Limits...
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

Histogram presentation of clusters of orthologous groups (COG) categories. Out of 23496 Nr hits, 8951 contigs were assigned at least one COG category among the 24 categories
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig4: Histogram presentation of clusters of orthologous groups (COG) categories. Out of 23496 Nr hits, 8951 contigs were assigned at least one COG category among the 24 categories

Mentions: 8,951 contigs were assigned with at least 1 COG category and 13 contigs had no homologous sequence in Nr database but matched homologous sequence in COG database (Fig. 3). Among the 24 COG categories, the cluster for “general function prediction only” accounted for the largest group (2380, 19.22 %), followed by “Replication, recombination and repair” (1251, 10.1 %) and “Transcription” (1000, 8.07 %). In addition, the following categories contained the minimum number of contigs: “Nuclear structure” (1), “Cell motility” (11, 0.0009 %), “RNA processing and modification” (77, 0.006 %). We even did not find any contig assigned to the category “Extracellular structures” (Fig. 4, Additional file 4).Fig. 4


De novo transcriptomic analysis of Chlorella sorokiniana reveals differential genes expression in photosynthetic carbon fixation and lipid production
Histogram presentation of clusters of orthologous groups (COG) categories. Out of 23496 Nr hits, 8951 contigs were assigned at least one COG category among the 24 categories
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig4: Histogram presentation of clusters of orthologous groups (COG) categories. Out of 23496 Nr hits, 8951 contigs were assigned at least one COG category among the 24 categories
Mentions: 8,951 contigs were assigned with at least 1 COG category and 13 contigs had no homologous sequence in Nr database but matched homologous sequence in COG database (Fig. 3). Among the 24 COG categories, the cluster for “general function prediction only” accounted for the largest group (2380, 19.22 %), followed by “Replication, recombination and repair” (1251, 10.1 %) and “Transcription” (1000, 8.07 %). In addition, the following categories contained the minimum number of contigs: “Nuclear structure” (1), “Cell motility” (11, 0.0009 %), “RNA processing and modification” (77, 0.006 %). We even did not find any contig assigned to the category “Extracellular structures” (Fig. 4, Additional file 4).Fig. 4

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