Plastid genome size and heterogeneous base composition of nuclear DNA from Ochrosphaera neapolitana (Prymnesiophyta)

Abstract

We have studied the plastid genome of Ochrosphaera neapolitana (Hymenomonadaceae, Prymnesiophyta), a member of the chlorophyll a + c--containing algae. Total DNA from O. neapolitana was fractionated in a CsCl density gradient, and the ‘lighter’ upper band (which is typically of plastid origin) was unusually abundant relative to the ‘heavier’ nuclear one. Denaturation and renaturation experiments done with DNA isolated from the upper band showed that it had a base composition of 43.6 mol% G + C (molar fraction of guanosine plus cytosine), compared with 60.5 mol% G + C in the lower band, and that it lacked a substantial fraction of repetitive sequences; this DNA had a size of c. 10 Mb, which is more than an order of magnitude larger than has been reported for any plastid genome. Using pulse field gel electrophoresis (PFGE) of total DNA, we resolved a plastid genome size of approximately 165 kb for O. neapolitana. Although this is within the range reported for other plastid genomes, there is an increase of about 40 kb compared with related algae. Using the upper band from the CsCl gradient as a probe for the PFGE blots, we showed that this upper band is apparently a mixture of nuclear DNA with a small fraction of plastid DNA. The nuclear genome of O. neapolitana thus appears to have a distinctive heterogeneity in G + C content, with two DNA types differing by c. 17 mol%.