Internal transcribed spacer primers and sequences for improved characterization of basidiomycetous orchid mycorrhizas

Taylor, D. Lee; McCormick, Melissa

doi:10.1111/j.1469-8137.2007.02320.x

Cited by 256 publications

(227 citation statements)

References 76 publications

(179 reference statements)

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“…see Tometella sublilacina clustering with species in Thelephora). Similar findings have been reported in several recent studies on Tomentella/Thelephora using ITS sequences (Haug et al, 2005;Taylor & McCormick, 2008). More detailed taxonomic investigations of their microscopic and macroscopic features coupled with the analyses of multiple additional genes from more species are needed to resolve these taxonomic issues.…”

Section: T Sha and Otherssupporting

confidence: 54%

Genetic diversity of the endemic gourmet mushroom Thelephora ganbajun from south-western China

Tao

Palanichamy

et al. 2008

Microbiology

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The ectomycorrhizal fungus Thelephora ganbajun is an endemic gourmet mushroom in Yunnan province, south-western China. However, despite its widespread consumer appeal, nutritional value and potential ecological role in natural forests, very little is known about its genetics, diversity and ecology. In this study, we investigated DNA sequence variation at the internal transcribed spacer (ITS) regions among 156 specimens collected from 23 sites of nine regions in Yunnan Province. Our analysis identified a total of 34 ITS haplotypes and these haplotypes were clustered into five distinct phylogenetic groups. The evolutionary divergences among these clades are similar to or greater than many known sister species pairs within the genus Thelephora and the closely related genus Tomentella. Among the 34 ITS haplotypes, 22 were represented by one specimen each and the remaining 12 were each shared by two or more specimens. The most common haplotype contained 68 specimens distributed in 21 of the 23 sites, a result consistent with gene flow among geographical populations. However, analysis of molecular variance (AMOVA) revealed low but significant genetic differentiation among local and regional populations. Interestingly, the Mantel test identified that the extent of genetic differentiation was not significantly correlated with geographical distance. Our study revealed significant genetic divergence within Th. ganbajun and limited but detectable gene flow among geographical populations of this endemic ectomycorrhizal gourmet mushroom.

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Section: T Sha and Otherssupporting

confidence: 54%

Genetic diversity of the endemic gourmet mushroom Thelephora ganbajun from south-western China

Tao

Palanichamy

et al. 2008

Microbiology

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“…Highly variable lengths and high evolutionary rates for the nuclear ribosomal cistron in species of Cantharellus, Tulasnella (Cantherellales, Basidiomycota) (61)(62)(63), and some lichens (53) may provide challenges for sequencing and analysis. The upper range of this ITS region variation is likely found in the Glomeromycota, with up to 20% divergence within a single multinucleate spore (64,65).…”

Section: Discussionmentioning

confidence: 99%

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

Schoch

Seifert

Huhndorf

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

4,258

2,910

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Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative proteincoding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter-and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.DNA barcoding | fungal biodiversity T he absence of a universally accepted DNA barcode for Fungi, the second most speciose eukaryotic kingdom (1, 2), is a serious limitation for multitaxon ecological and biodiversity studies. DNA barcoding uses standardized 500-to 800-bp sequences to identify species of all eukaryotic kingdoms using primers that are applicable for the broadest possible taxonomic group. Reference barcodes must be derived from expertly identified vouchers deposited in biological collections with online metadata and validated by available online sequence chromatograms. Interspecific variation should exceed intraspecific variation (the barcode gap), and barcoding is optimal when a sequence is constant and unique to one species (3, 4). Ideally, the barcode locus would be the same for all kingdoms. A region of the mitochondrial gene encoding the cytochrome c oxidase subunit 1 (CO1) is the barcode for animals (3, 4) and the default marker adopted by the Consortium for the Barcode of Life for all groups of organisms, including fungi (5). In Oomycota, part of the kingdom Stramenopila historically studied by mycologists, the de facto barcode internal transcribed spacer (ITS) region is suitable for identification, but the default CO1 marker is more reliable in a few clades of closely related species (6)...

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“…The case of reverse complementary sequences is handled separately below (Guideline 2); for the other three -and for the few fungi with truly divergent 5.8S/ITS region sequences, such as Cantharellus and Tulasnella (Feibelman et al 1994;Taylor and McCormick 2008) -a simple manual NCBI-BLAST search in INSD is likely to reveal the nature of the complication. The user is advised to pay attention to any sequences for which the 5.8S cannot be located, and not to make scientific use of those sequences until their nature has been clarified.…”

Section: Guideline 1 It Is Simple To Check That All Query Sequencesmentioning

confidence: 99%

Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences

Nilsson¹,

Tedersoo²,

Abarenkov³

et al. 2012

165

125

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Larsson K-H, Larsson E, Kõljalg U (2012) Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences. MycoKeys 4: 37-63. doi: 10.3897/mycokeys.4.3606 Abstract Molecular data form an important research tool in most branches of mycology. A non-trivial proportion of the public fungal DNA sequences are, however, compromised in terms of quality and reliability, contribut- Nilsson et al. / MycoKeys 4: 37-63 (2012) 38 ing noise and bias to sequence-borne inferences such as phylogenetic analysis, diversity assessment, and barcoding. In this paper we discuss various aspects and pitfalls of sequence quality assessment. Based on our observations, we provide a set of guidelines to assist in manual quality management of newly generated, near-full-length (Sanger-derived) fungal ITS sequences and to some extent also sequences of shorter read lengths, other genes or markers, and groups of organisms. The guidelines are intentionally non-technical and do not require substantial bioinformatics skills or significant computational power. Despite their simple nature, we feel they would have caught the vast majority of the severely compromised ITS sequences in the public corpus. Our guidelines are nevertheless not infallible, and common sense and intuition remain important elements in the pursuit of compromised sequence data. The guidelines focus on basic sequence authenticity and reliability of the newly generated sequences, and the user may want to consider additional resources and steps to accomplish the best possible quality control. A discussion on the technical resources for further sequence quality management is therefore provided in the supplementary material.

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Internal transcribed spacer primers and sequences for improved characterization of basidiomycetous orchid mycorrhizas

Cited by 256 publications

References 76 publications

Genetic diversity of the endemic gourmet mushroom Thelephora ganbajun from south-western China

Genetic diversity of the endemic gourmet mushroom Thelephora ganbajun from south-western China

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences

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