T2T genome of  Fujian Longyan Shan-ma duck (Anas platyrhynchos)
The domestic duck (Anas platyrhynchos) is an economically important poultry species and a valuable model for studying avian domestication and trait diversification. While high-quality reference genomes are available for meat-type breeds (e.g., Pekin duck), genomic resources for egg-laying breeds remain limited, constraining comparative analyses between divergent production types. Here, we present a near telomere-to-telomere (T2T) genome assembly of the female Fujian Longyan Shan-ma duck (A. platyrhynchos-FJLY), a representative laying-type breed. Using PacBio HiFi (~107×), Oxford Nanopore ultra-long (~35×), and Hi-C (~80×) sequencing, we assembled a 1.28 Gb genome anchored to 41 chromosomes (39 autosomes plus Z and W) with a scaffold N50 of 79.80 Mb and an anchoring rate of 98.55%. We predicted 18,749 protein-coding genes, of which 99.63% received functional annotations. Comparative analysis with the Pekin duck T2T genome revealed high collinearity across macrochromosomes but structural divergence in microchromosomes, including expansions in olfactory receptor gene clusters. Using this reference, re-analysis of public ovarian RNA-seq data identified 2,129 differentially expressed genes associated with egg number, with key follicular development and lipid metabolism regulators enriched on chr31–39. The genome exhibits high completeness (99.36% BUSCO) and base accuracy (QV > 39). This dataset fills the genomic resource gap for laying-type ducks and provides a foundation for investigating the genetic basis of egg production traits and avian microchromosome evolution.