European mink (Mustela lutreola) reference genome and population genomics

The European mink (Mustela lutreola) is considered as critically endangered in the IUCN red list, and is already extinct in large parts of its ancestral range. A chromosome-scale reference genome has been recently produced during the ERGA (European Reference Genome Atlas) pilot project, from an individual sampled in 2006 in Dordogne (France) in the framework of the first National Action Plan for European Mink. A fibroblast cell culture was derived from a skin biopsy on this animal, and then cryopreserved in liquid nitrogen in the Paris National Museum of Natural History cell collection. This frozen sample was used to generate fresh cell cultures for the production of high-quality DNA that was subsequently sequenced and assembled into a high-quality reference genome. This reference can now be used for genomic studies of this species that presents a very high risk of inbreeding depression especially in the western part of its geographic distribution. Inbreeding depression is a critical concern for conservation efforts as it is common in small, declining or fragmented populations. Demographic history of a population can also have an impact on inbreeding depression and shape the levels of genetic load. Interestingly, small populations with extremely low genetic diversity do not always present evidence of Inbreeding depression and may persist thanks to the purging of strong deleterious variants. One way to measure the extent of inbreeding is to scan genomes for runs of homozygosity (ROH). This method is becoming more commonly used to estimate inbreeding and could become a new index for conservation status in wild animals. For this study, we selected two European mink from France (LIFE VISON et PNA Vison), two from Romania, two from Estonia and two from Spain for whole genome re-sequencing (> 25x), each genomic sequence being compared to the reference genome. We expect to find long stretches of ROH that would indicate recent events of inbreeding. The results might have a direct impact on the current conservation program for the European mink.