Allelic diversity in alligator microsatellite loci is negatively correlated with GC content of flanking sequences and evolutionary conservation of PCR amplifiability

Abstract

Microsatellites are short tandem arrays of simple DNA sequences, having a basic repeat unit of 1-5 bp (Tautz and Schlbtterer 1994). Microsatellite loci are abundant in most complex genomes (Tautz and Schlötterer 1994) and are usually highly polymorphic when the basic repeat unit is duplicated more than 10 times (Weber 1990). Alíeles at a locus differ in length due to variation in the number of repeats, and slipped strand mispairing is considered to be the major mechanism by which length variants (new alíeles) are generated (Levinson and Gutman 1987; Strand et al. 1993). Variation at microsatellite loci can be assayed by PCR amplification using primers complementary to unique sequences flanking specific repetitive arrays, followed by electrophoretic sizing of the PCR products (Tautz 1989). Because microsatellites are highly polymorphic and amenable to PCR, multiplex PCR, and automated scoring, they often are the molecular genetic marker of choice (e.g., Bruford and Wayne 1993). Although microsatellites occur in all eukaryotes (Tautz and Schlotteret 1994), their distribution and overall fi^equency varies widely (e.g., Langercrantz, Ellegren, and Andersson 1993). Because primer development can be time-consuming and costly, many investigators attempt to use primers developed in one species to amplify orthologous loci in closely related species (e.g., Moore et al. 1991). Some of these studies show that this strategy can be quite successfiil, even in distantly related species (e.g., FitzSimmons, Moritz, and Moore 1995). Most such cross-species comparisons, however, have tested either a small number of primer pairs (e.g., FitzSimmons, Moritz, and Moore 1995) or a small number of taxa (e.g., Moore et al. 1991). Additionally, only loci that are polymorphic in the species from which they are developed are used in most studies. The selection and use of such loci biases cross-taxa comparisons (Ellegren, Primmer, and Sheldon 1995). In general, primers that exhibit low levels of variation, as well as those that yield complex or unclear patterns, are discarded without much investigation or hesitation. Thus, it is not known how a reasonably large random sample of microsatellite sequences evolves within a group of taxa. We have developed primers to amplify microsatellite loci from American alligators (Alligator mississippiensis).

Microsatellite variation among divergent populations of stalk-eyed flies, genus Cyrtodiopsis

“…Rates of both substitutions and insertions/deletions appear to be relatively high in microsatellite flanking regions and could increase the incidence of null alleles (Glenn et al, 1996 ;Ortı´et al, 1997;Hutter et al, 1998 ;Colson & Goldstein, 1999;Noor et al, 2001). An increase in null alleles with increasing genetic distance could account for some of our observed declines in number of alleles amplified, polymorphism and heterozygosity, particularly if mutation rates in the tandem repeat region were correlated with mutation rates in the flanking regions as proposed for crocodilians (Glenn et al, 1996). If null alleles were more common in populations distant from the source, we would expect to see departure from Hardy-Weinberg equilibrium owing to an excess of homozygotes in these populations.…”

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

“…Interspecific variation in local recombination rates may contribute to repeat instability (Pearson et al 2005). Characteristics of DNA repair mechanisms, flanking sequences, and proteins involved in chromatin remodeling may also direct lineage-specific rates and genome abundance of microsatellites (Glenn et al 1996;Mellon et al 1996). Due to their high abundance and homopolymeric tracts, several types of TEs (such as Alu SINEs and CR1 LINEs) are known to facilitate the expansion of microsatellites through microsatellite seeding in which TE activity can result in duplications of both flanking and endogenous microsatellite arrays.…”

Cross-species microsatellite amplification in South American Caimans (Caiman spp and Paleosuchus palpebrosus)

“…Microsatellite DNA markers are simple sequence repeats (Tautz et al, 1986) distributed along the genome (Litt and Luty, 1989) that have been used to assess genetic diversity and to study ecological behavioral characteristics such as mating system and dispersal pattern in reptiles and amphibians (Avise, 1994;Forstner and Forstner, 2002), including the timber rattlesnake Crotalus horridus (Villareal et al, 1995), Alligator mississipiensis (Glenn et al, 1996;Glenn et al, 1998;Davis et al, 2001a), and Crocodylus spp. (Dever et al, 2001;FitzSimmons et al, 2001;Verdade et al, 2002).…”