Long Reads de novo sequencing of the Anas diazi genome reveals changes in gene orthology in waterfowl

The Mexican duck (Anas diazi ) is the only duck species endemic to Mexico and is currently listed as threatened under NOM-059-SEMARNAT-2010. Its taxonomic status has long been controversial, historically considered a subspecies of Anas platyrhynchos due to their strong morphological similarity, particularly in females. In 2020, the American Ornithological Society formally recognized A. diazi as a distinct species; however, its genomic architecture remains largely unexplored. Here we present the first whole-genome analysis of A. diazi , based on PacBio HiFi long-read sequencing and a de novo assembly strategy. This represents the first genomic resource available for this endemic and threatened species. Genome size estimation based on K-mer and GenomeScope2 modeling revealed a haploid genome size of approximately 1.02 Gb, with a high model fit (> 96%), low repeat content (~ 7.4%), and moderate heterozygosity (~ 1.1%), values ​​consistent with other waterfowl genomes. Comparative alignment of reads with the A. platyrhynchos reference genome showed an alignment rate of approximately 86%, suggesting substantial lineage-specific genomic divergence. Gene prediction and functional annotation were performed using avian reference datasets (Anatidae and Gallus gallus ), generating nearly 4,000 highly reliable annotated proteins, the integrity of which was supported by BUSCO analysis. Using OrthoFinder and CAFE5, we investigated the evolution of gene families in A. diazi, A. platyrhynchos, Aix galericulata, Anser cygnoides , and G. gallus , identifying lineage-specific patterns of gene family expansion and contraction potentially associated with domestication, ecological specialization, and evolutionary divergence within Anatidae. Taken together, our results provide the first genomic framework for Anas diazi and lay the groundwork for future evolutionary, ecological, and conservation genomic studies of this waterbird endemic to Mexico.