A genome-wide screening of essential characteristics for long-term persistence in endangered fish species: a case study of Ryukyu-ayu

Abstract

In endangered species, inbreeding due to a reduction in population size is considered to be a cause of loss of genetic diversity. This process could prompt expression of deleterious recessive alleles that are present at low frequencies within populations, increasing the risk of extinction. However, recent studies have shown that some endangered species could have survived for a long time despite their extremely small effective population sizes. Comparative genomics studies of endangered species to estimate historical effective population size and to address genomic characteristics would provide a better understanding of their long-term persistence. Recent advances in a low-cost next generation sequencing library preparation method and a cost-effective low-coverage whole genome sequencing approach make it possible to conduct comparative population genomics for non-model organisms such as ayu, including endangered subspecies Ryukyu-ayu. Here, I introduce the preliminary results of the comparative genomic analyses between two subspecies using a low-coverage whole genome sequencing approach to identify genomic signatures likely involved in the long-time survival of this endangered fish subspecies Ryukyu-ayu.