Supporting data for "Genomic exploration of the endangered oriental stork, <i>Ciconia boyciana</i>, sheds light on migration adaptation and future conservation"

The oriental stork, <i>Ciconia boyciana</i>, is an endangered migratory bird listed on the IUCN Red List. The bird population has experienced a rapid decline in the past decades, with nest locations and stop-over sites largely degraded due to human-bird conflicts. Multipronged conservation efforts are required to secure the future of oriental storks. We propose that a thorough understanding of the genome-wide genetic background of this threatened bird species is critical to make future conservation strategies.<br>In this study, the first chromosome-scale reference genome was presented for the oriental stork with high quality, contiguity, and accuracy. The assembled genome size was 1.24 Gb with a scaffold N50 of 103 Mb, and 1.23 Gb contigs (99.32%) were anchored to 35 chromosomes. Population genomic analysis did not show a genetic structure in the wild population. Genome-wide genetic diversity ( = 0.0012) of the oriental stork was at a moderate to high level among threatened bird species and the inbreeding risk was also not significant (FROH = 5.56±5.30%). Reconstruction of demographic history indicated a rapid recent population decline likely driven by human activities. Genes that were under positive selection associated with the migratory trait were identified in related to the long-term potentiation, photoreceptor cell organization, circadian rhythm, muscle development and energy metabolism, indicating the essential interplay between genetic and ecological adaptation.<br>Our study presents the first chromosome-scale genome assembly of the oriental stork, provides a genomic basis for understanding genetic background of the oriental stork, the populations extinction risks and the migratory characteristics, which will facilitate the decision of future conservation plans for this species.