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An Evaluation of Rbcl, Tufa, UPA, LSU and ITS As DNA Barcode Markers

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An Evaluation of Rbcl, Tufa, UPA, LSU and ITS As DNA Barcode Markers 487_528_SAUNDERS.fm Page 487 Vendredi, 17. décembre 2010 11:21 11 Cryptogamie, Algologie, 2010, 31 (4): 487-528 ©2010 Adac. Tous droits réservés An evaluation of rbcL, tufA,UPA, LSU and ITS as DNA barcode markers for the marine green macroalgae Gary W. SAUNDERS* &Hana KUCERA Centre for Environmental and Molecular Algal Research, Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3 Canada Abstract —The universality and species discriminatory power of the plastid rubisco large subunit (rbcL) (considering 5’ and 3’ fragments independently), elongation factor tufA,and universal amplicon (UPA), and the nuclear D2/D3 region of the large ribosomal subunit (LSU) and the internal transcribed spacer of the ribosomal cistron (ITS) were evaluated for their utility as DNA barcode markers for green macroalgae. Excepting low success for ITS, all of these markers failed for the Cladophoraceae. For the remaining taxa, the 3’ region of the rbcL(rbcL-3P) and tufA had the largest barcode gaps (difference between maximum intra- and minimum inter-specific divergence). Unfortunately, moderate amplification success (80 %excluding Cladophoracae) caused, at least in part, by the presence of introns within the rbcL-3P for some taxa reduced the utility of this marker as auniversal barcode system. The tufA marker, on the other hand, had strong amplification success (95% excluding the Cladophoraceae) and no introns were uncovered. We thus recommend that tufA be adopted as the standard marker for the routine barcoding of green marine macroalgae (excluding the Cladophoraceae). During this survey we discovered cryptic species in Acrosiphonia, Monostroma,and Ulva indicating that significant taxonomic work remains for green macroalgae. Chlorophyta /DNA barcoding /green algae /ITS /LSU / rbcL/tufA /UP INTRODUCTION DNA barcoding, identifying organisms based on comparisons of short, standardized DNA sequences as agreed upon by the Consortium for the Barcode of Life (CBOL; http://barcoding.si.edu/), has been championed as arevolutionary system for the identification and discovery of all of the world’s eukaryotic organisms (Hebert et al., 2003a; Hebert et al., 2003b). The benefits of such an endeavour are multifold. First, developing adatabase of sequences against which unknown biological materials can be compared greatly increases the speed at which routine identification can be carried out. Across all taxa, DNA barcoding removes the reliance on morphological characters traditionally used to discriminate species. This is of particular importance for taxonomic groups that have few characters on which to base identification and for which expert taxonomists are required for even routine morphological identifications. Second, during diversity surveys, specimens may be flagged as potentially new species, alerting the taxonomist that further study is required, and ultimately leading to the discovery of new records and/or description of new species. The case of *Corresponding author: [email protected] 487_528_SAUNDERS.fm Page 488 Vendredi, 17. décembre 2010 11:21 11 488 G.W. Saunders &H.Kucera marine macroalgae is an excellent example of the value and strength of DNA barcoding; seaweeds are notoriously difficult to identify due to simple morphologies, phenotypic plasticity and convergent evolution (see Saunders, 2005). DNA barcoding has proven aphenomenal tool that has aided in species identification, discovery of cryptic species, or new records for red (Rhodophyta) and brown (Phaeophyceae) seaweeds (Saunders, 2005; Robba et al.,2006; Kucera &Saunders, 2008; Saunders, 2008; McDevit &Saunders, 2009; Saunders, 2009; Walker et al.,2009; Le Gall &Saunders, 2010). Whereas DNA barcoding has been advanced for the red and brown sea- weeds, the marine green macroalgae (most belong to one of the Bryopsido- phyceae, Trebouxiophyceae or Ulvophyceae) are the final group of marine macroalgae for which aDNA barcode marker remains to be developed. There are several requirements when choosing an appropriate marker for DNA barcoding. First, the genetic variability of the marker must be adequate for species level resolution. To this end, species discrimination is considered successful when spe- cimens from asingle species cluster together in distance analysis (Hebert et al., 2003a) and the largest intraspecific divergence is less than the smallest interspe- cific divergence –this difference termed the “barcoding gap” (Meier et al.,2008). Second, and of equal importance, the marker should be universally recoverable across taxa, meaning there is high PCR and sequencing success, ideally with a near-universal set of PCR primers. Given current technologies, it is also of ben- efit