The Complexities and Nuances of Analyzing the Genome of and Its Endosymbiont.

In "Retrotransposons Are the Major Contributors to the Expansion of the Muller F Element," Leung (2017) improved contigs attributed to the Muller F element from the original CAF1 assembly, and used them to conclude that most of the sequence expansion of the fourth chromosome of is due to a higher transposon load than previously thought, but is not due to DNA integrations. While we do not disagree with the first conclusion, the authors base their second conclusion on the lack of homology detected between their improved CAF1 genome assembly attributed to and reference genomes. While the consensus CAF1 genome assembly lacks any sequence similarity to the reference genome of the endosymbiont of (Mel), numerous studies from multiple laboratories provide experimental support for a large lateral/horizontal gene transfer (LGT) of a genome into this line. As such, we strongly suspect that the original whole genome assembly was either constructed after the removal of all reads, or that sequences were directly removed from the contigs in the CAF1 assembly. Hence, Leung (2017) could not have identified the LGT using the CAF1 assembly. This manuscript by Leung (2017) highlights that an assembly of the sequence reads and their mate pairs was erroneously attributed solely to the endosymbiont, albeit before we understood the extent of LGT in As such, we recommend that the sequences deposited at the National Center for Biotechnology Information (NCBI) under PRJNA13365 should not be attributed to endosymbiont of , but should have their taxonomy reclassified by NCBI as "Unclassified sequences." As our knowledge about genome biology improves, we need to reconsider and reanalyze earlier genomes removing the prejudice introduced from now defunct paradigms.