ArticleBMC evolutionary biology2011
Abundance of ultramicro inversions within local alignments between human and chimpanzee genomes.
Article in BMC evolutionary biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed.
- Characteristics and possible mechanisms of formation of microinversions distinguishing human and chimpanzee genomes.Scientific reports · 2022Article
- The Landscape of Micro-Inversions Provide Clues for Population Genetic Analysis of Humans.Interdisciplinary sciences, computational life sciences · 2020Article
- A simple method to control over-alignment in the MAFFT multiple sequence alignment program.Bioinformatics (Oxford, England) · 2016Article
- Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis.Briefings in bioinformatics · 2014Review
- On the structural plasticity of the human genome: chromosomal inversions revisited.Current genomics · 2012Article
- Reconstructing the demographic history of the human lineage using whole-genome sequences from human and three great apes.Genome biology and evolution · 2012Article
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2 authors.
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Abstract
backgroundChromosomal inversion is one of the most important mechanisms of evolution. Recent studies of comparative genomics have revealed that chromosomal inversions are abundant in the human genome. While such previously characterized inversions are large enough to be identified as a single alignment or a string of local alignments, the impact of ultramicro inversions, which are such short that the local alignments completely cover them, on evolution is still uncertain.
resultsIn this study, we developed a method for identifying ultramicro inversions by scanning of local alignments. This technique achieved a high sensitivity and a very low rate of false positives. We identified 2,377 ultramicro inversions ranging from five to 125 bp within the orthologous alignments between the human and chimpanzee genomes. The false positive rate was estimated to be around 4%. Based on phylogenetic profiles using the primate outgroups, 479 ultramicro inversions were inferred to have specifically inverted in the human lineage. Ultramicro inversions exclusively involving adenine and thymine were the most frequent; 461 inversions (19.4%) of the total. Furthermore, the density of ultramicro inversions in chromosome Y and the neighborhoods of transposable elements was higher than average. Sixty-five ultramicro inversions were identified within the exons of human protein-coding genes.
conclusionsWe defined ultramicro inversions as the inverted regions equal to or smaller than 125 bp buried within local alignments. Our observations suggest that ultramicro inversions are abundant among the human and chimpanzee genomes, and that location of the inversions correlated with the genome structural instability. Some of the ultramicro inversions may contribute to gene evolution. Our inversion-identification method is also applicable in the fine-tuning of genome alignments by distinguishing ultramicro inversions from nucleotide substitutions and indels.
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