The availability of high-quality chromosome-level genome assemblies of an increasing number of avian species holds significant promise for addressing longstanding questions in bird evolution and biology. In a recent issue of Communications Biology, Zhu, F., Yin, ZT., Zhao, QS. et al. (ZYZSJ)1 presented a chromosome-level assembly for the Silkie chicken using a multi-platform high-coverage dataset to obtain accurate and complete sequences spanning the chicken genome. A key finding from their genomic analysis is the reconstruction of the structure of the complex rearrangement at the Fm locus, the primary genetic change underlying the rare and conspicuous dermal hyperpigmentation phenotype generally called Fibromelanosis. However, in contrast to their identification of the *Fm_1 scenario (which the authors refer to as FM2) as the correct arrangement at the Fm locus, several previously published studies2-6 claim that *Fm_2 is the valid scenario. Our re-analysis of ZYZSJs new genome assembly (CAU_Silkie) demonstrates that *Fm_2 is indeed the correct scenario, and the *Fm_1 scenario favoured by ZYZSJ results from an assembly error caused by mosaic haplotypes generated during the de novo assembly step. We recommend that genome projects perform post-assembly validation and correction to safeguard biological interpretations from the impact of assembly artefacts.
