Thirteen different species of snakes live in the Catalan Countries, ranging from harmless grass snakes to venomous ones, such as the Pyrenean viper and the Iberian viper. Within the framework of the Catalan CBP Initiative, their complete genomes are being sequenced for the first time. "We are particularly interested in the genes for their venoms," explains Sergi Tulloch, a predoctoral researcher at the IBE (Institute of Biotechnology). They have already sequenced the genome of Vipera latastei , the viper endemic to the Iberian Peninsula, which is classified as vulnerable. "Knowing the genes associated with the toxins opens the door to the development of new drugs and antivenoms," notes Tulloch, who points out that snakebite is recognized as one of the neglected tropical diseases that causes many problems, especially in developing countries. They also sequenced the genome of a snake from Menorca that arrived in the Balearic Islands from North Africa with the Phoenicians, the Macroprotodon mauritanicus , or Balearic garrigue snake. Salvador Carranza, head of the IBE, also commented that the goal is to carry out an evolutionary study of the toxins using all the genomic data they are contributing to the Catalan initiative.
Objective: create Noah's Ark of the biodiversity of the Catalan Countries
Around twenty research centers are participating in an ambitious initiative that aims to sequence the genome of all eukaryotic species
For some time, a team of researchers from the Institute of Evolutionary Biology (IBE UPF-CSIC), led by Salvador Carranza, arguably the leading expert on reptiles and amphibians in Catalonia, had wanted to obtain the genome of one of the most endangered species in the country. Iberolacerta aurelioiThe Pyrenean lizard, an endemic species of the Pyrenees, is both a window into the glacial past and the evolution of mountain vertebrates. This small reptile, which inhabits only a very restricted area of three mountain ranges in Pallars Sobirà, southern France, and northwestern Andorra, was discovered in the late 1990s at Lake Sotllo, on the peak opposite. Its history—how it had managed to survive in the high mountains and why its habitat was so limited—was unknown. It was also unknown how climate change affected it or what other threats it faced.
To shed light on the situation, Carranza and his team traveled to Andorra, to the Comallempla valley, on the edge of the Comapedrosa Natural Park. Fortunately, on the very first day of the mission, after walking for a while on the ski slopes, they managed to locate an adult male in the scree at an altitude of nearly 2,500 meters. A tissue sample allowed them to obtain the genetic material (DNA and RNA) they needed to achieve a scientific milestone: constructing the first complete genome—a comprehensive instruction manual—of this Pallaresa lizard.
"Having its genome allows us to understand how it has evolved, how it relates to other species, and how it has adapted to its environment," Carranza, who is also the director of the IBE, enthusiastically told ARA, adding immediately: "It is a fundamental tool for reconstructing its history and establishing protection measures."
The genome of theIberolacerta aurelioi It has revealed a DNA very different from that of other lizards, with "curious" adaptations to life at high altitudes. The results "fit very well with what has been suspected for years: that these mountain lizards were confined to the summits long before the Pleistocene glaciations," Carranza points out.
Capture the biodiversity of the Catalan Countries
This emblematic species of the Pyrenees is part of the Catalan Initiative (CBP) for the Earth Biogenome Project (EBP), A very ambitious plan, launched in 2019, aims to produce a detailed catalog of the genomes of eukaryotic species—plants, animals, fungi, and diatoms (algae)—in the Catalan Countries. "This information [the genome] will contribute to a better understanding of the biodiversity of our territory and provide tools to help us with conservation, protection, and restoration policies," says Marta Riutort, professor and researcher at the Biodiversity Research Institute (IRBio) of the University of Barcelona.
Furthermore, she adds, it will allow for the cataloging of new species and the generation of knowledge about their biology and evolution, understanding how climate change affects them, and even discovering new molecules with potential applications in medicine, food, energy, or biotechnology. And above all, notes Teresa Garnatje, a researcher at the Botanical Institute of Barcelona, a joint center of the Spanish National Research Council (CSIC) and the Consortium of the Natural Science Museum of Barcelona, the initiative aims to help "raise awareness of the rich natural heritage we possess."
The initiative, involving more than 20 research centers throughout the Catalan-speaking territory, is promoted by the Catalan Society of Biology and developed jointly with the Catalan Institution of Natural History, within the framework of the Institute for Catalan Studies. Furthermore, the project is affiliated with theEBP —an international initiative that aims to describe the genome of all eukaryotic species that inhabit the Earth— and also in theEuropean Reference Genome Atlas (ERGA)
"[In the Catalan Countries] we have a very important naturalist tradition and many research groups working on evolution and biodiversity, as well as infrastructure that allows us to obtain sequences and perform bioinformatics analyses," such as the National Center for Genomic Analysis (CNAG) or the Supercomputing Center. Adding to this research context is the fact that Catalan-speaking territories concentrate a very large biodiversity, around 25% of the species present in Europe. In fact, "the Mediterranean arc is considered one of the centers of biodiversity on a planetary scale," this biologist points out.
