What distinguishes Homo sapiens from other living beings? And the group of mammals? What makes them different? These are the questions that researchers from the Hospital del Mar Medical Research Institute (IMIM) have been trying to answer, together with the Department of Experimental and Health Sciences at the Universitat Pompeu Fabra (UPF). To do this, they analysed the already-sequenced genomes of 68 mammals and identified 6,000 families of genes that are only found in these animals. These are genes with no homologues outside mammals, in other words, they are not present in other hairless species. In humans, it is estimated that they represent 2.5% of the genes that code for proteins. The work was led by Dr. José Luis Villanueva-Cañas, a member of the IMIM's Evolutionary Genomics research group, and currently a researcher at the Evolutionary Biology Institute (UPF-CSIC), and Dr. Mar Albà, an ICREA researcher at both the IMIM and the Biomedical Informatics Research Programme (GRIB). The study also involved Dr. David Andreu's group from the UPF's Department of Experimental and Health Sciences. It has been published in the journal Genome Biology and Evolution.
Dr. Villanueva-Cañas explains that the aim of the work was to "understand which genes define mammals as a class, in other words, which genes are only found in this group". To do this, he designed a set of programs that made it possible to compare the genomes of 68 mammals. These included Homo sapiens, as well as other primates and representatives of the main orders of this class of animals, including the Iberian lynx. With this data he generated a catalogue of genes exclusive to the mammals, of around 6,000 families of genes. At the same time, he assigned them a possible age of origin according to the species in which they are present. He also tried to figure out what these genes do, using expression data (RNA sequencing) from different tissues, to see where and how they are expressed, and proteomic data to check if they are translated, in other words, produce proteins.
Some of these genes have a de novo origin, and do not come from the duplication of pre-existing genes. De novo genes are important for acquiring new functions during evolution, as was demonstrated by another study led by Dr. Albà (Origins of de novo genes in human and chimpanzee, published in Plos Genetics). The new study has managed to identify the functions of some of these genes, related to how the skin is structured and why it is different from that of, for example, reptiles, as well as other genes involved in the mammary glands characteristic of mammals. They have also identified antimicrobial peptides, which participate in the body's defence against pathogens.
The researchers also stress that the genes they have found are short and usually only expressed in one, or just a few tissues. Dr. Albà wants to highlight that "Studies like this help us understand how new genes form during evolution and whether they play an important role in the adaptation of organisms to their environment". For this reason, "cataloguing mammal genes is the first step in understanding their functions" and "brings us closer to defining a set of pieces that originated at the start of their evolution and which are common to all of them, or some of their subgroups". Dr. Villanueva-Cañas explains that "We still we do not know the function of an important part of our genes, so it is necessary to make an effort to characterise them." This is the case of one that was identified during the study (neuronatin), which plays a so-far-unknown role in brain development.
Villanueva-Cañas, J.L., Ruiz-Orera, J., Agea, M.I., Gallo, M., Andreu, D. & Albà, M.M. (2017). New Genes and Functional Innovation in Mammals. Genome Biology and Evolution, 9, 1886-1900.