Genomic keys to the origin of vertebrates

Gene Expression and Morphogenesis (GEM-DCM2, CABD)
  • An international team of scientists reports how a more complex and specialised gene regulation was pivotal in the origin of vertebrates
  • Genomic, epigenomic and gene expression data from several species provides keys about the functional changes giving rise to greater complexity in vertebrates
  • Results shed light on how genomic duplications in the origin of vertebrates contributed to diversify gene function, allowing for more complex morphology

 

Large international team assembled to tackle a complex problem

Vertebrates are an extremely diverse group of living organisms that has colonised virtually all of the planet’s ecosystems. This group, to which the human species belongs, shares a unique, complex set of gene regulation systems. Such complex regulation has allowed the information contained in their genome to produce hundreds of specialised cells, tissues and organs. Which were the changes in vertebrate ancestor genomes that decisively gave rise to this, is a long-standing debate.

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Fossil of a bone fish skeleton, a testament to ancient vertebrates.

An international team of scientists addressed this, co-led by Spanish researchers from the Centre for Genomic Regulation (CRG), the Pompeu Fabra University (UPF), the National Centre for Scientific Research (CNRS, from France) and the Gene Expression and Morphogenesis unit at the Centro Andaluz de Biología del Desarrollo Spanish National Research Council (CSIC). The work enjoyed also of the participation of researchers of the University of Barcelona in Spain, as well as of research groups in many countries including France, the United Kingdom, Australia, the Czech Republic, The Netherlands, Japan, China, Portugal, Italy, Taiwan, Norway and the United States, making it a major international effort with manifold contributions.

 

On the differences between vertebrates and invertebrates

The international team contributed to the description of the processes that helped to obtain the complexity and diversity of gene function and regulation during the transition from invertebrates to vertebrates. As explains Manuel Irimia of the Centre for Genomic Regulation, and one of the principal investigators of this work, “we conducted an exhaustive analysis of the genomic regulation of different species, finding two key differences between vertebrates and invertebrates, firstly, we observed that generally speaking our gene regulation is much more complex than that of invertebrates. The second difference is that we have copies of genes that originally performed only very general functions, but which in vertebrates went on to specialise in much more specific functions, particularly in the brain”.

The researchers studied the genomes of several species of vertebrates, such as the zebrafish or the medaka fish, as well as that of frogs, chickens, mice and humans. However, in order to understand the origin of the genomic regulation mechanisms that characterise vertebrates, they needed equivalent data from a closely-related species that would furnish information about the evolutionary transition between invertebrates and vertebrates.

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The lancelet, a fish-like non-vertebrate organism that sheds light on the origins of vertebrates.

That living being was the amphioxus or lancelet, a non-vertebrate fish-like species commonly used for the study of vertebrate origin. They sequenced its genome generated gene data they used to study the regulation of lancelet genes. “The amphioxus is an organism that has been used as a research model system since the 19th Century. Its genome has evolved very slowly, without the whole genome duplications present in vertebrates. For this reason, the amphioxus can serve as a reference in evolutionary comparisons to understand our lineage”, says Héctor Escriva, one of the leaders of the work and a researcher at the Sorbonne and at the CNRS in Banyuls sur Mer, France.

 

Complex gene regulation allows taking evolution one step further

The work, published in Nature, not only compares genomes, but also provides gene expression data. This is enriched by the addition of epigenomic data, which is data about reversible but inheritable DNA modifications that do not change the identity of the DNA sequence (i.e. this influences the expression of certain genes, but does not change the genes’ identity per se).

Taken together, this work furnishes unique information about the functional changes that gave rise to higher complexity in vertebrates, particularly in the nervous system. The scientists observed that, while the regulation of genes that are responsible for the basic anatomy has been maintained between species, vertebrates incorporate more regulatory regions that enabled them to take on new functions.

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Jellyfish are among the oldest organisms alive, long preceding vertebrates in their appearance, and far simpler.

“Just like studies performed in human beings, our own study gives us an overview of the genome’s different regulatory layers and a detailed description of vertebrates’ unique genomic regulation characteristics that gave rise to organisms with a much more complex morphology”, states José Luis Gómez-Skarmeta, another of the leaders of the work, from the Gene Expression and Morphogenesis unit at the Centro Andaluz de Biología del Desarrollo (CSICUniversidad Pablo de Olavide).

A key contribution of this work is the understanding of how the genomic duplications that occurred in the origin of vertebrates contributed to diversify gene function. Almost 50 years ago, it was suggested that these duplications were key to our origin, although many of the associated predictions could not be proven until now.

 “We observed that in most cases, there are copies of genes whose function becomes specialised in specific tissues. This is particularly evident in the brain, which has incorporated new functions that have likely been essential to vertebrates’ evolutionary success”, adds Ignacio Maeso, a researcher of the same institution, and one of the leading authors of the work.

This work constitutes an unprecedented resource for the scientific community that will enable to explore the elements of functional genomics maintained between species in greater depth and to study the changes that have given rise to vertebrate complexity.

 

Image credits:

Fossil bone fish skeleton picture is in the public domain and was downloaded from Pexels.

Branchiostoma lanceolatum picture was downloaded from Wikimedia Commons and licensed via an Attribution-ShareAlike 4.0 International license (CC BY-SA 4.0).

Yellow jellyfish picture is in the public domain and was donwloaded from Public Domain Pictures.

 

 

 

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