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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.

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.

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PNJ tree (with bootstrap values from 100 replicates) for sequence-structure data from the nu ITS2 rRNA gene for a comprehensive sampling of the class Trebouxiophyceae.Major taxonomic groups are labelled and highlighted using differential color coding.
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pone-0016931-g002: PNJ tree (with bootstrap values from 100 replicates) for sequence-structure data from the nu ITS2 rRNA gene for a comprehensive sampling of the class Trebouxiophyceae.Major taxonomic groups are labelled and highlighted using differential color coding.

Mentions: Given the success of the experiment with data from the Chlorophyceae, the test was extended to include a comprehensive sampling of nu ITS2 rRNA sequence data from the green algal classes, Trebouxiophyceae (741 sequences) and Ulvophyceae (938 sequences). These data were analyzed under the same analytical conditions as the Chlorophyceae, including the use of prasinophycean data as the outgroup. The PNJ analysis resolved three principal clades of trebouxiophycean taxa (Fig. 2) that correspond to two sets of microthamnialean taxa (the Trebouxia alliance [Microthamniales I] and the Asterochloris alliance [Microthamniales II) and the Chlorellales which includes Chlorella, Parachlorella, Coccomyxa, Micractinium and Didymogenes. Bootstrap values for these three clades are 99%, 94% and 96%, respectively. Results of a third PNJ analysis (Fig. 3) revealed high bootstrap support for a Bryopsidales clade (92% bootstrap support; Halimeda and Caulerpa alliances). A Urospora/Acrosiphonia clade was resolved with 79% bootstrap support. Neither of the two ulvalean alliances (Ulvales I: Bolbocoelon, Blidingia, Monostroma, Umbraulva and one group of Ulva taxa; Ulvales II: a second group of Ulva taxa) were robustly resolved. However, the Ulvales II clade formed a sister group with the Urospora/Acrosiphonia alliance with 70% bootstrap support. As with the chlorophycean data (Fig. 1), the trebouxiophycean (Fig. 2) and ulvophycean (Fig. 3) data revealed numerous distinct branches that correspond to putative species.


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 (with bootstrap values from 100 replicates) for sequence-structure data from the nu ITS2 rRNA gene for a comprehensive sampling of the class Trebouxiophyceae.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-g002: PNJ tree (with bootstrap values from 100 replicates) for sequence-structure data from the nu ITS2 rRNA gene for a comprehensive sampling of the class Trebouxiophyceae.Major taxonomic groups are labelled and highlighted using differential color coding.
Mentions: Given the success of the experiment with data from the Chlorophyceae, the test was extended to include a comprehensive sampling of nu ITS2 rRNA sequence data from the green algal classes, Trebouxiophyceae (741 sequences) and Ulvophyceae (938 sequences). These data were analyzed under the same analytical conditions as the Chlorophyceae, including the use of prasinophycean data as the outgroup. The PNJ analysis resolved three principal clades of trebouxiophycean taxa (Fig. 2) that correspond to two sets of microthamnialean taxa (the Trebouxia alliance [Microthamniales I] and the Asterochloris alliance [Microthamniales II) and the Chlorellales which includes Chlorella, Parachlorella, Coccomyxa, Micractinium and Didymogenes. Bootstrap values for these three clades are 99%, 94% and 96%, respectively. Results of a third PNJ analysis (Fig. 3) revealed high bootstrap support for a Bryopsidales clade (92% bootstrap support; Halimeda and Caulerpa alliances). A Urospora/Acrosiphonia clade was resolved with 79% bootstrap support. Neither of the two ulvalean alliances (Ulvales I: Bolbocoelon, Blidingia, Monostroma, Umbraulva and one group of Ulva taxa; Ulvales II: a second group of Ulva taxa) were robustly resolved. However, the Ulvales II clade formed a sister group with the Urospora/Acrosiphonia alliance with 70% bootstrap support. As with the chlorophycean data (Fig. 1), the trebouxiophycean (Fig. 2) and ulvophycean (Fig. 3) data revealed numerous distinct branches that correspond to putative species.

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