nrDNA ITS Sequences Research Articles

Oxalis dreyerae (Oxalidaceae), a new species from South Africa

Oxalis dreyerae, a new species from the arid Richtersveld region of South Africa, is described. It is most similar to O. inconspicua from which it differs, among others, by having a larger plant body, larger and showier flowers with a broadly trumpet-shaped tube, much larger leaflets, petioles that are thicker than the peduncles, much larger lanceolate sepals and short, stubby teeth on the longer filaments. Its placement within the O. flava clade is supported by nrDNA ITS sequence evidence, which is also consistent with a close relationship to O. inconspicua. Oxalis dreyerae represents the eighth described species of Oxalis endemic to the arid Richtersveld of the Northern Cape, thus supporting the importance of the floristically diverse Gariep Centre of Endemism, of which the region forms a part.

Pastinaca erzincanensis (Apiaceae), A New Species from Eastern Turkey and Its Phylogenetic Position within Tordylieae

Pastinaca erzincanensis Menemen & Kandemir (Apiaceae) is described as a new species, restricted to a single location in Erzincan Province, Turkey. To describe the species and assess its phylogenetic placement, field-collected and herbarium specimens were examined for morphological, fruit anatomical/micromorphological and palynological variation and included in a molecular phylogenetic study. Comparisons of leaf morphology, palynology and fruit anatomy suggest an affinity with Pastinaca (Tordylieae tribe Tordyliinae), although the presence of vittae in the fruit ribs is unique within the genus. Maximum parsimony and maximum likelihood analyses of nrDNA ITS sequences from representative members of tribe Tordylieae show that P. erzincanensis nests within a well-supported clade comprising members of Pastinaca, Malabaila and Trigonosciadium. Within a poorly supported Pastinaca s. lato clade, P. erzincanensis is sister group to M. pastinacifolia, with P. pimpinellifolia, P. yildizii and M. brachytaenia placed a...

Resolving the phylogenetic placement of Porobeltraniella and allied genera in the Beltraniaceae

The circumscription of Beltraniaceae has thus far been based on the unique morphological characters of its genera, although these assumptions have never been tested phylogenetically because of a lack of DNA sequence data. The Indian Western Ghats is rich with diverse strains of Beltrania and similar genera, and therefore an attempt was made to re-collect as many species as possible, to study their taxonomy, and to resolve their phylogeny based on LSU and ITS nrDNA sequences. This study provides the first phylogenetic placement of genera Beltraniella, Porobeltraniella, Pseudobeltrania and Hemibeltrania in the Beltraniaceae based on fresh specimens, type studies and molecular phylogenetic analyses. Furthermore, Subramaniomyces appears to be phylogenetically related to beltranioid genera, and is therefore included in Beltraniaceae. However, the phylogenies of the hyphomycete genus Parapleurotheciopsis and the perithecial genus Pidoplitchkoviella appear to change with data selection and phylogenetic analytical method used, and remain unresolved.

Revising the Schizoparmaceae: Coniella and its synonyms Pilidiella and Schizoparme.

The asexual genera Coniella (1918) and Pilidiella (1927), including their sexual morphs in Schizoparme (1923), have a cosmopolitan distribution and are associated with foliar, fruit, leaf, stem and root diseases on a wide variety of hosts. Species of these genera sometimes occur as secondary invaders of plant tissues infected by other organisms or that are injured by other causes. Several studies published over the last few decades had conflicting ideas as to whether Coniella, Pilidiella and Schizoparme should be regarded as synonymous or as separate genera. The present study aims to resolve the generic classification of these genera through phylogenetic analyses of the concatenated alignment of partial LSU nrDNA, rpb2, ITS nrDNA and tef1 sequence data of 117 isolates, combined with their morphology. Results revealed that all strains cluster in a single well-supported clade. Conidial colour, traditionally the distinguishing character between Coniella and Pilidiella, evolved multiple times throughout the clade, and is not a good character at generic level in Schizoparmaceae. The three genera should therefore be regarded as synonymous, with the older name Coniella having priority. Furthermore, this study delineated 13 new species, and new combinations were proposed for a further 15 species.

Clavulina-Membranomyces is the most important lineage within the highly diverse ectomycorrhizal fungal community of Abies religiosa.

