Deep-level diagnostic value of the rDNA-ITS region

Abstract

The similarity of certain reported angiosperm rDNA internal transcribed spacer (ITS) region sequences to those of green algae prompted our analysis of the deep-level phylogenetic signal in the highly conserved but short 5.8S and hypervariable ITS2 sequences. We found that 5.8S sequences yield phylogenetic trees similar to but less well supported than those generated by a ca. 10-fold longer alignment from rDNA-18S sequences, as well as independent evidence. We attribute this result to our finding that, compared to 18S, the 5.8S has a higher proportion of sites subject to vary and greater among-site substitution rate homogeneity. We also determined that our phylogenetic results are not likely affected by intramolecular compensatory mutation to maintain RNA secondary structure nor by evident systematic biases in base composition. Despite historical homology, there appears to be no ITS2 primary sequence similarity shared sufficient similarity to cluster correctly on the basis of alignability. Our results indicate that groups, however, share sufficient similarity to cluster correctly on the basis of alignability. Our results indicate that ITS region sequences can diagnose organismal origins and phylogenetic relationships at many phylogenetic levels and provide a useful paradigm for molecular evolutionary study.

Molecular systematics, historical ecology, and phylogeography of Halimeda (Bryopsidales)

“…In Halimeda, however, elevated rates of SSU regions in comparison to those of other green algae (Zechman et al, 1999) close in on depressed rates among ITS regions. The depression is expected because of a relatively high proportion of conserved functional core positions Hershkovitz and Lewis, 1996) in the short sequences of Halimeda (this study) in comparison to much longer ones found in other green algae (e.g., Bakker et al, 1995a,b).…”

“…Secondary structure models generated with RNAdraw (Matzura and Wennborg, 1996) allowed adjustment of the alignment in variable regions. Delineation of subunit and spacer regions was according to Hershkovitz and Lewis (1996). Matrices of pair-wise Kimura 2-parameter distances were calculated (PAUP*) for each sequence region separately and then normalized by dividing obtained values by their corresponding entries in the matrix of ITS-2 distances.…”

“…Comparison of nrDNA sequences across the chlorophyll a+b algal diversity (e.g., Hershkovitz and Lewis, 1996;Mai and Coleman, 1997;Nakayama et al, 1998) reveals how unusual these regions in fact are in Halimeda. Inclusion of SSU nrDNA sequences of Halimeda and Caulerpa in phylogenetic analyses results in trees in which these taxa appear as close sisters on an extremely long branch (Zechman et al, 1999).…”

Toxic Pseudo-nitzschia multistriata (Bacillariophyceae) from the Gulf of Naples: morphology, toxin analysis and phylogenetic relationships with other Pseudo-nitzschia species

“…Sequences were aligned using Clustal W (Thompson et al 1994) in the Bioedit 4.5.8 computer package (Hall 1999). ITS regions recognition in the alignment was done according to Hershkovitz & Lewis (1996). The number of different haplotypes was calculated with the DAMBE computer program (Xia 2000), and the number of polymorphic sites was calculated using MEGA 2.1 (Kumar et al ).…”

Genetic variability in intergenic spacers of ribosomal DNA in Pisolithus isolates associated with pine, eucalyptus and Afzelia in lowland Kenyan forests

“…RFLP and sequencing of the intergenic spacers (ITS, IGS1) of the rDNA gene complex of Pisolithus collected beneath A. quanzensis, P. caribaea and E. camaldulensis were undertaken because these regions are known to be variable at the inter-and intraspecific level (Gardes et al, 1991 ;Henrion, Le Tacon & Martin, 1992 ;Appel & Gordon, 1996 ;Kretzer et al, 1996). In addition, ITS region sequences can diagnose phylogenetic relationships at many phylogenetic levels (Hershkovitz & Lewis, 1996). Our sampling identified three distinct RFLP haplotypes, each specific to a single host.…”