Ribosomal DNA Sequences and Angiosperm Systematics

Hershkovitz, Mark; Zimmer, Elizabeth A.; Hahn, William J.

doi:10.1201/9781439833278.ch14

Cited by 99 publications

(90 citation statements)

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“…The ITS region has been applied as a phylogenetic marker at the inter-and infra-generic level, but use at a higher level has also been suggested (Hershkovitz et al, 1999;Simmons and Freudenstein, 2003). High evolutionary rates are associated with several possible problems (Yang, 1998).…”

Section: Appropriateness Of Its Datamentioning

confidence: 99%

Conflicting phylogenies of balsaminoid families and the polytomy in Ericales: combining data in a Bayesian framework

Geuten

Smets

Schols

et al. 2004

Molecular Phylogenetics and Evolution

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The balsaminoid Ericales, namely Balsaminaceae, Marcgraviaceae, Tetrameristaceae, and Pellicieraceae have been confidently placed at the base of Ericales, but the relations among these families have been resolved differently in recent analyses. Sister to this basal group is a large polytomy comprising all other families of Ericales, which is associated with short internodes. Because there are more than 13 kb of sequences for a large sampling of representatives, a thorough examination of the available data with novel methods seemed in place. Because of its computational speed, Bayesian phylogenetics allows for the use of parameter-rich models that can accommodate differences in the evolutionary process between partitions in a simultaneous analysis. In addition, there are recently proposed Bayesian strategies of assessing incongruence between partitions. We have applied these methods to the current problems in Ericales phylogeny, taking into account reported pitfalls in Bayesian analysis such as model selection uncertainty. Based on our results we infer several, previously unresolved relationships in the order Ericales. In balsaminoid families, we find that the closest relatives of Balsaminaceae are Marcgraviaceae. In the Ericales polytomy, we find strong support for Pentaphylacaceae sensu APG II as the sister group of Maesaceae. In addition, Symplocaceae receive a position as sister to Theaceae and these families form a monophyletic group together with Styracaceae-Diapensiaceae. At the base of this clade are Actinidiaceae and Clethraceae. The positions of Ebenaceae and Lecythidaceae remain uncertain.

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Section: Appropriateness Of Its Datamentioning

confidence: 99%

Conflicting phylogenies of balsaminoid families and the polytomy in Ericales: combining data in a Bayesian framework

Geuten

Smets

Schols

et al. 2004

Molecular Phylogenetics and Evolution

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“…According to The Barcode of Life Data Systems (http://www.boldsystems.org), there were more than 1,100,000 DNA barcode records of 95,000 species published until now. Searching much evidence of alternative barcodes, the nuclear region of the internal transcribed spacer (ITS) possessing many advantages, is revealed to be the most frequently utilized DNA region in plants, fungi, and even animals (Hershkovitz et al 1999).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and hybridization of Pulsatilla tongkangensis based on the nrDNA ITS region sequence

Sun

Park

et al. 2013

Biologia

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Pulsatilla tongkangensis, a perennial medicinal herb growing on the cliffs of Tongkang, Kangwon Province, Korea, is accordingly named as P. tongkangensis as a new Pulsatilla species. Due to sharing similar morphological characters with other Pulsatilla species, how to accurately discriminate P. tongkangensis becomes a critical, urgently needed-solved problem. To understand the truth of P. tongkangensis derivation and the phylogenetic relationship in Pulsatilla, the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) as the most frequently used marker for distinguishing plant species was amplified from P. tongkangensis in this study. According to sequence alignment result, three P. tongkangensisspecific nucleotide sites were obtained to vary from other Pulsatilla species, particularly one at 417 bp showing completely homology among P. tongkangensis accessions and completely dissimilarity between P. tongkangensis and other Pulsatilla species. As known fungal contamination is common in herbal medicinal materials when improperly processed and stored, using universal primers of the ITS region could not only plant DNA but parasitic fungal DNA. Thus, to improve the amplification condition of the ITS region from P. tongkangensis and design plant-specific primer would the following focus of our study. This work will be useful for clearly understanding the phylogenetic relationship between P. tongkangensis and other species belonging to the genus Pulsatilla.

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“…As the development of plant systematic and identification, the discrimination through molecular identification approach has gradually replaced the traditional plant discrimination. And the ITS region, due to its high primer universality, has become the single most frequently utilized DNA region in plants, fungi, and even animals (Hershkovitz et al, 1999). However, high primer universality also has a disadvantage that these primers simplify a wide range of plant targets and work well to analyze DNA isolated from individual organisms, but do not exclude effectively the fungus sequences in mixed, phytosphere DNA extracts of fungus-associated plants.…”

Section: Resultsmentioning

confidence: 99%

Plant-specific primers for the amplification of the nrDNA ITS region in fungus-associated Pulsatilla species

Sun¹,

Park²,

Oh³

et al. 2013

J. Med. Plants Res.

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The internal transcribed spacer (ITS) region of nuclear ribosomal DNA is the most frequently used marker for distinguishing plant species. Previously published polymerase chain reaction (PCR) primers available for amplifying the ITS region from environmental plant samples provide a high degrees of success while maintaining a broad range of compatibility difficult to discriminate against fungal DNA. Thus, the plant-specific ITS primer design is required to achieve the preferential amplification of plant DNA with discrimination against fungal DNA from environmental plant samples. In this study, two primers, ITS1-F2 and ITS4-R, were newly designed and the specificity of these primers were tested against 14 accessions of Pulsatilla tongkangensis and 2 accessions of Pulsatilla cernua. Our results showed that ITS4-R, when paired with either a universal primer ITS5 or the newly designed primer ITS1-F2, efficiently amplified DNA from environmental P. cernua samples and discriminated against parasitic fungal DNAs, while another newly designed primer ITS1-F2, when paired with either a universal primer ITS4 or ITS4-R, could not preferentially amplify plant DNA or discriminate against fungal DNA. For P. tongkangensis, the dismatch of ITS5 primer resulted in noneffective or wrong amplification when paired with either ITS4-R or ITS4, while ITS1-F2, when paired with ITS4-R and ITS4, efficiently amplified plant DNA and both plant and fungal DNAs, respectively. This result suggested that the combination with ITS1-F2 and ITS4-R were intended to be specific to Pulsatilla species. This study will be particularly useful for detection and analysis of plant sequences from environmental or fungus-associated materials.

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Ribosomal DNA Sequences and Angiosperm Systematics

Cited by 99 publications

References 0 publications

Conflicting phylogenies of balsaminoid families and the polytomy in Ericales: combining data in a Bayesian framework

Conflicting phylogenies of balsaminoid families and the polytomy in Ericales: combining data in a Bayesian framework

Genetic diversity and hybridization of Pulsatilla tongkangensis based on the nrDNA ITS region sequence

Plant-specific primers for the amplification of the nrDNA ITS region in fungus-associated Pulsatilla species

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