A comprehensive microsatellite landscape of human Y-DNA at kilobase resolution

Abstract

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.

Microsatellite Density Landscapes Illustrate Short Tandem Repeats Aggregation in The Complete Reference Human Genome

“…More than 5% of the GRCh38 human genome consists of STRs instead of about 3% [43] (Table S2). Furthermore, the microsatellites landscapes at 1 Kbp resolution, as we displayed in the reference human Y-DNA previously [30], were comprehensively surveyed in the reference sequences of the GRCh38 human genome. Then, a total 58,769 SSRs landscape maps were obtained in the GRCh38 human genome (Fig.…”

“…IMEx 2.1 (Imperfect Microsatellite Extractor) was applied to identify STRs in the investigated genomes, which can find out relatively shorter STRs [31]. The threshold, which represents the lowest copy number of STR repeat units, was set at 6, 3, 3, 3, 3, 3 for extracting perfect mono-, di-, tri-, tetra-, penta- and hexanucleotide STRs respectively according to many previous STRs studies [30,32,33]. RepeatMasker and Tandem Repeat Finder were used as the reference tools for STRs identification [34,35].…”

“…The STRs landscape maps in the sample chromosomes were established by our developed method -Differential Calculator of Microsatellites (DCM) [29,30]; it could display the STRs density value in each genomic locational bin along the sample chromosome; this STRs density value was defined as STRs position-related differential relative density (pD n RD), and pD 1 RD represents the STRs density value at 1 Kbp differential resolution (pD 1 RD = (STRs size in each 1-Kbp bin /1-Kbp bin size) × 1000). The STRs landscape maps in the 2 genomes were based on the corresponding statistics of the STRs pD 1 RD and visualized by ggplot2 R package [36].…”

“…Recently, the Telomere-to-Telomere Consortium has firstly finished the sequencing of a complete human (female) genome without any gap called T2T-CHM13 (CHM13), with 3,054,815,472 bp in total sequence length, which contains all centromeric satellite arrays and the short arms of all 5 acrocentric chromosomes (chr13, 14, 15, 21 and 22), and this complete genome can provide a more comprehensive perspective to analyze microsatellites in human genome [25][26][27][28]. Previously, we investigated STRs landscape maps in the full human reference chromosome Y (GRCh38: NC_000024.10) at 1 kilo base pairs (Kbp) resolution by Differential Calculator of Microsatellite (DCM) method [29], revealing an exact distributional feature of STRs in every 1-Kbp locational bins of the chromosome Y [30]. In this study, we investigated STRs landscape maps in all chromosomes of human genome of GRC38 (p13 version) and CHM13 (1.1 version), and found that STRs tend to form HDMA peaks along each chromosome of GRCh38 and CHM13 human genomes.…”

Genome-wide development of intra- and inter-specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD

“…SSRs are ubiquitous in the genome of higher organisms and exhibit genetic polymorphism at inter- and intra-species levels (Bruford and Wayne 1993; Ellegren, 2004; Amiteye, 2021). Therefore, they have been widely used in population genetics (Chen et al, 2022; Sapkota et al, 2022;), genotyping, marker-assisted breeding, genome-wide association analysis (Li et al, 2014; Jha et al, 2021; Kim et al, 2021), forensic investigation (Li et al, 2021; Wang et al, 2022), evolutionary studies (Nowicki et al, 2021; Song et al, 2021; de Freitas et al, 2022), and conservation genetics (Rodríguez-Peña et al, 2018; Dong et al, 2022; Ming et al, 2022).…”