Nov 11, 2020.- A team coordinated by scientists from the Consejo Superior de Investigaciones Científicas (CSIC) and the Universidade de Vigo with participation of the CNAG-CRG, has sequenced the complete genome of the Mediterranean mussel (Mytilus galloprovincialis), a research that, in addition to revealing that the species contains 65,000 genes, more than double that those of the human being, has brought to light some keys to understanding the enormous capacity for adaptation and resistance to stress of this “marine superorganism”. The work, published in the journal Genome Biology has revealed a very unusual genomic architecture for an animal. This system is based on genes shared by all individuals of the species and on approximately 20% of “dispensable genes”, which are not shared by all and which are related to survival functions. This knowledge could be applied, for example, in the design of new treatments against diseases.

Mussels are constantly exposed to a wide range of potentially pathogenic microorganisms and other contaminants, as they are filter feeders. However, they show high resistance, unlike other bivalves. They also contain a large amount of antimicrobial peptides, molecules with antibacterial activity that also protect against viruses of different species, including some humans.

Mussels are constantly exposed to a wide range of potentially pathogenic microorganisms and other contaminants, as they are filter feeders. However, they show high resistance, unlike other bivalves. They also contain a large amount of antimicrobial peptides, molecules with antibacterial activity that also protect against viruses of different species, including some humans.

Researchers have assembled the 1.28 gigabase-sized mussel Mytilus galloprovincialis reference genome (that of humans is 3.3 gigabases) and found that this bivalve has approximately 65,000 genes, while humans have less than 30,000. In addition, they have sequenced the genome of another 14 individuals from two independent populations in Galicia and Italy.

“We have discovered that the mussel genome is a pangenome, composed of a core set of 45,000 genes plus some 15,000 dispensable genes. These are subject to variations in the presence or absence of genes, which means that they may be completely absent in some individuals ", explains the CSIC researcher and co-head of the project, Antonio Figueras, who works at the Instituto de Investigaciones Marinas (IIM- CSIC), in Vigo.

David Posada, a researcher at the Universidade de Vigo and co-main author with Antonio Figueras of the research, points out that “this type of genomic architecture is a new phenomenon in animals. That an animal has a 20% different genome than another of the same species is truly unheard of. At first we thought it was a mistake, but in the end we could see that it was true”.

Key contributors to this work included scientists from the University of Trieste, with Marco Gerdol as the first author, the University of Padua, the Institute of Evolutionary Biology (CSIC-UPF), and the Centro Nacional de Análisis Genómico (CNAG-CRG), whose scientists, led by Tyler Alioto and Marta Gut, have coordinated the assembly and sequencing of the genome.

The CNAG-CRG sequencing unit headed by Marta Gut performed the sequencing of the genome of the mussel Mytilus galloprovincialis, for which a fosmid-pool sequencing approach was taken. The high level of presence-absence variation within the genome complicated initial assembly efforts with shorts reads, but combining a clone based approach with additional long read data ultimately resulted in a contiguous reference genome sequence assembled and annotated by the team of Tyler Alioto.

 

An adaptive value

A pangenome contains a set of central genes present in all individuals of the same species, essential for survival, and dispensable genes, which are only found in a subset of individuals and generally have accessory functions. Furthermore, dispensable genes often belong to recently expanded families of "young" genes that have specialized in survival functions, which could be the key to explaining the mussel's resilience and invasiveness.

“This resistance to adverse environmental conditions, which even gives the mussel the name of invasive species, could be explained by the characteristics that we have discovered in the genome. It is possible that the pangenomic architecture of the mussel genome provides a selective advantage for its population”, emphasizes Figueras.

“We believe, after analyzing the functions of these genes, that it is an evolutionary strategy that allows them to adapt to all kinds of circumstances. Mussels are tough critters; There is practically no place with a temperate climate where there are no mussels”, says Posada.

First pangenome in animals

This research represents the first description of a pangenome in an animal (metazoan), as well as the existence of a massive phenomenon of absence and presence of genes in this kingdom, something that had only been discovered in microorganisms and occasionally in plants, microalgae and mushrooms.

In bacteria, dispensable genes provide evolutionary advantages that enhance the ability to migrate to new ecological niches and provide a significant contribution to phenotypic variation in plants. "We believe that the functions associated with the 15,000 dispensable genes of the mussel are also an invaluable resource for this species," says the CSIC researcher.

The sequencing of the mussel genome has also allowed scientists to delve further into the high variability of the sequences of the antimicrobial molecules they contain. On a practical level, this knowledge will allow scientists to understand how these molecules work and their diversity. "This work will allow the development of genomic tools that can be used in the future to protect them from possible diseases, or to improve their production and quality," explains the researcher from the Universidade de Vigo.

The mussel is the one with the highest production in aquaculture in Spain (Spain is the second largest producer in the world after China) and one of the most important in Europe, regularly reaching 250,000 tons per year. It is produced practically entirely in Galicia, a crop that is carried out in floating rafts or rafts arranged in polygons, the arrangement and number of which are controlled by the regional authorities.

Work of reference: Massive gene presence/absence variation shapes an open pan-genome in the Mediterranean mussel

This news item has been translated and adapted from the CSIC news. You can read it here.