Abies religiosa is an endemic conifer of Mexico, where its monodominant forests are the winter refuge of the monarch butterfly. Due to climate change, it has been estimated that by 2090, A. religiosa populations will decline by 96.5%. To achieve success, reforestation programs should consider its ectomycorrhizal (ECM) fungi. We used ITS nrDNA sequences to identify the ECM fungi associated with A. religiosa and, based on its abundance and frequency, determined the diversity and community structure in a pure A. religiosa forest near Mexico City. Using sequence metadata, we inferred the species geographic distribution and host preferences. We conducted phylogenetic analyses of the Clavulinaceae (the most important family). The ECM community held 83 species, among which the richest genera were Inocybe (21 species), Tomentella (10 species), and Russula (8 species). Besides its low species richness, the Clavulina-Membranomyces lineage was the most dominant family. Clavulina cf. cinerea and Membranomyces sp. exhibited the highest relative abundance and relative frequency values. Phylogenetic analyses placed the Clavulinaceae genotypes in three different clades: one within Membranomyces and two within Clavulina. A meta-analysis showed that the majority of the ECM fungi (45.78%) associated with A. religiosa in Mexico have also been sequenced from North America and are shared by Pinaceae and Fagaceae. In contrast, because they have not been sequenced previously, 32.2% of the species have a restricted distribution. Here, we highlight the emerging pattern that the Clavulina-Membranomyces lineage is dominant in several ECM communities in the Neotropics, including Aldinia and Dicymbe legume tropical forests in the Guyana Shield, the Alnus acuminata subtropical communities, and the A. religiosa temperate forests in Mexico.

Phylogenetic relationship of some Onobrychis taxa naturally grown in Turkey based on morphology and nuclear ribosomal DNA ITS Sequences

Phylogenetic relationships were studied based on morphology and nuclear ribosomal DNA internal transcript spacer (nrDNA ITS) sequences in 49 populations of 36 Onobrychis taxa belonging to 5 sections (Dendobrychis, Lophobrychis, Onobrychis, Heliobrychis and Hymenobrychis) naturally grown in Turkey. The morphological data (46 quantitative characters) were standardized and submitted for PCA analysis before the performance of hierarchical clustering analysis. In addition, a 577-bp region of the nrDNA ITS sequences was compared to generate a dendrogram using the neighbor-joining method. According to the obtained results, the Onobrychis genus is clearly divided into the Onobrychis and Sisyrosema subgenera both molecularly and morphologically; however, in terms of molecular data, while the Onobrychis subgenus showed polyphyletic features, the Sisyrosema subgenus had monophyletic features. Additionally, long-wing taxa belonging to Dendobrychis and Onobrychis and O. crista-galli belonging to Lophobrychis located in the same clade in Onobrychis showed polyphyletic features. This finding was confirmed in terms of long-wing taxa as well as morphology and indicated that these three sections were entangled with each other under the Onobrychis subgenus.

Genetic variation and phylogenetic relationship analysis of Jatropha curcas L. inferred from nrDNA ITS sequences

Genetic variation and phylogenetic relationships among 102 Jatropha curcas accessions from Asia, Africa, and the Americas were assessed using the internal transcribed spacer region of nuclear ribosomal DNA (nrDNA ITS). The average G+C content (65.04%) was considerably higher than the A+T (34.96%) content. The estimated genetic diversity revealed moderate genetic variation. The pairwise genetic divergences (GD) between haplotypes were evaluated and ranged from 0.000 to 0.017, suggesting a higher level of genetic differentiation in Mexican accessions than those of other regions. Phylogenetic relationships and intraspecific divergence were inferred by Bayesian inference (BI), maximum parsimony (MP), and median joining (MJ) network analysis and were generally resolved. The J. curcas accessions were consistently divided into three lineages, groups A, B, and C, which demonstrated distant geographical isolation and genetic divergence between American accessions and those from other regions. The MJ network analysis confirmed that Central America was the possible center of origin. The putative migration route suggested that J. curcas was distributed from Mexico or Brazil, via Cape Verde and then split into two routes. One route was dispersed to Spain, then migrated to China, eventually spreading to southeastern Asia, while the other route was dispersed to Africa, via Madagascar and migrated to China, later spreading to southeastern Asia.

