Ecology and evolution of mobile DNA
Dr. Supriya Khedkar
We are interested in studying how Mobile Genetic Elements (MGEs) - transposons, plasmids, integrons, bacterial viruses and their interactions shape bacterial genomes and communities in nature.
“Life did not take over the world by combat, but by networking” - Lynn Margulis
In the microbial world, much like in human societies, animal behavior, and ecological systems, networking (the exchange of information and or resources) facilitates adaptation, growth, and survival. For example, networking can rapidly spread antibiotic resistance genes to pathogenic microbes leading to clinically untreatable infections. The mechanism responsible for networking in microbes is Horizontal Gene Transfer (HGT) i.e, intercellular transfer of DNA, and Mobile Genetic Elements or MGEs are its key drivers. In the mobile DNA lab, MGEs - IS elements, transposons, integrons, phages, plasmids and Integrative Conjugative Elements are the model systems. We survey and study the diversity, ecology and evolution of microbial Mobile Genetic Elements with an overarching aim of applying our findings to address real world challenges such as MGE driven spread of antibiotic resistance to infection causing pathogens.
Research strategy
The mobile DNA lab works at the interface of mobile DNA and (meta)genomics research. We study Mobile Genetic Elements (MGEs) at gene, host-microbe genome and host-microbe community levels to get a holistic perspective of MGE ecology and evolution. To gather these insights, we analyse the wealth of genomics data in the public domain using approaches and principles from diverse biological sub-fields – microbiology, ecology, bioinformatics, machine learning, comparative, functional and evolutionary genomics. We specialize in using biology-based data-driven approaches to develop computational analyses and frameworks, that support hypothesis generation, biological insight inference and discovery. We generate publicly accessible data borne interactive platforms as web resources to support data exploration needs of the wider research community.

Our research is highly interdisciplinary and collaborative. We employ a combination of top down, bottom-up approaches and collaborations to access the necessary depth and breadth of knowledge to address research questions of interest.

Dr. Supriya Khedkar
- +49 (0)6221 54 51209
- khedkar@bioquant.uni-heidelberg.de
- BioQuant, Im Neuenheimer Feld 267, Room 543
Selected Publications
Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes
S. Khedkar*, G. Smyshlyaev, I. Letunic, O. M. Maistrenko, L. P. Coelho, A. Orakov, S. K. Forslund, F. Hildebrand, M. Luetge, T. S. B. Schmidt, O. Barabas, P. Bork
Nucleic Acids Research. 50, 3155–3168 (2022).
SMART: recent updates, new developments and status in 2020
I. Letunic, S. Khedkar, P. Bork
Nucleic Acids Research (2020).
S. Prabhakara, S. Khedkar, S. M. Shambat, R. Srinivasan, A. Basu, A. Norrby-Teglund, A. S. N. Seshasayee, G. Arakere
PLoS ONE. 8, e60013 (2013).
Draft Genome Sequence of Staphylococcus aureus ST672, an Emerging Disease Clone from India
S. Khedkar*, S. Prabhakara, R. M. Loganathan, C. S, M. Gowda, G. Arakere, A. S. N. Seshasayee
Journal of Bacteriology. 194, 6946–6947 (2012).