The Complexities and Nuances of Analyzing the Genome of Drosophila ananassae and Its Wolbachia Endosymbiont

G3 : Genes - Genomes - Genetics
Julie C Dunning Hotopp, Lisa Klasson

Abstract

In "Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element," Leung et al. (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 D. ananassae is due to a higher transposon load than previously thought, but is not due to Wolbachia 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 D. ananassae and reference Wolbachia genomes. While the consensus CAF1 genome assembly lacks any sequence similarity to the reference genome of the Wolbachia endosymbiont of Drosophila melanogaster (wMel), numerous studies from multiple laboratories provide experimental support for a large lateral/horizontal gene transfer (LGT) of a Wolbachia genome into this D. ananassae line. As such, we strongly suspect that the original whole genome assembly was either constructed after the removal of all Wolbachia reads, or that Wolbachia sequences were directly removed from the contigs in the CAF1 assembly. Hence, Leung et al. (2017) could ...Continue Reading

References

Mar 19, 2005·Genome Biology·Steven L SalzbergWilliam C Nelson
Nov 13, 2007·Nature·UNKNOWN Drosophila 12 Genomes ConsortiumIain MacCallum
Dec 7, 2007·Bioinformatics·Aleksey V ZiminJames A Yorke
Mar 25, 2009·Proceedings of the National Academy of Sciences of the United States of America·Lisa KlassonSiv G E Andersson
Dec 17, 2014·BMC Genomics·Lisa KlassonJulie C Dunning Hotopp
Jul 2, 2017·G3 : Genes - Genomes - Genetics·Wilson LeungSarah C R Elgin

❮ Previous
Next ❯

Citations

Oct 28, 2019·Microbiology Resource Announcements·Mark T GasserJulie C Dunning Hotopp
Apr 13, 2019·Scientific Reports·Emilie LefoulonBarton E Slatko
Mar 27, 2021·G3 : Genes - Genomes - Genetics·Eric S TvedteJulie C Dunning Hotopp

❮ Previous
Next ❯

Datasets Mentioned

BETA
PRJNA13365

Related Concepts

Related Feeds

Bioinformatics in Biomedicine

Bioinformatics in biomedicine incorporates computer science, biology, chemistry, medicine, mathematics and statistics. Discover the latest research on bioinformatics in biomedicine here.