Genome sequencing and assembly of feral chickens in the wild of Sulawesi, Indonesia

The feralization of domestic chicken makes the conservation and management of red jungle fowl (RJF, Gallus gallus) more complicated and challenging. We collected two Sulawesi feral chickens, located east of the Wallace Line, for whole-genome sequencing and de novo genome assembly. Phylogenetic and f4-statistics analyses indicated the Sulawesi feralized domestic chickens (G. g. domesticus) received gene flow from G. g. gallus. We integrated ~45x ultra-long Oxford Nanopore Technology reads and ~28x PacBio HiFi reads to generate a de novo genome assembly of a female Sulawesi feral chicken (GGsula) with a contig N50 of 19.88 Mbp. We characterized structural variations in GGsula, and found some were related to the nervous system. Our study provides the first genome assembly of feral chickens, which is a unique genomic resource to explore the process of chicken domestication and feralization.