Freshwater crayfish are keystone species of freshwater ecosystems andhave a significant impact on the biodiversity within their habitats. Freshwater crayfish are divided into 2 superfamilies, the Astacoidea and the Parastacoidea. Astacoidea includes Astacidae (European, Asian and North American species) and Cambaridae (North American species), while Parastacoidea includes only the family Parastacidae, representing the crayfish from the Southern Hemisphere. Despite their high ecological significance and their economic value as luxury food products, native European crayfish of the Astacidae family are still unexplored at the genomic level.
Towards the largest genome assembly in invertebrates
One of the main objectives of the GEODE project is to establish the first chromosome-level reference genome of the Astacidae family by assembling and annotating the genome of the noble crayfish A. astacus, an emblematic endangered native European crayfish species. With 17 Gb, the A. astacus genome would be one of the largest metazoan sequenced genomes. It will constitute an important milestone in the generation of high-quality reference genomes in non-model invertebrates and will aid to provide new understanding of genome expansion and gene functioning, notably in the context of the invertebrate immune system.
A high-quality assembly of such a huge genome will allow us to explore the evolution of gene repertoires and repetitive elements in Decapoda. Considering the huge genome size variation within the Astacidea infraorder, the A. astacus reference genome will be crucial to understand elements driving genome plasticity and evolution in Decapods.
An unprecedented effort to decipher genome evolution in Decapods
In parallel and in synergy with the genome assembly and comparative genomics approach, we aim to explore genome organization and karyotype evolution in a panel of crayfish species using cytogenomic approaches to gain deeper insight into genome evolution in Decapoda. In addition, understanding the landscape of repetitive DNAs can assist A. astacus genome assembly and will be precious for future assembly projects in other Decapod crustaceans.
So far, only 16 species out of the 669 species reported in the infraorder Astacidea have been investigated at the chromosomal level, including A. astacus with 176 chromosomes. Reported diploid chromosome numbers are generally higher than 170, positioning freshwater crayfish among the species with the highest chromosomal number among all Metazoans.
Exploring the molecular basis of immunity in Decapods
We aim to investigate the evolution of immunity-related genes in Decapoda, using the noble crayfish and the crayfish plague disease agent Aphanomyces astaci as well-established host-pathogen model. Ap. astaci belongs to the class Oomyceta and is a crustacean-specific pathogen with strains of varying virulence. Introduction of exotic (some invasive) North American crayfish species, which are natural carriers of Ap. astaci has caused high mortalities and numerous population collapses among all native European crayfish species, which are unable to resist the pathogen. However, some wild A. astacus populations have been shown to be latently infected with Ap. astaci, indicating elevated resistance against the pathogen. Within the GEODE project, we plan to leverage this host-pathogen model of special interest for biodiversity conservation to explore genes involved in the immune response in Decapoda.
Invertebrates generally rely on innate immunity for protection against various environmental and disease challenges. Pathogen recognition leads to activation of the molecular pathways involved in humoral and cellular response mechanisms. Effector cells of the crustacean immunity are the hemocytes. Currently, genes involved in the regulation of the hemocyte mediated immune responses are unknown or limited to reports of single targets. For a long time, it was generally accepted that immune memory is lacking in invertebrates. This notion was challenged by observations of immune memory responses in insects as well as in some Crustaceans. We plan to: (i) identify and annotate immune relevant genes in Decapoda; (ii) provide experimental evidence of immune memory in a time course immune priming experiment; (iii) associate traits of host resistance and pathogen virulence with specific genetic variants; and (iv) create an SNP array for screening and identification of the noble crayfish populations of a high conservation priority.
