Del Cortona A., Leliaert F., Bogaert K.A., Turmel M., Boedeker C., Janouskovec J., Lopez-Bautista J.M., Verbruggen H., Vandepoele K. & De Clerck O.
The plastid genome in Cladophorales green algae is encoded by hairpin chromosomes
Current Biology: accepted


Virtually all plastid genomes are double-stranded circular DNA molecules, typically between 100-200 kb in size and encoding circa 80-250 genes. Exceptions to this universal plastid genome architecture in eukaryotes are very few, and include dinoflagellates with a chloroplast genome that is largely transferred to the nucleus and the few genes that remain in the chloroplasts are located into single gene mini-circles. Here we report on the highly deviant chloroplast genome of Cladophorales green algae, which is entirely fragmented into hairpin plasmids. Short and long read high-throughput sequencing of DNA and RNA demonstrated that the chloroplast genome of Boodlea composita is fragmented with individual genes encoded on 1-7 kb DNA contigs, with an exceptionally high GC-content, each containing a long inverted repeat with one or two protein-coding genes and conserved non-coding regions putatively involved in replication and/or expression. We propose that these contigs correspond to linear single-stranded DNA molecules that fold onto themselves to form hairpin plasmids. The Boodlea chloroplast genes are highly divergent from their corresponding orthologs. The highly deviant chloroplast genome coincided with an elevated transfer of chloroplast genes to the nucleus. Interestingly, both in Cladophorales and dinoflagellates a similar set of genes is retained in the chloroplasts of these two unrelated eukaryotic lineages. A chloroplast genome that is composed only of linear DNA molecules is unprecedented among eukaryotes and highlights unexpected variation in the plastid genome architecture.

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