1. Species-specific metabolic networks
Our laboratory has developed species-specific metabolic pathways databases for strawberry ( FragariaCyc), grapevine (VitisCyc), eucalyptus (EucalyptusCyc) and cacao (CacaoCyc). These databases were made publicly available along with the reference BioCyc databases and species-specific metabolic networks for monocot plant species developed by Gramene project to facilitate cross-species comparison.
2. Gramene Database (supported by NSF)
Project Website: http://www.gramene.org
It is an open source, free-of-cost resource for comparative plant genomics and plant pathway knowledgebase. Dr. Naithani serves a an outreach coordinator for the Gramene project and senior biocurator for its pathway portal Plant Reactome (http://plantreactome.gramene.org). Plant Reactome features plant metabolic, signaling, transport, genetic, regulatory, developmental and stress-response pathways for 83 plant species, from unicellular photoautotrophs to higher plants. We utilize a combinatorial approach involving manual curation of reference pathways and automated gene orthology-based projection to rapidly scale up pathway knowledge from reference species rice (Oryza sativa) to all other species. Pathway clustering across the broad phylogenetic spectrum of photosynthetic organisms shows distinct gene-pathway association patterns reflecting evolutionary history and ploidy levels. Plant researchers can compare reference rice pathways with the projected pathways from any hosted plant species to discover species-specific pathway enrichment, regulatory events, and loss/gain of reactions, thereby providing necessary clues and hypotheses for building potential pathway engineering and synthetic biology strategies for the improvement of the physiology, utility, performance and synthesis of bioproducts. Users can also upload their data for pathway analysis, and visualization in the context of plant pathways hosted by Plant Reactome.
3. WikiPathways Collaboration
Project Website: http://www.wikipathways.org
We collaborate with the WikiPathways project on curating plant pathways.
4. Plant Genome and Transcriptome Analyses
We collaborate with genomics and transcriptomics project on improving/performing functional annotation phylogenetic analysis of genes and gene families and mapping and analysis of genes in the context of plant pathways.
5. Developing Big data Standards and Community Best Practices
We collaborate with AgBioData consortium (https://www.agbiodata.org) and Grape Information System (GrapeIS) on developing standards for genomic data formatting, biocuration and making data Findable, accessible, interoperable and re-usable (FAIR).