Omics analysis of Ehux CCMP1742 and CCMP2758 over time at different temperatures
In this study we sequenced the genome, analyzed the RNA expression and lipid production of two closely relate Emiliania huxleyi strains, CCMP1742 and CCMP2758.  Both strains are closely related since an unknown spontaneous mutation in Emiliania huxleyi CCMP1742 gave rise to CCMP2758. Their main phenotypic difference is the long chain alkenones (LCA) that they produce. Whilst strain CCMP1742 produces LCAs of 37 and 38 carbons, CCMP2758 also produces LCAs of 35 and 36 carbon atoms.  In this study we sequenced and assembled their genome, and analyzed their differential gene expression (RNAseq) and lipid profile at different growth temperatures (20C and 7C) and different growth stages.   RNA:  RNA sequencing:  RNA libraries were prepared usig TruSeq Stranded mRNA polyA kit. RNA fragments of CCMP1742 and CCMP2758 were barcoded using Unique Molecular Identifiers (UMIs) (9 bp length) during library preparation.   Samples were sequenced using either two runs of 1x 75bp on an Illumina Nextseq 500 platform (CCMP1516) or a S2, 2 x150 bp run on an Illumina NovaSeq 6000 platform   Transcripts data processing: For samples containing UMIS (CCMP1742 and CCMP2758) the UMI Identifiers were originally in a separate FastQ file. The original FASTQ file was modified to add the UMI identifiers to the FastQ header. Then adapters were removed using Trimmomatic, polyG tails were removed using Cutadapt and PCR duplicates using umi_tools dedup.   Raw and deduplicated reads were uploaded as follows: Raw RNA reads files contaning the UMI identifier in the FastQ header are labelled as: umis-SAMPLE_NAME RNA reads after deduplication files are labelled as: SAMPLE_NAME_dedup  DNA: DNA sequencing: The genome was assembled using short reads from Illumina platform (150 bp x Paired end) and long reads obtained from Nanopore. Genomes were assembled using SPAdesBio and annotated using Funannotate.  DNA reads processing: We provide the Illumina and Nanopore reads before (raw) and after the removal of likely contaminants. Each strain contains 7 runs:  - Nanopore raw reads (x1) - Illumina raw reads (x4, one for each sequencing alne used) - Nanopore reads after removing contamination (x1)  - Illumina raw reads after removing contamination (x1)
In this study we sequenced the genome, analyzed the RNA expression and lipid production of two closely relate Emiliania huxleyi strains, CCMP1742 and CCMP2758.  Both strains are closely related since an unknown spontaneous mutation in Emiliania huxleyi CCMP1742 gave rise to CCMP2758. Their main phenotypic difference is the long chain alkenones (LCA) that they produce. Whilst strain CCMP1742 produces LCAs of 37 and 38 carbons, CCMP2758 also produces LCAs of 35 and 36 carbon atoms.  In this study we sequenced and assembled their genome, and analyzed their differential gene expression (RNAseq) and lipid profile at different growth temperatures (20C and 7C) and different growth stages.   RNA:  RNA sequencing:  RNA libraries were prepared usig TruSeq Stranded mRNA polyA kit. RNA fragments of CCMP1742 and CCMP2758 were barcoded using Unique Molecular Identifiers (UMIs) (9 bp length) during library preparation.   Samples were sequenced using either two runs of 1x 75bp on an Illumina Nextseq 500 platform (CCMP1516) or a S2, 2 x150 bp run on an Illumina NovaSeq 6000 platform   Transcripts data processing: For samples containing UMIS (CCMP1742 and CCMP2758) the UMI Identifiers were originally in a separate FastQ file. The original FASTQ file was modified to add the UMI identifiers to the FastQ header. Then adapters were removed using Trimmomatic, polyG tails were removed using Cutadapt and PCR duplicates using umi_tools dedup.   Raw and deduplicated reads were uploaded as follows: Raw RNA reads files contaning the UMI identifier in the FastQ header are labelled as: umis-SAMPLE_NAME RNA reads after deduplication files are labelled as: SAMPLE_NAME_dedup  DNA: DNA sequencing: The genome was assembled using short reads from Illumina platform (150 bp x Paired end) and long reads obtained from Nanopore. Genomes were assembled using SPAdesBio and annotated using Funannotate.  DNA reads processing: We provide the Illumina and Nanopore reads before (raw) and after the removal of likely contaminants. Each strain contains 7 runs:  - Nanopore raw reads (x1) - Illumina raw reads (x4, one for each sequencing alne used) - Nanopore reads after removing contamination (x1)  - Illumina raw reads after removing contamination (x1)
royal netherlands institute for sea research (nioz)