Bioinformatics Protocol for Assessing Contamination Level and Quality on Genomics Data of Ensifer meliloti
Nitrogen (N) fixing bacteria have a symbiotic relationship with host plants. The legume plants provide sugar, a product of its photosynthesis, to rhizobacteria. Rhizobacteria, one of the various N fixing bacteria, utilize the sugar for its energy source needed for conversion of N2into NH4+. The rhizobacteria would provide fixed nitrogen to legume plant for its growth in exchange of energy source. There are various symbiotic relationships between microbes and plants, and the Heath Lab is especially interested in relationship between rhizobacteria and legume plants. Various genomic methods to study rhizobacteria require sequence data in Heath Lab. However, there is high possibility of contamination in the sequence data, which may lead to false result in research. Possible non-rhizobacteria that reside within the legume nodules, which don’t participate in N fixation but in survival of the legume plant, could affect the research as well. It was recently found that rhizobacteria other than Ensifer meliloti reside within the legume nodules. Due to the existence of other rhizobacteria, we need a protocol to differentiate between these bacteria. Here, we designed a protocol based on comparing the sequences of E.meliloti from the Heath Lab against public database to determine the level of contamination.
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Lee, Soohyun; Ceròn Romero, Mario; and Heath, Katy, "Bioinformatics Protocol for Assessing Contamination Level and Quality on Genomics Data of Ensifer meliloti" (2021). PRECS student projects. 56.
This research was conducted with the cooperation of the Department of Plant Biology, College of Integrative Biology, University of Illinois at Urbana-Champaign.
Financial support was provided by the National Science Foundation under grant #NSF REU 1950819/1950786, as part of the Phenotypic Plasticity Research Experience for Community College Students, through the University of Illinois at Urbana-Champaign Institute for Genomic Biology and Parkland College. http://precs.igb.illinois.edu/