abundance of ultramicro inversions within local alignments between human and chimpanzee genomes丰富的超微倒置在人类和黑猩猩的基因组之间的局部比对.pdfVIP

Hara and Imanishi BMC Evolutionary Biology 2011, 11:308 /1471-2148/11/308 RESEARCH ARTICLE Open Access Abundance of Ultramicro Inversions within Local Alignments between Human and Chimpanzee Genomes * Yuichiro Hara and Tadashi Imanishi Abstract Background: Chromosomal 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. Results: In 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. Conclusions: We defined ultramicro inversions as the inverted regions equal to or smaller than 125 bp buried within local alignments. Our observations suggest th