- A high proportion of “dispensable genes”, which are not found in all individuals, is related to survival and may explain the mussel’s capacity for adaptation.
- In addition to its commercial interest, this species contains molecules with antibacterial and antiviral activity.
Madrid, Wednesday 11 November 2020. A team coordinated by scientists from the Spanish National Research Council (CSIC) and the University of Vigo has sequenced the complete genome of the Mediterranean mussel (Mytilus galloprovincialis). In addition to revealing that the species contains 65,000 genes, more than twice as many as humans, the research has uncovered several keys to understanding the enormous adaptability and stress resistance of this “marine superorganism”. The study, published in Genome Biology and highlighted by Science, revealed a genomic architecture that is highly unusual for an animal.
This system is based on genes shared by all individuals of the species and on approximately 20% of “dispensable genes” that are not shared by all individuals and are related to survival functions. This knowledge could be applied, for example, to the design of new treatments against disease.
Mussels are constantly exposed to a wide range of potentially pathogenic microorganisms and other pollutants because they feed by filtration. Nevertheless, unlike other bivalves, they show very high resistance. They also contain a large number of antimicrobial peptides, molecules with antibacterial activity that also protect against viruses from different species, including some that affect humans.
The researchers assembled a 1.28-gigabyte reference genome for Mytilus galloprovincialis — the human genome is 3.3 gigabytes — and found that this bivalve has approximately 65,000 genes, compared with 30,000 in humans. They also sequenced the genomes of 14 other individuals from two independent populations in Galicia and Italy.
“We discovered that the mussel genome is a pan-genome, made up of a core set of 45,000 genes plus about 15,000 dispensable genes. These genes are subject to presence-or-absence variation, which means that they can be completely missing in some individuals,” explains CSIC researcher and project co-leader Antonio Figueras, who works at the Institute of Marine Research (IIM-CSIC) in Vigo.
David Posada, researcher at the University of Vigo and co-lead author of the study together with Figueras, notes that “this type of genomic architecture is a new phenomenon in animals”. “For one animal to have 20% of its genome different from another individual of the same species is truly unheard of. At first we thought it was an error, but in the end we were able to confirm that it was real,” he says.
The work also involved key contributions from scientists at the University of Trieste, with Marco Gerdol as first author, and the University of Padua, both in Italy; the Institute of Evolutionary Biology (CSIC-UPF); and the National Centre for Genomic Analysis (CNAG-CRG), whose scientists, led by Tyler Alioto and Marta Gut, coordinated genome assembly and sequencing.
Adaptive value
A pan-genome contains a set of core genes present in all individuals of a species, essential for survival, and dispensable genes that are found only in a subset of individuals and usually have accessory functions. Dispensable genes also tend to belong to recently expanded “new” gene families that have specialized in survival functions, which could be the key to explaining the mussel’s recovery and invasion capacity.
“This resistance to adverse environmental conditions, which even gives the mussel the status of an invasive species, could be explained by the characteristics we have discovered in its genome. The pan-genomic architecture of the mussel genome may provide a selective advantage for its population,” Figueras underlines.
“After analysing the functions of these genes, we believe this is an evolutionary strategy that allows mussels to adapt to all kinds of circumstances. Mussels are extremely tough organisms; practically anywhere with a temperate climate has mussels,” Posada says.
The first animal pan-genome
This research represents the first description of a pan-genome in an animal (a metazoan), as well as the existence of a massive phenomenon of gene absence and presence in this kingdom, something previously discovered only in microorganisms and occasionally in plants, microalgae and fungi.
In bacteria, dispensable genes provide evolutionary advantages that improve the ability to migrate to new ecological niches and make a significant contribution to phenotypic variation in plants. “We believe that the functions associated with the mussel’s 15,000 dispensable genes also represent an invaluable resource for this species,” says the CSIC researcher.
Sequencing the mussel genome also enabled scientists to study in greater depth the high variability of the antimicrobial molecules it contains. In practical terms, this knowledge will help scientists understand how these molecules work and how diverse they are. “This work will make it possible to develop genomic tools that could in the future help protect mussels from possible diseases, or improve their production and quality,” explains the University of Vigo researcher.
The mussel is the leading aquaculture species in Spain — the world’s second-largest producer after China — and one of the most important in Europe, regularly reaching 250,000 tonnes per year. Production is almost entirely concentrated in Galicia, where cultivation takes place on floating rafts arranged in areas whose layout and number are controlled by the regional authorities.
Alda Ólafsson/CSIC Communication