Limits...
Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics: towards an automated reconstruction of the green algal tree of life.

Buchheim MA, Keller A, Koetschan C, Förster F, Merget B, Wolf M - PLoS ONE (2011)

Bottom Line: 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.Results from analyses of the ITS2 data were robust at multiple nodes and showed considerable congruence with results from published phylogenetic analyses.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Science and the Mervin Bovaird Institute for Molecular Biology and Biotechnology, The University of Tulsa, Tulsa, Oklahoma, United States of America. mark-buchheim@utulsa.edu

ABSTRACT

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.

Show MeSH
PNJ tree for sequence-structure data from the nu ITS2 rRNA gene for a comprehensive sampling of the phylum Chlorophyta.Major taxonomic groups are labelled and highlighted using differential color coding.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3037400&req=5

pone-0016931-g004: PNJ tree for sequence-structure data from the nu ITS2 rRNA gene for a comprehensive sampling of the phylum Chlorophyta.Major taxonomic groups are labelled and highlighted using differential color coding.

Mentions: A composite, phylum-level analysis of ITS2 data (Fig. 4) derived from each of the class-level analyses reveals the same major clades for each class of green algae. However, the branching order of some of these clades differs between class-level and phylum-level analyses. The class level analyses, by default, present each class as monophyletic (Figs. 1–3). In contrast, the phylum level analysis challenges, albeit weakly, the monophyly of each of the classes (Fig. 4). For the Chlorophyceae, the Oedogoniales are allied with Ulvales I and Chlorellales III (Coccomyxa), a subset of the Sphaeropleales (Sphaeropleales II [Sphaeropleaceae]) are allied with Chlorellales I (Chlorella, Parachlorella, Micractinium, Didymogenes, Diacanthos, Closteriopsis, Actinastrum, Dictyosphaerium, Auxenochlorella, Lobosphaeropsis), II (Pseudochlorella, Koliella), and Microthamniales II (Fig. 4), and Sphaeropleales I (Desmodesmus and Scenedesmus) is sister to Ulvales I. The Chlamydomonadales are resolved as a monophyletic sister group to the latter alliance (Fig. 4). The Trebouxiophyceae form four distinct, non-monophyletic clades comprising the Microthamniales I, Microthamniales II, Chlorellales III, and Microthamniales II + Chlorellales I + Chlorellales II (Fig. 4). The Ulvophyceae also form four, non-monophyletic clades comprising the Bryopsidales II (Caulerpa), Ulvales + Urospora/Acrosiphonia, Bryopsidales I (Halimeda), and Ulvales I (Fig. 4).


Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics: towards an automated reconstruction of the green algal tree of life.

Buchheim MA, Keller A, Koetschan C, Förster F, Merget B, Wolf M - PLoS ONE (2011)

PNJ tree for sequence-structure data from the nu ITS2 rRNA gene for a comprehensive sampling of the phylum Chlorophyta.Major taxonomic groups are labelled and highlighted using differential color coding.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3037400&req=5

pone-0016931-g004: PNJ tree for sequence-structure data from the nu ITS2 rRNA gene for a comprehensive sampling of the phylum Chlorophyta.Major taxonomic groups are labelled and highlighted using differential color coding.
Mentions: A composite, phylum-level analysis of ITS2 data (Fig. 4) derived from each of the class-level analyses reveals the same major clades for each class of green algae. However, the branching order of some of these clades differs between class-level and phylum-level analyses. The class level analyses, by default, present each class as monophyletic (Figs. 1–3). In contrast, the phylum level analysis challenges, albeit weakly, the monophyly of each of the classes (Fig. 4). For the Chlorophyceae, the Oedogoniales are allied with Ulvales I and Chlorellales III (Coccomyxa), a subset of the Sphaeropleales (Sphaeropleales II [Sphaeropleaceae]) are allied with Chlorellales I (Chlorella, Parachlorella, Micractinium, Didymogenes, Diacanthos, Closteriopsis, Actinastrum, Dictyosphaerium, Auxenochlorella, Lobosphaeropsis), II (Pseudochlorella, Koliella), and Microthamniales II (Fig. 4), and Sphaeropleales I (Desmodesmus and Scenedesmus) is sister to Ulvales I. The Chlamydomonadales are resolved as a monophyletic sister group to the latter alliance (Fig. 4). The Trebouxiophyceae form four distinct, non-monophyletic clades comprising the Microthamniales I, Microthamniales II, Chlorellales III, and Microthamniales II + Chlorellales I + Chlorellales II (Fig. 4). The Ulvophyceae also form four, non-monophyletic clades comprising the Bryopsidales II (Caulerpa), Ulvales + Urospora/Acrosiphonia, Bryopsidales I (Halimeda), and Ulvales I (Fig. 4).

Bottom Line: 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.Results from analyses of the ITS2 data were robust at multiple nodes and showed considerable congruence with results from published phylogenetic analyses.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Science and the Mervin Bovaird Institute for Molecular Biology and Biotechnology, The University of Tulsa, Tulsa, Oklahoma, United States of America. mark-buchheim@utulsa.edu

ABSTRACT

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.

Show MeSH