I have isolated and purified a Green algae which was confirmed by its chloroplast 16S rRNA gene sequencing analysis. It is showing 85% sequence similarity with one of the existing algal type culture which is a nearest neighbour (NCBI). What genetic markers are actually used for taxonomic delineation of algal (eukaryotic) members. Which databases are to be used for their actual identification. Which journals accept the taxonomic paper of algae. My isolate is found to be genetically, physiologically, chemotaxonomically different from the most of the existing algal members. Please advise me regarding this.
A common marker region for chlorophytes is the 18S (small subunit, ribosomal). Another one is rbcL (large subunit, rubisco). There are lots of available reference sequenes for both regions in the NCBI genbank, and for 18S in http://ssu-rrna.org/ Most papers on new microalgal species I've seen are published in Phycologia, Protist, Journal of Plant Research, Phycological Research and European Journal of Phycology. Hope this helps!
In addition to mentioned above:
Marker: Internal transcribed spacers of ribosomal cistron (ITS1 and ITS2).
Journals: Journal of Phycology, BMC Evolutionary Biology, PLOS ONE
http://www.tandfonline.com/doi/abs/10.1080/09670262.2014.904524# This may help you!
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