5.8S-28S rRNA interaction and HMM-based ITS2 annotation

Sutherland

European Journal of Phycology

et al. 2013

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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

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“…Annotation of ITS2 sequences was according to the 5.8S-28S rDNA interaction during ribogenesis (Côté and Peculis 2001;Keller et al 2009). Optimal and suboptimal secondary structures for AG-3 potato strain sequences (AG-3 PT) were obtained by RNAstructure (Mathews et al 2004).…”

Section: Phylogenetic and Secondary Structure Analyses Of Sequencesmentioning

confidence: 99%

“…The ITS1, 5.8S rRNA and ITS2 sequences for AG-3 were reported to contain 218, 155 and 270 bases, respectively, but the original information used to annotate was difficult to trace. Annotation of ITS2 sequences was done according to the 5.8S-28S rDNA interaction (Côté and Peculis 2001;Keller et al 2009). The predicted secondary structure was used as criteria to refine the ITS2/28S junction in R. solani AG-3, as shown in Fig.…”

Section: Compensatory Base Changes In Secondary Structures Of Its2mentioning

confidence: 99%

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

et al. 2009

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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 rDNA plus the flanking 5.8S and 28S sequences were first annotated using the hidden Markov models (HMM)-based annotation to retrieve the exact sequence of the region (Keller et al, 2009) available at http://its2.bioapps.biozentrum.uniwuerzburg.de/. The output fasta format files from Bioedit were then entered into MEGA5 for phylogenetic tree construction using the distance-based Neighbour Joining (NJ) method and character-based Maximum Parsimony (MP).…”

Section: Phylogenetic Analysismentioning

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.