12460
2012
eng
e3806
61
article
1
2016-01-19
--
--
The ITS2 Database
The internal transcribed spacer 2 (ITS2) has been used as a phylogenetic marker for more than two decades. As ITS2 research mainly focused on the very variable ITS2 sequence, it confined this marker to low-level phylogenetics only. However, the combination of the ITS2 sequence and its highly conserved secondary structure improves the phylogenetic resolution1 and allows phylogenetic inference at multiple taxonomic ranks, including species delimitation.
The ITS2 Database presents an exhaustive dataset of internal transcribed spacer 2 sequences from NCBI GenBank accurately reannotated. Following an annotation by profile Hidden Markov Models (HMMs), the secondary structure of each sequence is predicted. First, it is tested whether a minimum energy based fold (direct fold) results in a correct, four helix conformation. If this is not the case, the structure is predicted by homology modeling. In homology modeling, an already known secondary structure is transferred to another ITS2 sequence, whose secondary structure was not able to fold correctly in a direct fold.
The ITS2 Database is not only a database for storage and retrieval of ITS2 sequence-structures. It also provides several tools to process your own ITS2 sequences, including annotation, structural prediction, motif detection and BLAST search on the combined sequence-structure information. Moreover, it integrates trimmed versions of 4SALE and ProfDistS for multiple sequence-structure alignment calculation and Neighbor Joining tree reconstruction. Together they form a coherent analysis pipeline from an initial set of sequences to a phylogeny based on sequence and secondary structure.
In a nutshell, this workbench simplifies first phylogenetic analyses to only a few mouse-clicks, while additionally providing tools and data for comprehensive large-scale analyses.
Journal of Visual Expression
10.3791/3806
urn:nbn:de:bvb:20-opus-124600
Journal of Visual Expression (61), e3806, doi:10.3791/3806 (2012)
Benjamin Merget
Christian Koetschan
Thomas Hackl
Frank Förster
Thomas Dandekar
Tobias Müller
Jörg Schultz
Matthias Wolf
eng
uncontrolled
homology modeling
eng
uncontrolled
molecular systematics
eng
uncontrolled
internal transcribed spacer 2
eng
uncontrolled
alignment
eng
uncontrolled
genetics
eng
uncontrolled
secondary structure
eng
uncontrolled
ribosomal RNA
eng
uncontrolled
phylogenetic tree
eng
uncontrolled
phylogeny
Datenverarbeitung; Informatik
Chemie und zugeordnete Wissenschaften
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Institut für Pharmazie und Lebensmittelchemie
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/12460/jove-61-3806.pdf
14086
2011
eng
e16931
2
6
article
1
2016-11-25
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--
Internal Transcribed Spacer 2 (nu ITS2 rRNA) Sequence-Structure Phylogenetics: Towards an Automated Reconstruction of the Green Algal Tree of Life
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, sequence-structure 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.
PLoS ONE
10.1371/journal.pone.0016931
urn:nbn:de:bvb:20-opus-140866
PLoS ONE 6(2): e16931. doi:10.1371/journal.pone.0016931
Mark A. Buchheim
Alexander Keller
Christian Koetschan
Frank Förster
Benjamin Merget
Matthias Wolf
eng
uncontrolled
RBCL Gene-sequences
eng
uncontrolled
Colonial volvocales chlorophyta
eng
uncontrolled
26S RDNA Data
eng
uncontrolled
Land plants
eng
uncontrolled
Molecular systematics
eng
uncontrolled
Secondary structure
eng
uncontrolled
Nuclear RDNA
eng
uncontrolled
DNA
eng
uncontrolled
Barcodes
eng
uncontrolled
Dasycladales chlorophyta
eng
uncontrolled
Profile distances
Datenverarbeitung; Informatik
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/14086/079_Buchheim_PLOS-ONE.PDF