So far, as presented at a recent conference where researchers reviewed the first five years of the project, initial expectations have been exceeded. The Initiative began with the goal of sequencing 150 representative species from the territories and has evolved into an active catalog of 199 species, ranging from Mediterranean corals to endemic plants, reptiles, birds, and subterranean fauna. Of these, 138 come directly from the 34 projects funded so far by the IEC's BioGenoma program, which, in turn, is supported by the Ministry of Universities and Research.
First, the emblematic
Mapping the genome of every species is a monumental task, which is why the Catalan initiative established as a starting criterion that the chosen species be native to the Catalan Countries and have some kind of application. This is, in fact, the same criterion used by the EBP (European Biological Programme), which stipulated that the species should be iconic, interesting, or important at an environmental, scientific, economic, or social level.
The first genome produced within the framework of the Catalan initiative was that of the Balearic shearwater (Puffinus mauretanicusThe Balearic shearwater (Central swan) is endemic to the Balearic Islands and is the most endangered seabird in Europe. In fact, if nothing changes, it is estimated that it will have completely disappeared in 60 years. Many pairs of this bird die each year due to longline fishing, as they descend to catch fish and become entangled in the fishermen's nets. Cats and other predators are also a significant threat to the bird's survival, as they eat the eggs and chicks.
"We sequenced the shearwater's genome a couple of years ago, and that has allowed us, in a new population-scale study, to establish its demographics, which colonies interbreed, and assess the level of hybridization. Now, with this information, we can also offer advice regarding planarians, a type of very small worm that lives in lakes and rivers."
Also in Catalan
Once the complete genome of a species has been sequenced, it is deposited in international repositories so that the entire scientific community can access and use it.
"We have managed to make publications available in Catalan as well," Garnatje proudly points out. "When we send the article to the scientific journal with the genome and its annotation [which genes are expressed and what function they perform], it is saved in the repositories." a copy in Catalan, so that anyone who wants to read it in Catalan can do so."
Some of the samples obtained through the Catalan Initiative are deposited at the Barcelona CryoZoo, a unique project worldwide that aims to safeguard and study biomaterial from multiple animal species, especially the most endangered, to preserve and gain a deeper understanding of animal diversity on the planet. This project is a joint effort of the Barcelona Zoo, Pompeu Fabra University, the European Molecular Biology Laboratory (EMBL), and the Barcelona Museum of Natural Sciences.
"The goal is to generate genomes of species that don't yet have a reference genome, as well as cell lines," explains ICREA researcher Tomàs Marquès-Bonet, from the IBE and professor at UPF. His laboratory is responsible for generating these genomes and cell lines. "The CryoZoo is ultimately a repository where we've generated biomaterials and digital data—the genomes—so that the scientific community can use them to investigate everything from parasitology to conservation, genetics, and zoonotic diseases."
For this expert in botany, the biodiversity of organisms goes hand in hand with the diversity of cultures and languages. "If we lose the names of plants, we end up losing the knowledge associated with them. It is crucial that we preserve the language, the name, and the traditional knowledge associated with each species," she asserts. In her case, Garnatje, along with Laura Botigué, a researcher at the Centre for Research in Agricultural Genomics (CRAG), contributes to the Catalan initiative with plant species. "In the case of plants, we set up a consortium of different universities and research groups from Catalonia, the Balearic Islands, and the Valencian Community, and we carried out several expeditions to collect plants," Garnatje explains.
Some of the samples obtained are stored in sheets at the herbarium of the Botanical Institute, the second most important plant repository on the Iberian Peninsula, a place that seems frozen in time, with plant specimens preserved in sheets that contain the scientific name of the species, the location where they were harvested, the date, and the person.
Another part of the samples goes to the CRAG, where the first—and very complicated—step is to extract quality DNA. "There are samples where we don't succeed, as has happened with Achillea pyrenaica, "Mountain chamomile," Botigué explains, adding that plant genomes are very complex. Unlike the human genome, which is diploid—meaning we receive two copies of DNA, one from our father and one from our mother—and has a total of 6 billion chemical bases, plants with more than 6 billion bases can have a redundant, repetitive genome, making it extremely difficult to complete the puzzle. "Bioinformatics algorithms are not capable," Botigué acknowledges.
Among the plant species included in the Catalan initiative is the popular arnica (Arnica montanaThis plant, which grows in high mountain areas, flowers sparsely and is widely used in folk medicine and pharmaceuticals to treat bruises, either as an ointment or macerated in alcohol. "Regulations are needed to protect it because it's being overexploited," Garnatje argues. "People often collect entire crates, but then only use a little and throw the rest away. Furthermore, the part used is the inflorescence—the flower—which prevents it from reproducing." That's why, she continues, "having its genome is crucial, to help raise awareness and also to establish conservation policies." Interestingly, because the plants don't move, they produce many products to defend themselves against herbivores, for example; therefore, their genetic material can lead to the discovery of molecules for making medicines.
Riutort insists that the Catalan atlas of the biodiversity genome "helps conserve organisms, which in turn implies conserving the surrounding environment." "Because, ultimately, we must all be aware that our health depends on our environment. It's all interconnected."