Why Nuclear Ribosomal DNA Spacers (ITS) Tell Different Stories in Quercus

Mayol, María; Rosselló, Josep A.

doi:10.1006/mpev.2001.0934

Cited by 151 publications

(118 citation statements)

References 47 publications

Supporting

Mentioning

109

Contrasting

Order By: Relevance

“…These data are in agreement with the accuracy tests of secondary structures of rRNAs , with the only published study involving ITS transcripts analysis of oak species (Mayol and Rossellò, 2001) and with what resulted from a computational analysis that was performed as a check on several Quercus ITS sequences deposited in GenBank. As in Mayol and Rossellò (2001), ITS1 from Q. ilex and Q. suber showed similar, sensibly lower absolute values of free energy than the other oak species.…”

Section: Its1 and Its2 Secondary Structure In Oakssupporting

confidence: 88%

“…Only small variation in length and loop size (helices III-V) could be detected, that seemingly reXect deeper level relationships within Quercus. No extra helices occur, contrary to the sample of Q. coccifera examined by Mayol and Rossellò (2001). The Angiosperm Universal Core motif (GGCRY-(n) 4-7 -GYGYC AAGGAA) of Liu and Schardl (1994) was detected in the ITS1 of all the oak species and is invariably present in helix V, in agreement with known predictions: 15 bases are stem paired, whereas the remaining AAGGA A is not.…”

Section: Its1 and Its2 Secondary Structure In Oakssupporting

confidence: 85%

“…Conversely, Manos et al (1999) provided gene trees with clades that corresponded to well deWned taxonomic groups and supported the recognition of the monophyly of the strictly Eurasian section Cerris. Mayol and Rossellò (2001) compared the two ITS data sets and detected high levels of variation in the G + C content, as well as large indels responsible for length variation, high rates of substitution in the conserved motifs and diVering secondary structures stability. The convincing explanation proposed for the contrasting phylogenetic history derived by Samuel et al (1998) was that it was generated by a spurious analysis, where some species were represented by ITS pseudogene sequences and only a few by functional orthologues.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Utility of ITS sequence data for phylogenetic reconstruction of Italian Quercus spp.

Bellarosa

Simeone

Papini

et al. 2005

Molecular Phylogenetics and Evolution

View full text Add to dashboard Cite

Nuclear ribosomal DNA sequences encoding the 5.8S RNA and the Xanking internal transcribed spacers (ITS1 and ITS2) were used to test the phylogenetic relationships within 12 Italian Quercus taxa (Fagaceae). Hypotheses of sequence orthology are tested by detailed inspection of some basic features of oak ITS sequences (i.e., general patterns of conserved domains, thermodynamic stability and predicted conformation of the secondary structure of transcripts) that also allowed more accurate sequence alignment. Analysis of ITS variation supported three monophyletic groups, corresponding to subg. Cerris, Schlerophyllodrys ( D Ilex group sensu Nixon) and Quercus, as proposed by Schwarz [Feddes Rep., Sonderbeih. D,. A derivation of the "Cerris group" from the "Ilex group" is suggested, with Q. cerris sister to the rest of the "Cerris group." Quercus pubescens was found to be sister to the rest of the "Quercus group." The status of hybrispecies of Q. crenata (Q. cerris £ Q. suber) and Q. morisii (Q. ilex £ Q. suber) was evaluated and discussed. Finally, the phylogenetic position of the Italian species in a broader context of the genus is presented. The utility of the ITS marker to assess the molecular systematics of oaks is therefore conWrmed. The importance of Italy as a region with a high degree of diversity at the population and genetic level is discussed. 

show abstract

Section: Its1 and Its2 Secondary Structure In Oakssupporting

confidence: 88%

Section: Its1 and Its2 Secondary Structure In Oakssupporting

confidence: 85%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Utility of ITS sequence data for phylogenetic reconstruction of Italian Quercus spp.

Bellarosa

Simeone

Papini

et al. 2005

Molecular Phylogenetics and Evolution

View full text Add to dashboard Cite

show abstract

“…These features of the 'b' copies are characteristic of rDNA pseudogenes, as observed in many other plant groups (e.g. Buckler et al 1997;Mayol and Roselló 2001;Bayly et al 2008;Burke et al 2008). Given this, our subsequent analyses focused purely on the 'a' copy amplified from a broader range of samples.…”

Section: Its Variation and Phylogenymentioning

confidence: 82%

“…However, numerous studies have reported the presence of divergent ITS paralogues within genomes, often including putative non-functional 'pseudogenes' (e.g. Buckler et al 1997;Mayol and Roselló 2001;Bayly et al 2008;Burke et al 2008). This also appears to be the case in Grevillea.…”

Section: Utility Of Its Sequences For Phylogeny Reconstructionmentioning

confidence: 98%

Phylogeny of the holly grevilleas (Proteaceae) based on nuclear ribosomal and chloroplast DNA

Holmes

Downing

James

et al. 2014

Aust. Systematic Bot.

View full text Add to dashboard Cite

Abstract. The holly grevilleas are an informal grouping of 15 species (19 taxa) of woody shrubs from south-eastern Australia, with a centre of distribution in central to western Victoria. Many of the species are narrowly endemic. The present study is the first molecular-phylogenetic analysis of the group, with the aim of providing an evolutionary framework for assessing species-level taxonomy and conservation priorities. Analyses using the nrDNA internal transcribed spacer (ITS) regions were complicated by the presence of divergent paralogues, including inferred pseudogenes; analyses restricted to presumed orthologous, functional ITS sequences were uninformative. Combined analyses of three chloroplast intergenic spacers (trnQ-5 0 rps16, trnL-trnF and rpoB-trnC) strongly support the monophyly of a core group of 16 taxa (the 'southern holly grevilleas') from Victoria and South Australia. However, nodes outside this group are poorly resolved and poorly supported, and the relationships of taxa from New South Wales and eastern Victoria (the 'northern holly grevilleas') are unclear. Among the southern holly grevilleas, the following four distinct and partly sympatric cpDNA clades are identified: the 'Grevillea ilicifolia', 'G. aquifolium', 'G. dryophylla' and 'G. repens' clades, among which the earliest and most strongly supported divergence is that of the western-most 'G. ilicifolia' clade. Variation in cpDNA is incongruent with current species-level taxonomy, especially for G. aquifolium (polyphyletic), G. montis-cole (polyphyletic, but the two subspecies each monophyletic) and G. microstegia (nested in G. aquifolium). The effects of incomplete chloroplast lineage sorting, gene flow through hybridisation or introgression, and inappropriate taxonomy are possible explanations for this incongruence. The formal conservation listing for some species within the holly grevillea group requires re-evaluation.

show abstract

Relationships in Taraxacum section Arctica s.l. (Asteraceae, Cichorieae) and allies based on nrITS

2009

View full text Add to dashboard Cite

show abstract

Why Nuclear Ribosomal DNA Spacers (ITS) Tell Different Stories in Quercus

Cited by 151 publications

References 47 publications

Utility of ITS sequence data for phylogenetic reconstruction of Italian Quercus spp.

Utility of ITS sequence data for phylogenetic reconstruction of Italian Quercus spp.

Phylogeny of the holly grevilleas (Proteaceae) based on nuclear ribosomal and chloroplast DNA

Relationships in Taraxacum section Arctica s.l. (Asteraceae, Cichorieae) and allies based on nrITS

Contact Info

Product

Resources

About