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Despite being a species of global conservation concern and subject to ex situ and in situ conservation efforts, genomic research has been limited, hindering our understanding of its population genetic status and evolutionary history. In this study, we present the first fully annotated, chromosome-level genome for the scaly-sided merganser, generated using Oxford Nanopore long reads, Illumina short reads, and Hi-C sequencing. The final assembly spans 1.1 Gb across 308 scaffolds, 64 of which are anchored into 35 chromosomes, plus the mitogenome, covering 99.5% of the genome. The assembly shows high contiguity (N50 = 84.3 Mb) and completeness, with a Benchmarking Universal Single-Copy Ortholog score of 98%. Repeat sequences comprise 9.55% of the genome. Homology-based gene annotation identified \u223c15,200 protein-coding genes. A complete 16,624 bp mitochondrial genome was also assembled and annotated. Synteny analysis revealed strong chromosomal conservation across the wider Anatidae family, with evidence of lineage-specific rearrangements. Pairwise Sequential Markovian Coalescence modeling indicates recent stability in the effective population size of the species, with past declines coinciding with Pleistocene glacial cycles. Our high-quality genome provides an essential resource for conservation genomic and evolutionary studies of the scaly-sided merganser, supporting ongoing efforts to manage and protect this globally threatened species.<\/jats:p>","DOI":"10.1093\/g3journal\/jkag268","type":"journal-article","created":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T05:03:02Z","timestamp":1790053382000},"source":"Crossref","is-referenced-by-count":0,"title":["Chromosome-level genome assembly of the threatened scaly-sided merganser\n                    <i>Mergus squamatus<\/i>\n                    with insight into its demographic history"],"prefix":"10.1093","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-9773-679X","authenticated-orcid":false,"given":"Joshua J","family":"Wright","sequence":"first","affiliation":[{"name":"School of Biological and Chemical Sciences, Manchester Metropolitan University , Chester Street, Manchester M1 5GD ,","place":["United 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