JGI and UNC Develop Functional Genomics Database for Plant Microbiome Studies

Scientists from the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and University of North Carolina (UNC) developed a catalog of bacterial genomes to help other researchers identify and characterize candidate genes that aid bacteria in thriving in plant environments, especially those involved in bacterial root colonization.

"If we want to engineer the right microbiome to support plant growth, we need to understand the real function of the microbiome and not just sequence marker genes," said study co-first author Asaf Levy, a research scientist at the JGI. "Here we used a massive genomic and computational effort to address the fundamental and important question: ‘How does the plant microbiome interact with the plant?'"

Scientists from various institutions have previously isolated novel bacterial from root environment of  Brassicaceae (191), poplar trees (135), and maize (51). The genomes of these 377 bacterial isolates, plus an additional 107 single bacterial cells from roots of Arabidopsis, were then sequenced, assembled, and annotated at the JGI. Then the JGI and UNC researchers combined the new genomes with publicly available genomes that represent the major types of plant-linked bacteria as well as those from non-plant environments. The combined data led to the formation of the database with 3,887 genomes, wherein 1,160 were from plants.

Read the media release of JGI for more details.


 

This article is part of the Crop Biotech Update, a weekly summary of world developments in agri-biotech for developing countries, produced by the Global Knowledge Center on Crop Biotechnology, International Service for the Aquisition of Agri-Biotech Applications SEAsiaCenter (ISAAA)

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