Abstract
We report the results of an extensive investigation of genomic structures in the human genome, with a particular focus on relatively large repeats (>50 kb) in adjacent chromosomal regions. We named such structures “Flowers” because the pattern observed on dot plots resembles a flower. We detected a total of 291 Flowers in the human genome. They were predominantly located in euchromatic regions. Flowers are gene-rich compared to the average gene density of the genome. Genes involved in systems receiving environmental information, such as immunity and detoxification, were overrepresented in Flowers. Within a Flower, the mean number of duplication units was approximately four. The maximum and minimum identities between homologs in a Flower showed different distributions; the maximum identity was often concentrated to 100% identity, while the minimum identity was evenly distributed in the range of 78% to 100%. Using a gene conversion detection test, we found frequent and/or recent gene conversion events within the tested Flowers. Interestingly, many of those converted regions contained protein-coding genes. Computer simulation studies suggest that one role of such frequent gene conversions is the elongation of the life span of gene families in a Flower by the resurrection of pseudogenes.
Highlights
We report the results of an extensive investigation of genomic structures in the human genome, with a particular focus on relatively large repeats (>50 kb) in adjacent chromosomal regions
A genomic structure is a region of repeats located on adjacent chromosomal regions and consists of combinations of tandem or/and inverted repeats and palindromes
Our method focused on identifying genomic structures, which are duplication-concentrated regions generated by genomic rearrangements
Summary
A genomic structure is a region of repeats located on adjacent chromosomal regions and consists of combinations of tandem or/and inverted repeats and palindromes. Genomic structures are generated by genomic rearrangements such as duplications, deletions, and inversions in a genome. If the genes are located within a rearrangement such as a duplication or deletion, the number of genes would vary between individuals, and expression levels of those genes could vary [1, 2]; this may affect phenotypic traits. Inversions do not result in changes in the copy number of genes, but could affect recombination frequency between an intact and inverted segment (haplotype). Recombination is suppressed, and both haplotypes accumulate specific mutations. This accumulation enhances genetic differentiation between genomes within a species. If genes in the recombination-suppressed region are involved in mating or adaptation to environmental changes, the inversion might affect reproductive isolation or speciation [4]
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