Fluorescence Assisted Capillary Electrophoresis of Glycans Enabled by the Negatively Charged Auxochromes in 1-Aminopyrenes

A compact and negatively charged acceptor group, N-(cyanamino)sulfonyl, is introduced for dye design and its influence on the absorption and emission spectra of the "push-pull" chromophores is demonstrated with 1,3,6-tris[(cyanamino)sulfonyl]-8-aminopyrene. The new sulfonamides, including O-phosphorylated (3-hydroxyazetidine)-N-sulfonyl, are negatively charged electron acceptors and auxochromes. 1-Aminopyrenes decorated with the new sulfonamides have three or six negative charges (pH ≥8), low m/z ratios, high mobilities in an electric field, and yellow to orange emission. We labeled maltodextrin oligomers by reductive amination, separated the products by electrophoresis, and demonstrated their high brightness in a commercial DNA analyzer and the distribution of the emission signal among the detection channels.

Globally distributed root endophyte Phialocephala subalpina links pathogenic and saprophytic lifestyles

BACKGROUND

Whereas an increasing number of pathogenic and mutualistic ascomycetous species were sequenced in the past decade, species showing a seemingly neutral association such as root endophytes received less attention. In the present study, the genome of Phialocephala subalpina, the most frequent species of the Phialocephala fortinii s.l. - Acephala applanata species complex, was sequenced for insight in the genome structure and gene inventory of these wide-spread root endophytes.

RESULTS

The genome of P. subalpina was sequenced using Roche/454 GS FLX technology and a whole genome shotgun strategy. The assembly resulted in 205 scaffolds and a genome size of 69.7 Mb. The expanded genome size in P. subalpina was not due to the proliferation of transposable elements or other repeats, as is the case with other ascomycetous genomes. Instead, P. subalpina revealed an expanded gene inventory that includes 20,173 gene models. Comparative genome analysis of P. subalpina with 13 ascomycetes shows that P. subalpina uses a versatile gene inventory including genes specific for pathogens and saprophytes. Moreover, the gene inventory for carbohydrate active enzymes (CAZymes) was expanded including genes involved in degradation of biopolymers, such as pectin, hemicellulose, cellulose and lignin.

CONCLUSIONS

The analysis of a globally distributed root endophyte allowed detailed insights in the gene inventory and genome organization of a yet largely neglected group of organisms. We showed that the ubiquitous root endophyte P. subalpina has a broad gene inventory that links pathogenic and saprophytic lifestyles.

Mitochondrial genome evolution in species belonging to the Phialocephala fortinii s.l. - Acephala applanata species complex

Background

Mitochondrial (mt) markers are successfully applied in evolutionary biology and systematics because mt genomes often evolve faster than the nuclear genomes. In addition, they allow robust phylogenetic analysis based on conserved proteins of the oxidative phosphorylation system. In the present study we sequenced and annotated the complete mt genome of P. subalpina, a member of the Phialocephala fortinii s.l. – Acephala applanata species complex (PAC). PAC belongs to the Helotiales, which is one of the most diverse groups of ascomycetes including more than 2,000 species. The gene order was compared to deduce the mt genome evolution in the Pezizomycotina. Genetic variation in coding and intergenic regions of the mtDNA was studied for PAC to assess the usefulness of mt DNA for species diagnosis.

Results

The mt genome of P. subalpina is 43,742 bp long and codes for 14 mt genes associated with the oxidative phosphorylation. In addition, a GIY-YIG endonuclease, the ribosomal protein S3 (Rps3) and a putative N-acetyl-transferase were recognized. A complete set of tRNA genes as well as the large and small rRNA genes but no introns were found. All protein-coding genes were confirmed by EST sequences. The gene order in P. subalpina deviated from the gene order in Sclerotinia sclerotiorum, the only other helotialean species with a fully sequenced and annotated mt genome. Gene order analysis within Pezizomycotina suggests that the evolution of gene orders is mostly driven by transpositions. Furthermore, sequence diversity in coding and non-coding mtDNA regions in seven additional PAC species was pronounced and allowed for unequivocal species diagnosis in PAC.

Conclusions

The combination of non-interrupted ORFs and EST sequences resulted in a high quality annotation of the mt genome of P. subalpina, which can be used as a reference for the annotation of other mt genomes in the Helotiales. In addition, our analyses show that mtDNA loci will be the marker of choice for future analysis of PAC communities.

