All Articles Projects Research

The Bat1K genome sequencing initiative

bat 1k project research genome

Prof. Emma Teeling and Dr. Nicole Foley introduce the Bat1K Project…

Just imagine. You’ve sequenced an animal’s genome. And within that genetic code lies the potential to uncover the secret of longer health-spans, flight, echolocation and disease resistance. It might not be as far fetched an idea as you could imagine. In fact, it might even be flying around your head at night.

Bats, amazing adaptations
One in every five living mammals is a bat. With an almost worldwide distribution (absent only at the poles), you can turn to face the night sky and be in with a chance of seeing one of more than 1,300 species of bat. Bats are extraordinary given their unique and peculiar adaptations. They are the only mammal capable of true powered flight and perceive the world very differently to us. Using laryngeal echolocation and ultrasound hearing, bats can orient in complete darkness, find their food and can even use it to help choose mates. Bats also possess an amazing immune system, despite being suspected reservoir species for deadly viruses with huge human health implications (e.g. Rabies, SARS, MERS, Ebola etc), bats do not show any outward declines in fitness, or indeed mass mortality, on infection, as seen in humans. Bats are also exceptionally long lived given their small size and high metabolic rate. In fact, in relation to body size, only 19 species of mammal are longer lived than humans,18 of these species are bats, living up to 10 times longer than expected given their small size and high metabolic rate. Most importantly, bats show negligible signs of senescence and age associated diseases are rarely reported in these taxa. Intriguingly, cancer, one of the best documented age-associated diseases in humans, is rarely reported in bat species. From a behavioural perspective bats are also unusual, using a wide diversity of social systems that encompasses solitary species, species forming harem structures and those which form the largest colonies of mammals known – Tadarida often roosting in caves containing up to 20 million individuals. Bats have evolved to thrive in diverse ecological niches and extant taxa now exhibit feeding specialisations on insects, blood, fruit, nectar, pollen and even species of small vertebrates including fish, birds, reptiles and amphibians. In tropical regions, bats provide important ecosystem services through their consumption of mosquitoes, feeding on various agricultural pests, seed dispersal and pollination. In the US alone, bats save the agricultural economy $3bn dollars that would otherwise be spent on pesticides. Forget Batman, bats are the real superheroes!

Threats
Despite their almost global distribution, diversity of unique adaptations and array of ecological services, 15% of all bat species are currently classified as threatened by the IUCN, with a further 105 species awaiting formal classification. Conservation threats to bats come in many guises. Perhaps the best known in recent times is White Nose Syndrome (WNS). An increase in arousals during hibernation, due to the external growth on wing, face and nose of a fungus called Pseudogymnoacsus destructans, the causative agent of WNS, has caused mass mortality of bats in the US. In contrast, P. destructans is found over large areas of continental Europe but the same mass mortality is not observed in European populations, suggestive of immunological resistance? In recent years, mass mortality is also reported at wind farm sites where bats have died in large numbers from collisions with turbines. While together, these two factors represent the leading cause of mortality in bats a host of other factors including light pollution and climate change have been shown to negatively impact bats. Given the huge array of adaptations exhibited by bats and the challenges facing the conservation of bat populations around the world, there is an urgent need to greatly expand our understanding of these magnificent mammals. Furthermore, advancing our understanding of the molecular basis of bats’ amazing adaptations will yield novel insights and solutions to the most urgent problems facing human populations.

Figure 1| Molecular phylogenetic tree for all bat families and their estimated times of divergence. Species for which genome data is currently available the National Centre for Biotechnology Information (NCBI) database. Bat illustrations by Fiona Reid. Taken from Teeling et al 2017.

Novel solutions to human problems?
The biggest challenges facing humanity in the next century are biological. Chief among these challenges will be improving the well-being of our large and rapidly ageing human populations, preventing the spread of emergent infectious diseases, maintaining agricultural productivity and restoring natural ecosystems worldwide. With their exceptional longevity, amazing immunity, diverse range of ecosystem services and their conservation status being impacted by habitat loss, studying bats will enable us to address all of these challenges, as many of their biological features mirror humans and their ecological roles both contribute to and prevent the spread of infectious diseases and structure functional ecosystems today and into the future.

Bat1K sequencing initiative
Despite the profound advantages to be gained from studying bats, many of the adaptations and unique characteristics of bats described above are not yet fully understood. In part, this is due to a relative lack of genome data for bats, relative to other species. In fact, of ~1,300 currently known bat species, only 14 species of bat have readily available genome assemblies in NCBI (Figure 1). The first bat genome to be sequenced was that of Myotis lucifugus which was sequenced using Sanger Chemistry by the Broad Institute in 2011 and to date this species has been the chiropteran representative in the vast majority of comparative mammalian studies conducted. The remaining bat genome assemblies vary greatly in quality and completeness, and so far, these factors have impeded biologists in fully understanding bats’ uniquely evolved traits.

