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De novo transcriptomic analysis of Chlorella sorokiniana reveals differential genes expression in photosynthetic carbon fixation and lipid production

View Article: PubMed Central - PubMed

ABSTRACT

Background: Microalgae, which can absorb carbon dioxide and then transform it into lipid, are promising candidates to produce renewable energy, especially biodiesel. The paucity of genomic information, however, limits the development of genome-based genetic modification to improve lipid production in many microalgae. Here, we describe the de novo sequencing, transcriptome assembly, annotation and differential expression analysis for Chlorella sorokiniana cultivated in different conditions to reveal the change of genes expression associated with lipid accumulation and photosynthetic carbon fixation.

Results: Six cultivation conditions were selected to cultivate C. sorokiniana. Lipid content of C. sorokiniana under nitrogen-limited condition was 2.96 times than that under nitrogen-replete condition. When cultivated in light with nitrogen-limited supply, C. sorokiniana can use carbon dioxide to accumulate lipid. Then, transcriptome of C. sorokiniana was sequenced using Illumina paired-end sequencing technology, and 244,291,069 raw reads with length of 100 bp were produced. After preprocessed, these reads were de novo assembled into 63,811 contigs among which 23,528 contigs were found homologous sequences in public databases through Blastx. Gene expression abundance under six conditions were quantified by calculating FPKM value. Ultimately, we found 385 genes at least 2-fold up-regulated while 71 genes at least 2-fold down-regulated in nitrogen-limited condition. Also, 204 genes were at least 2-fold up-regulated in light while 638 genes at least 2-fold down-regulated. Finally, 16 genes were selected to conduct RT-qPCR and 15 genes showed the similar results as those identified by transcriptomic analysis in term of differential expression.

Conclusions: De novo transcriptomic analyses have generated enormous information over C. sorokiniana, revealing a broad overview of genomic information related to lipid accumulation and photosynthetic carbon fixation. The genes with expression change under different conditions are highly likely the potential targets for genetic modification to improve lipid production and CO2 fixation efficiency in oleaginous microalgae.

Electronic supplementary material: The online version of this article (doi:10.1186/s12866-016-0839-8) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus

Characteristics of homology search of assembly against the Nr database. a: The length distribution of contigs assembled. b: The length distribution of contigs with match (with a cut-off E-value of 1.0E-5) in Nr database. c: Species distribution of the total homologous sequences with E-value ≤ 1.0E-5. d: E-value distribution of Blastx hits for each contigs with E-value ≤ 1.0E-5. We used the first hit of each search results for analysis
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Fig2: Characteristics of homology search of assembly against the Nr database. a: The length distribution of contigs assembled. b: The length distribution of contigs with match (with a cut-off E-value of 1.0E-5) in Nr database. c: Species distribution of the total homologous sequences with E-value ≤ 1.0E-5. d: E-value distribution of Blastx hits for each contigs with E-value ≤ 1.0E-5. We used the first hit of each search results for analysis

Mentions: After Illumina Hiseq2000 paired-end sequencing, over 244,291,069 raw reads were generated and are available at the NCBI SRA database (Table 1). All the raw reads were subjected to trimming based on base quality score and read length, and 229,288,757 clean reads were generated (Additional files 1 and 2), which were de novo assembled into 72,902 contigs with N50 of 2,502 bp. After clustered, 63,811 non-redundant contigs, ranging from 200 bp to 15,932 bp, were generated with an average length of 1,022 bp (Fig. 2a, Additional file 3), which was used for the following analysis. The Transcriptome Short Assembly project has been deposited at DDBJ/EMBL/GenBank under the accession GAPD00000000. The version described in this paper is the first version GAPD01000000.Fig. 2


De novo transcriptomic analysis of Chlorella sorokiniana reveals differential genes expression in photosynthetic carbon fixation and lipid production
Characteristics of homology search of assembly against the Nr database. a: The length distribution of contigs assembled. b: The length distribution of contigs with match (with a cut-off E-value of 1.0E-5) in Nr database. c: Species distribution of the total homologous sequences with E-value ≤ 1.0E-5. d: E-value distribution of Blastx hits for each contigs with E-value ≤ 1.0E-5. We used the first hit of each search results for analysis
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5037625&req=5

Fig2: Characteristics of homology search of assembly against the Nr database. a: The length distribution of contigs assembled. b: The length distribution of contigs with match (with a cut-off E-value of 1.0E-5) in Nr database. c: Species distribution of the total homologous sequences with E-value ≤ 1.0E-5. d: E-value distribution of Blastx hits for each contigs with E-value ≤ 1.0E-5. We used the first hit of each search results for analysis
Mentions: After Illumina Hiseq2000 paired-end sequencing, over 244,291,069 raw reads were generated and are available at the NCBI SRA database (Table 1). All the raw reads were subjected to trimming based on base quality score and read length, and 229,288,757 clean reads were generated (Additional files 1 and 2), which were de novo assembled into 72,902 contigs with N50 of 2,502 bp. After clustered, 63,811 non-redundant contigs, ranging from 200 bp to 15,932 bp, were generated with an average length of 1,022 bp (Fig. 2a, Additional file 3), which was used for the following analysis. The Transcriptome Short Assembly project has been deposited at DDBJ/EMBL/GenBank under the accession GAPD00000000. The version described in this paper is the first version GAPD01000000.Fig. 2

View Article: PubMed Central - PubMed

ABSTRACT

Background: Microalgae, which can absorb carbon dioxide and then transform it into lipid, are promising candidates to produce renewable energy, especially biodiesel. The paucity of genomic information, however, limits the development of genome-based genetic modification to improve lipid production in many microalgae. Here, we describe the de novo sequencing, transcriptome assembly, annotation and differential expression analysis for Chlorella sorokiniana cultivated in different conditions to reveal the change of genes expression associated with lipid accumulation and photosynthetic carbon fixation.

Results: Six cultivation conditions were selected to cultivate C. sorokiniana. Lipid content of C. sorokiniana under nitrogen-limited condition was 2.96 times than that under nitrogen-replete condition. When cultivated in light with nitrogen-limited supply, C. sorokiniana can use carbon dioxide to accumulate lipid. Then, transcriptome of C. sorokiniana was sequenced using Illumina paired-end sequencing technology, and 244,291,069 raw reads with length of 100 bp were produced. After preprocessed, these reads were de novo assembled into 63,811 contigs among which 23,528 contigs were found homologous sequences in public databases through Blastx. Gene expression abundance under six conditions were quantified by calculating FPKM value. Ultimately, we found 385 genes at least 2-fold up-regulated while 71 genes at least 2-fold down-regulated in nitrogen-limited condition. Also, 204 genes were at least 2-fold up-regulated in light while 638 genes at least 2-fold down-regulated. Finally, 16 genes were selected to conduct RT-qPCR and 15 genes showed the similar results as those identified by transcriptomic analysis in term of differential expression.

Conclusions: De novo transcriptomic analyses have generated enormous information over C. sorokiniana, revealing a broad overview of genomic information related to lipid accumulation and photosynthetic carbon fixation. The genes with expression change under different conditions are highly likely the potential targets for genetic modification to improve lipid production and CO2 fixation efficiency in oleaginous microalgae.

Electronic supplementary material: The online version of this article (doi:10.1186/s12866-016-0839-8) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus