Phylogenetic Relationships Among Members of Saxifragaceae Sensu Lato Based on rbcL Sequence Data

Morgan, David R.; Soltis, Douglas E.

doi:10.2307/2399851

Cited by 218 publications

(160 citation statements)

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“…PCR products were subjected to electrophoresis using 1% (wt/vol) agarose gels and Tris-acetate EDTA buffer, stained with ethidium bromide, and visualized using a GelDoc UV transilluminator and imager (Bio-Rad, Hercules, CA). Successful reactions were purified using polyethylene glycol precipitation (34). Sequencing reactions were run using a 10-l volume and BigDye Terminator master mix (version 3.1; Life Technologies, Carlsbad, CA) and an Applied Biosystems 3730XL DNA analyzer according to the manufacturer's directions.…”

Section: Methodsmentioning

confidence: 99%

Molecular Diversity of the Syndinean Genus Euduboscquella Based on Single-Cell PCR Analysis

Bachvaroff

Kim

Guillou

et al. 2012

Appl Environ Microbiol

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The genus Euduboscquella is one of a few described genera within the syndinean dinoflagellates, an enigmatic lineage with abundant diversity in marine environmental clone libraries based on small subunit (SSU) rRNA. The region composed of the SSU through to the partial large subunit (LSU) rRNA was determined from 40 individual tintinnid ciliate loricae infected with Euduboscquella sampled from eight surface water sites in the Northern Hemisphere, producing seven distinct SSU sequences. The corresponding host SSU rRNA region was also amplified from eight host species. The SSU tree of Euduboscquella and syndinean group I sequences from environmental clones had seven well-supported clades and one poorly supported clade across data sets from 57 to 692 total sequences. The genus Euduboscquella consistently formed a supported monophyletic clade within a single subclade of group I sequences. For most parasites with identical SSU sequences, the more variable internal transcribed spacer (ITS) to LSU rRNA regions were polymorphic at 3 to 10 sites. However, in E. cachoni there was variation between ITS to LSU copies at up to 20 sites within an individual, while in a parasite of Tintinnopsis spp., variation between different individuals ranged up to 19 polymorphic sites. However, applying the compensatory base change model to the ITS2 sequences suggested no compensatory changes within or between individuals with the same SSU sequence, while one to four compensatory changes between individuals with similar but not identical SSU sequences were found. Comparisons between host and parasite phylogenies do not suggest a simple pattern of host or parasite specificity.

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Section: Methodsmentioning

confidence: 99%

Molecular Diversity of the Syndinean Genus Euduboscquella Based on Single-Cell PCR Analysis

Bachvaroff

Kim

Guillou

et al. 2012

Appl Environ Microbiol

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“…Standard PCR conditions were used, although Ready-togo PCR beads (Amersham Pharmacia Biotech Inc.) were employed for a few taxa that were dif cult to amplify. PCR products were cleaned using PEG precipitation and ethanol cleaning (Morgan and Soltis 1993). Cycle sequencing used ABI Big Dye chemistry (Applied Biosystems, Foster City, CA), and was done in both directions using the same primers as for ampli cation.…”

Section: Methodsmentioning

confidence: 99%

Paraphyly in Tribe Onagreae: Insights into Phylogenetic Relationships of Onagraceae Based on Nuclear and Chloroplast Sequence Data

Levin¹,

Wagner²,

Hoch³

et al. 2004

Systematic Botany

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ABSTRACT. Onagraceae are a family of 17 genera in seven tribes, with the majority of species in tribes Onagreae and Epilobieae. Despite the species-richness of these two tribes, to date no phylogenetic study has been done with suf cient taxon sampling to examine relationships between and within these tribes. In this study, we used DNA sequence data from one nuclear region (ITS) and two chloroplast regions (trnL-trnF and rps16) to infer phylogenetic relationships among 93 taxa across the family, with concentrated sampling in the large tribe Onagreae. Results strongly suggest that tribe Gongylocarpeae is sister to tribes Epilobieae 1 Onagreae, both of which are monophyletic. Within Onagreae, Camissonia seems to be broadly paraphyletic, and Oenothera is also paraphyletic. In Oenothera there appear to be two lineages, one of which has Gaura 1 Stenosiphon nested within it. At the base of the Onagraceae phylogeny, we have clari ed previous confusion regarding con icting placements of Hauya and Lopezia based on nuclear versus chloroplast data. Results of these analyses are supported by morphology and suggest the need for new taxonomic delimitations, which are forthcoming.

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“…Single-stranded ''forward'' and ''reverse'' templates for the sequencing reaction were prepared via an asymmetric PCR amplification following the same protocol as above, except that only one of the two PCR-primers was included in the reaction. The singlestranded product was precipitated with 20% PEG/2.5 M NaCl, washed first with 70% EtOH, then with 95% EtOH before being suspended in 7 µl of TE (Morgan and Soltis, 1993).…”

Section: Methodsmentioning

confidence: 99%

Characterization of Mycobionts of Photomorph Pairs in the Peltigerineae (Lichenized Ascomycetes) Based on Internal Transcribed Spacer Sequences of the Nuclear Ribosomal DNA

Goffinet

Bayer

1997

Fungal Genetics and Biology

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Goffinet, B., and Bayer, R. J. 1997. Characterization of mycobionts of photomorph pairs in the Peltigerineae (lichenized ascomycetes) based on internal transcribed spacer sequences of the nuclear ribosomal DNA. Fungal Genetics and Biology 21, 228-237. The The ''one fungus-two photomorphs'' hypothesis suggests that certain lichenized fungi can establish a symbiotic relationship with either a eukaryotic or a prokaryotic photobiont. Such pairs of photomorphs are well know from cephalodiate Peltigerineae. Using an ascomycete-specific primer we amplified the internal transcribed spacer region of the nrDNA repeat of the mycobiont from total ''lichen DNA'' extracts of Peltigera malacea, photomorphs of P. aphthosa, P. britannica, and P. leucophlebia, Nephroma expallidum, and photomorphs of N. arcticum. Comparisons of 5.8S sequences suggest that the sequences obtained belong to the mycobiont and thus, that the ascomycetespecific primer is adequate for amplifying fungal DNA from total lichen-DNA extracts. The strict identity of nucleotide sequences of the internal transcribed spacer region of the nrDNA repeat between joined-photomorphs supports the one fungus-two photomorphs hypothesis. Photomorphs may thus primarily reflect phenotypic plasticity of photomorphic fungi in response to changing environmental conditions. The cyanomorph recently reported for P. leucophlebia is shown to be based on a misidentified specimen of P. aphthosa. Comparisons of the ITS sequences further supports recognizing P. aphthosa, P. britannica, and P. leucophlebia at the species rather than the infraspecific level. r 1997 Academic Press

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Phylogenetic Relationships Among Members of Saxifragaceae Sensu Lato Based on rbcL Sequence Data

Cited by 218 publications

References 0 publications

Molecular Diversity of the Syndinean Genus Euduboscquella Based on Single-Cell PCR Analysis

Molecular Diversity of the Syndinean Genus Euduboscquella Based on Single-Cell PCR Analysis

Paraphyly in Tribe Onagreae: Insights into Phylogenetic Relationships of Onagraceae Based on Nuclear and Chloroplast Sequence Data

Characterization of Mycobionts of Photomorph Pairs in the Peltigerineae (Lichenized Ascomycetes) Based on Internal Transcribed Spacer Sequences of the Nuclear Ribosomal DNA

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