EU - The Genome Analysis Centre (TGAC) together with the Universidad Nacional de Rio Cuarto (UNRC), Instituto de Agrobiotecnologica Rossario (INDEAR), and other European partners, have completed the genome sequence of a model strain of the soil bacterium Azospirillum brasilense to help improve farming productivity.
The soil bacterium, isolated from wheat roots in the central region of Argentina, has been used as a bio-fertiliser in agriculture during the last four decades. One of the main characteristics of the Azospirillum bacterium that aids plant health is its ability to be able to produce plant-growth regulators. By sequencing the genome of the bacterium's model strain, Azospirillum brasilense (Az39), the potential mechanisms responsible for growth improvement can be unravelled.
As the most-studied soil bacterium that encourages plant growth, Azospirillum brasilense is responsible for the major improvement of more than a hundred plant species' growth and yield productivity.
To sequence the genome, TGAC performed the optical mapping analysis with an OpGen Argus whole genome mapper to validate the final genome assembly.
Bernardo Clavijo, Project Leader of the Bioinformatics Algorithms Development Group at TGAC, explains the analytic process: "Optical mapping is a technology that produces a restriction map of a genome, which is essentially a list of distances at which a known sequence occurs within the DNA.
"Knowing where this tag lies allow you to anchor shorter assembled sequences from a sequencing experiment and confirm their validity, pretty much like how a few small clouds and their position on an image guide would give you the necessary hints to assemble an otherwise elusive blue sky in a jigsaw puzzle."
David Baker, Platforms and Pipelines Team Leader at TGAC, said: "Whole Genome Mapping is a powerful tool in validating sequencing of small genomes. We are privileged here at TGAC to have the equipment and expertise to run these types of samples. From receipt of sample material to alignment of the optical maps takes just several days' work."
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