Chromosome-level genome assembly of the critically endangered Baer’s pochard (Aythya baeri)

Baer’s pochard (Aythya baeri) is a critically endangered species historically widespread throughout East Asia, whose population according to a recent estimate has decreased to between 150 and 700 individuals, and faces a long-term risk of extinction. However, the lack of a reference genome limits the study of conservation management and molecular biology of this species. We therefore report the first high-quality genome assembly of Baer’s pochard. The genome has a total length of 1.14 Gb with a scaffold N50 of 85,749,954 bp and a contig N50 of 29,098,202 bp. We anchored 97.88% of the scaffold sequences onto 35 chromosomes based on the Hi-C data. BUSCO assessment indicated that 97.00% of the highly conserved Aves genes were completely present in the genome assembly. Furthermore, a total of 157.06 Mb of repetitive sequences were identified and 18,581 protein-coding genes were predicted in the genome, of which 99.00% were functionally annotated. This genome will be useful for understanding Baer’s pochard genetic diversity and facilitate the conservation planning of this species.