Characterization of novel extrachromosomal DNA from giant-celled marine green algae

Cloned HinfI fragments of the plasmid-like 2.2-kb DNA from the green alga Ernodesmis verticillata (Kützing) Borgesen hybridized solely to single or double bands within the 2.2-kb DNA in genomic Southern blots. Heterologous probes for nuclear and chloroplast genes hybridized only to high-molecular-weight (HMW) DNA. Thus, the low-molecular-weight (LMW) DNA is extrachromosomal and lacks extensive homology to nuclear or chloroplast genes. There was cross-hybridization to LMW DNA from other Caribbean isolates of E. verticillata, but not to that from a Pacific isolate. Under reduced stringency, cross-hybridization to LMW DNA from the related green alga Boergesenia forbesii (Harvey) Feldmann was also observed, suggesting that the LMW DNA may have a common origin and/or function in these algae. Six out of sixteen unique clones hybridized to discrete bands in northern blots, indicating that the LMW DNA may be actively transcribed in vivo. Four of the putatively transcribed clones have regions with significant deduced amino-acid sequence identity to psa and psb gene products, implying that the plasmid-like molecules might have originated from chloroplast DNA. Sequencing data also indicated a high G/C content, as well as the presence of frequent tandem and direct repeats in many of the cloned fragments. Sequencing and restriction analyses suggest that most of the cloned fragments are portions of different DNA molecules, providing evidence that the 2.2-kb extrachromosomal DNA in Ernodesmis is novel in that it represents a fairly heterogeneous population of molecules.