A highly contiguous de novo genome assembly of the Mexican Duck (Anas diazi) reveals fine-scale structural variation within the mallard complex
- 1Instituto de Ecología, Universidad Nacional Autónoma de México
- 2Postgrado en Ganadería, Colegio de Postgraduados Campus Montecillo
- 3Dirección del APFF Ciénegas del Lerma, Comisión Nacional de Áreas Naturales Protegidas, San Felipe Tlalmimilolpan
Abstract
The Mexican Duck (Anas diazi) is a quasi-endemic North American dabbling duck whose evolutionary history is marked by recent Pleistocene divergence and ongoing introgressive hybridization with the Mallard (Anas platyrhynchos). Because the two species are morphologically and genomically very similar, identifying where their genomes differ structurally is central to understanding how species integrity is maintained under gene flow. Here we present the first highly contiguous de novo genome assembly of A. diazi (PacBio HiFi) and use it to map chromosomal inversions across the phylogeny of the mallard complex. k-mer profiling revealed high heterozygosity (1.08%), and read-depth haplotype purging recovered an accurate 1.19 Gb haploid consensus (BUSCO 95.7%). Using independent, orientation-aware approaches—including read-based structural-variant detection and phylogenetic polarization—we find that structural differences between A. diazi and the Mallard are numerous but small (kb-scale), and strongly enriched on the Z chromosome. Loci within these species-specific inversions (e.g., PIK3C3, RIT2, and DIPK2B) exhibit high structural protein conservation, while functional annotation highlights post-transcriptional mechanisms. Furthermore, the capture of master non-coding RNAs within these rearrangements, including the spliceosomal U1 and the nucleolar SNORA5, provides a mechanism for species-specific alternative splicing and translational control. Ultimately, we find no evidence for macro-inversion ‘supergenes’; instead, the Mexican Duck maintains its divergence through fine-scale, Z-concentrated and post-transcriptional rewiring, consistent with the genomic architecture of recently diverged, hybridizing lineages.
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BibTeX
@article{padillaaguilar2026highly,
title = {{A highly contiguous de novo genome assembly of the Mexican Duck (Anas diazi) reveals fine-scale structural variation within the mallard complex}},
author = {Patricia Padilla-Aguilar and María Guadalupe Bravo-Vinaja and Edmundo Gutiérrez-Morales and David Colón-Quezada and Gastón Contreras-Jiménez and Marco Tulio Solano-De la Cruz},
journal = {BMC Genomics},
year = {2026},
month = jul,
doi = {10.1186/s12864-026-13219-3},
url = {https://doi.org/10.1186/s12864-026-13219-3},
note = {CC BY},
}
RIS
TY - JOUR
TI - A highly contiguous de novo genome assembly of the Mexican Duck (Anas diazi) reveals fine-scale structural variation within the mallard complex
AU - Patricia Padilla-Aguilar
AU - María Guadalupe Bravo-Vinaja
AU - Edmundo Gutiérrez-Morales
AU - David Colón-Quezada
AU - Gastón Contreras-Jiménez
AU - Marco Tulio Solano-De la Cruz
PY - 2026
DA - 2026/07/01
JO - BMC Genomics
DO - 10.1186/s12864-026-13219-3
UR - https://doi.org/10.1186/s12864-026-13219-3
AB - The Mexican Duck (Anas diazi) is a quasi-endemic North American dabbling duck whose evolutionary history is marked by recent Pleistocene divergence and ongoing introgressive hybridization with the Mallard (Anas platyrhynchos). Because the two species are morphologically and genomically very similar, identifying where their genomes differ structurally is central to understanding how species integrity is maintained under gene flow. Here we present the first highly contiguous de novo genome assembly of A. diazi (PacBio HiFi) and use it to map chromosomal inversions across the phylogeny of the mallard complex. k-mer profiling revealed high heterozygosity (1.08%), and read-depth haplotype purging recovered an accurate 1.19 Gb haploid consensus (BUSCO 95.7%). Using independent, orientation-aware approaches—including read-based structural-variant detection and phylogenetic polarization—we find that structural differences between A. diazi and the Mallard are numerous but small (kb-scale), and strongly enriched on the Z chromosome. Loci within these species-specific inversions (e.g., PIK3C3, RIT2, and DIPK2B) exhibit high structural protein conservation, while functional annotation highlights post-transcriptional mechanisms. Furthermore, the capture of master non-coding RNAs within these rearrangements, including the spliceosomal U1 and the nucleolar SNORA5, provides a mechanism for species-specific alternative splicing and translational control. Ultimately, we find no evidence for macro-inversion ‘supergenes’; instead, the Mexican Duck maintains its divergence through fine-scale, Z-concentrated and post-transcriptional rewiring, consistent with the genomic architecture of recently diverged, hybridizing lineages.
SN - 1471-2164
ER -