title: Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution.
abstract: The evolutionary dynamics of simple sequence repeats (SSRs or microsatellites) across the vertebrate tree of life remain largely undocumented and poorly understood. In this study, we analyzed patterns of genomic microsatellite abundance and evolution across 71 vertebrate genomes. The highest abundances of microsatellites exist in the genomes of ray-finned fishes, squamate reptiles, and mammals, while crocodilian, turtle, and avian genomes exhibit reduced microsatellite landscapes. We used comparative methods to infer evolutionary rates of change in microsatellite abundance across vertebrates and to highlight particular lineages that have experienced unusually high or low rates of change in genomic microsatellite abundance. Overall, most variation in microsatellite content, abundance, and evolutionary rate is observed among major lineages of reptiles, yet we found that several deeply divergent clades (i.e., squamate reptiles and mammals) contained relatively similar genomic microsatellite compositions. Archosauromorph reptiles (turtles, crocodilians, and birds) exhibit reduced genomic microsatellite content and the slowest rates of microsatellite evolution, in contrast to squamate reptile genomes that have among the highest rates of microsatellite evolution. Substantial branch-specific shifts in SSR content in primates, monotremes, rodents, snakes, and fish are also evident. Collectively, our results support multiple major shifts in microsatellite genomic landscapes among vertebrates.
authors.affiliation: a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA.
authors.forename: Richard H
authors.initials: RH
authors.lastname: Adams
authors.affiliation: b Department of Ecology, Evolution & Behavior, 1987 Upper Buford Cir., University of Minnesota, Saint Paul, MN 55108-6097, USA.
authors.forename: Heath
authors.initials: H
authors.lastname: Blackmon
authors.affiliation: a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA.
authors.forename: Jacobo
authors.initials: J
authors.lastname: Reyes-Velasco
authors.affiliation: a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA.
authors.forename: Drew R
authors.initials: DR
authors.lastname: Schield
authors.affiliation: a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA.
authors.forename: Daren C
authors.initials: DC
authors.lastname: Card
authors.affiliation: a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA.
authors.forename: Audra L
authors.initials: AL
authors.lastname: Andrew
authors.affiliation: a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA.
authors.forename: Nyimah
authors.initials: N
authors.lastname: Waynewood
authors.affiliation: a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA.
authors.forename: Todd A
authors.initials: TA
authors.lastname: Castoe
mesh_terms: D000818:Animals; D005075:Biological Evolution; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D016678:Genome; D023281:Genomics / Q000379:methods; D018895:Microsatellite Repeats; D010802:Phylogeny; D020080:Tandem Repeat Sequences; D014714:Vertebrates / Q000145:classification / Q000235:genetics*
keywords: comparative genomics; ensemencement de microsatellites; génomique comparée; microsatellite seeding; repeat elements; répétitions en tandem; simple sequence repeats; séquences simples répétées; tandem repeats; éléments répétés