High quality assemblies of four indigenous chicken genomes and related functional and genetics data resources

Abstract Many lines of evidence indicate that red jungle fowl (RJF) is the primary ancestor of domestic chickens. Although multiple versions of RJF (GRCg1~GRCg6a) and commercial chicken (GRCg7b/w) genomes have been assembled since 2004, no high-quality indigenous chicken genomes have been assembled, hampering the understanding of chicken domestication and evolution. To fill the gap, we sequenced the genomes of four indigenous chickens with distinct morphological traits in southwest China, using a combination of short, long and Hi-C reads. We assembled each genome (~1.0 Gb) into 42 chromosomes with chromosome N50 90.5~90.9 Mb, the highest quality of chicken genome assembly achieving so far. To provide resources for gene annotation and population genetic analysis, we also sequenced transcriptomes of 10 tissues for each of the four chickens and re-sequenced ~20 individuals for each of the four chicken breeds. Moreover, we corrected many mis-assemblies and assembled micro-chromosomes chr29 and chr34~chr39 for GRCg6a. Our assemblies, sequencing data and the correction of GRCg6a can be valuable resources for studying chicken domestication and evolution.