I have isolated various strains of microalgae from different wastewaters. I have been suggested to go for Colony PCR method by my lab mates. During literature survey, i have found that ITS regions give better resolution for identification and sequence similarity searching during BLAST. What is the significance of ITS regions in eukaryotic species and especially microalgae
I have quite a good experience with ITS2. There are 2 main problems:1. some algae (green, diatoms, Eustigmatophyceae, Xanthophyceae) have multiple variants of ITS in their genom so one may need cloning of PCR products before sequencing. 2. For many groups references are missing (so one would need to sequence 18S or rbcL in addition). ITS have deffinitely better resolution compared to 18S. There are mayn other aspects but they depends on your tasks and lab facilities.
The internal transcribed spacer 2 (ITS2) region of nuclear ribosomal DNA is frequently used as a target region in green algae, but there are also some other suitable target regions for barcoding. With respect to DNA barcoding of green microalgae there is a new publication in PLoS One.
Please see: Darienko T, Gustavs L, Eggert A, Wolf W2, Pröschold T. (2015) Evaluating the Species Boundaries of Green Microalgae (Coccomyxa, Trebouxiophyceae, Chlorophyta) Using Integrative Taxonomy and DNA Barcoding with Further Implications for the Species Identification in Environmental Samples. PLoS One 10(6):e0127838.