Genomic keys of origins of vertebrates revealed
The vertebrates, the animal group human species belong to, are extremely diverse and have colonized all ecosystems. Over the years, a debate was set on the changes in the genome of our ancestors that contributed to the successful evolution of vertebrates. Now, an international team of scientists, co-led by Spanish researchers from the Center for Genomic Regulation (CRG), the Spanish National Research Council (CSIC), and the French National Centre for Scientific Research (CNRS), has described the processes that enabled the diversity of functions and gene regulation during the transition from invertebrates to vertebrates. The study has been published in the scientific journal Nature and involves researchers and former researchers of the University of Barcelona (UB) and other research groups from twelve countries.
The vertebrates, the animal group human species belong to, are extremely diverse and have colonized all ecosystems. Over the years, a debate was set on the changes in the genome of our ancestors that contributed to the successful evolution of vertebrates. Now, an international team of scientists, co-led by Spanish researchers from the Center for Genomic Regulation (CRG), the Spanish National Research Council (CSIC), and the French National Centre for Scientific Research (CNRS), has described the processes that enabled the diversity of functions and gene regulation during the transition from invertebrates to vertebrates. The study has been published in the scientific journal Nature and involves researchers and former researchers of the University of Barcelona (UB) and other research groups from twelve countries.
The team of the UB, formed by researchers of the Biodiversity Research Institute (IRBio) and from the Evo-Devo-Genomics Group Ricard Albalat and Cristian Cañestro, and the Institute of Biomedicine of the UB (IBUB) Jordi Garcia-Fernàndez, Beatriz Albuixech, Carlos Herrera-Úbeda and Demián Bruguera, has taken part in the analysis of the non-coding DNA. “This analysis is a central part of the study to find gene regulation at the frontier between invertebrates and vertebrates”, says Jordi Garcia Fernández, professor at the Department of Genetics, Microbiology and Statistics of the UB. “Nowadays, -he continues- we know that knowing about genes is as important as understanding the way the genome works, and this is a regulatory DNA task. Also, understanding the way the genome works in evolution is essential to find out how it is altered in human diseases”.
Vertebrates share a unique set of gene regulation systems, which enables the stored information of our genome to produce many functions, and as a result, we have hundreds of specialized cells, tissues and organs. “We did a large analysis of genomic regulation in different species and we found two key differences. First, we saw that, generally speaking, our gene regulation is more complex than that of invertebrates. The second difference is that we have gene copies which were originally conducting general functions, but which have focused on specific functions in vertebrates, mainly in the brain” says Manuel Irimia, who also led the study and is head of the group at the Center for Genomic Regulation.
Scientists studied genomes from different species of vertebrates like zebra fish or the medaka, as well as frogs, chickens, mice and humans. However, in order to understand the origin of the mechanisms with genomic regulation that are common in vertebrates, they had to compare these with data from another related species with information on the evolution of the transition between invertebrates and vertebrates. Therefore, researchers sequenced the amphioxus genome and produced the necessary data to study the regulation of their genes. “Amphioxus is an organism used as a model in research since the 19th century. Its genome has evolved very slowly, without the whole duplications present in the vertebrates. For this reason, the amphioxus can serve as a reference in evolutionary comparisons to understand our lineage”, notes Héctor Escriva, who has also led the study and is a researcher at the Sorbonne University and CNRS in Banyuls-sur-Mer (France). The analysis of certain genic families that are important for the development -such as the Wnt family- made researchers qualify the amphioxus as “the conservative group in the chordates evolution, compared to the liberal group represented by urochordata, which have a high rate of evolutionary divergence”, conclude Ricard Albalat and Cristian Cañesterp, lecturers at the Department of Genetics, Microbiology and Statistics of the UB, and Ildiko SOmorjai, from the University of St Andrews (Scotland), the groups that took part in the analysis of the amphioxus genome.
The study Nature published does not only compare genomes but it also gathers epigenomic and genic expression data, and provides with unique information on the functional changes that have way to a larger complexity in vertebrates. The scientists saw that despite the regulation of the genes responsible for basic anatomy being kept among species, vertebrates added more regulatory regions that enabled them acquiring new functions. “In a similar way of the one in studies with humans, our analysis provides a global view of the different regulatory layers of the genome and describes the origins of the unique traits of genomic regulation in vertebrates, which gave way to organisms with a more complex morphology”, states José Luis Gómez-Skarmenta, who led the study in the Andalusian Center for Developmental Biology (CSIC - University Pablo de Olavide).
One of the most important results of the study is to understand how genomic duplications that took place in the origins of vertebrates contributed to the diversification of the gene functions. About fifty years ago researchers noted these duplications were key for our origins, but so far many of these predictions had not been proved. “We have seen that in many cases, there are gene copies that focus their function on specific tissues. This is clear in the brain, where many functions that proved essential for the evolutionary success of vertebrates have been incorporated”, adds Ignasi Maeso, researcher at the same center and one of the first authors of the study.
The study these Spanish scientists have published has the participation of laboratories from France, the United Kingdom, Australia, Czech Republic, the Netherlands, Japan, China, Portugal, Italy, Taiwan, Norway and the United States, and represents a unique resource for the scientific community that will serve to focus on the elements of functional genomics that were maintained among species as well as to study the changes that gave way to the complexity of vertebrates.
It should be noted that one of the co-supervisors of the study, Manuel Irimia, was a doctoral student in the Department of Genetics of the UB and received the Doctorsʼ Senate Award. Also, one of the first co-authors, Ignacio Maeso, holds the doctorate from the same Department like the other article signers Èlia Benito-Gutiérrez and Lluís Permanyer. On the other hand, the coauthors Stephanie Bertrand, Salvatore DʼAniello, David Ferrier, Ildiko Somorjai were postdoctoral researchers at the UB. Most of them being head of research groups in several European countries, which shows the training performance of the University of Barcelona on science, and specifically in the field of evo-devo, which comprises the study of the evolution of genetic mechanisms in the embryonic development.
Article reference:
Marletaz et al. "Amphioxus functional genomics and the origins of vertebrate gene regulation". Nature (20188) DOI: 10.1038/s41586-018-0734-6