Species delimitation in <i>Cladonia</i> (Ascomycota): a challenge to the DNA barcoding philosophy

The genus Curcuma L. is commonly used as spices, medicines, dyes and ornamentals. Owing to its economic significance and lack of clear-cut morphological differences between species, this genus is an ideal case for developing DNA barcodes. In this study, four chloroplast DNA regions (matK, rbcL, trnH-psbA and trnL-F) and one nuclear region (ITS2) were generated for 44 Curcuma species and five species from closely related genera, represented by 96 samples. PCR amplification success rate, intra- and inter-specific genetic distance variation and the correct identification percentage were taken into account to assess candidate barcode regions. PCR and sequence success rate were high in matK (89.7%), rbcL (100%), trnH-psbA (100%), trnL-F (95.7%) and ITS2 (82.6%) regions. The results further showed that four candidate chloroplast barcoding regions (matK, rbcL, trnH-psbA and trnL-F) yield no barcode gaps, indicating that the genus Curcuma represents a challenging group for DNA barcoding. The ITS2 region presented large interspecific variation and provided the highest correct identification rates (46.7%) based on BLASTClust method among the five regions. However, the ITS2 only provided 7.9% based on NJ tree method. An increase in discriminatory power needs the development of more variable markers.

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“…; Pino‐Bodas et al . ). However, none of the four chloroplast regions showed a barcode gap in our study.…”

Section: Discussionmentioning

confidence: 97%

Testing DNA barcodes in closely related species of Curcuma (Zingiberaceae) from Myanmar and China

Chen

Zhao

Erickson

et al. 2014

Molecular Ecology Resources

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“…For lichens a composite tree ( Figure B2) was created manually and adjusted according to recently published phylogenies (Helms et al 2003, Schmull et al 2011, Prieto and Wedin 2013 studies of the Cladoniaceae family (Stenroos 2002, Fontaine et al 2010, Pino-Bodas et al 2013 were included. No phylogenetic analysis was available for some species of the genus Cladonia: Cladonia bellidiflora, C. glauca and C. ramulosa.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Phylogenetic clustering found in lichen but not in plant communities in European heathlands

Geedicke¹,

Schultz²,

Rudolph³

et al. 2016

Community Ecology

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Species richness is a widespread measure to evaluate the effect of different management histories on plant communities and their biodiversity. However, analysing the phylogenetic structure of plant communities could provide new insights into the effects of different management methods on community assemblages and provide further guidance for conservation decisions. Heathlands require permanent management to ensure the existence of such a cultural landscape. While traditional management with grazing is time consuming, mechanical methods are often applied but their consequences on the phylogenetic community assemblages are still unclear. We sampled 60 vegetation plots in dry sandy heathlands (EU habitat type 2310) in northern Germany stratified by five different heathland management histories: fire, plaggen (turf cutting), mowing, deforestation and intensive grazing. Due to the distant relationship of vascular plants and lichens, we assembled two phylogenetic trees, one for vascular plants and one for lichens. We then calculated phylogenetic diversity (PD) and measures of phylogenetic community structure for vascular plant and lichen communities. Deforested areas supported significantly higher PD values for vascular plant communities. We found that PD was strongly correlated with species richness (SR) but the calculation of rarefied PD was uncorrelated to SR leading to a different ranking of management histories. We observed phylogenetic clustering in the lichen communities but not for vascular plants. Thus, management by mowing and intensive grazing promotes habitat filtering of lichens, while management histories that cause greater disturbance such as fire and plaggen do not seem to affect phylogenetic community structure. The set of management strategies fulfilled the goals of the managers in maintaining a healthy heathland community structure. However, management strategies that cause less disturbance can offer an additional range of habitat for other taxonomic groups such as lichen communities.

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“…In fungi, several regions have been utilized for phylogenetic studies including the ITS, 28S-LSU, and 18S-SSU of the rRNA cistron regions, as well as CO1 ( Penicillium ), MCM7 (ascomycetes), and RBP1 (Assembling the Fungal Tree of Life, AFToL project) [45], [58], [66]. Schoch et al recently reported that the ITS region was generally superior to the LSU in species discrimination and had a more clearly defined barcode gap, indicating that the ITS region should be designated as the universal barcode for fungi [45].…”

Section: Discussionmentioning

confidence: 99%

Phylogenetic Analysis of Phenotypically Characterized Cryptococcus laurentii Isolates Reveals High Frequency of Cryptic Species

et al. 2014

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BackgroundAlthough Cryptococcus laurentii has been considered saprophytic and its taxonomy is still being described, several cases of human infections have already reported. This study aimed to evaluate molecular aspects of C. laurentii isolates from Brazil, Botswana, Canada, and the United States.MethodsIn this study, 100 phenotypically identified C. laurentii isolates were evaluated by sequencing the 18S nuclear ribosomal small subunit rRNA gene (18S-SSU), D1/D2 region of 28S nuclear ribosomal large subunit rRNA gene (28S-LSU), and the internal transcribed spacer (ITS) of the ribosomal region.ResultsBLAST searches using 550-bp, 650-bp, and 550-bp sequenced amplicons obtained from the 18S-SSU, 28S-LSU, and the ITS region led to the identification of 75 C. laurentii strains that shared 99–100% identity with C. laurentii CBS 139. A total of nine isolates shared 99% identity with both Bullera sp. VY-68 and C. laurentii RY1. One isolate shared 99% identity with Cryptococcus rajasthanensis CBS 10406, and eight isolates shared 100% identity with Cryptococcus sp. APSS 862 according to the 28S-LSU and ITS regions and designated as Cryptococcus aspenensis sp. nov. (CBS 13867). While 16 isolates shared 99% identity with Cryptococcus flavescens CBS 942 according to the 18S-SSU sequence, only six were confirmed using the 28S-LSU and ITS region sequences. The remaining 10 shared 99% identity with Cryptococcus terrestris CBS 10810, which was recently described in Brazil. Through concatenated sequence analyses, seven sequence types in C. laurentii, three in C. flavescens, one in C. terrestris, and one in the C. aspenensis sp. nov. were identified.ConclusionsSequencing permitted the characterization of 75% of the environmental C. laurentii isolates from different geographical areas and the identification of seven haplotypes of this species. Among sequenced regions, the increased variability of the ITS region in comparison to the 18S-SSU and 28S-LSU regions reinforces its applicability as a DNA barcode.

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Species delimitation in Cladonia (Ascomycota): a challenge to the DNA barcoding philosophy

Cited by 63 publications

References 84 publications

Testing DNA barcodes in closely related species of Curcuma (Zingiberaceae) from Myanmar and China

Testing DNA barcodes in closely related species of Curcuma (Zingiberaceae) from Myanmar and China

Phylogenetic clustering found in lichen but not in plant communities in European heathlands

Phylogenetic Analysis of Phenotypically Characterized Cryptococcus laurentii Isolates Reveals High Frequency of Cryptic Species

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