Sequencing of RAPD fragments amplified from the genome of the prokaryote Prochlorococcus marinus (prochlorophyta).

DNA fingerprint patterns from the chlorophyll a and b containing prokaryote Prochlorococcus marinus were generated with the RAPD technique using two primers derived from repetitive sequence motifs, [(GATA)4 and M13] and a random primer (OPB-10]. Five RAPD fragments were reamplified, cloned and sequenced. The clones M13/1300 and OPB-10/1100 contained open reading frames, whereas the (GATA)4 fragments were interrupted by stop codons in all frames indicating their noncoding function and possessed a high AT score of 63% and 71%, respectively. With the two (GATA)4 clones and the M13/300 clone strain-specific signals were obtained in a Southern blot analysis of various Prochlorococcus strains. Clones M13/1300 and OPB-10/1100, containing the ORFs, produced RFLPs between the strains analyzed. All RAPD fragments are represented as single copy in the genome of Prochlorococcus.