DOI: 10.5061/dryad.qz612jmm7
title: MicrosatNavigator: Exploring nonrandom distribution and lineage-specificity of microsatellite repeat motifs on vertebrate sex chromosomes across 186 whole genomes

description: 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, considering their evolutionary variability
 and the simplicity of their evolutionary mechanisms. Using this tool,
 microsatellite repeat motifs in sex chromosomes of 186 vertebrates were
 identified. 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
 (≥50M% 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.
description: # MicrosatNavigator: Exploring nonrandom distribution and
 lineage-specificity of microsatellite repeat motifs on vertebrate sex
 chromosomes across 186 whole genomes Dataset DOI:
 [10.5061/dryad.qz612jmm7](10.5061/dryad.qz612jmm7) ## Description of the
 data and file structure The dataset contains all density and abundance
 data about the distribution of microsatellites in 186 whole genome
 sequences. Fasta sequence was collected from public databases (NCBI, DDBJ,
 ENA) and then processed by MicrosatNavigator. The output microsatellite
 data has been organized and structured in various TSV and Excel files. ##
 Description of the data and file structure The dataset contains: File S1:
 Supplementary_File_1_GC_Category_Python_script.zip: Python script allowing
 to categorize microsatellite category File S2:
 Supplementary_File_2_Simulated_fasta_files.zip: Simulated FASTA dataset
 used for benchmark testing of MicrosatNavigator
 Supplementary_table_1–14.zip: Table S1: List of genome assemblies that can
 be downloaded from public data repositories, such as NCBI, DDBJ, and ENA.
 These assemblies have chromosome-level information at the least Table S2:
 Relative abundance and relative density of microsatellite motif repeats
 Table S3: Relative density and fold difference of microsatellite motif
 repeats in autosomes and sex chromosomes Table S4: Summary of the top-five
 most significant microsatellites in the X, Y, Z, W, and autosomes Table
 S5: Assessment of accuracy and number of reported microsatellites in five
 simulated datasets Table S6: Comparison of pairs of the software's
 error rate using Tukey's Honest Significance Test Table S7:
 Comparison of the efficiency of MicrosatNavigator, KMER-SSR, PERF, and
 MISA for representative vertebrate genomes Table S8: The distribution of
 microsatellite repeat motif classes (mono-, di-, tri-, tetra-, penta-, and
 hexanucleotide) across 186 vertebrate genomes Table S9: Summary of the
 most common microsatellite repeat motifs in each class (mono-, di-, tri-,
 tetra-, penta-, and hexanucleotide) Table S10: Comparison of length
 differences among microsatellite repeat motif classes (mono-, di-, tri-,
 tetra-, penta-, and hexanucleotide) using Tukey’s Honest significance test
 Table S11: The length of individual microsatellites across 186 vertebrate
 genomes Table S12: Differences in the length of individual microsatellites
 between autosomes and sex chromosomes analyzed using Tukey’s Honest
 Significance Test Table S13: The relative abundance of each microsatellite
 GC% category in autosomes and sex chromosomes Table S14: The significance
 of the preference of each vertebrate lineage for a specific GC% category
 of microsatellite assessed using Tukey’s Honest test ## Code/Software
 Microsatellite distribution data has been generated by MicrosatNavigator
 and then processed by the Python script