The plastid genome in Cladophorales green algae is encoded by hairpin plasmids

Abstract

Virtually all plastid (chloroplast) genomes are circular double-stranded DNA molecules, typically between 100-200 kb in size and encoding circa 80-250 genes. Exceptions to this universal plastid genome architecture are very few and include the dinoflagellates where genes are located on DNA minicircles. 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 genes of Boodlea composita are 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 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 the plastid genome architecture.

Plastid genomes hit the big time

“…Like the Chlamydomonadales, members of the ulvophyte order Cladophorales, such as Boodlea composita , Dictyosphaeria cavernosa , and Valonia ventricosa , might have distended ptDNAs. The plastomes of these macro, multicellular, and multi‐nucleated algae are comprised of highly fragmented, single‐stranded linear chromosomes, of which only a few dozen have been well characterized, with an accumulative length of 91 kb (Del Cortona et al ., ). However, data suggest that these ptDNAs might contain many more unidentified chromosomes, most of which are probably ‘empty’, containing no genes, and meaning that the overall plastome length could be quite massive (Del Cortona et al ., ).…”

Convergence in the RNA processing of fractured algal organelle genomes

“…More recently, a second instance of chloroplast genome fragmentation has been detected in members of the Cladophorales (e.g., Boodlea , Pithophora ; Del Cortona et al 2017, Meade et al 2020). These species belong to an algal order different than the dinoflagellates in the alveolates, the chlorophytes, and possess chloroplasts of a primary endosymbiotic origin, in contrast to the dinoflagellate chloroplast acquired through the secondary or higher endosymbiotic acquisition of a red alga (Richardson et al 2015, Del Cortona et al 2017). Nevertheless, the Cladophorales have independently arrived on a fragmented chloroplast genome organization, consisting of a series of single‐stranded DNA chromosomes, folded in hairpin loops, that each contain one, or a small number of coding sequences (La Claire et al 1998, Del Cortona et al 2017).…”

“…In parallel, a wide range of unusual biochemical activities are associated with the peridinin chloroplast proteome, including the frequent addition of 3' poly(U) tails to mature, chloroplast‐encoded transcripts (Wang and Morse 2006, Dorrell et al 2019). These features place dinoflagellates in contrast to plants and to many other eukaryotic algae (e.g., diatoms), in which chloroplast genomes are more typically arranged in a single, circular chromosome (Green 2011, Del Cortona et al 2017), and chloroplast transcripts either do not receive 3' tails (Richardson et al 2014) or, in certain species, receive a 3' poly(A) tail as part of chloroplast RNA degradation (Lisitsky et al 1996, Záhonová et al 2014). Both chloroplast genome fragmentation and 3' poly(U) tail addition have subsequently been detected in close relatives of the dinoflagellates (the photosynthetic apicomplexan species Chromera and Vitrella; Janouskovec et al 2013, Dorrell et al 2014), and in non‐peridinin‐containing dinoflagellate chloroplasts (e.g., in the fucoxanthin‐containing chloroplasts of the dinoflagellates Karenia and Karlodinium , which have originated through the serial endosymbiotic replacement of the ancestral, peridinin dinoflagellate chloroplast; Espelund et al 2012, Richardson et al 2014).…”

“…These guide RNAs participate in the corrective insertion of internal uridines in mitochondrial coding RNAs, from a 3' reserve of uridine residues‐ hence, a poly(U) tail (Blum et al 1990). More recently, a second instance of chloroplast genome fragmentation has been detected in members of the Cladophorales (e.g., Boodlea , Pithophora ; Del Cortona et al 2017, Meade et al 2020). These species belong to an algal order different than the dinoflagellates in the alveolates, the chlorophytes, and possess chloroplasts of a primary endosymbiotic origin, in contrast to the dinoflagellate chloroplast acquired through the secondary or higher endosymbiotic acquisition of a red alga (Richardson et al 2015, Del Cortona et al 2017).…”

Integrated Genomic and Transcriptomic Analysis of the Peridinin Dinoflagellate Amphidinium carterae Plastid

“…Much is known about the organisation and expression of plastid genomes (Green 2011;Barbrook, et al 2018). The plastid genomes of photosynthetic eukaryotes retain fewer than 250 genes (Green 2011;Muñoz-Gómez 2017); these are typically organised as a single, circular chromosome, although some may have alternative linear or branched forms (Oldenburg and Bendich 2004;Barbrook, et al 2010;Janouskovec, et al 2013;Del Cortona, et al 2017). Genes are usually arranged in operons, and are co-transcribed before being cleaved into mature mRNAs (Barkan 2011;Luro, et al 2013;Hotto, et al 2015).…”