Biogeosciences Discuss., doi:10.5194/bg-2015-564-AC2, 2016 BGD © Author(s) 2016. CC-BY 3.0 License.

Interactive comment

Interactive comment on “Global analysis of gene expression dynamics within the marine microbial community during the VAHINE mesocosm experiment in the South West Pacific” by Ulrike Pfreundt et al.

Ulrike Pfreundt et al. [email protected]

Received and published: 6 June 2016

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Interactive comment on Biogeosciences Discuss., doi:10.5194/bg-2015-564, 2016. Printer-friendly version

Discussion paper

C1 BGD

11 mesocosm samples 11 lagoon samples Interactive subclusters of transcripts with similar comment RNA-Seq paired-end expresison changes sequencing reads Clustered cluster Heatmap adapter removal DE transcripts quality trimming (Figure 2) minimum length 20 nt differential expression (DE) analysis on each rRNA removal with matrix with edgeR SortMeRNA

separation into M1 and lagoon matrices 22 datasets with paired-end read non-ribosomal reads mapping with bowtie Raw count matrix (fragments per binning of all non- transcript per sample) ribososmal reads from transcript abundance all samples estimation with RSEM TMM-normalized Trinity De-novo TPM count matrix transcript assembly Taxonomic and KEGG Figures taxonomic and Trinity classification with KEGG affilitation transcripts Diamond for each transcript

FASTA file with find all transcripts taxonomic and integration of list of specific Function sequences of GOIs from mapping to GOIs functional classification TPM count data transcripts Heatmaps 147 relevant genomes with usearch of specific transcripts and classifications

Fig. 1. Flowchart describing the major steps in the bioinformatics workflow. Pre-processing of Printer-friendly version RNA-Seq reads was done separately for each dataset, leading to 22 datasets of non-ribosomal paired-end reads. Discussion paper

C2 Phase P0 BGD Sphingobacteriia Archaea SAR116_cluster Flavobacteriia Cytophagia Rhodobacterales Bacteroidetes SAR11_cluster root Actinobacteria Alphaproteobacteria Sphingomonadales Bacteria Planctomycetes Rhodospirillales M1 Viruses Proteobacteria Rhizobiales Interactive Verrucomicrobia Eukaryota Firmicutes Pseudomonadales comment Gammaproteobacteria Cyanobacteria Opisthokonta lagoon Nostocales Oceanospirillales Viridiplantae

Prochlorales Alteromonadales Alveolata Haptophyceae Vibrionales Oscillatoriophycideae Stramenopiles SAR86_cluster OMG_group

Phase P1 1 000 000

Sphingobacteriia SAR116_cluster Archaea Flavobacteriia Cytophagia Rhodobacterales SAR11_cluster Bacteroidetes Sphingomonadales 500 000 root Alphaproteobacteria Actinobacteria Rhodospirillales Bacteria Planctomycetes Rhizobiales 50 000 Proteobacteria Viruses Verrucomicrobia Pseudomonadales 5 000 Eukaryota Firmicutes Cyanobacteria Gammaproteobacteria Oceanospirillales Opisthokonta Nostocales Viridiplantae Alteromonadales Prochlorales Alveolata Haptophyceae Vibrionales Oscillatoriophycideae SAR86_cluster Stramenopiles OMG_group T Phase P2

Sphingobacteriia Archaea Rhodobacterales SAR116_cluster I Flavobacteriia Cytophagia Bacteroidetes SAR11_cluster Alphaproteobacteria root Actinobacteria Sphingomonadales M Bacteria Planctomycetes Rhodospirillales Proteobacteria Rhizobiales Viruses Verrucomicrobia E Firmicutes Eukaryota Pseudomonadales Cyanobacteria Gammaproteobacteria Oceanospirillales Viridiplantae Nostocales Opisthokonta Alteromonadales Haptophyceae Prochlorales Vibrionales

Alveolata SAR86_cluster Stramenopiles Oscillatoriophycideae OMG_group Printer-friendly version

Fig. 2. Figure 4. Comparison of the taxonomic affiliation of mRNA transcripts from M1 and the Discussion paper lagoon in the three chronological phases P0, P1, and P2, visualized with CoVennTree (Lott et al., 2015). C3