ITS2 and 18S rDNA sequence-structure phylogeny of.
ITS2 sequence-structure analysis in phylogenetics: A how-to manual for molecular systematics. (2010). ITS2 sequencestructure phylogeny in the Scenedesmaceae with special reference to Coelastrum (Chlorophyta, Chlorophyceae), including the new genera Comasiella and Pectinodesmus.
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There is a long tradition, especially in phycology, of using 18S rDNA sequences in inferring phylogenies, in particular for higher taxonomic level analysis. 18S like ITS2 displays a conserved RNA secondary structure which could be used simultaneously with the sequence to increase the amount of information available when inferring phylogenetic relationships.
Therefore we used highly variable internal transcribed spacer 2 (ITS2) sequences and conserved secondary structures, as deposited with the ITS2 Database, simultaneously. Findings: We built an accurate and in parts robustly resolved large scale phylogeny for 1,634 currently available hypnalean ITS2 sequence-structure pairs.
Secondary structure was predicted using Mfold software and sequence-structure was aligned by MARNA. RNAstat software transformed the secondary structures into 28 symbol code data for maximum parsimony (MP) analysis. The results showed that the ITS2 structures in our samples had a common four-helix folding type with some shared motifs.
ABSTRACTThere is an increasing interest in the Eustigmatophyceae, a class of stramenopile microalgae, because they offer a variety of high-value health-beneficial compounds, e.g. polyunsaturated fatty acids (PUFAs), while concomitantly producing high biomass. Clarification of the taxonomy of these organisms at the species level is important in order to achieve reproducible results and constant.
ITS2 had been suggested as a standard marker for fungi and integrating ITS2 based phylogenetic analysis with the morphological features of their primary sequences has been the recent trend, which has significantly enhanced the resolution and stability of the clades (35, 36, 37, 38).