New combinations in the genus Siler (Apiaceae) for the Italian Flora

On the basis of nrDNA ITS sequences and plastid markers (rps16 intron, rpoC1 intron and rpoB-trnC intergenic spacer), Banasiak et al. (2016) reconstructed the phylogeny of all the genera belonging to the subtribe Daucinae Dumortier (1827: 81), showing that the former tribe Laserpitieae Bentham in Bentham & Hooker (1867: 872) constitutes a paraphyletic grade at the base of the spiny-fruited members of Daucinae, while the traditionally delimited genera Daucus Linnaeus (1753: 242) and Laserpitium Linnaeus (1753: 248) are polyphyletic. The same authors proposed to maintain Daucus as monophyletic synonymizing several names at genus level, while Laserpitium was splitted into 5 genera—Laserpitium s.str. (now including only 6 species), Ekimia Duman & Watson (1999: 200), Laser Borkhausen ex Gaertner, Meyer & Scherbius (1799: 244, 384), Siler Miller (1754: without pagination), Silphiodaucus (Koso-Poljansky 1916: 211) Spalik, Wojewódska, Banasiak, Piwczyński & Reduron in Banasiak et al. (2016: 578), and Thapsia Linnaeus (1753: 261)—and nomenclatural changes were proposed (Banasiak et al. 2016).

Phylogeny of Apiaceae subtribe Daucinae and the taxonomic delineation of its genera

AbstractScandiceae subtribe Daucinae encompasses umbellifers that have fruits with prominent secondary ridges projecting into wings (former tribe Laserpitieae) or spines (former tribe Caucalideae pro parte). It comprises several economically or medicinally important genera including Cuminum, Daucus, Laser, Laserpitium and Thapsia among others. Recent molecular studies, based mostly on nrDNA ITS sequences, revealed that neither Daucus nor Laserpitium are monophyletic. To address issues of relationships and apply respective nomenclatural changes, we obtained additional ITS sequences as well as independent data from three plastid markers—rps16 intron, rpoC1 intron and rpoB‐trnC intergenic spacer—for a comprehensive sample of the subtribe. We examined data for 260 accessions representing all genera of Daucinae and 81 of its ca. 93 species. Phylogenetic trees were estimated using maximum likelihood and Bayesian inference methods. The results indicate that former Laserpitieae constitute a paraphyletic grade at the base of the spiny‐fruited members of Daucinae while traditionally delimited Daucus and Laserpitium are polyphyletic. To maintain a monophyletic Daucus, we suggest including the following genera and species into its synonymy: Agrocharis, Melanoselinum, Monizia, Pachyctenium, Pseudorlaya, Rouya, Tornabenea, Athamanta dellacellae and Cryptotaenia elegans. The species of Laserpitium occur in seven clades and only six species of the Laserpitium s.str. clade retain the generic name. Several species are transferred to Ekimia, Laser and Thapsia; additionally, a monospecific genus Siler is restored and a new genus, Silphiodaucus, is established. The inclusion of Ammodaucus into Thapsia suggested in an earlier study is not supported. The position of Laserpitium pseudomeum requires further study.

Diversity and taxonomy of Chaetomium and chaetomium-like fungi from indoor environments.

During a study of indoor fungi, 145 isolates belonging to Chaetomiaceae were cultured from air, swab and dust samples from 19 countries. Based on the phylogenetic analyses of DNA-directed RNA polymerase II second largest subunit (rpb2), β-tubulin (tub2), ITS and 28S large subunit (LSU) nrDNA sequences, together with morphological comparisons with related genera and species, 30 indoor taxa are recognised, of which 22 represent known species, seven are described as new, and one remains to be identified to species level. In our collection, 69 % of the indoor isolates with six species cluster with members of the Chaetomium globosum species complex, representing Chaetomium sensu stricto. The other indoor species fall into nine lineages that are separated from each other with several known chaetomiaceous genera occurring among them. No generic names are available for five of those lineages, and the following new genera are introduced here: Amesia with three indoor species, Arcopilus with one indoor species, Collariella with four indoor species, Dichotomopilus with seven indoor species and Ovatospora with two indoor species. The generic concept of Botryotrichum is expanded to include Emilmuelleria and the chaetomium-like species B. muromum (= Ch. murorum) in which two indoor species are included. The generic concept of Subramaniula is expanded to include several chaetomium-like taxa as well as one indoor species. Humicola is recognised as a distinct genus including two indoor taxa. According to this study, Ch. globosum is the most abundant Chaetomiaceae indoor species (74/145), followed by Ch. cochliodes (17/145), Ch. elatum (6/145) and B. piluliferum (5/145). The morphological diversity of indoor Chaetomiaceae as well as the morphological characteristics of the new genera are described and illustrated. This taxonomic study redefines the generic concept of Chaetomium and provides new insight into the phylogenetic relationships among different genera within Chaetomiaceae.

Evidence for hybridization and introgression in two Canadian Arctic louseworts: Pedicularis langsdorffii subsp. arctica and Pedicularis hirsuta

Hybridization and introgression between two closely related but taxonomically distinct Arctic lousewort species — the circumpolar Pedicularis hirsuta L. (predominantly eastern Arctic in Canada) and the amphi-Beringian, western Canadian Pedicularis langsdorffii Fisch. ex Steven subsp. arctica (R. Br.) Pennell ex Hultén — is documented here for the first time; only the second confirmed case of introgression in this widespread genus. Multivariate and univariate analysis of morphological characters successfully delineate the two species as morphologically similar but distinct taxa. Analysis of nrDNA ITS sequences likewise differentiate the two taxa in all sampled instances. Analysis of cpDNA atpI–atpH sequences also separate these taxa, except in 12 individuals of P. langsdorffii subsp. arctica, which possess the same haplotype as P. hirsuta. Where these two species overlap in range in the Canadian High Arctic, chloroplast transfer from P. hirsuta to P. langsdorffii subsp. arctica is detected, and morphologically intermediate hybids have been identified, indicating hybridization and subsequent backcrossing. Here we discuss the relationships between these two species, and provide a key that is useful for differentiating them.

Species identity of Phellinus linteus (sanghuang) extensively used as a medicinal mushroom in Korea.

Sanghuang is a medicinal mushroom that has gained particular attention in Korea. It has been extensively studied for the past few decades as a natural immune booster and cancer suppressor. Although the scientific name, Phellinus linteus, has been commonly used to refer to the sanghuang mushroom, the species identity of sanghuang has been called into question due to the ambiguity of its circumscription and the inadequacy of morphological distinctions within allied species. Because the species concept of sanghuang has been elucidated by recent molecular phylogenetic studies, it has become necessary to clarify the taxonomic positions of sanghuang strains extensively utilized in Korea. We conducted a phylogenetic analysis of 74 strains belonging to the P. linteus-baumii complex based on ITS nrDNA sequences. Parental stains of sanghuang varieties formally registered in the Korea Seed & Variety Service, including ASI 26046 (Corea sanghuang), 26114 (Boolro), and 26115 (HK 1-ho) were grouped with Sanghuangporus sanghuang instead of P. linteus in the inferred phylogeny.

Molecular phylogenetic analysis of key Jatropha species inferred from nrDNA ITS and chloroplast (trnL-F and rbcL) sequences

The genus Jatropha (Euphorbiaceae) contains species that are of significant economic and ornamental value. However, Jatropha breeding material is rather limited due to incomplete information regarding phylogenetic relationships among germplasm resources. Phylogenetic analyses were performed based on the internal transcribed spacer of nuclear ribosomal DNA (nrDNA ITS), two chloroplast regions (trnL-F and rbcL), and the combined (ITS+trnL-F+rbcL) dataset among twenty-five specimens representing six key Jatropha species. Phylogenetic relationships of Jatropha were well resolved between subgenus Curcas and subgenus Jatropha, and demonstrated the intermediate position of section Polymorphae among sections of both subgenera. Jatropha curcas and J. integerrima demonstrated a close phylogenetic relationship. The molecular data agreed with the morphological classification that recognized J. multifida and J. podagrica in sec. Peltatae. The distinct intraspecific divergence that occurred in J. curcas could be attributed to restricted gene flow caused by geographical isolation and different ecological conditions. Phylograms produced with trnL-F and rbcL sequence data suggested slow rates of sequence divergence among Jatropha spp., while the ITS gene tree had good resolution suggesting high genetic variation of ITS among Jatropha species.

Russula buyckii, a new species of Russula subgenus Incrustatula from Eastern Himalaya, India

Russula buyckii, a new species of Russula (subgen. Incrustatula, sect. Lilaceinae and subsect. Lilaceinae) is described from Eastern Himalaya, India. Its macro- and micro-morphological features are described in detail and compared with those of similar species. Identification and categorization of R. buyckii was supported by the molecular phylogenetic analysis based on the nrDNA ITS sequence data.

Tropicoporus stratificans sp. nov. (Hymenochaetales, Basidiomycota) from southern Brazil

Tropicoporus is a recently proposed genus that was segregated from Inonotus s.l. and includes species with important wood decay and medicinal functions. The description of T. stratificans sp. nov. is based on more than 10 specimens collected on fallen decayed wood in subtropical forests of Rio Grande do Sul State. The species is recognized by its resupinate, poroid, golden brown, perennial basidiomes that become multi-layered, dimitic hyphal system, abundant hymenial setae, and subglobose to ellipsoid, brownish-yellow to ferruginous-brown basidiospores. Based on nrDNA ITS sequences, Bayesian and maximum likelihood phylogenetic analyses of Tropicoporus nested the new taxon in the T. linteus clade. A description and illustrations of the new species are provided.

