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United States Department of Agriculture

Agricultural Research Service

Research Project: FORAGE SYSTEMS FOR SUSTAINABLE ANIMAL PRODUCTION IN THE MID-SOUTH Title: An Integrated Database for Grass and Endophyte Genomics at www.grassendophyte.org

Authors
item Zhao, Patrick -
item Dai, Xinbin -
item Li, Jun -
item Amarasinghe, Ranamalie -
item Young, Carolyn -
item Dinkins, Randy
item Hesse, Uljana -
item Jaromczyk, Jerzy -
item Schardl, Christopher -

Submitted to: International Symposium on Fungal Endophytes of Grasses
Publication Type: Abstract Only
Publication Acceptance Date: April 30, 2010
Publication Date: June 28, 2010
Citation: Zhao, P.X., Dai, X., Li, J., Amarasinghe, R., Young, C., Dinkins, R.D., Hesse, U., Jaromczyk, J., Schardl, C.L. 2010. An Integrated Database for Grass and Endophyte Genomics at www.grassendophyte.org. International Symposium on Fungal Endophytes of Grasses. pp 125-126.

Technical Abstract: The endophytic microbes are able to promote plant growth and health under various stresses via their symbiotic association with host plants. Genome-wide comparative analysis has been extensively employed to decipher complex mechanisms of interactions between endophytic microbes and host plants, resulting in fast accumulation of large scale genomics data. However, until recently, only a very limited amount of genomics information is publically available in scattered databases. We present an integrated database, which is freely available at http://www.grassendophyte.org/, to facilitate genomics study of grassendophyte symbiotic association. The database hosts a large volume of genomics data from model endophyte, Epichloe festucae, and associated Lolium and Festuca grasses, including gene models/unigenes, annotations and Illumina sequencing-based gene expression data from both fungi and plants. The genomic/Unigene sequences were annotated by BLASTX against 1) the Gene Ontology (http://www.geneontology.org/) sequence database and 2) the uniprot trembl database (http://www.ebi.ac.uk/uniprot/). The top five hits with meaningful annotations in uniprot tremble database were retrieved as effective annotations. Illumina reads were mapped to corresponding genes, providing gene expression data for different developmental stages of the endophyte. The database also integrates bioinformatics tools for mining genes of interest and the analysis of gene expression profiles.

Last Modified: 12/21/2014
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