Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes.

TitleWhole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes.
Publication TypeJournal Article
Year of Publication2014
AuthorsUdpa N, Ronen R, Zhou D, Liang J, Stobdan T, Appenzeller O, Yin Y, Du Y, Guo L, Cao R, Wang Y, Jin X, Huang C, Jia W, Cao D, Guo G, Claydon VE, Hainsworth R, Gamboa JL, Zibenigus M, Zenebe G, Xue J, Liu S, Frazer KA, Li Y, Bafna V, Haddad GG
JournalGenome Biol
Volume15
Issue2
PaginationR36
Date Published2014 Feb 20
ISSN1465-6914
Abstract

BACKGROUND: Although it has long been proposed that genetic factors contribute to adaptation to high altitude, such factors remain largely unverified. Recent advances in high-throughput sequencing have made it feasible to analyze genome-wide patterns of genetic variation in human populations. Since traditionally such studies surveyed only a small fraction of the genome, interpretation of the results was limited. RESULTS: We report here the results of the first whole genome resequencing-based analysis identifying genes that likely modulate high altitude adaptation in native Ethiopians residing at 3500 m above sea level on Bale Plateau or Chennek field in Ethiopia. Using cross-population tests of selection, we identify regions with a significant loss of diversity, indicative of a selective sweep. We focus on a 208 kbp gene-rich region on chromosome 19, which is significant in both of the Ethiopian subpopulations sampled. This region contains eight protein-coding genes and spans 135 SNPs. To elucidate its potential role in hypoxia tolerance, we experimentally tested whether individual genes from the region affect hypoxia tolerance in Drosophila. Three genes significantly impact survival rates in low oxygen: cic, an ortholog of human CIC, Hsl, an ortholog of human LIPE, and Paf-AHalpha, an ortholog of human PAFAH1B3. CONCLUSIONS: Our study reveals evolutionarily conserved genes that modulate hypoxia tolerance. In addition, we show that many of our results would likely be unattainable using data from exome sequencing or microarray studies. This highlights the importance of whole genome sequencing for investigating adaptation by natural selection.

DOI10.1186/gb-2014-15-2-r36
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/24555826?dopt=Abstract
PMCPMC4054780
Alternate JournalGenome Biol.
PubMed ID24555826