MicrosatNavigator: exploring nonrandom distribution and lineage-specificity of microsatellite repeat motifs on vertebrate sex chromosomes across 186 whole genomes

• Type: Article in International Scientific Journal
• Date: 2023

Authors

Rasoarahona, R (Author) Other; Wattanadilokchatkun, P (Author) Other; Panthum, T (Author) Other; Jaisamut, K (Author) Other; Lisachov, A (Author) Other; Thong, T (Author) Other; Singchat, W (Author) Other; Ahmad, SF (Author) Other; Han, KYD (Author) Other; Kraichak, E (Author) Other; Muangmai, N (Author) Other; Koga, A (Author) Other; Duengkae, P (Author) Other; Agostinho Antunes (Author) FCUP; Srikulnath, K (Author) Other

Journal

Title: Chromosome Research

Vol. 31

Initial page: 29

ISSN: 0967-3849

Publisher: Springer Nature

Indexing

ISI Web of Knowledge - 0 Citations

Scopus - 0 Citations

Other information

Authenticus ID: P-00Z-41W

DOI: 10.1007/s10577-023-09738-4

Abstract (EN): Microsatellites are short tandem DNA repeats, ubiquitous in genomes. They are believed to be under selection pressure, considering their high distribution and abundance beyond chance or random accumulation. However, limited analysis of microsatellites in single taxonomic groups makes it challenging to understand their evolutionary significance across taxonomic boundaries. Despite abundant genomic information, microsatellites have been studied in limited contexts and within a few species, warranting an unbiased examination of their genome-wide distribution in distinct versus closely related-clades. Large-scale comparisons have revealed relevant trends, especially in vertebrates. Here, MicrosatNavigator, a new tool that allows quick and reliable investigation of perfect microsatellites in DNA sequences, was developed. This tool can identify microsatellites across the entire genome sequences. Using this tool, microsatellite repeat motifs were identified in the genome sequences of 186 vertebrates. A significant positive correlation was noted between the abundance, density, length, and GC bias of microsatellites and specific lineages. The (AC)n motif is the most prevalent in vertebrate genomes, showing distinct patterns in closely related species. Longer microsatellites were observed on sex chromosomes in birds and mammals but not on autosomes. Microsatellites on sex chromosomes of non-fish vertebrates have the lowest GC content, whereas high-GC microsatellites (>= 50 M% GC) are preferred in bony and cartilaginous fishes. Thus, similar selective forces and mutational processes may constrain GC-rich microsatellites to different clades. These findings should facilitate investigations into the roles of microsatellites in sex chromosome differentiation and provide candidate microsatellites for functional analysis across the vertebrate evolutionary spectrum.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 22