The Case for the Charales

The phylogenetic significance of the Charales (Chara, Nitella, etc.) in the evolution of the embryophytes makes them a critical candidate for genome sequencing.  Moreover, these macrophytic algae play an important role in natural freshwater ecosystems and have been utilized for restoration of contaminated systems.  As a model organism, the Charales have also been extensively studied for cytological, physiological, and developmental research.  However, significant barriers have impeded progress in complete genome sequencing.  The first is the size of the genome (>2,000 Mb), likely due to genomic duplication combined with transposable element mediatied expansion.  While progress in sequencing technology makes obtaining the sequence of large and complex genomes less forbidding, assembly problems remain if there are redundancies in sequence.  Another difficulty with macro-algae is the problem of contaminating epiphytic and endophytic organisms (i.e., closely related green algae, diatoms, bacteria and fungi).  I report here progress from a number of labs in identifying species with relatively smaller (and therefore likely less redundant) genomes, in obtaining unialgal cultures, and in some significant questions that may be best answered at the genomic level.