Global abundance of short tandem repeats is non-random in rodents and primates

被引:7
作者
Arabfard, Masoud [1 ]
Salesi, Mahmood [1 ]
Nourian, Yazdan Hassani [1 ]
Arabipour, Iman [2 ]
Maddi, AliMohammad Ali [3 ]
Kavousi, Kaveh [3 ]
Ohadi, Mina [4 ]
机构
[1] Baqiyatallah Univ Med Sci, Chem Injuries Res Ctr, Syst Biol & Poisonings Inst, Tehran, Iran
[2] Islamic Azad Univ, Dept Biotechnol, Sci & Res Branch, Tehran, Iran
[3] Univ Tehran, Inst Biochem & Biophys IBB, Dept Bioinformat, Lab Complex Biol Syst & Bioinformat CBB, Tehran, Iran
[4] Univ Social Welf & Rehabil Sci, Iranian Res Ctr Aging, Tehran, Iran
来源
BMC GENOMIC DATA | 2022年 / 23卷 / 01期
关键词
Global; Short tandem repeat; Abundance; Non-random; Rodent; Primate; Hierarchical clustering; CORE PROMOTER; GENE-EXPRESSION; EVOLUTION; SEQUENCE; IDENTIFICATION; POPULATIONS; SELECTION; COMPLEX; GENOME; LENGTH;
D O I
10.1186/s12863-022-01092-4
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
Background While of predominant abundance across vertebrate genomes and significant biological implications, the relevance of short tandem repeats (STRs) (also known as microsatellites) to speciation remains largely elusive and attributed to random coincidence for the most part. Here we collected data on the whole-genome abundance of mono-, di-, and trinucleotide STRs in nine species, encompassing rodents and primates, including rat, mouse, olive baboon, gelada, macaque, gorilla, chimpanzee, bonobo, and human. The collected data were used to analyze hierarchical clustering of the STR abundances in the selected species. Results We found massive differential STR abundances between the rodent and primate orders. In addition, while numerous STRs had random abundance across the nine selected species, the global abundance conformed to three consistent < clusters>, as follows: <rat, mouse>, <gelada, macaque, olive baboon>, and <gorilla, chimpanzee, bonobo, human>, which coincided with the phylogenetic distances of the selected species (p < 4E-05). Exceptionally, in the trinucleotide STR compartment, human was significantly distant from all other species. Conclusion Based on hierarchical clustering, we propose that the global abundance of STRs is non-random in rodents and primates, and probably had a determining impact on the speciation of the two orders. We also propose the STRs and STR lengths, which predominantly conformed to the phylogeny of the selected species, exemplified by (t)10, (ct)6, and (taa4). Phylogenetic and experimental platforms are warranted to further examine the observed patterns and the biological mechanisms associated with those STRs.
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页数:11
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