Sex in the PAC: a hidden affair in dark septate endophytes?

BACKGROUND

Fungi are asexually and sexually reproducing organisms that can combine the evolutionary advantages of the two reproductive modes. However, for many fungi the sexual cycle has never been observed in the field or in vitro and it remains unclear whether sexual reproduction is absent or cryptic. Nevertheless, there are indirect approaches to assess the occurrence of sex in a species, such as population studies, expression analysis of genes involved in mating processes and analysis of their selective constraints. The members of the Phialocephala fortinii s. l. - Acephala applanata species complex (PAC) are ascomycetes and the predominant dark septate endophytes that colonize woody plant roots. Despite their abundance in many ecosystems of the northern hemisphere, no sexual state has been identified to date and little is known about their reproductive biology, and how it shaped their evolutionary history and contributes to their ecological role in forest ecosystems. We therefore aimed at assessing the importance of sexual reproduction by indirect approaches that included molecular analyses of the mating type (MAT) genes involved in reproductive processes.

RESULTS

The study included 19 PAC species and > 3, 000 strains that represented populations from different hosts, continents and ecosystems. Whereas A. applanata had a homothallic (self-fertile) MAT locus structure, all other species were structurally heterothallic (self-sterile). Compatible mating types were observed to co-occur more frequently than expected by chance. Moreover, in > 80% of the populations a 1:1 mating type ratio and gametic equilibrium were found. MAT genes were shown to evolve under strong purifying selection.

CONCLUSIONS

The signature of sex was found in worldwide populations of PAC species and functionality of MAT genes is likely preserved by purifying selection. We hypothesize that cryptic sex regularely occurs in the PAC and that further field studies and in vitro crosses will lead to the discovery of the sexual state. Although structurally heterothallic species prevail, it cannot be excluded that homothallism represents the ancestral breeding system in the PAC.

Negative effects on survival and performance of Norway spruce seedlings colonized by dark septate root endophytes are primarily isolate-dependent

Root endophytes are common and genetically highly diverse suggesting important ecological roles. Yet, relative to above-ground endophytes, little is known about them. Dark septate endophytic fungi of the Phialocephala fortinii s.l.-Acephala applanata species complex (PAC) are ubiquitous root colonizers of conifers and Ericaceae, but their ecological function is largely unknown. Responses of Norway spruce seedlings of two seed provenances to inoculations with isolates of four PAC species were studied in vitro. In addition, isolates of Phialocephala subalpina from two populations within and one outside the natural range of Norway spruce were also included to study the effect of the geographic origin of P. subalpina on host response. The interaction of PAC with Norway spruce ranged from neutral to highly virulent and was primarily isolate-dependent. Variation in virulence was much higher within than among species, nonetheless only isolates of P. subalpina were highly virulent. Disease caused by P. subalpina genotypes from the native range of Norway spruce was more severe than that induced by genotypes from outside the natural distribution of Norway spruce. Virulence was not correlated with the phylogenetic relatedness of the isolates but was positively correlated with the extent of fungal colonization as measured by quantitative real-time PCR.

Microsatellite-based quantification method to estimate biomass of endophytic Phialocephala species in strain mixtures

Fungi of the Phialocephala fortinii sensu lato-Acephala applanata species complex (PAC) are ubiquitous endophytic colonizers of tree roots in which they form genotypically diverse communities. Measurement of the colonization density of each of the fungal colonizers is a prerequisite to study the ecology of these communities. Up to now, there is no method readily available for the quantification of PAC strains co-colonizing the same root. The new DNA quantification method presented here is based on the amplification of microsatellites by competitive polymerase chain reaction (PCR). The method proved to be suitable to detect and quantify at least two strains within one single sample by the addition of a known amount of mycelium of a reference strain before DNA extraction. The method exploits the correlation between the reference/target ratio of light emitted during microsatellite detection (peak ratio) and the reference/target ratio of mycelial weights to determine the biomass of the target strain. Hence, calibration curves were obtained by linear regression of the peak ratios on the weight ratios for different mixtures of reference and target strains. The slopes of the calibration curves and the coefficients of determination were close to 1, indicating that peak ratios are good predictors of weight ratios. Estimates of fungal biomass in mycelial test mixtures of known composition laid within the 95% prediction interval and deviated on average by 16% (maximally 50%) from the true biomass. On average, 3-6% of the root biomass of Norway spruce seedlings consisted of mycelial biomass of either one of two inoculated PAC strains. Biomass estimates obtained by real-time quantitative PCR were correlated with the estimates obtained by the microsatellite-based method, but variation between the two estimates from the same root was high in some samples. The microsatellite-based DNA quantification method described here is currently the best method for strainwise estimation of endophytic biomass of PAC fungi in small root samples.

