Reply to Sasso et al.: Distribution and phylogeny of nonribosomal peptide and polyketide biosynthetic pathways in eukaryotes

We appreciate the complementary analysis and discussion presented by Sasso et al. (1) regarding our study (2). However, we would like to clarify a few issues that were raised in their letter (1).

There has been a huge explosion in the number of genome sequences available that make data mining studies possible. In our study, we aimed to systematically examine the distribution of nonribosomal peptide synthethase (NRPS) and type I polyketide synthase (PKS) biosynthetic gene clusters through the use of two genome mining tools (2). Complete genomes are usually sequenced to a much higher quality than partial genomes. They also have an intact gene repertoire that allows the identification of complete NRPS/PKS gene clusters. To obtain accurate and reliable information on the distribution of NRPS and type I PKS gene clusters, we used only complete genomes of bacteria, archaea, fungi, and protists (2). Incomplete plant and animal genomes were used because there were no complete plant and animal genomes available. Our analysis demonstrated the widespread distribution of NRPSs and PKSs across the three domains of life, even though we excluded a large amount of incomplete genomes in bacteria, archaea, and eukarya, including many fungal Basidiomycetes genomes (3). To reduce the potential false positives, we only counted the gene clusters identified by both software packages (2). Therefore, some NRPS and PKS enzymes identified by only one package were left out, including the 63-kb PKS gene described in ref. 1.

We admit analysis with partial genomes and alternative standards are necessary and useful. We also agree that the evidence obtained from incomplete genomes would support our conclusion (1). The absence of NRPSs and PKSs in basidiomycetes in figure 1 of ref. 2 and the 63-kb PKS gene in Chlorella variabilis are a reflection of our strict criteria in genome selection and analyzing and should not be interpreted as a misconstruction, given the clarified information in the Materials and Methods of ref. 2.

Sasso et al. (1) argue that we do not “provide sufficient evidence for horizontal gene transfer.” They claimed that we concluded “archaean and eukaryotic NRPSs and PKSs appeared to be acquired from bacteria via horizontal gene transfer.” In fact, we do not think there is enough evidence for horizontal gene transfer from our analysis (2).

The comments of Sasso et al. (1) strengthen our conclusion that NRPSs and PKSs have a widespread distribution (2). Our results can be further used by natural product chemists and other researchers for structure analysis and natural product discovery. The issues raised by Sasso et al. will be resolved once more complete and better-quality genomes, especially in eukaryotes, are released.