Supporting Information for Steffen MM Et Al

Supporting Information for Steffen MM et al.

Nutrients drive transcriptional changes that maintain metabolic homeostasis but alter genome architecture in Microcystis

Supplementary Table 1. Characteristics of RNA extracted and used for sequencing. Numbers in parentheses indicate standard deviation from triplicate measurements. Chlorophyll a fluorescence (fsu) is used as a proxy for biomass and was measured from cultures grown in 25 mL volumes on a Turner Designs TD-700™ fluorometer (Sunnyvale, CA, USA). n = 3 for all means reported. Growth rates were calculated using µ = Ln(N2/N1)/(t2-t1), with N1 = to biomass (fluorescence) at time t1(Guillard 1973).

Supplementary Figure 1. Log10 of the normalized mean expression values of genes established in the literature as common housekeeping genes (rnpB, trpA, gltX, gyrB, rrn5S_1, rrn5S_2, recA, rrn23S_1, rrn23S_2)(Alfonso et al. 2000, Christiansen et al. 2008, Humbert et al. 2013, López-López et al. 2005, Y et al. 2013) were plotted for each of the nutrient limited treatments against the corresponding values of the control treatment to validate normalization methods and calculation of expression values (Dillies et al. 2012).

Supplementary Figure 2. Community analysis at Kingdom and Phylum levels showing abundance across the three replicates of each treatment. Abundances are expressed in percentage of total reads that could not be recruited to the M. aeruginosa NIES 843 genome for comparative purposes.

Supplementary Figure 3. Recruitment plot (stacked) of transcriptomes to the Microcystis aeruginosa NIES 843 genome. Reads were binned into 100 kbp sections of the genome.

Supplementary Figure 65. Change in expression value (RPKM) of the mcy toxin gene cassette.

Supplementary Figure 6.Heat map depicting protein abundances of detected transposase enzymes in M. aeruginosa NIES 843 cultures grown under N-reduced and P-reduced conditions. For this study, only nitrate (NO3) was used as the N source. Modified normalized spectral abundance factor (NSAF) values from biological and technical duplicates were clustered based on Euclidean distance using average linkage.

Supplementary Table 2. Summary of information regarding general sequencing results. All sequence libraries had a mean read length of 50 base pairs.

Supplementary Table 3. Coordinates of elements in the M. aeruginosa NIES 843 genome highlighted in Figure 6.

Supplementary References

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