tufA gene as molecular marker for freshwater Chlorophyceae

Green microalgae from the class Chlorophyceae represent a major biodiversity component of eukaryotic algae in continental water. Identification and classification of this group through morphology is a hard task, since it may present cryptic species and phenotypic plasticity. Despite the increasing use of molecular methods for identification of microorganisms, no single standard barcode marker is yet established for this important group of green microalgae. Some available studies present results with a limited number of chlorophycean genera or using markers that require many different primers for different groups within the class. Thus, we aimed to find a single marker easily amplified and with wide coverage within Chlorophyceae using only one pair of primers. Here, we tested the universality of primers for different genes (tufA, ITS, rbcL, and UCP4) in 22 strains, comprising 18 different species from different orders of Chlorophyceae. The ITS primers sequenced only 3 strains and the UCP primer failed to amplify any strain. We tested two pairs of primers for rbcL and the best pair provided sequences for 10 strains whereas the second one provided sequences for only 7 strains. The pair of primers for the tufA gene presented good results for Chlorophyceae, successfully sequencing 21 strains and recovering the expected phylogeny relationships within the class. Thus, the tufA marker stands out as a good choice to be used as molecular marker for the class.