Polymorphism of nuclear DNA in selected species of Taraxacum sect. Palustria.
Ontology highlight
ABSTRACT:
SUBMITTER: Marciniuk J
PROVIDER: S-EPMC7714973 | biostudies-literature | 2020 Dec
REPOSITORIES: biostudies-literature
Publications
Polymorphism of nuclear DNA in selected species of <i>Taraxacum</i> sect. <i>Palustria</i>.
Marciniuk Jolanta J Rerak Joanna J Musiał Krystyna K Mizia Patryk P Marciniuk Paweł P Grabowska-Joachimiak Aleksandra A Joachimiak Andrzej J AJ
Saudi journal of biological sciences 20200728 12
This paper presents the results of research on nuclear DNA polymorphism in six apomictic species of marsh dandelions <i>(Taraxacum</i> sect. <i>Palustria): Taraxacum bavaricum, T. belorussicum, T. brandenburgicum, T. paucilobum, T. subdolum and T. vindobonense.</i> The studies demonstrated the existence of clear genetic differences between species and the existence of nuclear DNA polymorphism within each of the studied species. ...[more]
Similar Datasets
Project description:The species-rich and widespread genus Taraxacum F. H. Wiggers, 1780 (Asteraceae subfamily Cichorioideae) is one of the most taxonomically complex plant genera in the world, mainly due to its combination of different sexual and asexual reproduction strategies. Polyploidy is usually confined to apomictic microspecies, varying from 3x to 6x (rarely 10x). In this study, we focused on Taraxacum sect. Taraxacum (= T.sect.Ruderalia; T.officinale group), i.e., the largest group within the genus. We counted chromosome numbers and measured the DNA content for species sampled in Central Europe, mainly in Czechia. The chromosome number of the 28 species (T.aberrans Hagendijk, Soest & Zevenbergen, 1974, T.atroviride Štěpánek & Trávníček, 2008, T.atrox Kirschner & Štěpánek, 1997, T.baeckiiforme Sahlin, 1971, T.chrysophaenum Railonsala, 1957, T.coartatum G.E. Haglund, 1942, T.corynodes G.E. Haglund, 1943, T.crassum H. Øllgaard & Trávníček, 2003, T.deltoidifrons H. Øllgaard, 2003, T.diastematicum Marklund, 1940, T.gesticulans H. Øllgaard, 1978, T.glossodon Sonck & H. Øllgaard, 1999, T.guttigestans H. Øllgaard in Kirschner & Štěpánek, 1992, T.huelphersianum G.E. Haglund, 1935, T.ingens Palmgren, 1910, T.jugiferum H. Øllgaard, 2003, T.laticordatum Marklund, 1938, T.lojoense H. Lindberg, 1944 (= T.debrayi Hagendijk, Soest & Zevenbergen, 1972, T.lippertianum Sahlin, 1979), T.lucidifrons Trávníček, ineditus, T.obtusifrons Marklund, 1938, T.ochrochlorum G.E. Haglund, 1942, T.ohlsenii G.E. Haglund, 1936, T.perdubium Trávníček, ineditus, T.praestabile Railonsala, 1962, T.sepulcrilobum Trávníček, ineditus, T.sertatum Kirschner, H. Øllgaard & Štěpánek, 1997, T.subhuelphersianum M.P. Christiansen, 1971, T.valens Marklund, 1938) is 2n = 3x = 24. The DNA content ranged from 2C = 2.60 pg (T.atrox) to 2C = 2.86 pg (T.perdubium), with an average value of 2C = 2.72 pg. Chromosome numbers are reported for the first time for 26 species (all but T.diastematicum and T.obtusifrons), and genome size estimates for 26 species are now published for the first time.
