http://its2.bioapps.biozentrum.uni-wuerzburg.de/cgi-bin/index.pl?about Optimal global pairwise alignments from about 270,000 ribosomal RNA (rRNA) internal transcribed spacer 2 (ITS2) sequences - all against all - have been generated in order to model ITS2 secondary structures based on sequences with known structures. Via 60,000 known ITS2 sequences that fit a common core of the ITS2 secondary structure described for the eukaryotes (Schultz et al. 2005), homology based modeling (Wolf et al. 2005) and reannotation procedures revealed in addition more than 150,000 homologous structures that could not be predicted by standard RNA folding programs. en-en Happy Christmas with Euphorbia pulcherrima Tue, 01 Dec 2009 08:56:02 GMT There is a new Science E-letter about the ITS2 database available Wed, 16 Dec 2009 11:26:34 GMT In this study five different molecular markers were used to: (1) infer the phylogeographic differentiation of Thalassiosira weissflogii in the Atlantic and Pacific Oceans; and (2) address the biological species status of the inferred geographic lineages. The results of the ribosomal RNA data analyses suggested that the Hawaiian isolate evolved first after which the Indonesian and the Atlantic/California strains diverged. In contrast, the tree derived from the partial sexually induced gene 1 (Sig1) data exhibited an initial divergence between the Eastern Atlantic/Western Atlantic/California and the Hawaiian/Indonesian groups after which the latter evolved into the Hawaiian and Indonesian lineages. The partial beta-tubulin phylogeny discerns an early "split" between an Eastern Atlantic/Western Atlantic clade and an Indonesia/California/Hawaii group which later differentiated into distinct Hawaiian and Indonesian/California "branches". The number of compensatory base changes (CBCs) in the ITS2 indicated that the "Atlantic group", including the California isolate, constituted a single reproductive unit and that the Indonesian and Hawaiian T. weissflogii are two different biological species with regard to each other and to the "Atlantic clade". The beta-tubulin tree contradicts the reproductive units recovered by the compensatory base change analysis due to the close affinity of the California and Indonesia strains whereas the sexually induced gene 1 phylogeny supports the existence of three biological species, despite exhibiting a temporal sequence of geographic diversification that is different from that seen in topologies derived from the ribosomal RNA data. It is hypothesized that the tree derived from the sexually induced gene 1 reflects the relative order of the evolution of reproductive isolation in the different T. weissflogii strains while the lineages in the other phylogenies depict time elapsed since common ancestry. The current investigation is the first to have shown concordance in the pattern of variation between a reasonably good biological species marker (CBCs in the ITS2) and a protein hypothesized to be involved in sperm-egg recognition/adhesion in diatoms (Sig1). It was further discussed that the Pacific/Indonesian T. weissflogii species complex most likely evolved in the presence of gene flow and "local" environmental selection. Three hypotheses which potentially can explain the genetic diversification/similarity between the Atlantic T. weissflogii samples and the isolate obtained off the coast of California were proposed and discussed. Copyright 2009 Elsevier Ltd. All rights reserved. http://www.ncbi.nlm.nih.gov/pubmed/20018562 Tue, 22 Dec 2009 11:54:54 GMT Current molecular phylogenetic studies of Lepidoptera and most other arthropods are predominantly based on mitochondrial genes and a limited number of nuclear genes. The nuclear genes, however, generally do not provide sufficient information for young radiations. ITS2, which has proven to be an excellent nuclear marker for similarly aged radiations in other organisms like fungi and plants, is only rarely used for phylogeny estimation in arthropods, although universal primers exist. This is partly due to difficulties in the alignment of ITS2 sequences in more distant taxa. The present study uses ITS2 secondary structure information to elucidate the phylogeny of a species-rich young radiation of arthropods, the butterfly subgenus Agrodiaetus. One aim is to evaluate the efficiency of ITS2 to resolve the phylogeny of the subgenus in comparison with COI, the most important mitochondrial marker in arthropods. Furthermore, we assess the use of compensatory base changes in ITS2 for the delimitation of species and discuss the prospects of ITS2 as a nuclear marker for barcoding studies. http://www.biomedcentral.com/1471-2148/9/300 Thu, 07 Jan 2010 22:21:42 GMT Hidden Markov models (HMMs) play a major role in applications to unravel biomolecular functionality. Though HMMs are technically mature and widely applied in computational biology, there is a potential of methodical optimisation concerning its modelling of biological data sources with varying sequence lengths. Single building blocks of these models, the states, are associated with a certain holding time, being the link to the length distribution of represented sequence motifs. An adaptation of regular HMM topologies to bell-shaped sequence lengths is achieved by a serial chain-linking of hidden states, while residing in the class of conventional hidden Markov models. The factor of the repetition of states (r) and the parameter for state-specific duration of stay (p) are determined by fitting the distribution of sequence lengths with the method of moments (MM) and maximum likelihood (ML). Performance evaluations of differently adjusted HMM topologies underline the impact of an optimisation for HMMs based on sequence lengths. Secondary structure prediction on internal transcribed spacer 2 sequences demonstrates exemplarily the general impact of topological optimisations. In summary, we propose a general methodology to improve the modelling behaviour of HMMs by topological optimisation with ML and a fast and easily implementable moment estimator. http://www.bepress.com/sagmb/vol9/iss1/art6/ Thu, 07 Jan 2010 22:40:33 GMT Eat an apple on going to bed, and you will keep the doctor from earning his bread :-) Fri, 15 Jan 2010 15:33:52 GMT 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. http://www.biology-direct.com/content/5/1/4 Tue, 19 Jan 2010 15:07:24 GMT Xenopus laevis it is an important model organism in developmental biology. The species is found throughout most of Africa, and in isolated, introduced populations in North America, South America, and Europe. Tue, 02 Feb 2010 15:53:23 GMT Galanthus is a small genus of about 20 species in the family Amaryllidaceae commonly known as Snowdrops. Most flower in winter, before the spring equinox. Tue, 01 Mar 2010 14:35:35 GMT We added a new ITS2 highlight paper on barcoding from Chen et al. 2010 Thu, 18 Mar 2010 16:59:25 GMT An acknowledgements page is now provided by the ITS2 database Thu, 18 Mar 2010 16:59:25 GMT The links page was updated Thu, 18 Mar 2010 16:59:25 GMT We got a response to our Science E-letter Thu, 18 Mar 2010 16:59:25 GMT Fri, 19 Mar 2010 11:48:24 GMT Trametes versicolor is an extremely common polypore mushroom which can be found throughout the world. Wed, 07 Apr 2010 15:48:41 GMT We added a link list of Journals that cited the ITS2 Database Wed, 21 Apr 2010 11:18:23 GMT Mon, 26 Apr 2010 18:39:52 GMT We now support extended editing and loading of profiles, as well as a conversion from FigTree. Wed, 05 May 2010 10:43:24 GMT There are currently 234749 structures available! Wed, 05 May 2010 10:43:26 GMT The ITS2 database is now cited in more than 100 publications! Fri, 07 May 2010 08:28:52 GMT We now show a rotating 3D animation of Chlamydomonas reinhardtii Fri, 07 May 2010 08:28:54 GMT Channel catfish Ictalurus punctatus, is North America's most numerous catfish species. The popularity of channel catfish for food has contributed to the rapid growth of aquaculture of this species in the United States. Thi, 03 Jun 2010 13:07:24 GMT Agaricus bisporus is an edible basidiomycete mushroom native to grasslands in Europe and North America, and is one of the most commonly and widely consumed mushrooms in the world. Thi, 01 Jul 2010 12:02:42 GMT Biologen der Uni Stuttgart identifizieren drei neue Brtierchenarten - Vom Norden Alaskas bis zum Pazifik Thi, 01 Jul 2010 12:02:42 GMT The Golden-ringed Dragonfly (Cordulegaster boltonii) is a large, striking dragonfly and the longest British species, the only one of its genus in Britain. Mon, 06 Sep 2010 15:45:24 GMT Sunflowers (Helianthus annuus) are annual plants native to the Americas, that possess a large inflorescence (flowering head). Tue, 19 Oct 2010 22:12:34 GMT We will perform a major update of the ITS2 database! Tue, 19 Oct 2010 22:16:13 GMT During the last few weeks we added many new manuscripts citing the ITS2 database! See the cited-by region on the menu bar. Tue, 19 Oct 2010 22:23:52 GMT The ITS2 database now contains 274310 structures. Old versions are available on request! Tue, 02 Nov 2010 15:33:14 GMT Pathogenic strains of F. oxysporum have been studied for more than 100 years. The host range of these fungi is extremely broad, and includes animals, ranging from arthropods to humans, as well as plants, including a range of both gymnosperms and angiosperms. Tue, 02 Nov 2010 16:31:55 GMT We now offer the last 4 stable databases to be accessed through the webinterface. Mon, 08 Nov 2010 18:08:44 GMT Tue, 30 Nov 2010 10:04:44 GMT BACKGROUND:
Hypnales comprise over 50% of all pleurocarpous mosses. They provide a young radiation complicating phylogenetic analyses. To resolve the hypnalean phylogeny, it is necessary to use a phylogenetic marker providing highly variable features to resolve species on the one hand and conserved features enabling a backbone analysis on the other. Therefore we used highly variable internal transcribed spacer 2 (ITS2) sequences and conserved secondary structures, as deposited with the ITS2 Database, simultaneously.
FINDINGS:
We built an accurate and in parts robustly resolved large scale phylogeny for 1,634 currently available hypnalean ITS2 sequence-structure pairs.
CONCLUSIONS:
Profile Neighbor-Joining revealed a possible hypnalean backbone, indicating that most of the hypnalean taxa classified as different moss families are polyphyletic assemblages awaiting taxonomic changes. ]]> Tue, 30 Nov 2010 10:04:45 GMT Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential alignment problems. However, in general they are not biologically motivated and ignore our knowledge about the evolution of sequences. Thus, it is still a major open question how to define an evolutionary distance metric between divergent sequences that makes use of indel information and known substitution models without the need for a multiple alignment. Here we propose a new evolutionary distance metric to close this gap. It uses finite-state transducers to create a biologically motivated similarity score which models substitutions and indels, and does not depend on a multiple sequence alignment. The sequence similarity score is defined in analogy to pairwise alignments and additionally has the positive semi-definite property. We describe its derivation and show in simulation studies and real-world examples that it is more accurate in reconstructing phylogenies than competing methods. The result is a new and accurate way of determining evolutionary distances in and beyond the twilight zone of sequence alignments that is suitable for large datasets. ]]> Tue, 30 Nov 2010 10:04:46 GMT 5.8S-28S rRNA interaction and HMM-based ITS2 annotation
Gene 430(1-2):50-57]]> Tue, 30 Nov 2010 10:04:44 GMT Tue, 12 Jan 2011 10:04:24 GMT Background:
Chloroplast-encoded genes (matK and rbcL) have been formally proposed for use in DNA barcoding efforts targeting embryophytes. Extending such a protocol to chlorophytan green algae, though, is fraught with problems including non homology (matK) and heterogeneity that prevents the creation of a universal PCR toolkit (rbcL). Some have advocated the use of the nuclear-encoded, internal transcribed spacer two (ITS2) as an alternative to the traditional chloroplast markers. However, the ITS2 is broadly perceived to be insufficiently conserved or to be confounded by introgression or biparental inheritance patterns, precluding its broad use in phylogenetic reconstruction or as a DNA barcode. A growing body of evidence has shown that simultaneous analysis of nucleotide data with secondary structure information can overcome at least some of the limitations of ITS2. The goal of this investigation was to assess the feasibility of an automated, sequence-structure approach for analysis of IT2 data from a large sampling of phylum Chlorophyta.
Methodology/Principal Findings:
Sequences and secondary structures from 591 chlorophycean, 741 trebouxiophycean and 938 ulvophycean algae, all obtained from the ITS2 Database, were aligned using a sequence-structure-specific scoring matrix. Phylogenetic relationships were reconstructed by Profile Neighbor-Joining coupled with a sequence-structure specific, general time reversible substitution model. Results from analyses of the ITS2 data were robust at multiple nodes and showed considerable congruence with results from published phylogenetic analyses.
Conclusions/Significance:
Our observations on the power of automated, sequencestructure analyses of ITS2 to reconstruct phylum-level phylogenies of the green algae validate this approach to assessing diversity for large sets of chlorophytan taxa. Moreover, our results indicate that objections to the use of ITS2 for DNA barcoding should be weighed against the utility of an automated, data analysis approach with demonstrated power to reconstruct evolutionary patterns for highly divergent lineages.]]> Mon, 31 Jan 2011 19:19:35 GMT Mon, 31 Jan 2011 19:14:23 GMT Hyperbolic tree of Chlorophyta from Buchheim et al., Plos One (in press)]]> Mon, 31 Jan 2011 19:21:55 GMT Mon, 02 Mar 2011 17:15:24 GMT Mon, 01 Apr 2011 10:01:44 GMT Mon, 01 May 2011 18:17:19 GMT Mon, 30 May 2011 14:41:24 GMT Mon, 01 Jun 2011 09:37:11 GMT Mon, 01 Jul 2011 10:55:57 GMT Mon, 01 Aug 2011 12:00:45 GMT Mon, 19 Aug 2011 16:46:24 GMT Mon, 19 Aug 2011 16:46:26 GMT Mon, 07 Sep 2011 16:27:44 GMT Wed, 12 Oct 2011 11:08:11 GMT