Towards a complete diploid chicken genome

Trio sequencing enabled nearly complete, haplotype-resolved paternal and maternal chicken genome assemblies, leaving 14 residual gaps and missing telomeric sequences on 2 paternal and 4 maternal chromosomes.

• Why it matters: Repetitive and heterochromatic microchromosome and dot chromosome regions have blocked creation of a complete, haplotype-resolved chicken genome, limiting evolutionary and genetic analyses.
• What they did: Long reads from a female chick were combined with parental long-read data for haplotype phasing, producing assemblies that resolved over 50 Mb of previously unresolved regions, mainly in dot chromosomes.
• The result: Dot chromosomes show low nucleotide diversity but high structural-variant density between haplotypes, and centromere sizes/positions sometimes differ, implying comparative genomics must model these dynamic regions.

AI summary of the abstract · may contain errors · not medical advice · read the paper.