| S-EPMC6160755 | biostudies-other
Project description:The genus Taraxacum is one of the largest and taxonomically most complicated apomictic genera. Currently, it is considered to consist of over 2800 species placed within 60 sections. Due to the large number of species, and their uniform morphological design and plasticity of leaves, the identification of plants at the species level is challenging even for specialists. This problem significantly hinders the study of their properties and the rational use of these valuable medicinal and nutritional plants. This paper presents the results of research on the morphology and micromorphology of achenes of 28 Taraxacum species of sect. Palustria and for comparison one species per section of: Erythrosperma, Naevosa, Piesis, and Taraxacum. The achenes were measured with a stereoscopic microscope and a biometric program, and micromorphological studies were performed by scanning electron microscopy. It has been shown that traits associated with achene morphology and micromorphology have a high diagnostic value, allowing us to distinguish sections as well as species within the sect. Palustria. Based on the examined achene features, a dichotomous key for determining the studied species was constructed.
| S-EPMC7661953 | biostudies-literature
Project description:The Philippine island of Palawan is highly biodiverse. During fieldwork there in 2011 & 2014 we found five unknown species in the large genus Begonia. The species are similar in their rhizomatous stems, four-tepaled flowers, inferior two- or three-locular ovaries with bilamellate placentas, and are assignable to Begonia sect. Baryandra. Our observations support the recognition of these as five new species endemic to Palawan: B. elnidoensis, B. gironellae, B. quinquealata, B. tabonensis and B. tenuibracteata which are described here. The five new species were added to phylogenies based Bayesian analysis of nrDNA (ITS) and chloroplast DNA (ndhA, ndhF-rpl32, rpl32-trnL, trnC-trnD), along with 45 other allied ingroup species. A majority of the species show incongruent positions in the two phylogenies, with evidence of prevalent chloroplast capture. Models show chloroplast capture is more likely in plant populations with high levels of inbreeding following a reduction in selfing rate after hybridisation; we suggest that this is a possible explanation for the massive amount of chloroplast exchange seen in our phylogeny, as Begonia species often exist as small isolated populations and may be prone to inbreeding depression. Our data also indicate a level of nuclear genetic exchange between species. The high prevalence of hybrid events in Begonia is potentially an important factor in driving genomic change and species evolution in this mega-diverse genus.
| S-EPMC5931476 | biostudies-literature
Project description:Wild species related to cultivated tomato are essential genetic resources in breeding programs focused on food security to face future challenges. The ecogeographic analysis allows identifying the species adaptive ranges and most relevant environmental variables explaining their patterns of actual distribution. The objective of this research was to identify the diversity, ecological descriptors, and statistical relationship of 35 edaphoclimatic variables (20 climatic, 1 geographic and 14 edaphic variables) from 4,649 accessions of 12 wild tomato species and 4 closely related species classified in Solanum sect. Lycopersicon and clustered into four phylogenetic groups, namely "Lycopersicon group" (S. pimpinellifolium, S. cheesmaniae, and S. galapagense), "Arcanum group" (S. arcanum, S. chmielewskii, and S. neorickii), "Eriopersicon group" (S. habrochaites, S. huaylasense, S. corneliomulleri, S. peruvianum, and S. chilense), "Neolycopersicon group" (S. pennellii); and two phylogenetically related groups in Solanum sect. Juglandifolia (S. juglandifolium and S. ochranthum), and section Lycopersicoides (S. lycopersicoides and S. sitiens). The relationship between the climate and edaphic variables were determined by the canonical correlation analysis, reaching 89.2% of variation with the first three canonical correlations. The most significant climatic variables were related to humidity (annual evapotranspiration, annual precipitation, and precipitation of driest month) and physicochemical soil characteristics (bulk density, pH, and base saturation percentage). In all groups, ecological descriptors and diversity patterns were consistent with previous reports. Regarding edaphoclimatic diversity, 12 climate types and 17 soil units were identified among all species. This approach has promissory applications for biodiversity conservation and uses valuable genetic resources related to a leading crop.
