. braunii 779 transcriptome with that of B. braunii Bot-88 and Showa. (A) Venn diagram of B. braunii 779 ESTs sharing homology to those in B. braunii Bot-88 and Showa. Numbers in parentheses indicate the number of annotated ESTs. (B) Percentage of annotated sequences in various groups of ESTs. Percentage of annotated ESTs that share homology to Bot-88 only (or Bot-88), to both Bot-88 and Showa (or Both), to Showa only (or Showa), share no homology to either Bot-88 or Showa (or 779 uni or 779 unique), and 779 background level (or 779 all) are indicated.
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f0010: Comparative analysis of B. braunii 779 transcriptome with that of B. braunii Bot-88 and Showa. (A) Venn diagram of B. braunii 779 ESTs sharing homology to those in B. braunii Bot-88 and Showa. Numbers in parentheses indicate the number of annotated ESTs. (B) Percentage of annotated sequences in various groups of ESTs. Percentage of annotated ESTs that share homology to Bot-88 only (or Bot-88), to both Bot-88 and Showa (or Both), to Showa only (or Showa), share no homology to either Bot-88 or Showa (or 779 uni or 779 unique), and 779 background level (or 779 all) are indicated.

Mentions: Transcriptomes of A-race B. braunii Bot-88 and B-race Showa were first processed by removal of redundant ESTs using CD-Hit (i.e., identity > 90%). The resulting ESTs were subjected to BLASTN analysis against the transcriptome of B. braunii 779. At a threshold of e-value < 1E-05, we found that 1140 shared homology to those in both Bot-88 and Showa, 5860 were unique to Bot-88 [3], and 7489 unique to Showa [4] (Fig. 2).


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)

Comparative analysis of B. braunii 779 transcriptome with that of B. braunii Bot-88 and Showa. (A) Venn diagram of B. braunii 779 ESTs sharing homology to those in B. braunii Bot-88 and Showa. Numbers in parentheses indicate the number of annotated ESTs. (B) Percentage of annotated sequences in various groups of ESTs. Percentage of annotated ESTs that share homology to Bot-88 only (or Bot-88), to both Bot-88 and Showa (or Both), to Showa only (or Showa), share no homology to either Bot-88 or Showa (or 779 uni or 779 unique), and 779 background level (or 779 all) are indicated.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

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

f0010: Comparative analysis of B. braunii 779 transcriptome with that of B. braunii Bot-88 and Showa. (A) Venn diagram of B. braunii 779 ESTs sharing homology to those in B. braunii Bot-88 and Showa. Numbers in parentheses indicate the number of annotated ESTs. (B) Percentage of annotated sequences in various groups of ESTs. Percentage of annotated ESTs that share homology to Bot-88 only (or Bot-88), to both Bot-88 and Showa (or Both), to Showa only (or Showa), share no homology to either Bot-88 or Showa (or 779 uni or 779 unique), and 779 background level (or 779 all) are indicated.
Mentions: Transcriptomes of A-race B. braunii Bot-88 and B-race Showa were first processed by removal of redundant ESTs using CD-Hit (i.e., identity > 90%). The resulting ESTs were subjected to BLASTN analysis against the transcriptome of B. braunii 779. At a threshold of e-value < 1E-05, we found that 1140 shared homology to those in both Bot-88 and Showa, 5860 were unique to Bot-88 [3], and 7489 unique to Showa [4] (Fig. 2).

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.