Type II DNA Topoisomerase (Top2) as Promising Molecular Marker for Phylogenetic Analysis in Rhodophyta

Shimomura, K.; Yamamoto, Shuich; Harayama, Shigeaki; Saga, Naotsune

doi:10.1515/bot.2002.011

Cited by 2 publications

(1 citation statement)

References 9 publications

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“…Five primer pairs were designed based on nucleotide sequences of ß-tubulin, TOP2, EF-1 including 5 0 -untranslated region (UTR) and V-ATPase from P. yezoensis, as reported in previous studies (Kitade et al, 1999;Shimomura et al, 2002;Fukuda et al, 2003;Gong et al, 2005, Table 2). To evaluate the influence of the presence of introns on the level of polymorphism, we used three primer pairs that were not expected to span an intron for amplification, i.e.…”

Section: Caps Analysis: Pcr Amplification and Restriction Endonucleasmentioning

confidence: 99%

Genetic polymorphism withinPorphyra yezoensis(Bangiales, Rhodophyta) and related species from Japan and Korea detected by cleaved amplified polymorphic sequence analysis

Park

Fukuda

Endo

et al. 2007

European Journal of Phycology

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We investigated genetic diversity in 10 strains of Porphyra yezoensis and related species, collected from Japan and Korea, in order to identify an appropriate crossing partner for use in various genetic analyses. Firstly, the phylogenetic relationships among the 10 strains were examined using SSU rDNA sequences. All five Japanese strains (TU-1, TU-2, TUH-25, JHS and JHU) and two of the Korean strains (KGJ and KPH) were identified as P. yezoensis while the other three Korean strains (KTY1, KTY2 and KTY3) were identified as P. tenera. Using cleaved amplified polymorphic sequence analysis, genetic polymorphisms lying in five regions of four genes (ß-tubulin, TOP2, EF-1 and V-ATPase) were examined. Twenty out of 34 restriction endonucleases revealed genetic polymorphisms between the seven strains of P. yezoensis and the three strains of P. tenera in all five regions tested. Furthermore, when they were employed to digest the fragments of TOP2 and V-ATPase, 14 enzymes discriminated the two Korean strains of P. yezoensis (KGJ and KPH) from the five Japanese strains of this species. The level of polymorphism was much higher in the amplified fragment of V-ATPase (including four introns) than in that of TOP2 without an intron. The gene regions with detected polymorphisms would be useful molecular markers for confirmation of cross-fertilization in sporophytic thalli and for construction of a linkage map. A suitable combination of the strains in the cross experiment is discussed.

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Section: Caps Analysis: Pcr Amplification and Restriction Endonucleasmentioning

confidence: 99%

Genetic polymorphism withinPorphyra yezoensis(Bangiales, Rhodophyta) and related species from Japan and Korea detected by cleaved amplified polymorphic sequence analysis

Park

Fukuda

Endo

et al. 2007

European Journal of Phycology

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Phylogenetic positions of several amitochondriate protozoa——Evidence from phylogenetic analysis of DNA topoisomerase II

Dong

Wen

et al. 2005

Sci China Ser C

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Several groups of parasitic protozoa, as represented by Giardia, Trichomonas, Entamoeba and Microsporida, were once widely considered to be the most primitive extant eukaryotic group--Archezoa. The main evidence for this is their 'lacking mitochondria' and possessing some other primitive features between prokaryotes and eukaryotes, and being basal to all eukaryotes with mitochondria in phylogenies inferred from many molecules. Some authors even proposed that these organisms diverged before the endosymbiotic origin of mitochondria within eukaryotes. This view was once considered to be very significant to the study of origin and evolution of eukaryotic cells (eukaryotes). However, in recent years this has been challenged by accumulating evidence from new studies. Here the sequences of DNA topoisomerase II in G lamblia, T. vaginalis and E. histolytica were identified first by PCR and sequencing, then combining with the sequence data of the microsporidia Encephalitozoon cunicul and other eukaryotic groups of different evolutionary positions from GenBank, phylogenetic trees were constructed by various methods to investigate the evolutionary positions of these amitochondriate protozoa. Our results showed that since the characteristics of DNA topoisomerase II make it avoid the defect of 'long-branch attraction' appearing in the previous phylogenetic analyses, our trees can not only reflect effectively the relationship of different major eukaryotic groups, which is widely accepted, but also reveal phylogenetic positions for these amitochondriate protozoa, which is different from the previous phylogenetic trees. They are not the earliest-branching eukaryotes, but diverged after some mitochondriate organisms such as kinetoplastids and mycetozoan; they are not a united group but occupy different phylogenetic positions. Combining with the recent cytological findings of mitochondria-like organelles in them, we think that though some of them (e.g. diplomonads, as represented by Giardia) may occupy a very low evolutionary position, generally these organisms are not as extremely primitive as was thought before; they should be polyphyletic groups diverging after the endosymbiotic origin of mitochondrion to adapt themselves to anaerobic parasitic life.

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Type II DNA Topoisomerase (Top2) as Promising Molecular Marker for Phylogenetic Analysis in Rhodophyta

Cited by 2 publications

References 9 publications

Genetic polymorphism withinPorphyra yezoensis(Bangiales, Rhodophyta) and related species from Japan and Korea detected by cleaved amplified polymorphic sequence analysis

Genetic polymorphism withinPorphyra yezoensis(Bangiales, Rhodophyta) and related species from Japan and Korea detected by cleaved amplified polymorphic sequence analysis

Phylogenetic positions of several amitochondriate protozoa——Evidence from phylogenetic analysis of DNA topoisomerase II

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