| S-EPMC8635747 | biostudies-literature
Project description:Plant genomes vary greatly in composition and size mainly due to the diversity of repetitive DNAs and the inherent propensity for their amplification and removal from the host genome. Most studies addressing repeatome dynamics focus on model organisms, whereas few provide comprehensive investigations across the genomes of related taxa. Herein, we analyze the evolution of repeats of the 13 species in Melampodium sect. Melampodium, representing all but two of its diploid taxa, in a phylogenetic context. The investigated genomes range in size from 0.49 to 2.27 pg/1C (ca. 4.5-fold variation), despite having the same base chromosome number (x = 10) and very strong phylogenetic affinities. Phylogenetic analysis performed in BEAST and ancestral genome size reconstruction revealed mixed patterns of genome size increases and decreases across the group. High-throughput genome skimming and the RepeatExplorer pipeline were utilized to determine the repeat families responsible for the differences in observed genome sizes. Patterns of repeat evolution were found to be highly correlated with phylogenetic position, namely taxonomic series circumscription. Major differences found were in the abundances of the SIRE (Ty1-copia), Athila (Ty3-gypsy), and CACTA (DNA transposon) lineages. Additionally, several satellite DNA families were found to be highly group-specific, although their overall contribution to genome size variation was relatively small. Evolutionary changes in repetitive DNA composition and genome size were complex, with independent patterns of genome up- and downsizing throughout the evolution of the analyzed diploids. A model-based analysis of genome size and repetitive DNA composition revealed evidence for strong phylogenetic signal and differential evolutionary rates of major lineages of repeats in the diploid genomes.
| S-EPMC7136903 | biostudies-literature
Project description:Allopolyploidy has played an important role in the evolution of the flowering plants. Genome mergers are often accompanied by significant and rapid alterations of genome size and structure via chromosomal rearrangements and altered dynamics of tandem and dispersed repetitive DNA families. Recent developments in sequencing technologies and bioinformatic methods allow for a comprehensive investigation of the repetitive component of plant genomes. Interpretation of evolutionary dynamics following allopolyploidization requires both the knowledge of parentage and the age of origin of an allopolyploid. Whereas parentage is typically inferred from cytogenetic and phylogenetic data, age inference is hampered by the reticulate nature of the phylogenetic relationships. Treating subgenomes of allopolyploids as if they belonged to different species (i.e., no recombination among subgenomes) and applying cross-bracing (i.e., putting a constraint on the age difference of nodes pertaining to the same event), we can infer the age of allopolyploids within the framework of the multispecies coalescent within BEAST2. Together with a comprehensive characterization of the repetitive DNA fraction using the RepeatExplorer pipeline, we apply the dating approach in a group of closely related allopolyploids and their progenitor species in the plant genus Melampodium (Asteraceae). We dated the origin of both the allotetraploid, Melampodium strigosum, and its two allohexaploid derivatives, Melampodium pringlei and Melampodium sericeum, which share both parentage and the direction of the cross, to the Pleistocene ($<$1.4 Ma). Thus, Pleistocene climatic fluctuations may have triggered formation of allopolyploids possibly in short intervals, contributing to difficulties in inferring the precise temporal order of allopolyploid species divergence of M. sericeum and M. pringlei. The relatively recent origin of the allopolyploids likely played a role in the near-absence of major changes in the repetitive fraction of the polyploids' genomes. The repetitive elements most affected by the postpolyploidization changes represented retrotransposons of the Ty1-copia lineage Maximus and, to a lesser extent, also Athila elements of Ty3-gypsy family.
| S-EPMC6193527 | biostudies-literature
Project description:Phylogenetic reconstruction revealed that Mycena stirps Amparoina, which is traditionally classified in sect. Sacchariferae, should be treated at section level. Section Amparoina is characterised by the presence or absence of cherocytes, the presence of acanthocysts and spinulose caulocystidia. Eight species referred to Mycenasect.Amparoinasect. nov. are recognised in China. Of these taxa, four new species classified in the new section are formally described: M.bicystidiata sp. nov., M.griseotincta sp. nov., M.hygrophoroides sp. nov. and M.miscanthi sp. nov. The new species are characterised by the absence of both cherocytes and a basal disc, along with the presence of acanthocysts on the pileus, spinulose cheilocystidia and caulocystidia. Descriptions of the new species, accompanied by illustrations of morphological characters and comparisons with closely related taxa, are provided. A multi-locus analysis utilising the ITS + nLSU + SSU regions was carried out using maximum likelihood and Bayesian Inference. A key to the 12 species of sect. Amparoinasect. nov. and sect. Sacchariferae that are found in China is provided.
