Construction of High‐Precision Genomic Assembled Sequences and Assessment of the Effect of Its Quality to Population Genetic Analysis of Endangered Okinawa Rail and Japanese Golden Eagle

ABSTRACT Recent advances in whole genome sequencing (WGS) technology, particularly long‐read sequencing, have enabled the development of high‐precision reference genome assemblies for non‐model wild mammals and birds. The decreasing costs of WGS facilitate numerous global genomic initiatives, and genetic analysis based on genomic data is imperative for population genetics and conservation genetics. Genomic analysis provides precise insights into genetic diversity and inbreeding in endangered animals, but requires a high‐quality genome assembly. The absence of such assemblies can lead to a biased understanding of genetic diversity and misdirected conservation strategies. In this study, we developed high‐precision genome assemblies for two endangered Japanese animals, the Okinawa rail and the Japanese golden eagle, using a hybrid approach that combines short‐ and long‐read sequencing. This approach improved assembly contiguity, reduced missing data, and enhanced completeness. We also assessed how assembly quality influences genetic analysis by comparing results from population genetic analyses based on previous and newly established assemblies. The findings of this assessment indicated that genome‐wide heterozygosity and PSMC modeling were less sensitive to assembly quality. However, inbreeding analysis based on runs of homozygosity (ROH) was significantly affected by fragmentation of assembly. Consequently, high‐precision, contiguous assemblies are essential for accurate conservation genetic analyses, particularly for assessing inbreeding. In the absence of a high‐quality assembly, developing new ones is a viable alternative. Our hybrid approach combining Nanopore long‐read sequencing and short‐read sequencing enables the cost‐effective development of high‐quality genome assemblies, making it suitable for non‐model animals.