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, which are 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 unique inversion in chromosome 7 euchromatic region and other major translocations in chr17 and 20 in KIin1. 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 UK (ITU) population in IGSR is ethnically closest to KIn1, followed by the Srilankan Tamil from UK (STU) as representatives of South Asian ancestry.