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The use of 18S ribosomal DNA, ITS and rbcL molecular markers to study the genus Dunaliella (Dunaliellaceae) in Iranian samples : A phylogenetic approach

Dehghani Jaber, Atazadeh Ehsan, Omidi Yadollah, Movafeghi Ali

Oceanological and Hydrobiological Studies

2020

Vol. 49, No. 1

88--98

The microalga Dunaliella has been the focus of attention over recent decades owing to its high biotechnological potential for the production of β-carotene, biofuels and even as a good expression system for the production of recombinant proteins. Different species of this genus have unique features, biological characteristics and biotechnological potential. Therefore, it is necessary to have a clear and reliable taxonomic method to identify different species of Dunaliella. Although several taxonomic systems are available for Dunaliella based on morphological, physiological and molecular features, none of these methods are reliable enough and some controversies exist over different classification systems. In the current study, molecular techniques and bioinformatics tools have been used to re-assess the phylogenetic position of Dunaliella species based on 18S ribosomal DNA (18S rDNA), ITS and rbcL regions. The overall findings based on these markers provide a new and more reliable tool for phylogenetic analysis of Dunaliella species/strains.

Identification of diatom isolates from the Gulf of Gdańsk: testing of species identifications using morphology, 18S rDNA sequencing and DNA barcodes of strains from the Culture Collection of Baltic Algae (CCBA)

Pniewski F. F., Friedl T., Latała A.

Oceanological and Hydrobiological Studies

2010

Vol. 39, No.3

3-20

Eighteen strains of diatoms isolated from different phytoplankton and microphytobenthic assemblages in the Gulf of Gdańsk (Baltic Sea, Poland) and maintained at the Culture Collection of Baltic Algae (CCBA) were investigated for their species identifications. The latter were tested by phylogenetic analyses of nearly full 18S rDNA sequences as well as through sequence comparisons of 5.8S+ITS2 rDNA fragments for use as DNA barcode. The planktonic species were readily identified as a member of the Cyclotella meneghiniana species complex and Skeletonema marinoi, respectively, by both 18S phylogenies and DNA barcoding. In contrast, for the pennate diatom strains the suitability of DNA sequence comparisons for species identification appeared to be still rather limited. Only one strain could be identified to the species level (Navicula gregaria) using DNA barcodes, and no closest relative barcode sequences were available for the other strains. The 18S rDNA phylogenies supported species identification for only one strain (Bacillaria cf. paxillifera). In all other pennate strains identification was only possible to the genus level. Because for most species identified by morphology no closest neighbouring 18S rDNA sequences were available, the CCBA strains may serve as references to represent certain species which have been well characterized by morphology, 18S rDNA sequence analyses and DNA barcodes. Relatively high 18S rDNA differences between pairs of strains of Fistulifera saprophila and Navicula perminuta indicated that each species may represent a complex of several cryptic species. In contrast, the five isolates of Nitzschia microcephala had identical sequences as well as the two isolates of Nitzschia cf fonticola. With the addition of new species to the 18S rDNA phylogeny of pennate raphid diatoms, the monophyly of the genera Fistulifera, Haslea and Navicula s.str. were confirmed, while Nitzschia appeared paraphyletic. The traditional family Naviculaceae was paraphyletic, in agreement with previous phylogenetic studies.