TreeBASE Search-Matrices for study 12863

@ARTICLE{TreeBASE2Ref20831, author = {Suman Keerthi and Uma Devi Koduru and Sarma S Nittala}, title = {Ribosomal DNA typing in the genus Dunaliella (Chlorophyceae) ? A reliable barcode for species identification?}, year = {2012}, keywords = {18S rRNA gene, carotenogenic Dunaliella, D. salina, introns, ITS regions, phylogenetic analysis, rDNA primers}, doi = {}, url = {http://}, pmid = {}, journal = {Phycological Research}, volume = {}, number = {}, pages = {}, abstract = {Dunaliella salina (Dunal)Teodoresco, a unicellular cell wall less halophilic commercially important microalga is difficult to identify based on morphology. Typing rDNA is reported as a means for its identification. Sixteen carotenogenic Dunaliella isolates from south east Indian coast were rDNA typed. Primers specific for 18S rRNA of chlorophycean microalgae also amplified the 18S rRNA of ciliate grazer- Euplotes euryhalinus Valbonesi & Luporini in Dunaliella cultures. The position of the primers developed for amplification of whole length 18S rRNA gene and species specific introns in Dunaliella was also found to differ in different Dunaliella isolates. Carotenogenic Dunaliella isolates with and without an intron in 18S rRNA gene were found. Among the Dunaliella isolates with one intron, some were found to have intron 1 type described in a majority of D. salina isolates while some had intron 2 type found in Dunaliella species with two introns and D. salina ABRIINW-M1/2 strain. Two types of ITS1 not previously recognized in Dunaliella were discovered. They were amplified from B32 isolate as ~650bp and ~500bp products; the former matched several ITS sequences from Dunaliella species and the latter showed similarity with sequences accessioned as ITS1 from D. bardawil Ben-Amotz & Avron (a nomen nudum of D. salina) and D. viridis Teodoresco . This ITS1 had sequence similarity over some length with U6RNA gene with transposon activity. Analysis of highly conserved region of ITS2 region from B32 and I3 isolates revealed great differences with six compensatory base changes between them and eight with other D. salina isolates compared. Phylogenetic analysis of 18S rRNA and ITS1?5.8S rRNA?ITS2 sequences showed no clustering of D. salina isolates. The genetic distances between Dunaliella species within carotenogenous and non carotenogenous group far exceeded the differences between the two groups. Thus rDNA typing was found not suitable for identification of D. salina. The primers developed for characterization of rDNA were found to be neither genus nor species specific. } }