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Berlin Brandenburg

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  • 1
    Language: English
    In: International Journal of Plant Sciences October 2007, Vol.168(8), pp.1157-1160
    Description: The increasing number of pseudogenic internal transcribed spacer (ITS) regions (ITS1, 5.8S rDNA, ITS2) reported for plant taxa raises questions—for example, concerning the proportion of functional copies. Our application of quantitative PCR (qPCR) with genomic DNA under stringent conditions revealed that 〈3% of the copies of the ITS region were putatively functional in the genomic PCR pool in Mammillaria . The selective amplification of functional copies of the ITS region was possible through the utilization of conserved angiosperm motifs (ITS1 motif and 5.8S motif) as primer annealing sites. Our study displays that it is possible to quantify the proportion of functional copies of repetitive DNA regions through their selective amplification by qPCR.
    Keywords: Polymerase Chain Reaction -- Genetic Aspects ; Genomic Libraries -- Evaluation ; Angiosperms -- Genetic Aspects ; Genetic Polymorphisms -- Evaluation;
    ISSN: 10585893
    E-ISSN: 15375315
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  • 2
    In: PLoS ONE, 2016, Vol.11(4)
    Description: Most flowers display distinct colour patterns comprising two different areas. The peripheral large-area component of floral colour patterns attracts flower visitors from some distance and the central small-area component guides flower visitors towards landing sites. Whereas the peripheral colour is largely variable among species, the central colour, produced mostly by anthers and pollen or pollen mimicking floral guides, is predominantly yellow and UV-absorbing. This holds also for yellow flowers that regularly display a UV bull’s eye pattern. Here we show that yellow-flowering Crocus species are a noticeable exception, since yellow-flowering Crocus species–being entirely UV-absorbing–exhibit low colour contrast between yellow reproductive organs and yellow tepals. The elongated yellow or orange-yellow style of Crocus flowers is a stamen-mimicking structure promoting cross-pollination by facilitating flower visitors’ contact with the apical stigma before the flower visitors are touching the anthers. Since Crocus species possess either yellow, violet or white tepals, the colour contrast between the stamen-mimicking style and the tepals varies among species. In this study comprising 106 Crocus species, it was tested whether the style length of Crocus flowers is dependent on the corolla colour. The results show that members of the genus Crocus with yellow tepals have evolved independently up to twelve times in the genus Crocus and that yellow-flowering Crocus species possess shorter styles as compared to violet- and white-flowering ones. The manipulation of flower visitors by anther-mimicking elongated styles in Crocu s flowers is discussed.
    Keywords: Research Article ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Research And Analysis Methods ; Biology And Life Sciences
    E-ISSN: 1932-6203
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  • 3
    Language: English
    In: Molecular Phylogenetics and Evolution, 2006, Vol.41(3), pp.579-593
    Description: Molecular studies of 21 species of the large Cactaceae genus representing a variety of intrageneric taxonomic levels revealed a high degree of intra-individual polymorphism of the internal transcribed spacer region (ITS1, 5.8S rDNA, ITS2). Only a few of these ITS copies belong to apparently functional genes, whereas most are probably non-functional (pseudogenes). As a multiple gene family, the ITS region is subjected to concerted evolution. However, the high degree of intra-individual polymorphism of up to 36% in ITS1 and up to 35% in ITS2 suggests a non-concerted evolution of these loci in . Conserved angiosperm motifs of ITS1 and ITS2 were compared between genomic and cDNA ITS clones of . Some of these motifs (e.g., ITS1 motif 1, ‘TGGT’ within ITS2) in combination with the determination of GC-content, length comparisons of the spacers and ITS2 secondary structure (helices II and III) are helpful in the identification of pseudogene rDNA regions.
