Toward a complete diploid chicken genome.

Authors

Shiyu Fan, Jiao Liu, Na Kang, Diyan Li, Zhuanjian Li, Naiyi Xu, Luohao Xu

Published in

Cell reports. Volume 45. Issue 11. Pages 118280. Nov 12, 2026. Epub Nov 12, 2026.

Abstract

The repetitive and heterochromatic parts of microchromosomes and dot chromosomes have impeded the creation of a complete, haplotype-resolved chicken genome. To overcome these challenges, we employed a trio-sequencing approach, utilizing long reads from a female chick, supplemented by parental long-read data for accurate haplotype phasing. This strategy generated nearly complete, haplotype-resolved paternal and maternal assemblies, with 14 residual gaps. Telomeric sequences remain missing from two paternal and four maternal chromosomes, suggesting a still incomplete assembly. GGswu2 resolved more than 50 Mb of previously unresolved regions, predominantly within dot chromosomes. The dot chromosomes exhibit low nucleotide diversity but a high density of structural variants between haplotypes. We found that the centromere sizes and relative positions of centromere cores sometimes differ between the two haplotype genomes. These findings suggest that comparative genomics must incorporate high-resolution analyses of these dynamic and complex regions to fully understand avian genome evolution and genetic complexity.

PMID:
43019056
Bibliographic data and abstract were imported from PubMed on 13 Nov 2026.

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