Academic literature on the topic 'TrnQ-rps16'

AbstractThe fruits of Xanthium sibiricum have been widely used in traditional Chinese medicine for the treatment of nasal sinusitis and headaches. The genus Xanthium (cocklebur) is a taxonomically complex genus. Different taxonomic concepts have been proposed, some including several species, others lumping the different taxa in a few extremely polymorphic species. Due to the morphological similarities between species, the correct authentication of X. sibiricum is very difficult. Therefore, we established a polymerase chain reaction-restriction fragment length polymorphism method and diagnostic PCR based on nuclear internal transcribed spacer and chloroplast trnQ-rps16 barcodes to differentiate X. sibirium from related species.Results from the phylogenetic analyses based on sequence information from four marker regions (plastidal psbA-trnH and trnQ-rps16 and nuclear ITS and D35) support those taxonomic concepts accepting a reduced number of species, as four to five major clades are revealed in the phylogenetic reconstructions. X. sibiricum, together with some accessions from closely related taxa, is always supported as monophyletic, constituting a well-defined genetic entity. Allele-specific primer pairs for ITS and trnQ-rps16 were designed to amplify diagnostic products from the genomic DNA of X. sibiricum. Specific PCR in combination with digestion using the restriction enzyme MseI allowed for the identification of X. sibiricum by producing specific restriction patterns. The results demonstrate that the applied techniques provide effective and accurate authentication of X. sibiricum.

Phylogeography in plants is hampered by lack of DNA-sequence regions that detect sufficient variation in intra-specific lineages to reveal historical patterns. We tested 13 putatively highly variable non-coding chloroplast regions in six species complexes, from four different angiosperm families, where phylogeographic patterns have previously been identified using restriction fragment length polymorphism analysis of the chloroplast genome. All regions tested amplified in most of the species. The intergenic spacer regions trnQ–rps16, trnS–trnG, psbA–trnH, psbD–trnT and ndhC–trnV were the five most promising regions for phylogeographic analysis in terms of variability, and petB and rpl16 were variable, given the utility of being amplified in a single reaction. The trnQ–rps16 and psbA–trnH intergenic spacer regions and the rpl16 D4-loop intron showed variation between known lineages in all species. The psbA–trnH intergenic spacer that has been suggested as a suitable barcoding gene for plants, generally showed a level of variation similar to that in other variable regions in the species investigated here, suggesting that some caution is required in the use of this region for barcoding applications. The present analysis identified a set of seven chloroplast regions that are a useful basis for informed selection of sequences for assessment of phylogeographic structure in plants.

Aizoaceae is the largest succulent plant family in the world, including in excess of 1800 species. Despite its richness, a large proportion of its taxa are listed as data deficient and as such, has been identified as the top priority for taxonomic research in South Africa. Limitations to accurate taxonomic identification of taxa in the family may be partly attributed to the degree of technical knowledge required to identify taxa in the Aizoaceae. DNA barcoding may provide an alternative method of identification; however, the suitability of commonly used gene regions has not been tested in the family. Here, we analyse variable and parsimony informative characters (PIC), as well as the barcoding gap, in commonly used plastid regions (atpB-rbcL, matK, psbA-trnH, psbJ-petA, rpl16, rps16, trnD-trnT, trnL-trnF, trnQ-rps16, and trnS-trnG) and the nuclear region ITS (for Aizooideae only) across two subfamilies and two expanded clades within the Aizoaceae. The relative percentage of PIC was much greater in subfamilies Aizooideae and Mesembryanthemoideae than in Ruschioideae. Although nrITS had the highest percentage of PIC, barcoding gap analyses identified neither ITS nor any chloroplast region as suitable for barcoding of the family. From the results, it is evident that novel barcoding regions need to be explored within the Aizoaceae.

The infrageneric taxonomy and evolution of Ranunculus are still not well understood. In this regard, we investigated the origin and genetic diversity of the Iberian endemic plant Ranunculus bupleuroides s.l. by analysis of nuclear internal transcribed spacers (ITS) and plastid (rpl32-trnL, rps16-trnQ, trnK-matK, ycf6-psbM) sequence data. Phylogenetic analysis reveals two geographically well supported subclades: one formed by high mountain plants and another by more typical samples of Ranunculus bupleuroides from the lowlands of the western Iberian Peninsula. The subclade of montane plants includes both plants originating in Gredos and Béjar (Ranunculus cherubicus subsp. cherubicus) and those from Sierra Nevada (R. cherubicus subsp. girelai). In the light of the new molecular results obtained, combined with an assessment of morphological, geographical and ecological characters, a new systematic treatment is proposed.

