Background Though interest in human simple sequence repeats (SSRs) is increasing, little is known about the exact distributional features of numerous SSRs in human Y-DNA at chromosomal level. Herein, totally 540 maps were established, which could clearly display SSR landscape in every bin of 1 k base pairs (Kbp) along the sequenced part of human reference Y-DNA (NC_000024.10), by our developed differential method for improving the existing method to reveal SSR distributional characteristics in large genomic sequences. Results The maps show that SSRs accumulate significantly with forming density peaks in at least 2040 bins of 1 Kbp, which involve different coding, noncoding and intergenic regions of the Y-DNA, and 10 especially high density peaks were reported to associate with biological significances, suggesting that the other hundreds of especially high density peaks might also be biologically significant and worth further analyzing. In contrast, the maps also show that SSRs are extremely sparse in at least 207 bins of 1 Kbp, including many noncoding and intergenic regions of the Y-DNA, which is inconsistent with the widely accepted view that SSRs are mostly rich in these regions, and these sparse distributions are possibly due to powerfully regional selection. Additionally, many regions harbor SSR clusters with same or similar motif in the Y-DNA. Conclusions These 540 maps may provide the important information of clearly position-related SSR distributional features along the human reference Y-DNA for better understanding the genome structures of the Y-DNA. This study may contribute to further exploring the biological significance and distribution law of the huge numbers of SSRs in human Y-DNA.
Background The ubiquitous presence of short tandem repeats (STRs) in virtually all genomes implicates their functional relevance, while a widely-accepted definition of STR is yet to be established. Previous studies majorly focus on relatively longer STRs, while shorter repeats were generally excluded. Herein, we have adopted a more generous criteria to define shorter repeats, which has led to the definition of a much larger number of STRs that lack prior analysis. Using this definition, we analyzed the short repeats in 55 randomly selected segments in 55 randomly selected genomic sequences from a fairly wide range of species covering animals, plants, fungi, protozoa, bacteria, archaea and viruses. Results Our analysis reveals a high percentage of short repeats in all 55 randomly selected segments, indicating that the universal presence of high-content short repeats could be a common characteristic of genomes across all biological kingdoms. Therefore, it is reasonable to assume a mechanism for continuous production of repeats that can make the replicating process relatively semi-conservative. We have proposed a folded replication slippage model that considers the geometric space of nucleotides and hydrogen bond stability to explain the mechanism more explicitly, with improving the existing straight-line slippage model. The folded slippage model can explain the expansion and contraction of mono- to hexa- nucleotide repeats with proper folding angles. Analysis of external forces in the folding template strands also suggests that expansion exists more commonly than contraction in the short tandem repeats. Conclusion The folded replication slippage model provides a reasonable explanation for the continuous occurrences of simple sequence repeats in genomes. This model also contributes to the explanation of STR-to-genome evolution and is an alternative model that complements semi-conservative replication.
We systematically built more than 100,000 microsatellites landscape-maps with identifying 3,433 and 5,306 high density microsatellites accumulation (HDMA) peaks in the human reference genome (GRCh38, p13 version) and the first complete human genome (T2T-CHM13, 1.1 version) at 1 kilobase resolution. Intuitive HDMA peak-locus maps were constructed for every chromosome of the 2 genomes, revealing that these HDMA peaks are distributed regularly along every chromosome. Data mining and comparison of HDMA peaks illustrated that most of the HDMA peaks may play biological roles with highly variable genomic sequences. Therefore, comparing the variation of HDMA peaks will provide an unprecedented approach to study human genetic variation.
Simple sequence repeats (SSRs) are found ubiquitously in almost all genome, and their formation mechanism is ambiguous yet. Here, the SSRs were analyzed in 55 randomly selected segments of genomes from a fairly wide range of species, with introducing more open standard for extensively mining repeats. A high percentage of repeats were discovered in these segments through that open standard and verified that they are not random. However, the current theory suggested that repeats tend to disappear over long-term evolution, which is inconsistent with such high proportion of SSRs remained in the genomes, inferring that there is most probably a mechanism for continually producing repeats during replicating process to balance continuous repeat disappearance. It can be inferred that there is most probably a mechanism for continually producing repeats during replicating process to balance continuous repeats disappearance, which certainly makes the base numbers of replication strand unequal to template strand. Therefore, the accepted straight-line slippage model is necessary to improve for explaining occurrence of simple sequence repeats. We proposed a folded slippage model to explain the high percent microsatellite occurrence with considering the geometric space of nucleotides and hydrogen bond stability, which can describe microsatellite expansion and contraction more reasonably. And analysis of external forces in the folding template strands showed the microsatellites tend to expand than contract. Our research may provide implements for the contribution of microsatellites to genome evolution and complement the semi-conservative replication.
BackgroundSimple sequence repeats (SSRs) are found ubiquitously in almost all genome, and their formation mechanism is ambiguous yet.ResultsHere, the SSRs were analyzed in 55 randomly selected segments of genomes from a fairly wide range of species, with introducing more open standard for extensively mining repeats. A high percentage of repeats were discovered in these segments, which is inconsistent with the current theory suggested that repeats tend to disappear over long-term evolution. Therefore, a mechanism is most probably responsible for continually producing repeats during replication to balance continuous repeat disappearance, which may makes the replicating process relatively semi-conservative. To improve the current straight-line slippage model, we proposed a folded slippage model involving the geometric space of nucleotides and hydrogen bond stability to explain the high-percent SSR occurrence, which can describe SSR expansion and contraction more reasonably. And analysis of external forces in the folding template strands suggested that the microsatellites tend to expand than contract.ConclusionOur research may provide implements for contributions of microsatellites to genome evolution and complement semi-conservative replication.
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