The first assembled chromosome-level genome of an individual from Karnataka, India

We present the first chromosome-level assembled genome of an individual from Karnataka, India (KIn1), using de novo assembly of 12x coverage of PacBio HiFi reads generated in-house and 30x Hi-C data from the most ethnically related individual to KIn1 from Andhra Pradesh (HG04712), publicly available under International Genome Sample Resource (IGSR). We achieved an N50 of 137 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. A comparison of the KIn1 assembly with assemblies of four other individual genomes from a Puerto Rican (PR1), Ashkenazi (Ash1), Hans Chinese (Hans1), and Northern European (T2T) reported to date from resources like IGSR and/or Genome-in-a-Bottle (GIBR) collections shows that the longest scaffolds from KIn1 cover 80-90% of the reference chromosomes and exhibit near collinearity. We find a unique inversion in the chromosome 7 euchromatic region and other major translocations in chromosomes 17 and 20 in KIn1. We also produced a chromosome-level assembly for another individual from Punjab, Lahore (HG03492), for use in our comparison. The analysis of variants among select IGSR individuals using the KIn1 assembly as a reference reveals that the Indian Telugu from the UK (ITU) population in IGSR is ethnically closest to KIn1, followed by the Sri Lankan Tamil from the UK (STU) as representatives of South Asian ancestry.