Plant Associated and Environmental Microbes Database


Multilocus Sequence Typing (MLST) and Multilocus Sequence Analysis (MLSA)

MLST is a typing scheme based on the DNA sequence of typically four to 10 loci in a bacterial genome to identify and classify bacterial strains and to unravel population genetics, molecular evolution, and epidemiology of the species the strains belong to. MLST was first proposed in 1998 by Maiden and colleagues.

In MLST, allele sequences at each locus are assigned numbers. Strains that have the same alleles at all loci are considered to belong to the same sequence type. Also every sequence type has a number. Most of the downstream analyses in MLST are based on allele numbers and sequence types. In MLSA instead, the actual DNA sequences are used in the downstream analyses. Moreover, MLST is usually applied to strains that belong to a well-defined species while MLSA is more often used when species boundaries are not well known and MLSA data are used to improve species descriptions.

The following papers describe MLST/MLSA studies in plant pathogens:

  1. Castillo, J.A. and J.T. Greenberg, Evolutionary Dynamics Of Ralstonia Solanacearum. Appl Environ Microbiol, 2006.
  2. Feng, J., Schuenzel, E. L., Li, J., Schaad, N. W., Multilocus sequence typing reveals two evolutionary lineages of Acidovorax avenae subsp. Citrulli Phytopathology, 2009. 99(8):913-20.
  3. Goss, E.M., M. Kreitman, and J. Bergelson, Genetic diversity, recombination and cryptic clades in Pseudomonas viridiflava infecting natural populations of Arabidopsis thaliana. Genetics, 2005. 169(1): p. 21-35.
  4. Hwang, M.S., R.L. Morgan, S.F. Sarkar, P.W. Wang, and D.S. Guttman, Phylogenetic characterization of virulence and resistance phenotypes of Pseudomonas syringae. Appl Environ Microbiol, 2005. 71(9): p. 5182-91.
  5. Sarkar, S.F. and D.S. Guttman,Evolution of the core genome of Pseudomonas syringae, a highly clonal, endemic plant pathogen. Appl Environ Microbiol, 2004. 70(4): p. 1999-2012.
  6. Scally, M., E.L. Schuenzel, R. Stouthamer, and L. Nunney, Multilocus sequence type system for the plant pathogen Xylella fastidiosa and relative contributions of recombination and point mutation to clonal diversity. Appl Environ Microbiol, 2005. 71(12): p. 8491-9.
  7. Yan, S., H. Liu, T.J. Mohr, J. Jenrette, R. Chiodini, M. Zaccardelli, J.C. Setubal, and B.A. Vinatzer, Role of recombination in the evolution of the model plant pathogen Pseudomonas syringae pv. tomato DC3000, a very atypical tomato strain. Appl Environ Microbiol, 2008. 74(10): p. 3171-81.
  8. Young, J.M., D.C. Park, H.M. Shearman, and E. Fargier, A multilocus sequence analysis of the genus Xanthomonas. Syst Appl Microbiol, 2008. 31(5): p. 366-77.