The Chlorella Genome: Big Surprises from a Small Package

Green algae in the genus Chlorella are widely distributed in freshwater environments. They are typically small, nonmotile, unicellular organisms with a single chloroplast and a rigid cell wall. The term Chlorella has long been applied to a large group of unrelated chlorophyte microalgae, which molecular analysis has separated into two classes: the Trebouxiophyceae (containing the true Chlorella genus) and the Chlorophyceae. Chlorella spp are photosynthetic endosymbionts of a variety of freshwater organisms, such as the protozoan Paramecium bursaria (see figure), and have also been used as a model system for studying large double-stranded DNA viruses that infect green algae in freshwater ecosystems. Therefore, genomic analysis is of interest to the study of both algal symbioses and algal–viral interactions.

Chlorella endosymbionts inside the single-celled protozoan Paramecium bursaria.

In a new report, Blanc et al. (pages 2943–2955) present the genome sequence of Chlorella variabilis NC64A. The genome size of 46.2 Mb places the NC64A genome midway between other sequenced chlorophyte genomes, including Chlamydomonas reinhardtii (121 Mb), two species of Ostreococcus (∼12 to 13 Mb), and two species of Micromonas (∼20 to 21 Mb). Repeated sequences were found to make up just 12% of the genome, making NC64A repeat-poor compared with land plants (which comprise 20 to 30% repeat sequence in Arabidopsis to over 90% in large genomes such as wheat). Interestingly, half of the repeated sequences identified showed no resemblance to known repeat families.

A total of 9791 protein-encoding genes were predicted in the NC64A genome. Surprisingly, these included a number of genes encoding known meiosis-specific proteins, despite the fact that NC64A has been observed only in the haploid phase and has long been assumed to be asexual. In addition, homologs were found of proteins that promote the disassembly of the gametic cell walls and allow gamete fusion in Chlamydomonas. These findings suggest that NC64A might have a diploid phase and a cryptic sexual reproductive cycle that has been overlooked, such as recently reported in Ostreococcus (Grimsley et al., 2010).

Also unexpected was the presence of homologs of many Chlamydomonas flagellar proteins, although flagella have not been observed in Chlorella. Specifically, the results suggested that NC64A has retained an almost complete set of outer-arm dynein proteins previously found only in eukaryotes that have motile cilia or flagella. This led to the intriguing hypothesis that Chlorella may retain the ability to form rudimentary flagella-like structures, which might function in the putative cryptic sexual phase, for example, in the recognition of the mating partner and initiation of cell fusion. Alternatively, the flagellar apparatus could have been lost and conserved flagella-like proteins acquired other biological functions.

Another interesting feature of the NC64A genome was the presence of homologs of receptors and biosynthetic enzymes of land plant hormones, such as abscisic acid, auxin, and cytokinin. The presence of these homologs does not necessarily imply the existence of plant hormones and their related functions in Chlorella but supports the hypothesis that genes involved in phytohormone biosynthesis and perception were established in ancestral organisms prior to the appearance of land plants.

Finally, the analysis revealed surprising observations with respect to genes involved in cell wall metabolism. The Chlorella cell wall contains glucosamine polymers, such as chitin and chitosan, instead of cellulose and hemicelluloses that make up the cell walls of land plants. The genomic analysis indeed revealed no homologs of Arabidopsis genes involved in synthesis of cellulose or hemicelluloses. However, homologs were found to chitin metabolism genes present in Chlorella DNA viruses, leading to the remarkable hypothesis that components of Chlorella chitin metabolism could have been acquired via lateral gene transfer from viruses. If this is indeed the case, large DNA viruses predominantly associated with microalgae and marine protists might have played a larger role in the evolution of their hosts than previously recognized. Thus, Chlorella NC64A yields up a small bag of surprises and plenty of intriguing hypotheses for future investigation.