Suitability of quantitative real-time PCR to estimate the biomass of fungal root endophytes

A nested single-copy locus-based quantitative PCR (qPCR) assay and a multicopy locus-based qPCR assay were developed to estimate endophytic biomass of fungal root symbionts belonging to the Phialocephala fortinii sensu lato-Acephala applanata species complex (PAC). Both assays were suitable for estimation of endophytic biomass, but the nested assay was more sensitive and specific for PAC. For mycelia grown in liquid cultures, the correlation between dry weight and DNA amount was strong and statistically significant for all three examined strains, allowing accurate prediction of fungal biomass by qPCR. For mycelia colonizing cellophane or Norway spruce roots, correlation between biomass estimated by qPCR and microscopy was strain dependent and was affected by the abundance of microsclerotia. Fungal biomass estimated by qPCR and microscopy correlated well for one strain with poor microsclerotia formation but not for two strains with high microsclerotia formation. The accuracy of qPCR measurement is constrained by the variability of cell volumes, while the accuracy of microscopy can be hampered by overlapping fungal structures and lack of specificity for PAC. Nevertheless, qPCR is preferable because it is highly specific for PAC and less time-consuming than quantification by microscopy. There is currently no better method than qPCR-based quantification using calibration curves obtained from pure mycelia to predict PAC biomass in substrates. In this study, the DNA amount of A. applanata extracted from 15 mm of Norway spruce fine root segments (mean diameter, 610 microm) varied between 0.3 and 45.5 ng, which corresponds to a PAC biomass of 5.1 +/- 4.5 microg (estimate +/- 95% prediction interval) and 418 +/- 264 microg.

Microsatellite size homoplasies and null alleles do not affect species diagnosis and population genetic analysis in a fungal species complex

The suitability of 13 microsatellite loci for species diagnosis and population genetics in 11 species of the Phialocephala fortinii s.l.-Acephala applanata species complex (PAC) was assessed. Two data sets were compared to test possible biases in species typing and clone detection resulting from null alleles and size homoplasies. The first data set was based on fragment lengths derived from a multiplex polymerase chain reaction (PCR) assay and the second data set was received from singleplex PCR at lower stringency and sequencing. Most null alleles observed in the multiplex PCR assay could be amplified during singleplex PCR under less stringent conditions. Size homoplasies resulting from mutations in flanking regions and differences in microsatellite structures were observed. For example, Phialocephala uotolensis possessed a (CT)(13) in addition to the (GT)(x) motif at locus mPF_0644. Despite the occurrence of null alleles and size homoplasies, species diagnosis and population genetic analysis studies were not affected. These markers will facilitate studies on population biology, ecology and biogeography of PAC species.

Phylogeny of Phaeomollisia piceae gen. sp. nov.: a dark, septate, conifer-needle endophyte and its relationships to Phialocephala and Acephala

Dark, septate endophytes (DSE) were isolated from roots and needles of dwarf Picea abies and from roots of Vaccinium spp. growing on a permafrost site in the Jura Mountains in Switzerland. Two of the isolates sporulated after incubation for more than one year at 4 degrees C. One of them was a hitherto undescribed helotialean ascomycete Phaeomollisia piceae gen. sp. nov., the other was a new species of Phialocephala, P. glacialis sp. nov. Both species are closely related to DSE of the Phialocephala fortinii s. lat.-Acephala applanata species complex (PAC) as revealed by phylogenetic analyses of the ITS and 18S rDNA regions. Morphologically dissimilar fungi, such as Vibrissea and Loramyces species, are phylogenetically also closely linked to the new species and the PAC. Cadophora lagerbergii and C. (Phialophora) botulispora are moved to Phialocephala because Phialocephala dimorphospora and P. repens are the closest relatives. Several Mollisia species were closely related to the new species and the PAC according to ITS sequence comparisons. One DSE from needles of Abies alba and one from shoots of Castanea sativa formed Cystodendron anamorphs in culture. Their identical 18S sequences and almost identical ITS sequences indicated Mollisia species as closest relatives, suggesting that Mollisia species are highly euryoecious.

Isolation and characterization of microsatellite markers for the tree-root endophytes Phialocephala subalpina and Phialocephala fortinii s.s

Species of the Phialocephala fortinii s.l.-Acephala applanata complex are the dominant dark septate endophytes (DSE) in roots of species belonging to the Pinaceae. The two species Phialocephala subalpina and P. fortinii s.s. belong to the most widely distributed species within this complex. In the present study, 15 polymorphic microsatellite loci were developed for these two closely related species. Strains of a community which were analysed previously using single-copy restriction fragment length polymorphism were screened with the new markers. Microsatellites were suitable to classify the two species and to recognize individuals within species.

Assignment of species rank to six reproductively isolated cryptic species of the Phialocephala fortinii s.1.-Acephala applanata species complex

Phialocephala fortinii s.1. and Acephala applanata are the dominant dark septate endophytes (DSE) in roots of many trees and shrubs. Population genetic analysis led to the discovery of morphologically indistinguishable but reproductively isolated cryptic species (CSP) within Phialocephala fortinii s.1. In the present study we show that sequence data of two coding (beta-tubulin and translation elongation factor [EF-lalpha]) and three noncoding DNA loci confirm subdivision of P. fortinii s.1. and allow to differentiate seven CSP of P. fortinii. In addition we show that strains collected throughout Europe can be classified correctly based on these sequence markers. Statistically significant differences in growth response on different media were observed among CSP of P. fortinii and A. applanata. Growth inhibition on MEA amended with 100 mgl(-1) cycloheximide had the strongest differential effect of all physiological traits examined. In contrast exoenzyme production (laccase, proteinase, pectinase, phenol-oxidase, amylase, cytochrome oxidase and tyrosinase) rarely helped to differentiate CSP of P. fortinii. However A. applanata was a strong producer of amylases, laccases and proteinases. Based on these data we propose to assign species rank to six CSP of P. fortinii: P. turiciensis, P. letzii, P. europaea, P. helvetica, P. uotolensis, P. subalpina spp. nov. and P. fortinii s.s.

Suitability of methods for species recognition in the Phialocephala fortinii-Acephala applanata species complex using DNA analysis

Sequence data of two coding and three non-coding loci were used to study the taxonomic identity within and relatedness among seven previously defined cryptic species (CSP) of Phialocephala fortinii and Acephala applanata using two approaches of species recognition. Identification of taxonomic groups corresponding to CSP was ambiguous in some cases when applying solely the genealogical concordance phylogenetic species recognition (GCPSR) concept. The definition of groups corresponding to CSP using GCPSR was complicated due to shared sequence haplotypes between CSP, unresolved CSP for several loci, and possible introgression. GCPSR in conjunction with a population genetic approach improved resolution significantly and the CSP status could be confirmed for all seven CSP of P. fortinii s.l. The most critical step in both analyses was the definition of groups. The combination of several classes of markers differing in resolution helped to define species boundaries.

Population genetic analysis of Phialocephala fortinii s.l. and Acephala applanata in two undisturbed forests in Switzerland and evidence for new cryptic species

The genetic structure of the root endophytes Phialocephala fortinii s.l. and Acephala applanata was analyzed in two undisturbed forests. A total of 606 strains isolated from surface-sterilized, fine roots of Picea abies and Vaccinium myrtillus were examined. Two new cryptic species of P. fortinii were recognized and host specialization of A. applanata was confirmed. This species was almost exclusively isolated from roots of P. abies. The index of association did not deviate significantly from zero within any population, suggesting that recombination occurs or had occurred. Significant gene but no genotype flow was detected among study sites for P. fortinii s.l. In contrast, several isolates of A. applanata with both identical multi-locus haplotype and identical ISSR fingerprint were found in both study sites indicating genotype flow or a recent common history.

