Simultaneous acclimation to nitrogen and iron scarcity in open ocean cyanobacteria revealed by sparse tensor decomposition of metatranscriptomes

Description

This dataset contains all of the supplementary files necessary to reproduce the findings published in the research article entitled Simultaneous acclimation to nitrogen and iron scarcity in open ocean cyanobacteria revealed by sparse tensor decomposition of metatranscriptomes. The scripts necessary for reproducing the published analyses can be found in the GitHub repository associated with the article. Below is the article abstract and a description of the files included in this dataset.

Abstract

Microbes respond to changes in their environment by adapting their physiology through coordinated adjustments to the expression levels of functionally related genes. To detect these shifts in situ, we developed a sparse tensor decomposition method that derives gene co-expression patterns from inherently complex whole community RNA-sequencing data. Application of the method to metatranscriptomes of the abundant marine cyanobacteria Prochlorococcus and Synechococcus identified responses to scarcity of two essential nutrients, nitrogen and iron, including increased transporter expression, restructured photosynthesis and carbon metabolism, and mitigation of oxidative stress. Further, expression profiles of the identified gene clusters suggest that both cyanobacteria populations experience simultaneous nitrogen and iron stresses in a transition zone between North Pacific oceanic gyres. The results demonstrate the power of our approach to infer organism responses to environmental pressures, hypothesize functions of uncharacterized genes, and extrapolate ramifications for biogeochemical cycles in a changing ecosystem.

Legends for data S1 to S11

Data S1. Prochlorococcus component profiles.

Median weight profiles for each Prochlorococcus component, including list of associated CyCOGs with corresponding gene weight, bootstrap support, and consensus annotation.

Data S2. Synechococcus component profiles.

Median weight profiles for each Synechococcus component, including list of associated CyCOGs with corresponding gene weight, bootstrap support, and consensus annotation.

Data S3. Enrichment analysis.

Significantly enriched KEGG pathways associated with each component, and compiled consensus annotations for each CyCOG.

Data S4. MED4 CyCOGs.

Mapping of Prochlorococcus MED4 genes to associated CyCOGs.

Data S5. Nitrogen and iron acclimation clusters.

CyCOGs, genes, and annotations for clusters associated with acclimation to nitrogen and iron scarcity.

Data S6. Sample metadata.

Metadata file detailing sampling conditions for all metatranscriptomes used in this study.

Data S7. Genome metadata.

Metadata file for CyCOG v6 reference genomes, including updated clade assignments.

Data S8. CyCOG v6 database.

Tarball of CyCOG v6 database, including reference genomes and annotation data.

Data S9. Reference sequence phylogenies.

Tarball of Prochlorococcus and Synechococcus reference genome phylogenies, used to update clade assignments.

Data S10. Prochlorococcus transcript abundance data.

A netCDF file of raw and normalized Prochlorococcus transcript abundance data, aggregated by CyCOG and organized into an `xarray.Dataset' tensor data structure.

Data S11. Synechococcus transcript abundance data.

A netCDF file of raw and normalized Synechococcus transcript abundance data, aggregated by CyCOG and organized into an `xarray.Dataset' tensor data structure.