    Keywords: Internal Transcribed Spacer ; Non-Concerted Evolution ; Mammillaria ; Pseudogene ; Its Motifs ; Its2 Secondary Structure ; Biology
    ISSN: 1055-7903
    E-ISSN: 1095-9513
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  • 4
    Language: English
    In: Molecular Phylogenetics and Evolution, October 2018, Vol.127, pp.891-897
    Description: Phylogenetic relationships among the taxa of series are still unclear, preventing the understanding of species diversity and the evolution of the important spice saffron ( ). Therefore, we analyzed sequences of two chloroplast ( L- F, K- K) and three nuclear (TOPO6, ribosomal DNA ETS and ITS) marker regions to infer phylogenetic relationships among all species belonging to series . Our phylogenetic analyses resolved the relationships among all taxa of the series. and the former subspecies appeared polyphyletic. The latter deserve elevating the subspecies to species rank, while for a detailed study of species boundaries is necessary. Multi-locus and also genome-wide single nucleotide polymorphism data obtained through genotyping-by-sequencing placed within with no indication that other species contributed to the evolution of the triploid. Our analyses thus made an autotriploid origin of from very likely.
    Keywords: Crocus Series Crocus ; Evolution ; GBS ; Multi-Locus Analysis ; Phylogeny ; Saffron ; Biology
    ISSN: 1055-7903
    E-ISSN: 1095-9513
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  • 5
    Language: English
    In: Molecular Phylogenetics and Evolution, March 2013, Vol.66(3), pp.617-627
    Description: ► We provide the first exhaustive phylogeny of crocuses based on nuclear sequences. ► We reconstruct chromosome number evolution and polyploidization in . ► 8 out of 15 series of are monophyletic, as well as probably both sections. ► Chromosome numbers increased multiple times independently by polyploidization. ► Supernumerary B chromosomes evolved at least five times independently within consists of about 100 species distributed from western Europe and northern Africa to western China, with the center of diversity on the Balkan Peninsula and in Asia Minor. Our study focuses on clarifying phylogenetic relationships and chromosome number evolution within the genus using sequences of the chloroplast L-F region, the nuclear ribosomal DNA internal transcribed spacer (ITS) region, and a part of the nuclear single-copy gene . In a combined dataset of ITS and L-F sequences, 115 individuals representing 110 taxa from both subgenera and all sections and series of were analyzed with Bayesian phylogenetic inference. For 79 individuals representing 74 taxa were included, and for the majority of them PCR amplicons were cloned and up to eight clones per individual were sequenced to detect allopolyploidization events. species were included as outgroup in both analyses. Characteristics of seed surface structures were evaluated by scanning electron microscopy. Phylogenetic analysis of ITS/ L-F data resulted in a monophyletic genus , probably monophyletic sections and , and inferred monophyly for eight of the 15 series of the genus. The aggregate, thought to be consisting of closely related subspecies, was found to be polyphyletic, the taxa occurring within three major clades in the phylogenetic tree. Cloning of resulted in the detection of homoeologous copies in about one third of the taxa of section , indicating an allotetraploid origin of this section. Reconstruction of chromosome number evolution along the phylogenetic tree using a probabilistic and a parsimony approach arrived at partly contradictory results. Both analyses agreed however on the occurrence of multiple polyploidization and dysploidy events. B chromosomes evolved at least five times independently within the genus, preferentially in clades characterized by karyotype changes.
    Keywords: B Chromosome ; Chromosome Number ; Crocus ; Evolution ; Internal Transcribed Spacer (Its) ; Pcosat103 ; Phylogeny ; Trnl-F ; Seed Testa ; Whole Genome Duplication ; Biology
    ISSN: 1055-7903
    E-ISSN: 1095-9513
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  • 6
    Language: English
    In: PLoS ONE, 01 January 2017, Vol.12(6), p.e0178402
    Description: Cistanthe longiscapa is an endemic annual herb and characteristic element of the Chilean Atacama Desert. Principal threats are the destruction of its seed deposits by human activities and reduced germination rates due to the decreasing occurrence of precipitation events. To enable population genetic and phylogeographic analyses in this species we performed paired-end shotgun sequencing (2x100 bp) of genomic DNA on the Illumina HiSeq platform and identified microsatellite (SSR) loci in the resulting sequences. From 29 million quality-filtered read pairs we obtained 549,174 contigs (average length 614 bp; N50 = 904). Searching for SSRs revealed 10,336 loci with microsatellite motifs. Initially, we designed primers for 96 loci, which were tested for PCR amplification on three C. longiscapa individuals. Successfully amplifying loci were further tested on eight individuals to screen for length variation in the resulting amplicons, and the alleles were exemplarily sequenced to infer the basis for the observed length variation. Finally we arrived at 26 validated SSR loci for population studies in C. longiscapa, which resulted in 146 bi-allelic SSR markers in our test sample of eight individuals. The genomic sequences were also used to assemble the plastid genome of C. longiscapa, which provides an additional set of maternally inherited genetic markers.
