Hundreds of new genome sequences fill gaps in the fruit fly tree of life

Fruit flies are classic model organisms in biological research and were among the first species to have their entire genome sequenced. With more than 4,400 species, the diversity of the fruit fly family could provide insight into evolutionary patterns and processes. But only a fraction of these species have had their genomes sequenced, and most published fruit fly genome sequences are from a very limited set of species with representative inbred laboratory strains.

To address this, researchers sequenced the genomes of 179 fly species from the Drosophilidae family, including wild-caught flies, preserved museum specimens and laboratory-reared species. Using a hybrid sequencing approach that combines the latest short- and long-read sequencing technologies, they were able to produce low-cost, high-quality genome sequences from limited material. They used the new genome sequences and previously published data to produce a phylogenetic tree for 360 species from the Drosophilidae family, refining our understanding of the evolutionary relationships of these species. They also aligned nearly 300 fruit fly genomes as an open source tool for future comparative genomics research, such as a whole-genome alignment.

While large-scale sequencing efforts for larger organisms such as mammals are well underway, this study shows that genome sequencing for small organisms such as individual flies – even those kept in museums for up to twenty years – is now possible.

The authors add: “It is now entirely possible to think about assembling genomes for hundreds or thousands of species, even with the research budget of a single laboratory. This kind of large-scale sampling at the clade level will give us an unprecedented level of resolution for studying the genome sequences of diverse groups such as fruit flies and beyond, which will certainly improve our understanding of the evolutionary process.”