After more than 10 years of research, and sequencing millions of reads, we were finally able to uncover secrets of the chloroplast genome of Cladophorales green algae. In stark contrast to other algae, little was known about the gene content and structure of the chloroplast genome in this ecologically important group of marine and freshwater green algae. Most previous attempts to amplify common chloroplast genes have failed, and an atypical plastid genome has been suggested by the presence of abundant plasmid-like DNA in the chloroplasts of several species. Pioneering work of John La Claire and colleagues in the 1990-ies revealed that these structures are single-stranded DNA molecules of 1.5-3.0 kb that fold in a hairpin configuration, and contain putatively transcribed sequences with similarity to chloroplast genes.
In a recent study, we describe intriguing features of the plastid genome of Cladophorales. Through the integration of different DNA sequencing methods, combined with RNA sequencing, we found that chloroplast protein-coding genes are highly expressed and encoded on 1-7 kb linear single-stranded DNA molecules. Due to the wide-spread presence of inverted repeats, these molecules fold into a hairpin configuration. The chloroplast genes are highly divergent from their corresponding orthologs, and display an alternative genetic code. The origin of this highly deviant chloroplast genome likely occurred before the emergence of the Cladophorales, and coincided with an elevated transfer of chloroplast genes to the nucleus. A chloroplast genome that is composed only of linear DNA molecules is unprecedented among eukaryotes and highlights unexpected variation in plastid genome architecture.
Del Cortona A, Leliaert F, Bogaert KA, Turmel M, Boedeker C, Janouškovec J, Lopez-Bautista JM, Verbruggen H, Vandepoele K, De Clerck O. 2017. The plastid genome in Cladophorales green algae is encoded by hairpin chromosomes. Current Biology 24:3771–3782 doi:10.1016/j.cub.2017.11.004.
Smith DR. 2017. Evolution: In Chloroplast Genomes, Anything Goes. Current Biology 27:R1305-R1307 doi:10.1016/j.cub.2017.10.049.