Whole human genome sequencing initiatives help us understand population history
and the basis of genetic diseases. Current data mostly focuses on Old World
populations, and the information of the genomic structure of Native Americans,
especially those from the Southern Cone is scant. Here we present annotation and
variant discovery from high-quality complete genome sequences of a cohort of 11
Mapuche-Huilliche individuals (HUI) from Southern Chile. We found approximately
3.1 × 106 single nucleotide variants (SNVs) per individual and identified
403,383 (6.9%) of novel SNVs events. Analyses of large-scale genomic events
detected 680 copy number variants (CNVs) and 4,514 structural variants (SVs),
including 398 and 1,910 novel events, respectively. Global ancestry composition
of HUI genomes revealed that the cohort represents a sample from a marginally
admixed population from the Southern Cone, whose main genetic component derives
from Native American ancestors. Additionally, we found that HUI genomes contain
variants in genes associated with 5 of the 6 leading causes of noncommunicable
diseases in Chile, which may have an impact on the risk of prevalent diseases in
Chilean and Amerindian populations. Our data represents a useful resource that
can contribute to population-based studies and for the design of early
diagnostics or prevention tools for Native and admixed Latin American
populations.
