BioBam Scholarship Supported Project – with OmicsBox.
- Mr. Arun Arumugaperumal
- Mr. Sayan Paul and Miss Saranya Lathakumari, PhD students
- Dr. Sudhakar Sivasubramaniam
The earthworm Eisenia fetida has a symbiotic bacteria named Verminephrobacter eiseniae in its nephridia. A new strain of V. eiseniae msu was found out and the genome of the bacteria was found hidden in the genome sequencing reads of Eisenia fetida. We separated the bacteria specific reads and assembled the draft genome. The protein coding genes were identified and annotated and further the metabolites that could benefit the earthworm were also identified.
The project involved
- Isolation of bacterial reads from the sequencing reads of earthworm
- Genome assembly and statistical analysis of completeness
- Species demarcation of the bacteria and genome map preparation
- Functional annotation and pathway analysis
- Functional enrichment analysis between the new strain and the type strain
- Identification of symbiosis-associated genes
- Multiple genome alignment and phylogeny
- Pan genome analysis to determine openness of genome
Verminephrobacter eiseniae (JGI Genome Portal)
Contribution of OmicsBox
The functional annotation of the genes were carried out using OmicsBox. It helped to identify the protein domains through the InterProsSan option. Functional enrichment analysis helped to identify the specific genes that were present in the newly identified bacterial strain compared to the type strain.
The bacteria was found to have genes for the production of vitamin B2, thiamine, biotin, propionate, pyruvate, folate, and pantothenate which might help in the embryogenesis and overall fitness of the worm. The bacteria was found to possess several virulence genes that might help in the successful colonization of the earthworm nephridia in a way similar to that of Mycobacterium infection.
Arumugaperumal, A., Paul, S., Lathakumari, S. et al. The draft genome of a new Verminephrobacter eiseniae strain: a nephridial symbiont of earthworms. Ann Microbiol 70, 3 (2020).
Department of Biotechnology at Manonmaniam Sundaranar University, TamilNadu, India