High similarity between flanking regions of different microsatellites detected within each of two species of Lepidoptera:Parnassius apolloandEuphydryas aurinia

Abstract

Microsatellite flanking regions have been compared in two butterfly species. Several microsatellite flanking regions showed high similarity to one another among different microsatellites within a same species, but very few similarities were found between species. This can be the consequence of either duplication/multiplication events involving large regions containing microsatellites or of microsatellites imbedded in minisatellite regions. The multiplication of microsatellites might also be linked to mobile elements. Furthermore, crossing over between nonhomologous microsatellites can lead to the exchange of the flanking regions between microsatellites. The same phenomenon was observed in both studied butterfly species but not in Aphis fabae (Hemiptera), which was screened at the same time using the same protocol. These findings might explain, at least partially, why microsatellite isolation in Lepidoptera has been relatively unsuccessful so far.

High‐throughput sequencing and graph‐based cluster analysis facilitate microsatellite development from a highly complex genome

“…A number of studies reached this conclusion on the basis of post hoc analyses of flanking sequence similarities revealed by all‐against‐all BLAST analysis (Meglecz et al. 2004; McInerney et al. 2011) and through comparison to the Repbase database of known transposable elements (McInerney et al.…”

“…1997), butterflies (Meglecz et al. 2004), squat lobsters (Bailie et al. 2010), and parasitic nematodes (Grillo et al.…”

A Helitron-Like Transposon Superfamily from Lepidoptera Disrupts (GAAA)n Microsatellites and is Responsible for Flanking Sequence Similarity within a Microsatellite Family

“…Polymorphic microsatellite markers from Lepidoptera have been used for linkage mapping (Miao et al 2005) and population genetic studies (Reddy et al 1999;Prasad et al 2005;Malausa et al 2007), but problems often arise during genotype analyses. PCR coamplification of fragments primed at [1 microsatellite locus often occur due to the presence of multilocus microsatellites (microsatellite families) that share nucleotide sequence similarity at genome regions that flank the tandem repeat (Zhang 2004;Meglécz et al 2004; Van't Hof et al 2007). Difficulties are encountered because alleles that originate from independently segregating loci typically are scored, and render genetic markers unsuitable for population or linkage analysis (Anthony et al 2001;Fauvelot et al 2006;Anderson et al 2007).…”

“…Also, the wheat genome is composed of microsatellite loci with flanking nucleotide sequences that contain TEs (Ramsey et al 1999), whereas rice (TA) n microsatellites are a known target for the insertion of the Micron family of MITEs (Akagi et al 2001;Temnykh et al 2001). TE associations with microsatellite loci often result in molecular markers that are non-Mendelian, show PCR co-amplification of [1 locus, or weak PCR amplification due to oligonucleotide primer competition (Economou et al 1990;Zhang 2004;Meglécz et al 2004; Van't Hof et al 2007), and are problematic during the development of genetic and genomic marker loci.…”

Introgression as a likely cause of mtDNA paraphyly in two allopatric skippers (Lepidoptera: Hesperiidae)

“…Specifically, it is possible that although the primers developed to amplify microsatellite repeats in E. propertius do yield PCR products for E. horatius, those fragments may not be homologous and can represent a different tandem repeat within a microsatellite family. This phenomenon is believed to exist in many Lepidoptera (Meglécz et al, 2004;Zhang, 2004).…”