Comparison of the Microsatellite Distribution Patterns in the Genomes of Euarchontoglires at the Taxonomic Level

Abstract

Microsatellite or simple sequence repeat (SSR) instability within genes can induce genetic variation. The SSR signatures remain largely unknown in different clades within Euarchontoglires, one of the most successful mammalian radiations. Here, we conducted a genome-wide characterization of microsatellite distribution patterns at different taxonomic levels in 153 Euarchontoglires genomes. Our results showed that the abundance and density of the SSRs were significantly positively correlated with primate genome size, but no significant relationship with the genome size of rodents was found. Furthermore, a higher level of complexity for perfect SSR (P-SSR) attributes was observed in rodents than in primates. The most frequent type of P-SSR was the mononucleotide P-SSR in the genomes of primates, tree shrews, and colugos, while mononucleotide or dinucleotide motif types were dominant in the genomes of rodents and lagomorphs. Furthermore, (A)n was the most abundant motif in primate genomes, but (A)n, (AC)n, or (AG)n was the most abundant motif in rodent genomes which even varied within the same genus. The GC content and the repeat copy numbers of P-SSRs varied in different species when compared at different taxonomic levels, reflecting underlying differences in SSR mutation processes. Notably, the CDSs containing P-SSRs were categorized by functions and pathways using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes annotations, highlighting their roles in transcription regulation. Generally, this work will aid future studies of the functional roles of the taxonomic features of microsatellites during the evolution of mammals in Euarchontoglires.

Mutation and selection processes regulating short tandem repeats give rise to genetic and phenotypic diversity across species

“…Interestingly, it was reported that hexamers are the most abundant type of STR in intergenic, intronic and exonic regions in Srivastava et al ( 2019 ). This is in contrast with previous literature, where hexamers were typically found to be among the rarest types of STRs (Ding et al, 2017 ; Song et al, 2021 ; Willems et al, 2014 ). The way in which STR abundances were quantified may be at the root of this apparent discrepancy: Srivastava et al ( 2019 ) compared abundances of different repeat types based on the fraction of all STR bases covered by STRs of a particular motif size.…”

“…Recent years have seen several comparative genomics studies aimed at investigating patterns of STR characteristics across eukaryotes at various evolutionary distances. From these investigations, we can learn that while it is true that larger genomes tend to have more and longer STRs (Ding et al, 2017 ; Song et al, 2021 ; Yuan et al, 2018 ), the STR density per megabase seems to be rather constant (Srivastava et al, 2019 ), with some exceptions noted below. Furthermore, G/C content in STRs is generally representative of the corresponding genomic G/C content, which is not correlated to the overall STR density (Srivastava et al, 2019 ).…”

The Landscape of Genome-Wide and Gender-Specific Microsatellites in Indo-Pacific Humpback Dolphin and Potential Applications in Cetacean Resource Investigation

“…AC/GT motifs were the most abundant in the dinucleotide microsatellites (Figure 1B). On the whole, the composition of the microsatellites of the S. chinensis genome was consistent with that in mammals such as humans, primates, rats, camels, and pigs [35][36][37][38][39][40]. To date, genome-wide microsatellites have been deciphered and mined for many aquatic species such as jellyfish, catfish and eel fish, etc.…”

First record of the spatial organization of the nucleosome‐less chromatin of dinoflagellates: The nonrandom distribution of microsatellites and bipolar arrangement of telomeres in the nucleus of Gambierdiscus australes (Dinophyceae)

“…Our results indicate that trinucleotide repeats constitute a larger proportion of the microsatellites in the genome of Gambierdiscus australes than either monoor AC and AG dinucleotide repeats. In most eukaryotes, especially higher vertebrates such as birds and mammals, mononucleotides as well as AC and AG dinucleotides are the most common microsatellites (e.g., Song et al 2021). The exception is in green algae and some of the protists and fungi analyzed by Srivastava et al (2019), in which trinucleotides accounted for a large proportion of the motif types and were second in abundance only to hexamers.…”

“…In most eukaryotes, especially higher vertebrates such as birds and mammals, mononucleotides as well as AC and AG dinucleotides are the most common microsatellites (e.g., Song et al. 2021). The exception is in green algae and some of the protists and fungi analyzed by Srivastava et al.…”