Hugo Volkaert, Center for Agricultural Biotechnology Kasetsart University
14 April 2008
Lateral gene transfer is an intriguing phenomenon. The fungal isolate studied in this report is apparently a mixture of hyphae derived from two species, and seems not to behave like either species. If the observations about the number of nuclei in the cells and the pathogenicity tests tell us anything, it is that something is going on... but what?
Arguments are presented to show evidence of possible LGT.
However, in the case presented in this study, it cannot be ruled out that PCR recombination is responsible for the observation that some sequences apparently have one part derived from one species and the other part from the other species. Though (one of) the primers may be highly specific for either species, the intervening sequence (5.8S rRNA) is not. As a result, using only one T. cucumeris specific primer, incompletely amplified fragments of the T. cucumeris DNA, containing (part of ) the 5.8S region could easily anneal to the apparently more common DNA of C. oryzae-sativae and in a following round of DNA polymerase activity result in a chimaeric fragment. That is probably why a high proportion of apparent chimeric fragments appear when a T. cucumeris specific primer is used. When the C. oryzae-sativae primer is used, many more cloned fragments are obtained (500 vs 66) indicating much more efficient PCR amplification (because of more C. oryzae-sativae DNA?) and only one appears to be a chimaera.
Since the obtained clones were only tested by PCR amplification for the presence of different species specific primers, it cannot be unambiguously stated that they are the result of LGT, or PCR recombination.
Several authors have reported PCR recombinants when amplifying from heterogeneous DNA mixes (such as interspecific hybrid plants).
see e. g. Meyerhans A, et al. 1990 DNA recombination during PCR. NAR18:1687–1691
Bradley RD, Hillis DM. 1997 Recombinant DNA sequences generated by PCR amplification. MBE14:592–593
Cronn et al., 2002 PCR-mediated recombination in amplification products derived from polyploid cotton. TAG104: 482-489
Horizontal gene transfer or PCR recombination?
14 April 2008
Lateral gene transfer is an intriguing phenomenon. The fungal isolate studied in this report is apparently a mixture of hyphae derived from two species, and seems not to behave like either species. If the observations about the number of nuclei in the cells and the pathogenicity tests tell us anything, it is that something is going on... but what?
Arguments are presented to show evidence of possible LGT.
However, in the case presented in this study, it cannot be ruled out that PCR recombination is responsible for the observation that some sequences apparently have one part derived from one species and the other part from the other species. Though (one of) the primers may be highly specific for either species, the intervening sequence (5.8S rRNA) is not. As a result, using only one T. cucumeris specific primer, incompletely amplified fragments of the T. cucumeris DNA, containing (part of ) the 5.8S region could easily anneal to the apparently more common DNA of C. oryzae-sativae and in a following round of DNA polymerase activity result in a chimaeric fragment. That is probably why a high proportion of apparent chimeric fragments appear when a T. cucumeris specific primer is used. When the C. oryzae-sativae primer is used, many more cloned fragments are obtained (500 vs 66) indicating much more efficient PCR amplification (because of more C. oryzae-sativae DNA?) and only one appears to be a chimaera.
Since the obtained clones were only tested by PCR amplification for the presence of different species specific primers, it cannot be unambiguously stated that they are the result of LGT, or PCR recombination.
Several authors have reported PCR recombinants when amplifying from heterogeneous DNA mixes (such as interspecific hybrid plants).
see e. g. Meyerhans A, et al. 1990 DNA recombination during PCR. NAR18:1687–1691
Bradley RD, Hillis DM. 1997 Recombinant DNA sequences generated by PCR amplification. MBE14:592–593
Cronn et al., 2002 PCR-mediated recombination in amplification products derived from polyploid cotton. TAG104: 482-489
Competing interests
none