For the first time, the raw genetic material that codes for bats’ unique adaptations and superpowers, such as the ability to fly, to use sound to move effortlessly in complete darkness, to survive and tolerate deadly diseases and to resist ageing and cancer, has been fully revealed and published in Nature.
Bat1K, a global consortium of scientists led by Dr Sonja Vernes and Professor Emma Tealing dedicated to sequencing the genomes of every one of the 1421 living bat species has generated and analysed six highly accurate bat genomes that are ten times more complete than any bat genome published to date, in order to begin to uncover bats’ unique traits.
Senior author Dr Sonja Vernes, Co-Founding Director of Bat1K, Max Planck Research Group Leader at the Max Planck Institute for Psycholinguistics and recently appointed UKRI Fellow at St Andrews, said: “These are the first reference-quality genomes for bats. Having such complete and well annotated genomes allowed us unprecedented insight into the genetic and evolutionary abilities seen in bats.”
Professor Emma Teeling, University College Dublin, Co-Founding Director of Bat1K and senior author, added: “Given these exquisite bat genomes, we can now better understand how bats tolerate viruses, slow down ageing, and have evolved flight and echolocation. These genomes are the tools needed to identify the genetic solutions evolved in bats that ultimately could be harnessed to alleviate human ageing and disease.”
To generate these bat genomes, the team used new technologies to sequence the bat’s DNA and developed new methods to assemble these pieces into the correct order and to identify the genes present.
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 Ferreuungulata that consists of carnivores (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 team also found evidence that bats’ ability to tolerate viruses is reflected in their genomes. The exquisite genomes revealed “fossilised viruses”, evidence of surviving past viral infections, and showed that bat genomes contained a higher diversity than other species providing a genomic record of historical tolerance to viral infection.
Given the quality of the bat genomes, the team uniquely identified and experimentally validated several non-coding regulatory regions that may govern bats’ key evolutionary innovations.
These latest findings mark only the beginning of the team’s work. The remaining ~1400 living bat species exhibit an incredible diversity in ecology, longevity, sensory perception and immunology, and numerous questions still remain regarding the genomic basis of these spectacular features. Bat1K aims to answer these questions as more and more bat genomes are sequenced, further uncovering the genetic basis of bats’ rare and wonderful superpowers.
Professor Eugene Myers, Director of the Max Planck Institute of Molecular Cell Biology and Genetics and the Center for Systems Biology in Dresden, Germany, and senior author, said: “Using the latest DNA sequencing technologies and new computing methods for such data, we have 96 to 99% of each bat genome in chromosome level reconstructions – an unprecedented quality akin to, for example, the current human genome reference which is the result of over a decade of intensive ‘finishing’ efforts.
“As such, these bat genomes provide a superb foundation for experimentation and evolutionary studies of bats’ fascinating abilities and physiological properties.”
Dr Michael Hiller, Max Planck Research Group Leader at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, Max Planck Institute for the Physics of Complex Systems, the Center for Systems Biology, Dresden, and senior author said: “Our genome scans revealed changes in hearing genes that may contribute to echolocation, which bats use to hunt and navigate in complete darkness.
“Furthermore, we found expansions of anti-viral genes, unique selection on immune genes, and loss of genes involved in inflammation in bats. These changes may contribute to bats’ exceptional immunity and points to their tolerance of coronaviruses.”
This study was funded in part by the Max Planck Society, the European Research Council, the Irish Research Council, and the Human Frontier Science Program, NSF.
Dr Vernes is to lead a £1.5m seven-year study at the University of St Andrews on the way bats communicate to shed light on the evolution of human language.
The funding, announced by the UKRI Future Leaders Fellowships scheme, will allow Dr Vernes to examine the vocalisations of bats and, by comparing them with other mammals, to understand more clearly the mechanisms by which human language has evolved.
The £1.5m grant will fund the first four years of the seven-year project, with further funding to follow.
Future Leaders Fellowships is a £900 million fund that is helping to establish the careers of world-class research and innovation leaders across UK business and academia.
The paper, Six reference-quality genomes reveal evolution of bat adaptation, by David Jebb, Zixia Huang, Martin Pippel, Graham M Hughes, Ksenia Lavrichenko, Paolo Devanna, Sylke Winkler, Lars S Jermiin, Emilia C Skirmuntt, Aris Katzourakis, Lucy Burkitt-Gray, David A Ray, Kevin A M Sullivan, Juliana G Roscito, Bogdan M Kirilenko, Liliana M Dávalos, Angelique P Corthals, Megan L Power, Gareth Jones, Roger D Ransome, Dina K N Dechmann, Andrea G Locatelli, Sébastien J Puechmaille, Olivier Fedrigo, Erich D Jarvis, Michael Hiller, Sonja C Vernes, Eugene W Myers & Emma C Teeling is published in Nature available online.
Issued by the University of St Andrews Communications Office.Research