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Background  The water-bloom-forming cyanobacterium  Microcystis aeruginosa  is a known producer of various kinds of toxic and bioactive chemicals. Of these, hepatotoxic cyclic heptapeptides microcystins have been studied most intensively due to increasing concerns for human health risks and environmental damage. More than 70 variants of microcystins are known, and a single microcystin synthetase ( mcy ) gene cluster consisting of 10 genes ( mcyA  to  mcyJ ) has been identified to be responsible for the production of all known variants of microcystins. Our previous multilocus sequence typing (MLST) analysis of the seven housekeeping genes indicated that microcystin-producing strains of  M. aeruginosa  are classified into two phylogenetic groups.    Results  To investigate whether the  mcy  genes are genetically structured similarly as in MLST analysis of the housekeeping genes and to identify the evolutionary forces responsible for the genetic divergence of these genes, we used 118  mcy -positive isolates to perform phylogenetic and population genetic analyses of  mcy  genes based on three  mcy  loci within the  mcy  gene cluster ( mcyD ,  mcyG , and  mcyJ ), none of which is involved in the production of different microcystin variants. Both individual phylogenetic analysis and multilocus genealogical analysis of the  mcy  genes divided our isolates into two clades, consistent with the MLST phylogeny based on seven housekeeping loci. No shared characteristics within each clade are known, and microcystin analyses did not identify any compositional trend specific to each clade. Statistical analyses for recombination indicated that recombination among the  mcy  genes is much more frequent within clades than between, suggesting that recombination has been an important force maintaining the cryptic divergence of  mcy  genes. On the other hand, a series of statistical tests provided no strong evidence for selection to explain the deep divergence of the  mcy  genes. Furthermore, analysis of molecular variance (AMOVA) indicated a low level of geographic structuring in the genetic diversity of  mcy .    Conclusion  Our phylogenetic analyses suggest that the  mcy  genes of  M. aeruginosa  are subdivided into two cryptic clades, consistent with the phylogeny determined by MLST. Population genetic analyses suggest that these two clades have primarily been maintained as a result of homology-dependent recombination and neutral genetic drift.

bmc evolutionary biology

Recombination, cryptic clades and neutral molecular divergence of the microcystin synthetase (mcy) genes of toxic cyanobacterium Microcystis aeruginosa