Abstract
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.
Highlights
Sequencing complete human genomes has greatly expanded the knowledge of our genetic diversity, providing insights into the evolutionary history of man and the bases of human diseases
Global ancestry composition revealed that Huilliche individuals (HUI) genomes sequenced have a minimal contribution of European, East and South Asian and African founder populations (K = 5) and represent an original source of genetic variation for modern admixed individuals living in America
We found that contemporary American populations, including admixed Latinos from Chile and Peruvians from Lima (PEL) have a high genetic component of an unknown ancestral genetic contribution identified only in HUI genomes
Summary
Sequencing complete human genomes has greatly expanded the knowledge of our genetic diversity, providing insights into the evolutionary history of man and the bases of human diseases. While current high-coverage full genome efforts have mostly focused on Europeans, Asians and Africans, there is still limited information concerning the genetic structure of Native American groups[4]. Whole genome/exome and large-scale genotyping data has been used to study the genetic history, multiple streams of migration and population-genomic variables that underlie patterns of deleterious variation for African, Asian, European, and Native American ancestry in populations of Latin America and the Caribbean[7,8,9,10], as well as the Pacific Northwest[11]. We sequenced at high-coverage and analyzed the complete genome of 11 individuals belonging to a native Mapuche-Huilliche population from Southern Chile
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