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Ribosomal Its Sequences And Plant Phylogenetic Inference Pdf

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We identified eight putative ITS pseudogenes from four taxa with low predicted secondary structure stability and high substitution rates. Maximum likelihood ML and neighbor-joining NJ methods were used for phylogenetic reconstruction. In the former clade, most tetraploid taxa appear to be polyphyletic; sequences from individual plants did not correspond to recognized taxonomic units.

Agarwood is a type of wood that is used in traditional Thai medicines and has been applied in several recipes; in particular, this wood is considered as a costly resinous non-wood product. However, the morphological characteristics of the plant in the genus Aquilaria are quite similar, and so the authentication steps need a botanical expert for the purposes of identification and then also require an efficient tool for species-level discrimination. DNA barcoding is an approved molecular technique which uses a short sequence as a barcoding region specific for identified species.

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Ribosomal ITS sequences and plant phylogenetic inference

In this paper, we discuss the possibility of using a short nuclear DNA sequence as a barcode to identify a wide range of medicinal plant species. First, the PCR and sequencing success rates of ITS and ITS2 were evaluated based entirely on materials from dry medicinal product and herbarium voucher specimens, including some samples collected back to 90 years ago. Our results supported the hypothesis that ITS2 can be used as a minibarcode to effectively identify species in a wide variety of specimens and medicinal materials. DNA barcoding takes advantage of short standard sequences to discover and identify species [ 1 ]. An ideal DNA barcode should be short enough to be amplified from archival specimens using universal primers. The results of that study showed that minibarcodes can be isolated from different types of specimens, including museum samples, trace tissue samples with degraded DNA and other specimens, from which the acquisition of a full-length barcode CO1 is not feasible [ 2 ]. The amplification of DNA from herbarium specimens is also important for barcoding studies because it is often necessary to confirm the species identification of fresh specimens by comparing their sequences with those of older museum specimens [ 3 ].

Phylogenetic analyses were conducted to evaluate relationships of 7 taxa of Korean Carpesium including three outgroup Inula britannica L. Phylogenetic studies used maximum parsimony, neighbor-joining and maximum likelihood methods analysis. The total number of variable sites was for the entire sequences, and a parsimony informative sites of 64 are valid. As the result, Korean Carpesium were formed monophyletic group and C. The results show that C. These results suggest that the ITS data used in this study could be useful for the phylogenetic analysis of Korean Carpesium. Download PDF.

Either your web browser doesn't support Javascript or it is currently turned off. In the latter case, please turn on Javascript support in your web browser and reload this page. All relevant data are within the paper and its Supporting Information file. Molecular morphometrics is an emerging third dimensional aspect of fungal species delimitation. They have been demonstrated to be more informative than conventional barcoding methods. Hence in this study, foliar endophytic fungal FEF assemblages in three Magnoliopsida plants were delimited using nuclear ribosomal internal transcribed spacer 2 ITS2 sequence—secondary structural features based phylogenetic analysis, also known as molecular morphometrics.


One of the most popular sequences for phylogenetic inference at the generic and infrageneric levels in plants is the internal transcribed spacer (ITS) region of.


Flowering times in Viburnum. Arnoldia PDF Donoghue, M. Growth patterns in woody plants with examples from the genus Viburnum.

Separate and combined analyses were performed. ITS-variation was extensive and, because of alignment ambiguities, some sites were excluded from the analyses. Several topologies from the rbc L analysis that conflicted with earlier classifications are corroborated by the ITS data: 1 Posoqueria should be excluded from Gardenieae. Incongruities found between the two data sets may be caused by density of taxon sampling, different evolutionary rates, phylogenetic sorting, homoplasy caused by functional constraints, or sampling of non-orthologous ITS types. This is a preview of subscription content, access via your institution.

Barcode of nuclear ribosomal internal transcribed spacer regions ITS as a useful tool to recognize a newly naturalized and potentially invasive weed, Chloris pilosa Schumach. Poaceae , in Taiwan. PDF Download Appendix. Akaike, H. A new look at the statistical model identification.

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