It's time to sequence everything

What can we gain by collecting the genomes of every animal, plant, fungi and protozoa species on the planet?

 
Insects are by far the most diverse animal group, with more than a million known species.   Barta IV/Flickr  (CC BY 2.0)

Insects are by far the most diverse animal group, with more than a million known species. Barta IV/Flickr (CC BY 2.0)

 

Biology is about to make a fundamental leap in the understanding of life on earth. The Earth BioGenome Project, officially launched in November 2018, aims to sequence the genome of every known eukaryotic species on the planet. The project is expected to cost US$4.7 billion over the next 10 years, which is similar to the US$5 billion price tag, adjusted for inflation, of the Human Genome Project, which finished in 2003. This monumental effort will involve a large number of research institutions around the world, from Brazil to Australia and the UK to the US.

There are currently about 1.5 million eukaryotic species described, and the Earth BioGenome Project aims to sequence them all. Eukaryotic species are those that have their DNA enclosed inside a nucleus, which includes animals, plants, fungi and protozoa. Currently, there are about 3,500 eukaryotic genomes available on major platforms for download, which represent less than 0.2% of known species. To date, the study of genetics has given us an incredible wealth of information about how all life is related, and how different species have undergone evolution over time, but this work is far from complete. New species, such as the Type D killer whales, are constantly being discovered. By rough estimates, there are potentially 10-20 million undiscovered eukaryotic species, many of which can only be identified based on subtle differences at the genetic level.

 
Conniff's shrub frog , Pseudophilautus conniffae,  was only identified as a distinct species in 2019.   Batuwita, De Silva, and Udugampala (2019)/Wikimedia Commons  (CC BY 4.0)

Conniff's shrub frog, Pseudophilautus conniffae, was only identified as a distinct species in 2019. Batuwita, De Silva, and Udugampala (2019)/Wikimedia Commons (CC BY 4.0)

 

There are several reasons why now is the time to do this. First and foremost, the technology has improved to the point where such a lofty goal is within reach. There will still need to be some improvements to the methods and technology involved, but these changes are already underway. In January, the Wellcome Sanger Institute and Pacific Biosystems produced the first reference level genome for the Aedes aegypti mosquito. Typically, these reference genomes are created by cultivating large numbers of insects and inbreeding them to create effective clones, producing a host of individuals with similar enough genomes that any differences are negligible. Although this method has previously produced valuable data, it is not realistic for a project of this size; capturing and breeding every insect on the planet would be a very large task.

However, this study pioneered a new protocol that decreased the amount of DNA needed for accurate sequencing. Having a method that allows single wild-captured individuals to be used for the creation of new genomes is invaluable. Although this change is relatively small, it will mean a lot for sequencing the genomes of small animals, such as mosquitoes and flies.

 
New protocols make it quicker and less expensive to sequence insect genomes.   Muhammad Mahdi Karim/Wikimedia Commons  (GNU 1.2)

New protocols make it quicker and less expensive to sequence insect genomes. Muhammad Mahdi Karim/Wikimedia Commons (GNU 1.2)

 

Another reason for pursuing the Earth BioGenome Project now is that we are currently amid what is being called the sixth mass extinction event. Some estimates suggest that 50% of the species on earth will be extinct by 2050. This project, therefore, will represent a slice in time of the biodiversity on this planet. Even if we can’t keep all these species from going extinct, we would still hold genomic information that could potentially allow us to resurrect them in the future, similar to what is being attempted with the woolly mammoth.

Aside from starting up Jurassic Park in real life, having a clear view of biodiversity will create data-driven plans for conservation. A global genomic database would allow projects like the Forest Global Earth Observatory, a network of sites and scientists that study forest function and diversity, to more accurately track biodiversity and changes in species abundance. This would help us better understand how the environment is changing due to climate change and other human impacts.

The ever-growing human population is modifying our planet like nothing else has in the past; there is an increased need for food and for more efficient ways to produce it. Having the genomes of every plant on earth — not just those that are important to agriculture — will give insight into ways to improve crop yields and disease resistance. Researchers may even identify new crops that could be grown for future generations.

 
An extensive library of plant genomes may help us identify new crops to sustain the growing human population .  3268zauber/Wikimedia Commons  (CC BY-SA 3.0)

An extensive library of plant genomes may help us identify new crops to sustain the growing human population. 3268zauber/Wikimedia Commons (CC BY-SA 3.0)

 

One of the overlooked benefits of this kind of work is the potential for new pharmaceuticals. The vast majority of our modern drugs are sourced from nature; even if they are synthetically produced now, the blueprint was most likely copied from the wild. New pharmaceuticals could potentially be used not only to cure cancers but also to stave off the oncoming issue of antibiotic resistance.

Perhaps the most exciting aspect of this project is that it may give us a clearer understanding of evolution itself. The fundamental level at which evolution acts is in genetics, and having genomic information for every species would help us understand the evolutionary process and allow for more a robust tree of life. It is impossible to know how a more thorough understanding of evolution will affect our understanding of life.

This project, expected to be completed in 10 years, will generate an entirely new view of biology and the process of evolution. The history of life is intricate, and will require serious and thorough work to fully understand, but the rewards for doing so will be great. From the small insights we have gained since 1977, when we first learnt how to read genomes, our world has become much richer and our appreciation for the complexity of life has grown deeper. The wealth of information gained through this endeavour will not only benefit humanity but will also influence how we interact with all other life on earth.

Edited by Andrew Katsis