[PDF] PhotoEukStein: Towards an omics-based definition of unicellular eukaryote phototrophs functional traits via metabolic modelling-论文阅读讨论-ReadPaper

摘要

Defining biological functional traits for unicellular organisms relies on comprehending the set and combination of the biochemical reactions their genomes encode for. This network of biochemical reactions defines the metabolic strategy organisms and communities used to grow in a given environment. While prokaryotes have been the ideal target for reconstructing and analysing these metabolic networks, eukaryotes lagged behind due to the complexity of their genomes and the paucity of knowledge on their metabolism. Here, we developed PhotoEukstein, a meta-metabolic model for unicellular phototroph eukaryotes allowing a fast and automated top-down derivation of Genome-Scale Metabolic models directly from genomes. We applied it to a diverse collection of 559 environmental genomes and transcriptomes of marine eukaryote unicellular plankton. We show these models allow to predict functional traits that cannot be purely deducted from taxonomic information or listing of metabolic reactions encoded by the genome. They provide the opportunity to build connections with Earth System Models to pinpoint environmental parameters needed to parametrise specific functional traits.

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