Lateral gene transfer (LGT) is the movement of DNA between diverse organisms other than via vertical transmission. LGT is synonymous with horizontal gene transfer (HGT). Recognized within the bacteria domain of life for decades8, 11 inter-domain transfers are increasingly described1,2,3,4,6,7,9,10,13, particularly between bacteria and complex multicellular organisms. With the sequencing of more endosymbiont-colonized arthropods,5,14 the growing appreciation for the prevalence of recent LGT events,11 along with indication of medically significant gene transfers,13 the interest in identifying LGT events is only likely to increase over the coming years. Standard methods for identifying all LGTs must be made available that consider the likelihood of contamination while not being so stringent as to perform genome cleansing of all but older, functional LGTs. Through funding by the United States National Science Foundation (NSF), our analysis tools are being made available for genomic LGT analysis:
These analysis tools have been designed (LGTSeek and LGTView) or modified (TwinBLAST) such that the bioinformatically savvy as well as naive users can adopt them to their particular project and infrastructure. As big computing is expensive, the analysis runs are time consuming, and the resources necessary to run genome level analyses are not readily available to all researchers, the tools offered here do not require the user to have massive computational resources. The individual’s raw or processed data will not be hosted. Rather, the user maintains control over, and responsibility for, their data as the virtual machine (VM) is run on local machines, institutional grids/clusters, and on cloud infrastructures such as the Amazon EC2. With some knowledge about the donor and/or recipient genome, the integration of recent DNA can be detected.
- Acuña, R., Padilla, B. E., Flórez-Ramos, C. P., Rubio, J. D., Herrera, J. C., Benavides, P., … & Rose, J. K. (2012). Adaptive horizontal transfer of a bacterial gene to an invasive insect pest of coffee. Proceedings of the National Academy of Sciences, 109(11), 4197-4202.
- Boto, Luis. “Horizontal gene transfer in the acquisition of novel traits by metazoans.” Proc. R. Soc. B. Vol. 281. No. 1777. The Royal Society, 2014.
- Dunning Hotopp, J. C., Clark, M. E., Oliveira, D. C., Foster, J. M., Fischer, P., Torres, M. C. M., … & Ingram, J. (2007). Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science, 317(5845), 1753-1756.
- Dunning Hotopp, J. C. (2011). Horizontal gene transfer between bacteria and animals. Trends in Genetics, 27(4), 157-163.
- i5K Consortium. (2013). The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment. Journal of Heredity, 104(5), 595-600.
- Keeling, P. J., & Palmer, J. D. (2008). Horizontal gene transfer in eukaryotic evolution. Nature Reviews Genetics, 9(8), 605-618.
- Klasson, L., Kambris, Z., Cook, P. E., Walker, T., & Sinkins, S. P. (2009). Horizontal gene transfer between Wolbachia and the mosquito Aedes aegypti. Bmc Genomics, 10(1), 33.
- Koonin, E. V., Makarova, K. S., & Aravind, L. (2001). Horizontal gene transfer in prokaryotes: quantification and classification 1. Annual Reviews in Microbiology, 55(1), 709-742.
- Moran, N. A., & Jarvik, T. (2010). Lateral transfer of genes from fungi underlies carotenoid production in aphids. science, 328(5978), 624-627.
- Nelson, K. E., Clayton, R. A., Gill, S. R., Gwinn, M. L., Dodson, R. J., Haft, D. H., … & McDonald, L. (1999). Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima.Nature, 399(6734), 323-329.
- Ochman, H., Lawrence, J. G., & Groisman, E. A. (2000). Lateral gene transfer and the nature of bacterial innovation. Nature, 405(6784), 299-304.
- Richards, T. A., & Monier, A. (2016). A tale of two tardigrades. Proceedings of the National Academy of Sciences, 113(18), 4892-4894.
- Riley, D. R., Sieber, K. B., Robinson, K. M., White, J. R., Ganesan, A., Nourbakhsh, S., & Dunning Hotopp, J. C. (2013). Bacteria-human somatic cell lateral gene transfer is enriched in cancer samples. PLoS Comput Biol, 9(6), e1003107.
- Zug, R., & Hammerstein, P. (2012). Still a host of hosts for Wolbachia: analysis of recent data suggests that 40% of terrestrial arthropod species are infected. PloS one, 7(6), e38544.