Molecular and phenotypic description of the widespread root symbiont Acephala applanata gen. et sp. nov., formerly known as dark-septate endophyte type 1

Acephala applanata gen. et sp. nov. is described. A. applanata is a dark-septate endophyte (DSE) of conifer roots and belongs to the Phialocephala fortinii species complex. Several genetic markers, including isozymes, inter-simple-sequence-repeat (ISSR) fingerprints, single-copy restriction fragment length polymorphisms (RFLP) and sequences of the internal transcribed spacers (ITS), let us unambiguously separate isolates of A. applanata from isolates of P. fortinii s.l. and other dark-septate endophytes. Alleles at four RFLP loci and two fixed nucleotides in the ITS region were diagnostic for A. applanata. One of the fixed nucleotides resulted in the addition of an Afa I restriction site. PCR amplification with primers prITS4 and the newly developed primer PF-ITS_F (ACT CTG AAT GTT AGT GAT GTC TGA GT) and restriction digestion with Afa I yielded three fragments (203 bp, 117 bp, 56 bp) in A. applanata but only two (260 bp and 117 bp) in P. fortinii s.l. Population differentiation (GST) between A. applanata and other cryptic species of P fortinii was pronounced, and the index of association (IA) did not deviate significantly from zero, showing that recombination occurs or had occurred in A. applanata. Although isolates of A. applanata never were observed to sporulate, it can be distinguished morphologically from P fortinii s.l. by the scarcity of aerial mycelium, significantly slower growth and denser mycelium on cellophane overlaid on water agar. These phenotypic characteristics, combined with diagnostic RFLP alleles and/or PCR-RFLP of the ITS fragment with the fixed Afa I restriction site, unequivocally allow identification of A. applanata.

Monitoring the spatial and temporal dynamics of a community of the tree-root endophyte Phialocephala fortinii s.l

Phialocephala fortinii sensu lato was isolated from Picea abies roots that had been collected from the same 3 x 3-m forest plot in 2001 and 2004, to examine the spatial and temporal dynamics of this fungal community. RFLP analysis was used to define the multilocus haplotype (MLH) of each isolate. Pielou's measure of association and chi(2) tests of independence were employed to examine the randomness of patterns of spatial distribution of MLH observed in 2001 and 2004. Population differentiation between the two samplings was tested using the G(ST) statistic. In 2001, 144 strains of 28 MLH were isolated; in 2004, 139 strains of 29 MLH. Abundant MLH in 2001 also prevailed in 2004, and the same two cryptic species were dominant in both collections. The probability of being isolated in both years increased with increasing frequency of an MLH. The patterns of spatial distribution of most MLH did not differ between years. The G(ST) values indicated identity of the two collections. Communities of P. fortinii sensu lato remain spatially and genetically stable for at least 3 yr.

Evidence for subdivision of the root-endophyte Phialocephala fortinii into cryptic species and recombination within species

The genetic structure of the root-endophyte Phialocephala fortinii was analyzed in three study sites using 11 single-copy RFLP probes. A total of 541 strains isolated from surface-sterilized, fine roots (diameter 0.5-3 mm) of Norway spruce (Picea abies) were examined. The average gene diversity (H) was high in all three study sites. Cluster analysis showed that up to four well-separated clusters of multi-locus haplotypes were present within the sites. Significant population subdivision was detected among these clusters, suggesting that groups of multi-locus haplotypes were reproductively isolated and that P. fortinii is a species complex composed of several cryptic species. This hypothesis was supported by ISSR-PCR which showed clusters consistent with those of the multi-locus haplotypes identified by RFLP analysis. In contrast, ITS sequence analysis did not allow to separate the species as clearly. The index of association (IA) did not deviate significantly from zero within any cryptic species, suggesting that recombination occurs within these species. Cryptic species occurred sympatrically. Thalli of two cryptic species were detected in the same 5-mm-long root segment in one instance. No significant differentiation was observed among populations of the same cryptic species in forest stands located approximately 5 km from each other. This finding is consistent with significant gene flow over this spatial scale. In addition, several isolates with both identical multi-locus haplotype and identical ISSR fingerprint were found at each study site indicating genotype flow or a recent common history between study sites.