To deliver the promise and potential of gleaning evolutionary solutions from bats’ genome, Bat1K was established, comprising a global effort to sequence and annotate chromosome-level genome assemblies of all living bat species. The main goal of this consortium is to uncover the genes and genetic mechanisms behind the unusual adaptations of bats, essentially mine the bat genome to uncover their secrets. Using the newest of genetic tools, Bat1K will deep sequence the blue print and genetic code of every species of bat in the world. It took over 13 years and $3 billion US dollars to sequence the first human genome and given the great advances in the field, it is now much faster and cheaper. The publication of the Bat1K White paper in Annual Reviews of Animal Biosciences set out to provide information to the scientific community about the Bat1K effort; to encourage participation; to set standards for tissue collection and vouchering, assembly quality and data release; and to outline the major research endeavours that we anticipate will benefit from Bat1K.

Building a consortium
At the time of the white paper publication, the Bat1K consortium had >148 members. Central to the success of Bat1K is wide involvement from bat researchers and enthusiasts across diverse research areas and interests. Indeed, this project is only possible through the mobilisation of bat researchers, volunteers, students and bat lovers around the globe; it is only by using this approach that we will be able to identify and locate all species of bat, so that we can uncover the secrets that lie within their genetic code. Essentially, Bat1K will form an active vibrant community of individuals united by a common drive to conserve, better understand and promote bats. To facilitate wide-ranging participation, Bat1K launched the Bat1k website (http://bat1k.com/) to encourage and welcome every interested party to sign up as a member of the Bat1k consortium; from the person who simply enjoys watching bats on summer evening walks, grass-roots conservation organisations, field biologists, professional ecologists and bat researchers from every scientific discipline.

Figure 2 | Myotis myotis (Greater mouse-eared bat) in flight in a forest in North West France. The sequencing of this bats genome is currently underway as part of the Bat1k project. Photo courtesy of Olivier Farcy.

Tissue Collection: Quality Considerations
Given that historically some bat genomes sequenced to date have suffered from poor quality or a lack of completeness, one of the key goals of the Bat1k project is to produce bat genomes of the highest possible quality. That is a chromosome level assembly, however, even among all vertebrate genomes sequenced today, few have yet to be sequenced to this level. Given the ambitious quality standards set out for Bat1k genomes in the white paper, starting sample quality needs to be exquisite. To meet these rigorous quality standards, Bat1K have members of grass-roots conservation organisations, field biologists, professional ecologists and any other groups who maintain close proximity to bats on a regular basis over the course of their work. Once any organism dies, its DNA begins to degrade, shearing into ever smaller pieces, much like disassembling a jigsaw. Indeed, building a jigsaw could be likened to building a genome, where it’s much easier to put the jigsaw back together again if there are larger intact parts to reassemble. To maintain the highest DNA integrity possible samples should be frozen, ideally at around -200 degree celcius using liquid nitrogen, or frozen as soon and at as cold a temperature as possible as field conditions allow (see white paper for details).

This ambitious project is divided into three phases, (I) all bat families (n=21); (II) all genera (n~220); (III) remaining species (n~1000). Currently, appropriate tissue are pledged for all bat families and six pilot genomes are in the process of being seqeunced and assembled. Bat1K will produce high quality, chromosome-level genomes for hundreds of bat species and will make this data publicly available to everyone. This will be a “genomic ark” for all living bat species, which is essential to capture the legacy of our current natural heritage, moving into a uncertain future. Bats face a variety of global pressures that threaten populations with regional or global extinction. The IUCN (International Union for Conservation of Nature) Red List currently classifies 71 bat species as Critically Endangered or Endangered because of significant population declines from conservation threats. Lack of knowledge about bat species hampers our ability to assess population stability in many cases, and 201 bat species are considered ‘Data Deficient’ by the IUCN, meaning that their status cannot yet be determined. By sequencing to our proposed standard the genome of every living bat species, including those that are currently threatened and endangered, we can ascertain the genomic consequence of decreasing population size and whether there is an increase in deleterious mutations in smaller populations, which may drive future extinction events. This can direct future management plans in terms of conservation priority and could direct future genomic conservation interventions.

How to be involved
To become a member of the Bat1k consortium we would encourage you to sign up, in particular, if you have access to the high-quality samples needed at this phase of the project or indeed just to show your enthusiasm for bats and add your voice to the project.

To sign up as a member, simply go to Bat1k.com and click on the sign-up tab. On the short sign-up form you will then be asked for some basic contacts details. Immediately below this there are further questions for people who may be able to contribute specific expertise or facilitate access to tissue samples for particular species.

Regular updates on the projects progress are posted on the website and we can be found regularly tweeting about Bat1k and all things bats on twitter, @bat1kgenomes.

About the Authors: Prof. Emma Teeling established the Laboratory of Molecular Evolution and Mammalian Phylogenetics in 2005 and is the Founding Director of the Centre for Irish Bat Research at University College Dublin, Ireland. Here, she successfully leads a prolific, internationally renowned research team focused on studying the evolution and genomic basis of adaptation in bats and other mammals. She is listed in top 100 female Irish scientists and her TEDx talk has been viewed >5.8K times on YouTube. Prof. Teeling is the Co-Founder and Director of the Bat1K genome sequencing initiative.

Dr. Nicole Foley is a recent graduate of the Teeling lab where she combined field biology, molecular techniques and bioinformatics to address a diversity of questions relating to the taxonomy, phylogenetics and exceptional longevity of bats. She is currently a Post Doctoral Researcher at Texas Tech University, USA where she is using next generation sequencing data to understand the molecular mechanisms underpinning bats’ amazing adaptations.

Leave a Comment