The native mussel Mytilus chilensis genome reveals adaptative molecular signatures facing the marine environment.

The blue mussel Mytilus chilensis is a key socioeconomic species inhabiting the southern coast of Chile. This endemic marine mussel supports a booming aquaculture industry, which entirely relies on artificially collected seeds from natural beds that are translocated to a diverse physical-chemical ocean conditions for farming. Furthermore, mussel production is threatened by a broad range of microorganisms, pollution, and environmental stressors that eventually impact its survival and growth. Herein, understanding the genomic basis of the local adaption is pivotal to developing sustainable shellfish aquaculture. We present a high-quality reference genome of M. chilensis, which is the first chromosome-level genome for a Mytilidae member in South America. The assembled genome size was 1.93 Gb, with a contig N50 of 134 Mb. Through Hi-C proximity ligation, 11,868 contigs were clustered, ordered, and assembled into 14 chromosomes in congruence with the karyological evidence. The M. chilensis genome comprises 34,530 genes and 4,795 non-coding RNAs. A total of 57% of the genome contains repetitive sequences with predominancy of LTR-retrotransposons and unknown elements. Comparative genome analysis was conducted among M. chilensis and M. coruscus, revealing genic rearrangements distributed into the whole genome. Notably, Steamer-like elements associated with horizontal transmissible cancer were explored in reference genomes, suggesting putative phylogenetic relationships at the chromosome level in Bivalvia. Genome expression analysis was also conducted, showing putative genomic differences between two ecologically different mussel populations. Collectively, the evidence suggests that local genome adaptation can be analyzed to develop sustainable mussel production. The genome of M. chilensis provides pivotal molecular knowledge for the Mytilus complex evolution and will help to understand how climate change can impact mussel biology.