The ITS2 Database II: homology modelling RNA structure for molecular systematics

Sutherland

European Journal of Phycology

et al. 2013

The status of the green algal genera Haematococcus and Stephanosphaera has been a source of debate among algal systematists. A phylogenetic alliance between Haematococcus (sensu lato) and the colonial Stephanosphaera was affirmed by earlier molecular phylogenetic investigations. Although the data suggested that the genus Haematococcus may not be a monophyletic group, taxon sampling limited the scope of any potential taxonomic revision. Results from new molecular phylogenetic analyses of data from the 18S and 26S rRNA genes support the establishment of a separate genus, Balticola, as originally proposed by Droop in 1956. Haematococcus remains as a valid genus, with H. pluvialis as its only member. The monotypic status of H. pluvialis is supported both by molecular phylogenetic analyses of the ribosomal RNA genes and assessments of molecular evolution in the ITS2 sequences of H. pluvialis strains. The near-complete absence of compensatory base changes in a sequencestructure analysis of the highly variable ITS2 gene from more than 40 geographically diverse isolates of H. pluvialis corroborates the unity of the species inferred from molecular phylogenetic analyses of 18S and 26S rRNA gene sequence data.

Section: Sequence Analysis and Its2 Secondary Structure Predictionmentioning

confidence: 99%

The blood alga: phylogeny ofHaematococcus(Chlorophyceae) inferred from ribosomal RNA gene sequence data

Sutherland

European Journal of Phycology

et al. 2013

“…One of the suboptimal structures followed the common core of eukaryotic ITS2 secondary structures (Schultz et al 2005) and was used as a template for homology modelling. Homology modelling (Wolf et al 2005b) of all secondary structures from sequences of AG strains used in further analyses was done using the ITS2 PAM 50 matrix with the custom modelling option (Selig et al 2008) available at the ITS2 Database (Schultz et al 2005;Wolf et al 2005a;Selig et al 2008). Secondary structures were displayed with 4SALE (Seibel et al 2008).…”

Section: Phylogenetic and Secondary Structure Analyses Of Sequencesmentioning

confidence: 99%

“…With ITS sequences, there are also additional reasons because structural features of ITS1 and ITS2 may be important for positioning the transcriptprocessing machinery on the pre-rRNA, the precursor of the 18S, 5.8S and 28S rRNAs (Côté and Peculis 2001;Abeyrathne and Nazar 2005). Hence, the secondary structures of ITS RNA sequences provide additional evolutionary information (Coleman 2000;2003;Coleman and Vacquier 2002;Wolf et al 2005a) and a rather simple molecular marker, which may be particularly useful when studying closely related species (Müller et al 2007;Selig et al 2008). …”

Section: Introductionmentioning

confidence: 99%

Evolutionary Diversification Indicated by Compensatory Base Changes in ITS2 Secondary Structures in a Complex Fungal Species, Rhizoctonia solani

et al. 2009

The rRNA cistron (18S-ITS1-5.8S-ITS2-28S) is used widely for phylogenetic analyses. Recent studies show that compensatory base changes (CBC) in the secondary structure of ITS2 correlate with genetic incompatibility between organisms. Rhizoctonia solani consists of genetically incompatible strain groups (anastomosis groups, AG) distinguished by lack of anastomosis between hyphae of strains. Phylogenetic analysis of internal transcribed spacer (ITS) sequences shows a strong correlation with AG determination. In this study, ITS sequences were reannotated according to the flanking 5.8S and 28S regions which interact during ribogenesis. One or two CBCs were detected between the ITS2 secondary structure of AG-3 potato strains as compared to AG-3 tobacco strains, and between these two strains and all other AGs. When a binucleate Rhizoctonia species related to Ceratobasidiaceae was compared to the AGs of R. solani, which were multinucleate (3-21 nuclei per cell), 1-3 CBCs were detected. The CBCs in potato strains of AG-3 distinguish them from AG-3 tobacco strains and other AGs yielding further evidence that the potato strains of AG-3 originally described as R. solani are a species distinct from other AGs. The ITS1-5.8S-ITS2 sequences were analyzed by direct sequencing of PCR products from 497 strains of AG-3 isolated from potato. The same 10 and 4 positions in ITS1 and ITS2, respectively, contained variability in 425 strains (86%). Nine different unambiguous ITS sequences (haplotypes) could be detected in a single strain by sequencing cloned PCR products indicating that concerted evolution had not homogenized the rRNA cistrons in many AG-3 strains. Importantly, the sequence variability did not affect the secondary structure of ITS2 and CBCs in AG-3.

“…The ITS2 secondary structure is typically a four-helix model, which is common to almost all eukaryotic taxa (Coleman, 2003;Schultz et al, 2005) and is true for digenean trematodes as well (Morgan & Blair, 1998). The conserved nature of ITS2 secondary structural core allows utility in inferring phylogenies at higher taxonomic levels, in addition to its role for low-level phylogenetic analyses on the species and genus levels Selig et al, 2008). The identical nature of the ITS2 secondary structure can be attributed to similarity in rRNA biogenesis among eukaryotes; its folding pattern plays an important role in processing of mature rRNA (Joseph et al, 1999) and structures are maintained during evolution through transitions/transversions, although mutations occur frequently (Coleman, 2007;Keller et al, 2010).…”

Section: Discussionmentioning

confidence: 99%

Morphological and molecular characterization of Posthodiplostomum sp. (Digenea: Diplostomidae) metacercaria in the muscles of snakeheads (Channa punctata) from Manipur, India

Athokpam

Tandon

2014

Helminthologia

141 SummaryThe spotted snakehead, Channa punctata Bloch, 1793, is a locally important fish species commonly consumed by the natives in the state of Manipur, Northeast India. The fish host C. punctata from Lamphel area revealed a diplostomid metacercarial infection. Morphologically, the recovered metacercaria was identified as a species of Posthodiplostomum Dubois, 1936. Molecular characterization using the ribosomal RNA genes (rDNA 18S, ITS2 and 28S regions) and the mitochondrial CO1 region supplements the identification. Molecular analysis revealed the metacercaria to be closely related to Posthodiplostomum sp. Japan isolate, with sequence similarity variation from 97.5 -99.7 % while considering for the three rDNA markers. The secondary structure of the ITS2 region further corroborated these results; the typical four-helix model, when compared to the taxon from Japan, showed differences only in twelve bases (with seven transitions and five transversions). In phylogenetic analysis also, the metacercaria claded with the genus Posthodiplostomum, coming closer to the Japanese isolate, thus supplementing the morphological identification of the metacercaria.