| S-EPMC6533235 | biostudies-literature
Project description:DNA testing for food authentication and quality control requires sensitive species-specific quantification of nuclear DNA from complex and unknown biological sources. We have developed a multiplex assay based on TaqMan® real-time quantitative PCR (qPCR) for species-specific detection and quantification of chicken (Gallus gallus), duck (Anas platyrhynchos), and turkey (Meleagris gallopavo) nuclear DNA. The multiplex assay is able to accurately detect very low quantities of species-specific DNA from single or multispecies sample mixtures; its minimum effective quantification range is 5 to 50 pg of starting DNA material. In addition to its use in food fraudulence cases, we have validated the assay using simulated forensic sample conditions to demonstrate its utility in forensic investigations. Despite treatment with potent inhibitors such as hematin and humic acid, and degradation of template DNA by DNase, the assay was still able to robustly detect and quantify DNA from each of the three poultry species in mixed samples. The efficient species determination and accurate DNA quantification will help reduce fraudulent food labeling and facilitate downstream DNA analysis for genetic identification and traceability.
| S-EPMC4252418 | biostudies-literature
Project description:We tested the performance of DNA barcoding in Acridoidea and attempted to solve species boundary delimitation problems in selected groups using COI barcodes. Three analysis methods were applied to reconstruct the phylogeny. K2P distances were used to assess the overlap range between intraspecific variation and interspecific divergence. "Best match (BM)", "best close match (BCM)", "all species barcodes (ASB)" and "back-propagation neural networks (BP-based method)" were utilized to test the success rate of species identification. Phylogenetic species concept and network analysis were employed to delimitate the species boundary in eight selected species groups. The results demonstrated that the COI barcode region performed better in phylogenetic reconstruction at genus and species levels than at higher-levels, but showed a little improvement in resolving the higher-level relationships when the third base data or both first and third base data were excluded. Most overlaps and incorrect identifications may be due to imperfect taxonomy, indicating the critical role of taxonomic revision in DNA barcoding study. Species boundary delimitation confirmed the presence of oversplitting in six species groups and suggested that each group should be treated as a single species.
| S-EPMC3869712 | biostudies-literature
Project description:Conservation and sustainable use of species diversity require a description of the environment where they develop. The objectives were to determine ecological descriptors and climatic diversity of areas along the distribution range of 12 species of wild tomatoes (Solanum sect. Lycopersicon) and four wild species of phylogenetically related groups (Solanum sect. Juglandifolia and sect. Lycopersicoides), as well as their ecological similarity in Latin America. With 4228 selected tomato accessions and an environmental information system (EIS) composed of 21 climatic variables, diversity patterns of the distribution areas were identified for each species, as well as ecological descriptors through the use of geographic information systems (GIS). The contribution of climatic variables to the species geographical distribution was identified by principal component analysis (PCA), and similarity in species distribution as a function of the variables identified with cluster analysis (CA). Climatic characteristics and the environmental amplitude of wild tomatoes and related species along their distributional range were satisfactorily determined by ecological descriptors. Eleven climate types were identified, predominantly BSk (arid, steppe, cold), BWh (arid, desert, hot), and Cfb (temperate, no dry season, warm summer). PCA determined 10 most important variables were the most important for the geographical distribution. Six groups of species were identified according to CA and climatic distribution similarity. This approach has shown promissory applications for biodiversity conservation of valuable genetic resources for tomato crop breeding.
| S-EPMC8145878 | biostudies-literature