Intergeneric phylogenetic relationships within Apiaceae tribe Oenantheae were investigated using sequence data from the chloroplast DNA psbI–5′trnK(UUU) and nuclear ribosomal DNA internal transcribed spacer regions. One hundred and thirty-one accessions were examined, representing all 17 genera of the tribe and approximately one-half of its species. The cpDNA region includes four intergenic spacers and the rps16 intron and these noncoding loci were analyzed separately to assess their relative utility for resolving relationships. Separate maximum parsimony analyses of the entire psbI–5′trnK(UUU) and ITS regions, each with and without scored indels, yielded concordant trees. Phylogenies derived from maximum parsimony, Bayesian, or maximum likelihood analyses of combined chloroplast and nuclear DNA sequences for 82 accessions were highly resolved, well supported, and consistent. Among the five noncoding loci examined, the trnQ(UUG)–5′rps16 and 3′rps16–5′trnK(UUU) intergenic spacers are the most variable, with the latter contributing the greatest total number of parsimony informative characters relative to its size. The North American genera Atrema , Cynosciadium , Daucosma , Limnosciadium , Neogoezia , Oxypolis , Ptilimnium , and Trepocarpus ally with the western hemispheric and Australasian genus Lilaeopsis in a strongly supported North American Endemics clade that is a sister group to a clade composed primarily of Old World taxa ( Berula sensu lato, Cryptotaenia , Helosciadium , and Sium ). Oxypolis and Ptilimnium are not monophyletic, with the rachis-leaved members of each comprising a clade separate from their compound-leaved congeners. Dispersal-vicariance analysis suggests that the ancestors of the North American Endemics clade probably originated in Canada and the USA or in a broader ancestral area including Mexico and South America.

Prior taxonomic studies in subtribe Pleurothallidinae have suggested a close relationship between miscellaneous species featuring long-repent, segmented rhizomes, abbreviated ramicauls, few-flowered inflorescences, and flowers with partially connate sepals and trilobed lip. The lack of phylogenetic information for most species has prevented further conclusions or changes in their taxonomy; and as a result, they are currently assigned to several unrelated genera: Anathallis, Madisonia, Pabstiella, Pleurothallis, Sansonia and Specklinia. We performed phylogenetic analyses using nuclear (nrITS) and five plastid (matK, psbD-trnT, rps16-trnQ, trnH-psbA and trnS-trnG) markers and demonstrated that these species form an isolated clade which requires generic recognition. The name Madisonia, previously a monotypic genus endemic of the Amazon basin, is re-circumscribed and expanded to include nine species distributed in the Atlantic Rainforest and the Caribbean. Eight new nomenclatural combinations are proposed.

Abstract Merostachys is a Neotropical woody bamboo genus that occurs in the understory and along forest borders. Our taxonomic studies of its species and morphological analyses have allowed us to recognize morphological groups in the genus. Previous molecular analyses, which included relatively few species, supported Merostachys as monophyletic and sister to Actinocladum or Athroostachys. We here provide a phylogenetic estimation for Merostachys based on a broader taxon sampling and seven plastid markers (one coding: ndhF 3′ end; four intergenic spacers: rps16-trnQ, trnC-rpoB, trnD-trnT and trnT-trnL; and two introns: rpl16 and rps16). We aimed to test the monophyly of the genus, to verify its relationship with other genera of Arthrostylidiinae, mainly Athroostachys and Actinocladum, and to test whether the previously identified morphological groups were congruent with the molecular data. The monophyly of the genus was confirmed, as was its sister relationship with Athroostachys, although alternate hypothesis testing could not reject a sister relationship with Actinocladum. Two well-supported clades in Merostachys were recovered, one of which encompasses a polytomy. These clades did not exhibit consistent morphological synapomorphies and were not congruent with the morphological groups; however, floret surface (shiny vs. dull) was correlated with the two clades. The lack of resolution in Merostachys, as exemplified by the polytomy, can be attributed mainly to incomplete lineage sorting, suggesting a recent radiation in this group.