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 7
    Language: English
    In: Organisms Diversity & Evolution, 2011, Vol.11(5), pp.387-407
    Description: A new region of speciation for the genus Gagea (Liliaceae) was investigated (Bogda-Shan and Urumqi; northwestern Xinjiang, China). Two species were recorded as new for the region ( G. rufidula , G. davlianidzeae ); three species are described as new to science ( G. angelae, G. jensii and G. huochengensis ). The description of G. nigra is emendated. Sequence data (cpDNA: trn L- trn F IGS+ psb A- trn H IGS, nrDNA: ITS), including representatives of all Gagea sections, were used to compare the new species with closely related taxa. A nuclear single copy gene region (pCOS At 103) was analysed for representatives of the Sects. Minimae and Gagea . Network analysis of cpDNA and nDNA indicates hybridization and recent speciation in Xinjiang. ITS and pCOS At 103 sequences reveal gene flow between G. davlianidzeae and G. nigra . A cpDNA haplotype network constructed from representatives of Sect. Gagea was highly informative phylogenetically. Gagea angelae and G . huochengensis , sharing gene flow, are related closely to a basal clade represented by G. ancestralis , G. xiphoidea and G. capusii , which may include the putative progenitor of all other taxa of the large Eurasian Sect. Gagea . Whereas speciation in Sect. Minimae seems to be driven mainly by hybridization, speciation in the Sect. Gagea may be influenced by both hybridization and geographical separation. We confirm the monophyly of Sects. Bulbiferae and Minimae .
    Keywords: cpDNA ; Gagea ; hybridization ; ITS ; Liliales ; At ; speciation
    ISSN: 1439-6092
    E-ISSN: 1618-1077
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  • 8
    Language: English
    In: Journal of Plant Research, 2008, Vol.121(3), pp.261-270
    Description: The internal transcribed spacer (ITS) region (ITS1, 5.8S rDNA, ITS2) represents the most widely applied nuclear marker in eukaryotic phylogenetics. Although this region has been assumed to evolve in concert, the number of investigations revealing high degrees of intra-individual polymorphism connected with the presence of pseudogenes has risen. The 5.8S rDNA is the most important diagnostic marker for functionality of the ITS region. In Mammillaria , intra-individual 5.8S rDNA polymorphisms of up to 36% and up to nine different types have been found. Twenty-eight of 30 cloned genomic Mammillaria sequences were identified as putative pseudogenes. For the identification of pseudogenic ITS regions, in addition to formal tests based on substitution rates, we attempted to focus on functional features of the 5.8S rDNA (5.8S motif, secondary structure). The importance of functional data for the identification of pseudogenes is outlined and discussed. The identification of pseudogenes is essential, because they may cause erroneous phylogenies and taxonomic problems.
    Keywords: 5.8S rDNA ; Intra-individual variability ; Mammillaria ; Pseudogene ; Secondary structure
    ISSN: 0918-9440
    E-ISSN: 1618-0860
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  • 9
    Language: English
    In: Canadian Journal of Botany, March, 2008, Vol.86(3), p.300(6)
    Keywords: Phylogeny -- Research ; Pseudogenes -- Identification And Classification ; Plant Genetics -- Research
    ISSN: 0008-4026
    Source: Cengage Learning, Inc.
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  • 10
    In: Phytotaxa, 05/11/2016, Vol.260(2), p.131
    ISSN: 1179-3155
    E-ISSN: 1179-3163
    Source: CrossRef
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