Monumental project underway to sequence the genome of all complex species on Earth

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the Terrestrial Biogenome Project, a global consortium that aims to sequence the genomes of all complex life on earth (some 1.8 million described species) in ten years, is gaining momentum.

Projects Origins, goals and progress are detailed in two multi-author articles published to January 18, 2022. When complete, it will forever change the way biological research is done.

Concretely, researchers will no longer be limited to a few “model species” and will be able to exploit the DNA database of sequences of any organism with characteristics of interest. This new information will help us understand how complex life has evolved, how it functions and how biodiversity can be protected.

The project was first offers in 2016, and I had the privilege of speaking to his launch in London in 2018. It is currently moving from its start-up phase to full-scale production.

The objective of the first phase is to sequence a genome of each taxonomic family on earth, some 9,400 of them. By the end of 2022, a third of these species should be done. Phase two will see the sequencing of one representative of all 180,000 genera, and phase three will mark the completion of all species.

Genetic DNA Sequence

DNA sequence.

The importance of strange species

The overarching goal of the Earth Biogenome Project is to sequence the genomes of the 1.8 million described species of complex life on Earth. This includes all plants, animals, fungi, and single-celled organisms with true nuclei (i.e. all “eukaryotes”).

While model organisms like mice, rock cress, fruit flies and nematodes have been extremely important in our understanding of gene functions, it is a huge advantage to be able to study other species that can function a little differently.

Many important biological principles have evolved from the study of obscure organisms. For example, genes were discovered by Gregor Mendel in peas, and the rules that govern them were discovered in red bread mold.

DNA was first discovered in salmon sperm, and our knowledge of some of the systems that keep it safe comes from research on tardigrades. Chromosomes were first observed in mealworms and sex chromosomes in a beetle (the action and evolution of sex chromosomes has also been explored in fish and platypus). And telomeres, which cap the ends of chromosomes, have been discovered in pond scum.

Responding to biological questions and protecting biodiversity

Comparing near and distant species offers tremendous power to discover what genes do and how they are regulated. For example, in another PNAS article, coincidentally also published on January 18, my colleagues at the University of Canberra and I found that Australian dragon lizards regulated sex by the chromosomal neighborhood of a sex gene, rather than the DNA sequence itself.

Scientists also use species comparisons to trace genes and regulatory systems back to their evolutionary origins, which can reveal startling conservation of gene function over nearly a billion years. For example, the same genes are involved in retinal development in humans and in Drosophila photoreceptors. And the mutated BRCA1 gene in breast cancer is responsible for repairing DNA breaks in plants and animals.

The genome of animals is also much more conserved than previously thought. For example, several colleagues and I recently demonstrated that animal chromosomes are 684 million years old.

It will also be exciting to explore the “dark matter” of the genome and reveal how DNA sequences that do not code for proteins may still play a role in the functioning and evolution of the genome.

Another important focus of the Earth Biogenome project is conservation genomics. This field uses DNA sequencing to identify endangered species, which comprise approximately 28% of the world’s complex organisms, which helps us monitor their genetic health and advise on their management.

It’s no longer an impossible task

Until recently, sequencing large genomes took years and millions of dollars. But there have been huge technical advances that now make it possible to sequence and assemble large genomes for a few thousand dollars. The entire Earth Biogenome Project will cost less in today’s dollars than the Human Genome Project, which was worth about $3 billion in total.

In the past, researchers had to chemically identify the order of the four bases on millions of tiny DNA fragments and then piece together the entire sequence. Today, they can register different bases based on their physical properties or by binding each of the four bases to a different dye. New sequencing methods can scan long DNA molecules that are tied up in tiny tubes or squeezed through tiny holes in a membrane.

Illustration of chromosomal DNA

Chromosomes are made up of long double helix arrays of the four base pairs whose sequence specifies the genes. DNA molecules are capped at their ends by telomeres.

Why sequence everything?

But why not save time and money by sequencing only the main representative species?

Well, the whole point of the Earth Biogenome project is to exploit the variation between species to make comparisons, and also to capturing remarkable innovations in the outliers.

There is also the fear of missing out. For example, if we only sequence 69,999 of the 70,000 species of nematodes, we risk missing the one that could unlock the secrets of how nematodes can cause disease in animals and plants.

Currently, 44 affiliated institutions in 22 countries are working on the Earth Biogenome project. There are also 49 affiliated projects, including huge projects such as the California Conservation Genomics Project, the Bird 10,000 Genomes Project and UK Darwin’s tree of life Project, as well as numerous projects on particular groups such as bats and butterflies.

Written by Jenny Graves, Emeritus Professor of Genetics and Fellow Vice-Chancellor, La Trobe University.

This article was first published in The conversation.The conversation

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