Characterization of a highly repetitive DNA sequence in Camellia sinensis (L.) O. Kuntze genome

Tea is a widely consumed non-alcoholic natural beverage grown mostly in tropical asia and Africa. It is a vegetatively propagated crop and thus has low genetic variability. Repetitive DNA sequences in the genome, although, are commonly recognised very useful to differentiate individuals, they have not been explored extensively in tea genome. Here we report characterization of novel repetitive motiffs in a genomic DNA clone, designated as pMST11. It was isolated and sequenced from a genomic library of Camellia sinensis (L.) O. Kuntze by reverse genomic hybridisation approach. Sequence analysis of the insert displayed a highly A+T rich (66.8%) fragment of 894 base pairs (bp) containing a 168 bp single open reading frame in minus strand. The insert exhibited twelve 15-45 bp long direct repeats, of which, six were novel, non-overlapping and more than 30 bp long. The insert sequence of the clone displayed two unique microsatellite loci, having dinucleotide repeats (AG)15 and (AG)17. Interestingly, both microsatellites contained a 15 bp-consensus sequence attached to their 3' ends. Hybridization of the pMST11 clone with the tea genomic DNA, digested individually with 17 restriction endonucleases, exhibited a continuous smear suggesting that one or more repeats are highly dispersed through-out the tea genome. Dot blot analysis of the 894 bp insert sequence with genomes of 10 out of 12 different plant species exhibited positive signals of various intensities. Human and animal genomes exhibited negligible signals suggesting plant-specific nature of the repeats. The role of these repeat sequences in context of evaluating genetic variation in vegetatively propagated tea is discussed.