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

Abstract

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.Key words: comparative genomics, microsatellite seeding, repeat elements, tandem repeats, simple sequence repeats.Résumé : La dynamique évolutive des séquences simples répétées (SSR ou microsatellites) au sein des vertébrés demeure largement non-documentée et mal connue. Dans ce travail, les auteurs ont analysé l'abondance et l'évolution des microsatellites chez 71 génomes de vertébrés. Les abondances de microsatellites les plus grandes ont été rencontrées au sein des génomes des poissons dotés de nageoires à rayons, des reptiles à écailles et des mammifères, tandis que les génomes des crocodiliens, des tortues et des oiseaux présentaient le moins de microsatellites. Les auteurs ont employé des méthodes comparatives pour inférer les taux de changements évolutifs en matière d'abondance des microsatellites parmi les vertébrés et pour mettre en évidence des lignages qui ont connu des taux exceptionnellement élevés ou faibles. Globalement, la majeure partie de la variation en matière de contenu, d'abondance et de taux d'évolution des microsatellites a été observée au sein des grands groupes de reptiles, et pourtant, les auteurs ont noté que certains clades très distants (p. ex. les reptiles à écailles et les mammifères) présentaient des compositions génomiques semblables en matière de microsatellites. Les reptiles archosauromorphes (tortues, crocodiliens et oiseaux) affichaient une teneur réduite en microsatellites et les plus faibles taux évolutifs au sein des microsatellites, tandis que les génomes des reptiles à écailles avai...

Insights into the Evolution of a Snake Venom Multi-Gene Family from the Genomic Organization of Echis ocellatus SVMP Genes

“…These non-coding elements are abundant in major lineages of vertebrates. Mammalian, fish, and squamate reptile genomes appear to be relatively microsatellite rich [ 74 ]. However, besides Hts35, RepeatMasker only identified few SSR tracks in introns 1 (5× GTTT; 28× TC) and 2 (13× ATTT; 4× TAA) of the PII-SVMP gene ( Figure A1 ), and introns 1 (11× GTTT; 21× AG) and 2 (9× GTTT; 4× TAA) of the PI-SVMP gene ( Figure A2 ).…”

Of Men and Mice: Modeling the Fragile X Syndrome

“…Due to their high variability, tandem tracts are thought to serve as a substrate for evolution (reviewed in Kashi and King, 2006 ; Hannan, 2012 ; Plohl et al, 2012 ). Most microsatellites are nonetheless only maintained by chance and total microsatellite numbers are rather species or clade specific than related to vertebrate evolution (Buschiazzo and Gemmell, 2010 ; Adams et al, 2016 ). Yet, tract length polymorphism turned out to be a major source for the emergence of variability and complexity in species: recent research revealed that tandem tracts located in regulatory regions contribute to the genesis of complexity (Liu H. et al, 2012 ; Namdar-Aligoodarzi et al, 2015 ).…”

A genome-wide investigation of microsatellite mismatches and the association with body mass among bird species

“…Microsatellites, also known as simple sequence repeats (SSRs), are tandem repeats of simple nucleotide motifs, which have wide coverage in eukaryotic and prokaryotic genomes ( Tóth, Gáspári & Jurka, 2000 ; Ellegren, 2004 ; Adams et al, 2016 ). One feature of microsatellites is that they have a high mutation rate (10 −7 to 10 −3 mutations per locus per generation), leading to high heterozygosity and extensive length polymorphisms ( Kruglyak et al, 2000 ).…”

“…Many studies on microsatellites have explored the frequencies, abundance and polymorphism of microsatellites in the genomes ( Wang et al, 2014 ; Qi et al, 2015 ; Adams et al, 2016 ). Few, if any, have correlated these microsatellite characters to the life history traits of a species.…”