Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution

Richard H. Adams, Heath Blackmon, Jacobo Reyes-Velasco, Drew R. Schield, Daren C. Card, Audra L. Andrew, Nyimah Waynewood, Todd A. Castoe

Research output: Contribution to journalArticlepeer-review

17 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)295-310
Number of pages16
JournalGenome
Volume59
Issue number5
DOIs
StatePublished - 2016

Bibliographical note

Publisher Copyright:
© 2016 Published by NRC Research Press.

Keywords

  • Comparative genomics
  • Microsatellite seeding
  • Repeat elements
  • Simple sequence repeats
  • Tandem repeats

Fingerprint Dive into the research topics of 'Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution'. Together they form a unique fingerprint.

Cite this