PlantSEED enables automated annotation and reconstruction of plant primary metabolism with improved compartmentalization and comparative consistency

Plant J. 2018 Sep;95(6):1102-1113. doi: 10.1111/tpj.14003. Epub 2018 Aug 9.


Genome-scale metabolic reconstructions help us to understand and engineer metabolism. Next-generation sequencing technologies are delivering genomes and transcriptomes for an ever-widening range of plants. While such omic data can, in principle, be used to compare metabolic reconstructions in different species, organs and environmental conditions, these comparisons require a standardized framework for the reconstruction of metabolic networks from transcript data. We previously introduced PlantSEED as a framework covering primary metabolism for 10 species. We have now expanded PlantSEED to include 39 species and provide tools that enable automated annotation and metabolic reconstruction from transcriptome data. The algorithm for automated annotation in PlantSEED propagates annotations using a set of signature k-mers (short amino acid sequences characteristic of particular proteins) that identify metabolic enzymes with an accuracy of about 97%. PlantSEED reconstructions are built from a curated template that includes consistent compartmentalization for more than 100 primary metabolic subsystems. Together, the annotation and reconstruction algorithms produce reconstructions without gaps and with more accurate compartmentalization than existing resources. These tools are available via the PlantSEED web interface at, which enables users to upload, annotate and reconstruct from private transcript data and simulate metabolic activity under various conditions using flux balance analysis. We demonstrate the ability to compare these metabolic reconstructions with a case study involving growth on several nitrogen sources in roots of four species.

Keywords: flux balance analysis; metabolic modeling; metabolic reconstruction; plant genomes; plant metabolism.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Computational Biology / methods*
  • Databases, Factual*
  • Genome, Plant / genetics
  • High-Throughput Nucleotide Sequencing
  • Metabolic Networks and Pathways
  • Metabolomics / methods*
  • Plants / genetics
  • Plants / metabolism*
  • Transcriptome