A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants.

ABSTRACT:

Background

The red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many of which have accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited to cataloging simple variants such as single-nucleotide changes and short insertions and deletions, it is mostly inadequate to discover more complex structural variation in the genome.

Methods

We present a pangenome for the domestic chicken consisting of thirty assemblies of chickens from different breeds and res

SUBMITTER: Rice ES 

PROVIDER: S-EPMC10664547 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature