Identical Internal Transcribed Spacer Research Articles

First Report of Aspergillus tubingensis Causing Leaf Spot on Pogostemon cablin in China

Patchouli (Pogostemon cablin (Blanco) Benth) is an important medicinal and aromatic plant widely cultivated in China, India, and other Southeast Asian countries. It is renowned for its diverse applications in traditional medicine and its detoxification, antibacterial, anti-inflammatory, and other pharmacological properties (Wu et al. 2016; Fang et al. 2022). In May 2023, a severe leaf spot disease was observed on Pogostemon cablin plants grown in most plantations in Yulin, Guangxi, China (22°26′N; 109°83′E), with over 50% incidence rate. Symptoms began as small, circular, brown spots on leaves, enlarging with yellow halos. Lesions expanded into irregular shapes with necrotic centers. Advanced stages showed extensive yellowing, browning, and leaf senescence. A total of 20 symptomatic plants were sampled from 5 different locations within the detected area, with 4 plants sampled per location. To isolate the pathogen, 20 affected leaves were collected from these plants and preliminarily washed with sterile distilled water (SDW). Five small tissue pieces (5×5 mm) were excised from the lesion edge of each leaf, surface-disinfected with 75% ethanol and 1% NaClO, rinsed thrice with SDW, and placed on potato dextrose agar (PDA) at 28 °C in darkness for 7 days. Out of these, 18 plants (90%) yield fungal isolate with recurrent and similar morphological characteristics. Four representative isolates (X5-1-1, X5-1-3, X5-1-5, and X5-1-7) were selected for further analysis. On PDA, colonies were initially white, gradually turning black on the surface, with light yellow on the reverse side of the plate. Conidia were brown to black, globose, rough-walled, and 2.6 to 5.2 µm in diameter. Conidial heads were brown-black, and conidiophores were smooth and hyaline. Morphological characteristics matched those of Aspergillus sp. (Guo et al. 2017). For molecular identification, the internal transcribed spacer (ITS) region and the β-tubulin (TUB) gene of all four isolates were sequenced (Lim et al. 2019). All four isolates (X5-1-1, X5-1-3, X5-1-5, and X5-1-7) showed consistent morphological characteristics and 100% identical ITS and TUB sequences. Representative sequences from isolate X5-1-5 were submitted to GenBank (ITS: PP789632; TUB: PP798205). The obtained ITS and TUB sequences showed 99% similarity to Aspergillus tubingensis (ITS: OP737633; TUB: MG991377). Based on morphological and molecular analyses, the fungus was identified as A. tubingensis (Palmer et al. 2019). For pathogenicity tests, a spore suspension (1 × 10^6 conidia/mL) was prepared from 7-day-old cultures of A. tubingensis grown on PDA. The suspension was sprayed onto leaves of 10 healthy Pogostemon cablin plants until runoff. Control plants were sprayed with SDW. All plants were kept in a controlled greenhouse (12/12h light/dark, 25 ± 2 °C, 90% humidity). After 7 d, symptoms identical to those observed in the field developed on all pathogen inoculated plants, while control plants remained asymptomatic. The fungus was successfully re-isolated from infected leaves in three successive trials, fulfilling Koch's postulates. Notably, A. tubingensis has previously been reported causing field diseases on strawberry in California, Jatropha curcas and Helleborus species in China (Palmer et al. 2019; Guo et al. 2017, Liaquat et al. 2019), and vine canker on table grape in Italy (Vitale et al. 2012). To our knowledge, this is the first report of A. tubingensis causing leaf spot on Pogostemon cablin in China. This finding provides a foundation for further investigate into the biology, epidemiology, and management of this disease.

First record of Diplodia gallae causing branch cankers on declining scarlet oak (Quercus coccinea) in Virginia.