Morphological and phylogenetic clarification of Peziza arvernensis, P. pseudovesiculosa, P. pseudosylvestris, and P. domiciliana

The concepts of the morphologically similar species Peziza arvernensis, P. pseudovesiculosa, P. pseudosylvestris, and P. domiciliana are revisited in light of new morphological and molecular data from freshly collected and herbarium specimens. Phylogenetic inference based on ITS nrDNA sequences suggests that P. arvernensis, P. pseudovesiculosa, and P. pseudosylvestris are monophyletic and that P. domiciliana represents an independent taxon.

Xyloselinum laoticum (Umbelliferae), a new species from Laos, and taxonomic placement of the genus in the light of nrDNA ITS sequence analysis

A new species of Xyloselinum, X. laoticum, endemic to the Vientiane province of Laos, is described and illustrated. Similar to two previously described species of Xyloselinum from limestone ridges of Northern Vietnam, the new species is subshrub with 2–3 pinnatisect leaves having petiolulate basal segments and broadly lanceolate terminal segments, solitary or binary mericarp vallecular vittae, almost flat on the commissural side endosperm. The new species is more closer to X. vietnamense than to X. leonidii. Xyloselinum laoticum differs from X. vietnamense in irregularly toothed or laciniate terminal leaf segments without bladders on lower surface, solid (not fistulose) petioles, globose umbels and umbellets, almost glabrous (not densely covered by scattered short prickles) pedicels, always entire bracteoles, and conical (not shortly conical) stylopods. It is supported by the nrDNA ITS data that Xyloselinum is treated as an independent genus and placed in Selineae Clade together with some S and E Asian genera separated from Peucedanum s.l. or Ligusticum/Selinum complex.

Molecular identification and pathogenicity assessment of a rust fungus infecting common ragweed (Ambrosia artemisiifolia) in its native North American range

A rust fungus collected from common ragweed (Ambrosia artemisiifolia) in Texas, USA, was identified as belonging to the Puccinia xanthii morphospecies based on its nrDNA ITS sequence. Pathogenicity studies carried out with this rust accession under quarantine conditions in the UK showed that the fungus was highly virulent on A. artemisiifolia plants from Australia. Recently, P. xanthii has been proposed as a potential classical biological control agent (CBCA) for common ragweed in its invasive range, focusing on Europe, despite previous doubts about its biocontrol potential. The results of the pathogenicity tests reported here support the suitability of this pathogen as a CBCA for common ragweed.

A polyphasic contribution to the knowledge of Auxarthron (Onygenaceae)

In a survey of coprophilous fungi in Italy, two interesting ascomycetes were recovered from hedgehog dung. These fungi showed a sexual morph characterized by gymnothecia, globose reticulate ascospores, a Malbranchea asexual state, and a keratinolytic ability, and were identified morphologically and molecularly as Auxarthron umbrinum and A. concentricum of the Onygenaceae. The history, ecology, and morphology of the genus Auxarthron as a whole, and of A. umbrinum and A. concentricum in particular, are revised. A preliminary evaluation of the antagonistic properties of A. umbrinum and A. concentricum against phytopathogenic fungi has been performed in dual cultures. Growth inhibition of some plant pathogenic fungi was recorded, and the effects were growth medium dependent. When solid-state fermentation (SSF) substrate of both Auxarthron isolates has been submitted to extraction, both the organic extract residues (n-hexane and CH2Cl2) and the lyophilized aqueous phases were used for the antibiotic test against plant pathogenic fungi. Significant antifungal activity was obtained by organic fractions and aqueous residue of A. concentricum against Alternaria brassicicola and Botrytis cinerea, whereas A. umbrinum appeared to be less effective. The analysis of ITS nrDNA sequences suggests that an extensive phylogenetic revision of the genus Auxarthron is necessary.

Pseudodidymosphaeria gen. nov. in Massarinaceae

Didymosphaeria spartii was collected from dead branches of Spartium junceum in Italy. Multi-gene phylogenetic analyses of ITS, 18S and 28S nrDNA sequence data were carried out using maximum likelihood and Bayesian analysis. The resulting phylogenetic trees showed this to be a new genus in a well-supported clade in Massarinaceae. A new genus Pseudodidymosphaeria is therefore introduced to accommodate this species based on molecular phylogeny and morphology. A illustrated account is provided for the new genus with its asexual morph and the new taxon is compared with Massarina and Didymosphaeria.