Patterns of microsatellite distribution across eukaryotic genomes

BMC Genomics
Surabhi SrivastavaRakesh Kumar Mishra

Abstract

Microsatellites, or Simple Sequence Repeats (SSRs), are short tandem repeats of 1-6 nt motifs present in all genomes. Emerging evidence points to their role in cellular processes and gene regulation. Despite the huge resource of genomic information currently available, SSRs have been studied in a limited context and compared across relatively few species. We have identified ~ 685 million eukaryotic microsatellites and analyzed their genomic trends across 15 taxonomic subgroups from protists to mammals. The distribution of SSRs reveals taxon-specific variations in their exonic, intronic and intergenic densities. Our analysis reveals the differences among non-related species and novel patterns uniquely demarcating closely related species. We document several repeats common across subgroups as well as rare SSRs that are excluded almost throughout evolution. We further identify species-specific signatures in pathogens like Leishmania as well as in cereal crops, Drosophila, birds and primates. We also find that distinct SSRs preferentially exist as long repeating units in different subgroups; most unicellular organisms show no length preference for any SSR class, while many SSR motifs accumulate as long repeats in complex organisms,...Continue Reading

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Citations

Oct 11, 2019·Nucleic Acids Research·Akshay Kumar AvvaruDivya Tej Sowpati
Oct 11, 2019·Molecular Ecology Resources·Lianming DuZhenxin Fan
Jul 27, 2021·Physiology and Molecular Biology of Plants : an International Journal of Functional Plant Biology·Aman DabralManeesh S Bhandari
Oct 20, 2021·Genome Biology and Evolution·Hsiao-Pei YangFay-Wei Li
Nov 10, 2021·Functional & Integrative Genomics·Karine E Janner de FreitasAntonio Costa de Oliveira
Sep 25, 2020·Chemico-biological Interactions·Rohit SatyamMohammad Amjad Kamal

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Software Mentioned

house Python script
R
Morpheus
SciPy package
TimeTree
house
in
Python
iTOL ( interactive Tree of Life )
aov

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