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Genome wide RNA-Seq of CsubMADS1 OX and wildtype Coccomyxa subellipsoidea C-169 cultures

ABSTRACT: Genome wide RNA-Seq of CsubMADS1 OX and wildtype Coccomyxa subellipsoidea C-169 cultures

PROVIDER: PRJNA885080 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21740188_1.fastq.gz	Fastqsanger.gz
	SRR21740188_2.fastq.gz	Fastqsanger.gz
	SRR21740189_1.fastq.gz	Fastqsanger.gz
	SRR21740189_2.fastq.gz	Fastqsanger.gz
	SRR21740190_1.fastq.gz	Fastqsanger.gz

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Genome wide RNA-Seq of CsubMADS1 OX and wildtype Coccomyxa subellipsoidea C-169 cultures

Project description:To assess the significant downstream pathways affected by the overexpression of CsubMADS1 in Coccomyxa, transcriptome analysis was carried out using RNA sequencing of three biological replicates each from WT and CsubMADS1 OX at stationary phase (3h before dark phase). The stationary phase was chosen for the analysis because this is when the nutrients start depleting in the medium and starvation stress is induced.

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Transcriptome analysis reveals global regulation in response to CO2 supplementation in oleaginous microalga Coccomyxa subellipsoidea C-169

Project description:The microalga Coccomyxa subellipsoidea C-169 possesses some features that may be valuable for lipid production, and, as demonstrated in this study, can be greatly induced to produce a high amount of fatty acid by CO2 supplementation. Here we have compared the transcriptome of air group (AG, cells cultured under 0.04% CO2) and CO2-supplemented group (CG, cells cultured under 2% CO2), and found that dramatic and collaborative regulation in central metabolic pathways as well as biochemical processes occured in response to CO2 supplementation. This study gains a broad understanding of how CO2 stress regulates gene expression and eventually reveals a fine-tuned strategy adopted by C-169 to sustain rapid cell growth and lipid production, which will be helpful for the implementation of biofuels production from oleaginous microalgae. Transcriptomic profiles of Coccomyxa subellipsoidea C-169 cultured for 4 days under two CO2 levels (0.04% and 2%, v/v) were generated by digital gene expression (DGE) analysis, in triplicate, using Illumina Hiseq2000.

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Transcriptome analysis reveals global regulation in response to CO2 supplementation in oleaginous microalga Coccomyxa subellipsoidea C-169

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Project description:Transcriptome analysis reveals global regulation in response to CO2 supplementation in oleaginous microalga Coccomyxa subellipsoidea C-169

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Identification and Characterization of MiRNAs in Coccomyxa subellipsoidea C-169.

Project description:Coccomyxa subellipsoidea C-169 (C-169) is an oleaginous microalga which is promising for renewable biofuel production. MicroRNAs (miRNAs), as the pivotal modulators of gene expression at post-transcriptional level, are prospective candidates for bioengineering practice. However, so far, no miRNA in C-169 has been reported and its potential impact upon CO2 supplementation remains unclear. High-throughput sequencing of small RNAs from C-169 cultured in air or 2% CO2 revealed 124 miRNAs in total, including 118 conserved miRNAs and six novel ones. In total, 384 genes were predicted as their potential target genes, 320 for conserved miRNAs and 64 for novel miRNAs. The annotated target genes were significantly enriched in six KEGG pathways, including pantothenate and CoA biosynthesis, C5-branched dibasic acid metabolism, 2-oxocarboxylic acid metabolism, butanoate metabolism, valine, leucine and isoleucine biosynthesis and alpha-linolenic acid metabolism. The miRNAs' target genes were enriched in lipid metabolism as well as RNA-interacting proteins involved in translation, transcription and rRNA processing. The pioneering identification of C-169 miRNAs and analysis of their putative target genes lay the foundation for further miRNA research in eukaryotic algae and will contribute to the development of C-169 as an oleaginous microalga through bioengineering in the future.

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