Thus, the fact that SSRs in carrot transcripts generally had fewer repeat units than SSRs in genomic sequence, even for trinucleotide repeats (trinucleotides were twice as frequent in ESTs compared to genomic data), suggests a negative selection pressure against microsatellite size increase in protein-coding sequences.
RNA editing in protein-coding transcripts.
* Only substitutions in protein-coding genes considered.
Although together with trinucleotides some reports also indicated a predominance of hexanucleotides in protein-coding sequences [ 3, 18, 51], this has not been consistently reported due to differences in the program parameters and criteria used for microsatellite detection, as discussed above.
An increasing number of microsatellites have been characterized in protein coding sequences (CDSs) and non-coding untranslated regions (UTRs) of genes for several plant species.
Again, the majority of imperfect microsatellite markers (85%) were found in protein coding sequences, with the rest being found in transposable elements.
Using Drosophila Reference Genetic Panel data, we further show that pattern of allelic variation modulates motif heterogeneity of microsatellites, and provide estimates of allele age of specific imperfect microsatellites found within protein-coding genes.
Among PCR-amplified markers, microsatellite (or simple sequence repeat, SSR) markers are commonly used in large-scale genomic studies owing to their ubiquitous distribution in both protein-coding and non-coding regions and the high degree of length polymorphism among individuals [ 5].
Interestingly, 1,094 microsatellites were identified in 801 predicted protein-coding regions, 99% of them being trinucleotides.
In addition to microsatellites [ 14- 18], several polymorphic protein-coding loci have been used to examine genetic diversity of P. vivax populations, including genes encoding the merozoite surface proteins (MSP) [ 19- 28]; the circumsporozoite protein (CSP) [ 21, 24, 26, 28- 30]; and the locus encoding apical membrane antigen 1 (AMA-1) [ 20, 31- 36].