for the DNA barcode marker to be short enough to be sequenced in asingle read (<700bp) (see Hollingsworth et al., 2009b). Markers in which intra-individual heterogeneity is common, or which can exhibit microsatellites or single nucleotide runs (particularly of thymine or adenine) are not preferred because these cause problems with direct sequencing of PCR product (Gribble &Anderson, 2007). The ideal marker consists of ahighly variable region, which provides for species discrimination, flanked by highly conserved regions from which primers can be designed. During the development of DNA barcoding, several markers have been proposed for different phyla. In animals, red and brown algae, the 5’ end of the cytochrome coxidase 1gene (COI-5P) provides resolution at the species level among most groups tested, and has come to be accepted as the barcode marker and is now being applied to biodiversity and taxonomic studies across the globe (e.g., Hebert et al.,2004; Saunders, 2005; Ferri et al.,2009; McDevit &Saunders, 2009). For the green macroalgae, COI-5P was our first marker of interest; however, preliminary investigations failed to generate successful amplification, despite extensive primer testing (Kucera &Saunders, unpublished data). Our failure in designing primers for the successful amplification of green algal COI-5P may be in part attributable to the lack of available mitochondrial sequences; only two published ulvophycean mitochondrial genomes were available at the time of study (Pombert et al.,2004; Pombert et al.,2006). However, the presence of introns within the cytochrome coxidase 1ofulvophycean taxa (Watanabe et al., 1998; Pombert et al.,2004; Pombert et al.,2006) may be the largest obstacle to developing the COI-5P as aDNA barcode marker for marine green macroalgae. These difficulties make COI-5P unsuitable for DNA barcoding in green macroalgae, leading us to ultimately abandon it as apotential marker (also see Hall et al. (2010) in this volume). Similarly, difficulties in applying the COI-5P have been encountered in land plants and fungi. In fungi, the presence of introns (Seifert et al.,2007) and lack of species level resolution (Geiser et al.,2007) meant that the COI-5P could not be applied universally. The internal transcribed spacer region (ITS) had been 487_528_SAUNDERS.fm Page 489 Vendredi, 17. décembre 2010 11:21 11 Assessing green algal barcode markers 489 used for fungal identification for at least adecade before the advent of DNA barcoding in 2003, and is now recommended as the marker for barcoding fungi (see Seifert, 2009). Finding amarker that is both universal and which provides sufficient species discrimination was much more difficult in land plants. After four years of extensive debate, the Plant Working Group members of CBOL have settled on two plastid markers, the rubisco large subunit (rbcL) and matK, as the DNA barcodes for plants (Hollingsworth et al.,2009b). Since 2005, the debate over which marker (and eventually which combination of makers) would be used for land plant barcoding has produced awealth of data on avariety of markers and some interesting conclusions. Firstly, atrade-off between universality and species discrimination has affected the search for the plant barcode as there has been no single marker studied to date that can achieve both of these criteria as well as COI-5P does for animals, and therefore, typically two or more markers have been recommended to be used in concert. Secondly, the optimal marker (or marker combination) tends to vary based on the taxonomic group studied (Hollingsworth et al.,2009b). We selected several markers to investigate as potential DNA barcode markers for the marine green macroalgae. The rbcLwas an obvious choice for testing since its utility as aDNA barcode has been established among plant groups (Hollingsworth et al.,2009b) and because it has formed the basis of several taxonomic and phylogenetic studies in marine green macroalgae. As an example, in the genus Ulva the rbcLhas been employed extensively to resolve taxonomic issues (e.g., Hayden &Waaland, 2002; Hayden et al.,2003; Hayden &Waaland, 2004). Unfortunately, the presence of introns in the rbcLofsome marine green macroalgae (Hanyuda et al.,2000) may negatively affect the universality of rbcL as abarcode marker since the ability to amplify and sequence large fragments with asingle bidirectional read will be hampered. Given the fact that green algae are particularly prone to acquiring intron sequences (Bhattacharya et al.,1996; Haugen et al.,2005), and that the extent to which introns are present among their rbcLgenes is unknown, the wider applicability of this marker as abarcode needs to be evaluated empirically. The plastid elongation factor tufA has similarly been used for phylo- genetic analyses and to discriminate among green algal species and is known to lack
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