Filtern
Volltext vorhanden
- ja (23)
Gehört zur Bibliographie
- ja (23)
Erscheinungsjahr
Dokumenttyp
Sprache
- Englisch (23)
Schlagworte
- Phylogenie (2)
- bee decline (2)
- foraging (2)
- honey bees (2)
- metabarcoding (2)
- next generation sequencing (2)
- solitary bees (2)
- 16S metabarcoding (1)
- 26S RDNA Data (1)
- Algen (1)
- Alps (1)
- AmGr1 (1)
- AmGr2 (1)
- AmGr3 (1)
- American foulbrood (1)
- Angiopoietin-like 4 (1)
- Anticoagulants (1)
- Bacillus (1)
- Barcodes (1)
- Biologie (1)
- Bocas-del-Toro (1)
- Bone disease (1)
- COI (1)
- Coagulation factor IX (1)
- Coexpression (1)
- Colonial volvocales chlorophyta (1)
- Coumarin (1)
- DNA (1)
- DNA barcoding (1)
- DNS-Sequenz (1)
- Dasycladales chlorophyta (1)
- Endothelial growth-factor (1)
- European foulbrood (1)
- Evolution (1)
- Gene expression profiling (1)
- Halictidae (1)
- ITS2 (1)
- Land plants (1)
- Llullaillaco Volcano (1)
- Meliponini (1)
- Mesenchymal stem cells (1)
- Molecular systematics (1)
- Multiple myeloma (1)
- NGS (1)
- Nuclear RDNA (1)
- Orthoptera (1)
- Osmia bicornis (1)
- Osteogenic precursor cells (1)
- Paenibacillus (1)
- Paenibacterin (1)
- Pollen (1)
- Polymerase chain reaction (1)
- Profile distances (1)
- RBCL Gene-sequences (1)
- Ribosomale RNS (1)
- Secondary structure (1)
- Sekundärstruktur (1)
- Sporosarcina (1)
- Subtercola vilae (1)
- VKORC1 (1)
- Vitamin K epoxide reductase (1)
- Warfarin (1)
- Williamsia sp. ARP1 (1)
- adaption (1)
- aerobiology (1)
- allergy (1)
- angiogenic cytokines (1)
- annotation (1)
- anti-microbial activit (1)
- arabidopsis thaliana (1)
- assembly (1)
- bacteria (1)
- bacterial genomics (1)
- bacterial pathogens (1)
- bacterial transmission (1)
- bee disease (1)
- bees (1)
- bioassays (1)
- biodiversity (1)
- biodiversity exploratories (1)
- chemical mimicry (1)
- chrysididae (1)
- cold adaptation (1)
- cuticular chemistry (1)
- cuticular hydrocarbons (1)
- dendrobates pumilio (1)
- diet breadth (1)
- distance‐based specialization index (1)
- diversity (1)
- draft genome (1)
- elevational gradient (1)
- environmental monitoring (1)
- evolutionary arms race (1)
- floral resources (1)
- food safety (1)
- foraging patterns (1)
- functional complementarity (1)
- functional redundancy (1)
- gene-expression (1)
- genome analysis (1)
- gray tree frogs (1)
- gustatory receptors (Grs) (1)
- gut bacteria (1)
- herbivores (1)
- high throughput sequencing (1)
- honeybee taste perception (1)
- hymenoptera (1)
- illumina MiSeq platform (1)
- in-vitro (1)
- interaction networks (1)
- larvae (1)
- male mating success (1)
- marrow stromal cells (1)
- mesenchymal stem-cells (1)
- microbiome (1)
- microbiome metabarcoding (1)
- microclimate (1)
- monoclonial gammopathy (1)
- nest microbiota (1)
- nutrition (1)
- nutritional ecology (1)
- oophaga pumilio (1)
- operational sex ratio (1)
- osmia (1)
- paleoecology (1)
- palynolog (1)
- palynology (1)
- pathogen (1)
- pathogen vector (1)
- peripheral-blood (1)
- philanthidae (1)
- phyllosphere (1)
- phylogenetics (1)
- phylogenomics (1)
- phylogeny evolution (1)
- pied flycatchers (1)
- plant richness (1)
- plant-insect interactions (1)
- plant–insect interactions (1)
- plant–microbe–pollinator triangle (1)
- pollen (1)
- pollen metabarcoding (1)
- pollen nutrients (1)
- pollen provisions (1)
- pollination (1)
- pollination ecology (1)
- pollination network (1)
- pollinator decline (1)
- precedes multiple-myeloma (1)
- proboscis extension response (PER) (1)
- rRNA (1)
- sampling behavior (1)
- season (1)
- secondary invader (1)
- secondary structure (1)
- sequence (1)
- sequential mate choice (1)
- solitary bee (1)
- sugar responsiveness (1)
- systematic affiliation (1)
- temperature gradient (1)
- treefrogs hyla-gratiosa (1)
- undetermined significance (1)
- whole genome sequencing (1)
- wild bees (1)
Institut
- Theodor-Boveri-Institut für Biowissenschaften (23) (entfernen)
Sonstige beteiligte Institutionen
ResearcherID
- D-1221-2009 (1)
EU-Projektnummer / Contract (GA) number
- 289706 (1)
The internal transcribed spacer 2 (ITS2) is a widely used phylogenetic marker. In the past, it has mainly been used for species level classifications. Nowadays, a wider applicability becomes apparent. Here, the conserved structure of the RNA molecule plays a vital role. We have developed the ITS2 Database (http://its2.bioapps .biozentrum.uni-wuerzburg.de) which holds information about sequence, structure and taxonomic classification of all ITS2 in GenBank. In the new version, we use Hidden Markov models (HMMs) for the identification and delineation of the ITS2 resulting in a major redesign of the annotation pipeline. This allowed the identification of more than 160 000 correct full ength and more than 50 000 partial structures. In the web interface, these can now be searched with a modified BLAST considering both sequence and structure, enabling rapid taxon sampling. Novel sequences can be annotated using the HMM based approach and modelled according to multiple template structures. Sequences can be searched for known and newly identified motifs. Together, the database and the web server build an exhaustive resource for ITS2 based phylogenetic analyses.
Background: In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is lacking. Results: This is the first study to counter this deficiency. We inspected the accuracy and robustness of phylogenetics with individual secondary structures by simulation experiments for artificial tree topologies with up to 18 taxa and for divergency levels in the range of typical phylogenetic studies. We chose the internal transcribed spacer 2 of the ribosomal cistron as an exemplary marker region. Simulation integrated the coevolution process of sequences with secondary structures. Additionally, the phylogenetic power of marker size duplication was investigated and compared with sequence and sequence-structure reconstruction methods. The results clearly show that accuracy and robustness of Neighbor Joining trees are largely improved by structural information in contrast to sequence only data, whereas a doubled marker size only accounts for robustness. Conclusions: Individual secondary structures of ribosomal RNA sequences provide a valuable gain of information content that is useful for phylogenetics. Thus, the usage of ITS2 sequence together with secondary structure for taxonomic inferences is recommended. Other reconstruction methods as maximum likelihood, bayesian inference or maximum parsimony may equally profit from secondary structure inclusion. Reviewers: This article was reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. Open peer review: Reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. For the full reviews, please go to the Reviewers’ comments section.
Biodiversity may be investigated and explored by the means of genetic sequence information and molecular phylogenetics. Yet, with ribosomal genes, information for phylogenetic studies may not only be retained from the primary sequence, but also from the secondary structure. Software that is able to cope with two dimensional data and designed to answer taxonomic questions has been recently developed and published as a new scientific pipeline. This thesis is concerned with expanding this pipeline by a tool that facialiates the annotation of a ribosomal region, namely the ITS2. We were also able to show that this states a crucial step for secondary structure phylogenetics and for data allocation of the ITS2-database. This resulting freely available tool determines high quality annotations. In a further study, the complete phylogenetic pipeline has been evaluated on a theoretical basis in a comprehensive simulation study. We were able to show that both, the accuracy and the robustness of phylogenetic trees are largely improved by the approach. The second major part of this thesis concentrates on case studies that applied this pipeline to resolve questions in taxonomy and ecology. We were able to determine several independent phylogenies within the green algae that further corroborate the idea that secondary structures improve the obtainable phylogenetic signal, but now from a biological perspective. This approach was applicable in studies on the species and genus level, but due to the conservation of the secondary structure also for investigations on the deeper level of taxonomy. An additional case study with blue butterflies indicates that this approach is not restricted to plants, but may also be used for metazoan phylogenies. The importance of high quality phylogenetic trees is indicated by two ecological studies that have been conducted. By integrating secondary structure phylogenetics, we were able to answer questions about the evolution of ant-plant interactions and of communities of bacteria residing on different plant tissues. Finally, we speculate how phylogenetic methods with RNA may be further enhanced by integration of the third dimension. This has been a speculative idea that was supplemented with a small phylogenetic example, however it shows that the great potential of structural phylogenetics has not been fully exploited yet. Altogether, this thesis comprises aspects of several different biological disciplines, which are evolutionary biology and biodiversity research, community and invasion ecology as well as molecular and structural biology. Further, it is complemented by statistical approaches and development of informatical software. All these different research areas are combined by the means of bioinformatics as the central connective link into one comprehensive thesis.