Abstract
BackgroundThe rationale for gathering information from plants procuring nitrogen through symbiotic interactions controlled by a common genetic program for a sustainable biofuel production is the high energy demanding application of synthetic nitrogen fertilizers. We curated sequence information publicly available for the biofuel plant sugarcane, performed an analysis of the common SYM pathway known to control symbiosis in other plants, and provide results, sequences and literature links as an online database.MethodsSugarcane sequences and informations were downloaded from the nucEST database, cleaned and trimmed with seqclean, assembled with TGICL plus translating mapping method, and annotated. The annotation is based on BLAST searches against a local formatted plant Uniprot90 generated with CD-HIT for functional assignment, rpsBLAST to CDD database for conserved domain analysis, and BLAST search to sorghum's for Gene Ontology (GO) assignment. Gene expression was normalized according the Unigene standard, presented as ESTs/100 kb. Protein sequences known in the SYM pathway were used as queries to search the SymGRASS sequence database. Additionally, antimicrobial peptides described in the PhytAMP database served as queries to retrieve and generate expression profiles of these defense genes in the libraries compared to the libraries obtained under symbiotic interactions.ResultsWe describe the SymGRASS, a database of sugarcane orthologous genes involved in arbuscular mycorrhiza (AM) and root nodule (RN) symbiosis. The database aggregates knowledge about sequences, tissues, organ, developmental stages and experimental conditions, and provides annotation and level of gene expression for sugarcane transcripts and SYM orthologous genes in sugarcane through a web interface. Several candidate genes were found for all nodes in the pathway, and interestingly a set of symbiosis specific genes was found.ConclusionsThe knowledge integrated in SymGRASS may guide studies on molecular, cellular and physiological mechanisms by which sugarcane controls the establishment and efficiency of endophytic associations. We believe that the candidate sequences for the SYM pathway together with the pool of exclusively expressed tentative consensus (TC) sequences are crucial for the design of molecular studies to unravel the mechanisms controlling the establishment of symbioses in sugarcane, ultimately serving as a basis for the improvement of grass crops.
Highlights
The rationale for gathering information from plants procuring nitrogen through symbiotic interactions controlled by a common genetic program for a sustainable biofuel production is the high energy demanding application of synthetic nitrogen fertilizers
The understanding of mechanisms involved in the evolution of arbuscular mycorrhiza (AM) and root nodule symbiosis (RNS) has in recent years faced dramatic advances through genetic analysis of the plant host
Gene Ontology terms were assigned to the tentative consensus (TC) based on their similarity to UniprotKB protein accessed through the BLASTx and mapped to Gene Ontology association (GOA) [12]
Summary
The rationale for gathering information from plants procuring nitrogen through symbiotic interactions controlled by a common genetic program for a sustainable biofuel production is the high energy demanding application of synthetic nitrogen fertilizers. We curated sequence information publicly available for the biofuel plant sugarcane, performed an analysis of the common SYM pathway known to control symbiosis in other plants, and provide results, sequences and literature links as an online database. 400 Myr later, the nitrogen-fixing root nodule symbiosis (RNS) with rhizobacteria (rhizobia) evolved in association with a subset of the dicotyledonous angiosperms (mostly legumes). It is evident that the common SYM pathway evolved in the context of AM and became secondarily involved in RNS [1]. Besides of being capable of AM symbiosis, sugarcane (Saccharum officinarum) associates with rhizhospheric, associative and endophytic nitrogen fixing bacteria [2], that posses unique features yet to be characterized, but as occurred with RNS, it is possible that this system of beneficial plant-microbial association evolved already in the context of AM symbiosis
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