We're going to learn a lot more about how bats do all of the things they do, in part due to the work of the Bat1K consortium to sequence the genome of six widely divergent living bat species.

Other bat genomes have been published but these genomes are 10 times more complete than any published to date.

Most relevant during the SARS-CoV-2 virus and the COVID-19 it brought in humans is showing evolution through gene expansion and loss in a family of genes, APOBEC3, which is known to play an important role in immunity to viruses in other mammals. The details in the paper that explain this evolution set the groundwork for investigating how these genetic changes, found in bats but not in other mammals, could help prevent the worst outcomes of viral diseases in other mammals, including humans.

Phyllostomus discolor, the pale spear-nosed bat. Credit: Brock and Sherri Fenton

To generate the bat genomes, the team used the newest technologies of the DRESDEN-concept Genome Center, a shared technology resource in Dresden, Germany to sequence the bat's DNA, and generated new methods to assemble these pieces into the correct order and to identify the genes present. While previous efforts had identified genes with the potential to influence the unique biology of bats, uncovering how gene duplications contributed to this unique biology was complicated by incomplete genomes.

The team compared these bat genomes against 42 other mammals to address the unresolved question of where bats are located within the mammalian tree of life. Using novel phylogenetic methods and comprehensive molecular data sets, the team found the strongest support for bats being most closely related to a group called Fereuungulata that consists of carnivorans (which includes dogs, cats and seals, among other species), pangolins, whales and ungulates (hooved mammals).

To uncover genomic changes that contribute to the unique adaptations found in bats, the team systematically searched for gene differences between bats and other mammals, identifying regions of the genome that have evolved differently in bats and the loss and gain of genes that may drive bats' unique traits.

The researchers found evidence the exquisite genomes revealed "fossilized viruses," evidence of surviving past viral infections, and showed that bat genomes contained a higher diversity of these viral remnants than other species providing a genomic record of ancient historical interaction with viral infections. The genomes also revealed the signatures of many other genetic elements besides ancient viral insertions, including 'jumping genes' or transposable elements.