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Simple sequence repeats (SSRs) are
becoming standard DNA markers for plant genome analysis and are being used as
markers in marker assisted breeding. And hence because of its great
significance we have initiated first time this study to analyze complete
sequence of Arabidopsis thaliana for the prevalence of mono-,di-, tri-,
tetra-, penta-, and hexa- mer repeats. We
have developed a programme, which can search a repeat of any length and also
their frequency of occurrence in the genome
A maximum number of these repeats were found in chromosome 1, 2 and 4 whereas,
chromosome 3 and 5 contain relatively less number of these repeats. Moreover,
none of the penta nucleotide repeats was present is chromosome 5. Among the
SSRs, hexamers and dimmers were more predominant except in the chromosome 5.
Overall data showed that Chromosome 5 has minimum number of these repeats.
Repeats of A, AT, AAT, AAAC, AAAG, AAAT, AAAAT, AAAAAG, AAAAAT are predominant,
whereas repeats of C, AC, ACC, AGC, AATT, ACAT, AGAT, AACCG, AAAATT, AAACAC,
AAAGAG, and AAATTT are rare. The abundance or rarity of various simple repeats
in different chromosomes is not explained by nucleotide composition of sequence
or potential repeated motifs to form alternative DNA structures. This suggests
that in addition to nucleotide composition of repeat motifs, characteristic DNA
replication / repair / recombination machinery might play an important role in
genesis of repeats.
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