What is the correct genomic structure of the complex chromosomal rearrangement at the Fm locus in Silkie chicken?

ARISING FROM Zhu, F., Yin, ZT., Zhao, QS. et al. Communications Biology https://doi.org/10.1038/s42003-023-05619-y (2023) High-quality chromosome-level genome assemblies for numerous avian species promise to address 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 entire 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, several previously published studies2-6 claim that *Fm_2 is the valid scenario. Our re-analysis of ZYZSJs new assembly (CAU_Silkie) using long-read data from multiple black-bone chickens demonstrates that *Fm_2 is the correct scenario. 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 post-assembly validation and correction in genome projects to prevent misinterpretation due to assembly artefacts. Enhancing the assembly of haplotypes in such complex regions is essential for unravelling the genetic foundations of traits governed by genes within these areas.