Identification and evaluation of chloroplast uni- and trinucleotide sequence repeats in citrus

A cpDNA fragment of 34 genotypes belonging to Citrus and four related genera was amplified and sequenced. Chloroplast microsatellites were revealed with the length of repeats ranging from 25 to 44 bases. Other than the normal uninucleotide poly(A) repeats, a trinucleotide poly(TAA) motif was also found, the first report of such repeats in a plant chloroplast genome. According to SSR structure variations, 18 Chloroplast SSR Types (CST) were identified. The CST sequences were informative for better understanding the genetic relationships of chloroplast genomes among the analyzed genotypes and confirmed some previous hypotheses about the female parent of several hybrid accessions.