The Karnataka Individual Genome Project expands the human reference landscape to include South Asia

Assembling individual genomes remains an expensive endeavor, hindering large-scale comparative human genomics. So far, chromosome-level assemblies of only a few individuals, including PR1 (Puerto Rican), Ash1 (Ashkenazi Jew), Han1 (Southern Han Chinese), and CHM13 (Northern European) have been reported. Here, we present a chromosome-level genome assembly of a non-International Genome Sample Resource (IGSR) and non-Genome in a Bottle individual from the Indian subcontinent (KIn1) obtained using a cost-effective approach. We achieved an N50 of 141 Mb and an L50 of 9-very close to the maximum achievable N50 of 147 Mb and minimum achievable L50 of 8, respectively, for human genomes. We also generated chromosome-level assemblies for other individuals from the Indian diaspora, including PJL1 from Punjab, Lahore (HG03492), GIH1 from Gujarat (NA20847), BIB1 from Bangladesh (HG03009), and ITU1 from Andhra Pradesh (HG04217), all represented in IGSR, by scaffolding the publicly available respective contigs and Hi-C data. Here, we demonstrate that by comparing these individual genomes with those reported elsewhere, the configuration of inversion 8p23.1 in KIn1, Han1, GIH1, and BIB1 is similar to that in hg38, here to referred as 8p23.1std. The inverted configuration, 8p23.1inv, is present in CHM13, PJL1, Ash1, and PR1. We also find evidence of all three large known inversions in the p-arm of chromosome 16, with prevalence among South Asians. In chromosome 5, one of the reported inversions is present in all assemblies except hg38 and Ash1. Finally, we investigate the large inversions that are unique to KIn1.