Towards a complete diploid chicken genome
- 1Southwest University
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 produced nearly complete, haplotype-resolved paternal and maternal assemblies, with 14 residual gaps. Telomeric sequences remain missing in 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 the high-resolution of these dynamic complex regions to fully understand avian genome evolution and genetic complexity.
Related
- The complete chloroplast genome of diploid Hieracium tomentosum (Asteraceae, Cichorieae)
- Haplotype-resolved DiMeLo-seq maps centromeric chromatin in a complete diploid human genome
- A first complete catalog of highly expressed genes in eight chicken tissues reveals uncharacterized gene families specific for the chicken testis
- DipSkmer: Reference-free population genomics with diploid genome skims
- The revised diploid genome sequence of an individual human: A workflow for near telomere-to-telomere assemblies using only Oxford Nanopore Technologies Simplex-reads
BibTeX
@misc{fan2026towards,
title = {{Towards a complete diploid chicken genome}},
author = {S. Fan and J. Liu and N. Kang and D. Li and Z. Li and N. Xu and L. Xu},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.25.761615},
url = {https://www.biorxiv.org/content/10.64898/2026.10.25.761615v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Towards a complete diploid chicken genome
AU - S. Fan
AU - J. Liu
AU - N. Kang
AU - D. Li
AU - Z. Li
AU - N. Xu
AU - L. Xu
PY - 2026
DA - 2026/10/25
PB - bioRxiv
DO - 10.64898/2026.10.25.761615
UR - https://www.biorxiv.org/content/10.64898/2026.10.25.761615v1
AB - 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 produced nearly complete, haplotype-resolved paternal and maternal assemblies, with 14 residual gaps. Telomeric sequences remain missing in 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 the high-resolution of these dynamic complex regions to fully understand avian genome evolution and genetic complexity.
ER -