2023-10-09 23:48:07
“Trying to understand how species are related during evolution, and how their genome has evolved, is a major challenge for biology in the decades to come. »
You are a biologist specializing in evolutionary genomics. What does your current research consist of and how does it fit into contemporary issues in your discipline?
Hugues Roest Crollius : The genome of an individual, that is to say the DNA contained in its cells, is inherited from a long evolutionary lineage which goes back to the origin of life more than 3.7 billion years ago of years. It is this history, on the scale of the evolution of the genomes of vertebrate animals in particular, that we are trying to reconstruct. To do this, we are attempting to computationally reconstruct the genomes of ancestral species, whose DNA is no longer available to be sequenced, which existed millions of years ago, in order to document these intermediate states of evolutionary history. some change.
Today, numerous national and international research programs aim to sequence the genomes of tens of thousands of species. Trying to understand how these are linked during evolution, and how their genome evolved, is a major challenge for biology in the decades to come.
CNRS research director, you are also the scientific manager of the bioinformatics platform of the Computational Biology Center of the ENS Institute of Biology (IBENS). What does this entity consist of and what is exceptional regarding it?
Hugues Roest Crollius : It is above all a scientific computing platform dedicated to biology, open primarily to the laboratories which initially contributed to setting it up: theInstitute of Biology of the ENS-PSL (GOING), le Interdisciplinary Center for Research in Biology (CIRB) of the Collège de France and a CNRS unit of theESPCI-PSL.
Following the idea of Auguste Genovesio who was its first director, this platform is shared, that is to say that the research teams who install computers purchased with their own funds have free computing hours. , while the others pay an annual contribution relating to their use of it. As a result, we now have a high-performance “computing cluster” with more than 4,000 nodes and 18 terabytes of memory. A bioinformatics engineer trains users when they are beginners, helps them launch their calculations, carries out part of the maintenance of the machines and monitors that everything goes well. A management unit meets monthly to establish the strategy, arbitrate expenses, and think regarding the future. Because computing platforms of this type are destined to be concentrated more and more in regional “computer centers”, and we must anticipate these changes.
Who can access the resources of this platform?
Hugues Roest Crollius : The calculations that we carry out in biology are quite different from those carried out in physics or mathematics. We work a lot with software developed by the international community and freely shared, of which more than 200 are installed on the cluster. The platform is open to all biologists from the 3 founding institutes, but we also open it to other ENS-PSL laboratories for which it makes sense, such as those of department of cognitive studies.
You have used this platform in particular to carry out work on the early diversification of teleost fish. A few months ago, these were the subject of a publication in the prestigious scientific journal Science (1). How does this research constitute a major advance for the phylogenomic community and the evolutionary history of fish?
Hugues Roest Crollius : Teleosts include 99.8% of fish species, or 30,000 different identified species, which represent half of all vertebrate species. These fish are grouped into three large families: the group which includes the eels, the group which includes the so-called “bony tongue” fish, including the arapaima from South America, and finally the large group of clupeocephali, which includes all other species.
For more than 50 years, debates between paleontologists and evolutionary biologists have raged over the order in which these three groups appeared. This is one of the oldest enigmas in evolution, which molecular phylogeny has so far failed to resolve. In this article, we present an answer to this question, strongly supported by multiple and independent evolutionary evidence. All our results converge towards an unexpected evolutionary scenario that resolves the topology of the first branches of the fish tree of life.
For this work, you used bioinformatics methods developed in your research group. What is new regarding them and how do they allow for a more conclusive analysis?
Hugues Roest Crollius : This breakthrough was made possible by two major advances. First of all, our colleagues at INRAE in Rennes and Toulouse sequenced the genomes of seven fish from the eel group, little known until now. Second, in the laboratory, we implemented for the first time methods that use the structure of the genome, such as the order of genes on chromosomes, the organization of chromosomes… and not the sequence of genes, as an evolutionary trait. The idea that genomic structures might be used to answer difficult questions regarding evolution generated much enthusiasm, and has since been adopted by other studies of similar questions.
“I am convinced that this dynamic between researchers from different generations is one of the keys to tackling difficult problems in science. »
Among the co-signatories of this scientific publication are two young researchers, trained with you at the ENS: Elise Parey, first author and Camille Berthelot. What are the benefits of such an intergenerational scientific dynamic?
Hugues Roest Crollius : Élise Parey carried out her thesis in my research team, in co-supervision with Camille Berthelot, who had also already completed her thesis in the laboratory a few years ago and who then joined it as a researcher. They are both extraordinary scientists. Together and with other lab members and collaborators, we did some other nice work before this article in Science. I am very proud of what they accomplished, and I was very fortunate to welcome them to my research team.
They are now pursuing their careers, Élise Parey as a post-doctoral researcher in London and Camille Berthelot as team leader at the Pasteur Institute. I’m sure they will be talked regarding in the near future. I am convinced that this dynamic between researchers from different generations is one of the keys to tackling difficult problems in science.
As a CNRS research director, what do you get from working at the École normale supérieure?
Hugues Roest Crollius : The Institute of Biology of the ENS (IBENS) where I work is closely linked to the Department of Biology of the ENS where bachelor’s and master’s courses are taught. It’s this symbiosis that I find really crucial. Through the lessons that researchers can provide, we are led to constantly test and update our own knowledge. We have the opportunity to transmit knowledge to very motivated students and sometimes, we have the chance to transmit to them the passion for our subjects of study and to welcome them into our laboratories. IBENS is also a very friendly place, rich in many disciplines in biology, very well equipped, where it is good to do research!
What advice might you give to any young person wishing to enter your fields?
Hugues Roest Crollius : First of all, to have a natural curiosity for biological phenomena, and an interest in evolution as a lever to answer the questions that arise. Then, given the mass and considerable complexity of the data that we manipulate, we must acquire know-how, or have an appetite for IT tools, and a little in statistics. But if I come back to my own career, you must already choose your master’s courses carefully, do several if you can, test different subjects, because being passionate regarding a question, a theme, is an inexhaustible but essential driving force to lead the life of a researcher.
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Bibliography
(1) Genome structures resolve the early diversification of teleost fishes, Parey E., Louis A., Montfort J. et al. (2023), Science, 9 février 2023 – Vol 379, Issue 6632, pp. 572-575
DOI: 10.1126/science.abq4257
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