Dataset Information

The Landscape of Micro-Inversions Provide Clues for Population Genetic Analysis of Humans.

ABSTRACT:

Background

Variations in the human genome have been studied extensively. However, little is known about the role of micro-inversions (MIs), generally defined as small (ResultsIn this paper, we explored the distribution of MIs in genomes from 26 human populations and 7 nonhuman primate genomes and analyzed the phylogenetic structure of the 26 human populations based on the MIs. We further investigated the functions of the MIs located within genes associated with human health. With hg19 as the reference genome, we detected 6968 MIs among the 1937 human samples and 24,476 MIs among the 7 nonhuman primate genomes. The analyses of MIs in human genomes showed that the MIs were rarely located in exonic regions. Nonhuman primates and human populations shared only 82 inverted alleles, and Africans had the most inverted alleles in common with nonhuman primates, which was consistent with the "Out of Africa" hypothesis. The clustering of MIs among the human populations also coincided with human migration history and ancestral lineages.

Conclusions

We propose that MIs are potential evolutionary markers for investigating population dynamics. Our results revealed the diversity of MIs in human populations and showed that they are essential to construct human population relationships and have a potential effect on human health.

SUBMITTER: Qu L

PROVIDER: S-EPMC7658078 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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Publications

The Landscape of Micro-Inversions Provide Clues for Population Genetic Analysis of Humans.

Qu Li L Wang Luotong L He Feifei F Han Yilun Y Yang Longshu L Wang May D MD Zhu Huaiqiu H

Interdisciplinary sciences, computational life sciences 20200914 4

<h4>Background</h4>Variations in the human genome have been studied extensively. However, little is known about the role of micro-inversions (MIs), generally defined as small (< 100 bp) inversions, in human evolution, diversity, and health. Depicting the pattern of MIs among diverse populations is critical for interpreting human evolutionary history and obtaining insight into genetic diseases.<h4>Results</h4>In this paper, we explored the distribution of MIs in genomes from 26 human populations ...[more]

PMID: 32929667

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Project description:BackgroundPatterns of homozygosity can be influenced by several factors, such as demography, recombination, and selection. Using the goat SNP50 BeadChip, we genotyped 3171 goats belonging to 117 populations with a worldwide distribution. Our objectives were to characterize the number and length of runs of homozygosity (ROH) and to detect ROH hotspots in order to gain new insights into the consequences of neutral and selection processes on the genome-wide homozygosity patterns of goats.ResultsThe proportion of the goat genome covered by ROH is, in general, less than 15% with an inverse relationship between ROH length and frequency i.e. short ROH (<?3 Mb) are the most frequent ones. Our data also indicate that ~?60% of the breeds display low FROH coefficients (<?0.10), while ~?30 and ~?10% of the goat populations show moderate (0.10?<?FROH?<?0.20) or high (>?0.20) FROH values. For populations from Asia, the average number of ROH is smaller and their coverage is lower in goats from the Near East than in goats from Central Asia, which is consistent with the role of the Fertile Crescent as the primary centre of goat domestication. We also observed that local breeds with small population sizes tend to have a larger fraction of the genome covered by ROH compared to breeds with tens or hundreds of thousands of individuals. Five regions on three goat chromosomes i.e. 11, 12 and 18, contain ROH hotspots that overlap with signatures of selection.ConclusionsPatterns of homozygosity (average number of ROH of 77 and genome coverage of 248 Mb; FROH?<?0.15) are similar in goats from different geographic areas. The increased homozygosity in local breeds is the consequence of their small population size and geographic isolation as well as of founder effects and recent inbreeding. The existence of three ROH hotspots that co-localize with signatures of selection demonstrates that selection has also played an important role in increasing the homozygosity of specific regions in the goat genome. Finally, most of the goat breeds analysed in this work display low levels of homozygosity, which is favourable for their genetic management and viability.

Dataset Information

The Landscape of Micro-Inversions Provide Clues for Population Genetic Analysis of Humans.

Background

Conclusions

Publications

The Landscape of Micro-Inversions Provide Clues for Population Genetic Analysis of Humans.

Similar Datasets

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