Toward a complete diploid chicken genome.

Trio sequencing produced 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 reference.
• What they did: A trio-sequencing design used long reads from a female chick plus parental long-read data to phase haplotypes and assemble nearly complete genomes.
• The result: GGswu2 resolved more than 50 Mb of previously unresolved regions, and dot chromosomes show low nucleotide diversity but high structural-variant density between haplotypes, with centromere size/position differences sometimes present.

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