Allium toksanbaicum from South East Kazakhstan is described as a new species. Molecular markers reveal a close relationship to A. obliquum and some other central Asian species of the section Oreiprason. We investigated the phylogenetic relationship of the new species based on sequences of two chloroplast spacers (rpl32-trnL and trnQ-rps16) and the nuclear ribosomal DNA internal transcribed spacer (ITS) region. The new species is diploid with a chromosome number of 2n = 2x = 16. A detailed morphological description, illustrations and karyotype features of the new species are given. With its falcate leaves, the new species is very similar to A. carolinianum from the section Falcatifolia, but in the shape of the inflorescence and flowers it is very different from it. From A. obliquum it differs for the purple colour of flowers and filaments, as well as the presence of teeth at the base of inner stamens.

Submitted by Renata Lopes (renatasil82@gmail.com) on 2017-03-23T19:08:09Z No. of bitstreams: 1 fernandasampaio.pdf: 1013409 bytes, checksum: a971117fc3bdd9c19272fe04cac30974 (MD5)
Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2017-03-24T12:55:01Z (GMT) No. of bitstreams: 1 fernandasampaio.pdf: 1013409 bytes, checksum: a971117fc3bdd9c19272fe04cac30974 (MD5)
Made available in DSpace on 2017-03-24T12:55:01Z (GMT). No. of bitstreams: 1 fernandasampaio.pdf: 1013409 bytes, checksum: a971117fc3bdd9c19272fe04cac30974 (MD5) Previous issue date: 2009-02-13
O gênero Lippia é um dos principais da família Verbenaceae e em sua maior parte está concentrado no Brasil, México, Paraguai e Argentina com poucas espécies endêmicas na África. O objetivo deste trabalho foi a construção de uma hipótese filogenética para 39 espécies do gênero Lippia ocorrentes no Brasil, Argentina, Bolívia, Paraguai e Uruguai com base em dados moleculares das regiões ITS, Waxy, TrnL-F e trnQ-rps16. As sequências foram amplificadas e purificadas para posterior seqüenciamento. As análises foram feitas utilizando-se Máxima Verossimilhança e Inferência Bayesiana. O presente trabalho revelou, pela primeira vez, aspectos filogenéticos de espécies do gênero Lippia com base em caracteres moleculares. De modo geral, as árvores filogenéticas baseadas nas diferentes regiões gênicas estudadas revelaram questões importantes como é o caso do monofiletismo da seção Goniostachyum. Outro ponto importante envolve a falta de resolução das seções Dipterocalix, Rhodolippia e Zapania. Dentre elas destaca-se a seção Zapania que constitui em vários aspectos estudados, a seção mais diversa. Embora o presente trabalho tenha mostrado aspectos inéditos com relação à organização filogenética de espécies e seções do gênero Lippia, a questão da especiação no gênero permanece em aberto. É possível que para resolver este problema sejam necessários estudos populacionais e filogeográficos, embasados por uma análise filogenética com maior número de genes e principalmente, envolvendo um maior número de espécies.
Lippia is one of the most important genus of the Verbenaceae family. It is mainly concentrated in Brazil, Mexico, Paraguay and Argentina with few endemic species in Africa. The present study was done in order to construct a phylogenetic hypothesis for 39 species of the genus Lippia from Brazil, Argentina, Bolivia, Paraguay and Uruguay based on molecular data of regions ITS, Waxy, TrnL-F and rps16-trnQ. The sequences were amplified and purified for subsequent sequencing. The phylogenetic analyses were done using the Maximum Likelihood and Bayesian Inference. It was possible to show for the first time, phylogenetic aspects of the genus Lippia based on molecular data. In general, the phylogenetic trees based on different gene regions revealed important points such as the monophyly of Goniostachyum section. Another important point involves the lack of resolution of the sections Dipterocalix, Rhodolippia and mainly Zapania which is the most diverse among them. Although this work has shown new aspects about the phylogenetic organization of sections and species of the genus Lippia, the speciation process of the genus remains an open question. To resolve this problem, additional studies using phylogeographic and population genetics approaches, based on a phylogenetic analysis with greater numbers of genes and mainly involving a great number of species should be necessary.