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 × 10 6 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.
Bibliographical noteFunding Information:
The authors thank the Mapuche-Huilliche community of Huapi Island (Ranco Lake), without whose participation and encouragement this work would not have been made possible. This work was funded by grants from Fondo de Areas Prioritarias (FONDAP) Center for Genome Regulation (number 1509000), FONDAP Center for intercultural and indigenous research (number 15110006), Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT) numbers 1130303 to J.F.M., 1140353 and 1180848 to G.V.D., 3160400 to E.R, and 1120813 and 1160833 to S.E.
© 2019, The Author(s).