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The black-necked crane (Grus nigricollis) which inhabits high-altitude areas has the largest body size of the world's 15 crane species, and is classified as threatened by the IUCN. To support further studies on population genetics and genomics, we present a high-quality genome assembly based on both Illumina and nanopore sequencing. In total, 54.59 Gb Illumina short reads and 116.5 Gb nanopore long reads were generated. The 1.23 Gb assembled genome has a high contig N50 of 17.89 Mb, and has a longest contig of 87.83 Mb. The completeness (97.7%) of the draft genome was evaluated with single-copy orthologous genes using BUSCO. We identified 17,789 genes and found that 8.11% of the genome is composed of repetitive elements. In total, 84 of the 2,272 one-to-one orthologous genes were under positive selection in the black-necked crane lineage. SNP-based inference indicated two bottlenecks in the recent demographic trajectories of the black-necked crane. The genome information will contribute to future study of crane evolutionary history and provide new insights into the potential adaptation mechanisms of the black-necked crane to its high-altitude habitat.

A High-quality Draft Genome Assembly of the Black-necked Crane (Grus nigricollis) Based on Nanopore Sequencing