Characterization of Guignardia mangiferae isolated from tropical plants based on morphology, ISSR-PCR amplifications and ITS1–5.8S-ITS2 sequences

Phenotypic and genotypic variability of 18 endophytic Guignardia strains from different host plants (Anacardiaceae: Anacardium giganteum, Myracrodruon urundeuva, Spondias mombin; Apocynaceae: Aspidosperma polyneuron; Ericaceae: Rhododendron sp.; Fabaceae: Bowdichia nitida; Leguminosae: Cassia occidentalis; Rutaceae: Citrus aurantium) growing in different sites in Brazil was assessed by means of morphometric measurements and inter-single-sequence-repeat-anchored polymerase chain reaction (ISSR-PCR) amplifications of the DNA. Morphology of conidia and ascospores and growth rates of the Brazilian isolates corresponded well with those of G. mangiferae. Multiple correspondence analysis (MCA) of the ISSR-PCR data yielded three groups of strains, which did, however, not correspond either to the host or to the geographic origin. The same individual tree hosted genotypically different strains indicating multiple infections. Phylogeny based on ITS1-5.8S-ITS2 sequence analyses confirmed conspecificity of the Brazilian isolates with G. mangiferae (syn. G. endophyllicola).

Development of single-copy RFLP markers for population genetic studies of Phialocephala fortinii and closely related taxa

Single-copy RFLP markers were developed for the root endophytic fungus Phialocephala fortinii. After an initial screening of 40 probes with four restriction enzymes, EcoRV and HindIII were chosen to analyse 31 strains of P. fortinii and nine strains of a closely related morphotype (Type 1) which have known ISSR-PCR or allozyme phenotypes. Type 1 isolates and a single genetically different isolate with Type 1 like morphology, a representative of a possible third taxon, showed unique alleles with several probes and both restriction enzymes. Consequently, both taxa were easily distinguishable from P. fortinii isolates. Whereas EcoRV in combination with seven probes revealed only eight multi-locus haplotypes among 17 ISSR phenotypes, HindIII in combination with 12 probes was able to distinguish all ISSR and/or allozyme phenotypes except two pairs of strains. Strains of P. fortinii showed a high gene diversity, and up to 15 alleles per locus were observed among the 31 strains of P. fortinii. The 12 probes used in combination with HindIII were (partially) sequenced and BLAST searches showed no similarities with known sequences indicating that they probably are non-coding regions of the genome. Enzyme-probe combinations suitable to indicate the genetic structure of P. fortinii and Type 1 populations were easily identified in the present study. This opens up avenues to study communities of the P. fortinii complex exposed to various environments and management intensities, and will help to promote the understanding of these extremely successful organisms.

Genetic variability among strains of Phialocephala fortinii and phylogenetic analysis of the genus Phialocephala based on rDNA ITS sequence comparisons

Two methods to determine variability among strains of Phialocephala fortinii and sterile DSE (dark septate endophyte) Type 1 were compared: inter-simple sequence repeat polymerase chain reaction analysis (ISSR–PCR) and sequence analysis of the two internal transcribed spacers and the 5.8S ribosomal DNA (ITS1-5.8S-ITS2). Both methods showed similar results for some strains, but different results for others. Phylogenetic analysis of various strains of P. fortinii and Type 1 based on ITS1-5.8S-ITS2 sequence information showed that Type 1 strains, with the exception of one Type 1 strain and a strain with a Type-1-like culture morphology, form a well-supported clade, whereas P. fortinii strains are much more variable and the relative position of many strains on the tree are unresolved. Two sterile DSE strains with Type 1 culture morphology form a well-supported clade, separate from the P. fortinii – Type 1 clade. Phylogenetic analysis of some species of the Leotiales and of Phialocephala and related species based on ITS1-5.8S-ITS2 sequences indicate that the genera Phialocephala and Sporendocladia are polyphyletic. One major clade, supported by a high bootstrap value, is positioned as a well-separated lineage among members of the Leotiales. Phialocephala fortinii, Phialocephala dimorphospora, Phialocephala compacta, Phialocephala scopiformis, and Type 1, all known as endophytes of woody plant species, are positioned in this clade. A second well-supported clade including Phialocephala humicola, Phialocephala xalapensis, and Phialocephala fusca was positioned outside the Leotiales. Phialocephala xalapensis and P. humicola had identical sequences and were not separable based on morphology. The two taxa were, therefore, considered to represent the same species. Phialocephala virens, Phialophora finlandia, Sporendocladia foliicola, and Leptodontidium orchidicola were not included in either of the two Phialocephala clades.Key words: Phialocephala, phylogenetic analysis, internal transcribed spacer, DSE.