Members of Botryosphaeria s.l. have an extensive history as cankering pathogens of stressed and declining oak trees in the eastern United States (Ferreira et al. 2021). The host range, distribution, and virulence among two closely related species, Diplodia corticola and D. gallae, remains unclear (Brazee et al. 2023). On 15 August 2023, a survey was conducted at a declining natural hardwood site in Shenandoah County, Virginia (GPS coordinates 38.922089, -78.606125). One mature Quercus coccinea tree that displayed scorched leaf margins and branch dieback was felled and a cankered branch from the crown was sampled (Fig. 1A and B). A 4-mm piece of necrotic tissue was selected from the margin of the canker, disinfected with 2.5% NaOCl, again with 70% ethanol, and air-dried before being placed on half-strength acidified PDA medium (pH 4.8) and incubated in the dark at 22 ± 2°C. After 5 days, four colonies were transferred to full-strength PDA medium and incubated in the dark at 22 ± 2°C. After 10 days, all four colonies displayed thick, gray, floccose mycelium and pigmented hyphae (Fig. 1C). Mycelia was harvested from 10-day-old colonies with a sterile pin and DNA was extracted using a Qiagen DNeasy Plant Pro Kit (Germantown, MD) according to the manufacturer's instructions. A fragment of the internal transcribed spacer (ITS) and translation elongation factor 1-α (tef1) loci were amplified using ITS4/ITS5 (White et al. 1990) and EF1-728F/EF1-986R (Carbone and Kohn 1999) primer sets, respectively. The PCR amplicons were purified with ExoSap-IT (Affymetrix, Santa Clara, CA) and sequenced at Eurofins (Louisville, KY).&xa0; The raw nucleotide sequences were analyzed using Geneious 11.1.5 software (Biomatters, Auckland, NZ). All four colonies had identical ITS sequences. A 523 and 276-bp fragment of the ITS and tef1 loci, respectively, from isolate R1.2 was deposited into the GenBank database (accessions OR934498 and OR961039). A dataset of 43 strains consisting of 38,658 characters was aligned using MAFFT v7.49 (Katoh et al. 2013), and a concatenated ITS + tef1 maximum likelihood phylogenetic tree (1000 bootstraps) was built with PhyML 3.0 (Guindon et al. 2010) using the GTR substitution model. Isolate R1.2 was grouped with isolates of D. gallae although the species failed to form a well-supported clade (BS = 67) due to intraspecific variation (Fig. 1D). Koch's postulates were fulfilled by inoculating five healthy, containerized Q. coccinea trees (average stem caliper 5.3 cm) with isolate R1.2, with five plants as controls. After disinfecting the bark with 70% ethanol, a 0.5 mm section of the bark was removed 13 cm above the soil line with a sterile scalpel, and a 0.5 mm agar plug taken from the edge of a 10-day-old PDA culture was placed in the wound with the mycelium facing the cambial tissue, sealed with Parafilm, and maintained at 22 ± 4°C. The same procedure was performed on the control plants using sterile PDA plugs. After five weeks the bark was removed, and all five stems treated with R1.2 had necrotic lesions with a mean linear growth ([length+width]/2) of 9.2 ± 2.72 mm from the edge of the wound, which was significantly larger (P = 0.003) than the controls (1 ± 0.66 mm; Fig. 1E - L). Necrotic stem tissue was sampled as previously described, and the isolate recovered was confirmed as D. gallae based on morphology and 100% ITS sequence homology to isolate R1.2. D. gallae was not recovered from the control plants. In the United States, D. gallae has been isolated from Q. rubra and Q. velutina twig cankers in Maine, Massachusetts, New Hampshire, New York, and Vermont (Brazee et al. 2023). This is the first report of the species in Virginia causing branch cankers on Q. coccinea.

First Report of Kiwifruit Root Rot Caused by Globisporangium spinosum in China.

Kiwifruit is widely cultivated for its high vitamin C content and nutritional value. In January 2022, root rot symptoms were found in about 30% of Actinidia chinensis cv. Jinyan plants grafted on A. deliciosa rootstocks in an orchard located in Sanming (26.32°N, 117.23°E), Fujian Province of China. The affected plants appeared stunted, with brown and decaying roots, some of which were covered with white hyphae. To isolate the pathogen, the surfaces of typical symptomatic roots were sterilized for 30 s using 75% ethanol, followed by four rinses in sterile water, placing on potato dextrose agar (PDA), and incubating away from light at 25°C for 7 days. 16 Globisporangium-like isolates were obtained through hyphal tip isolation, displaying a milky-white appearance with irregular protuberances on the surface, and yellow-white backs with radial fold lines. The isolates were then cultured on corn meal agar for 5 days at 25°C in dark for morphological characteristics. Under microscope, the hyphae appeared as long strips without septa and 4.1 to 8.2 µm wide (average 6.7 µm), containing irregularly sized spherical droplets. Both terminal and intercalary hyphae swellings were observed; these appeared either spherical or subspherical, with some having projections. Their dimensions were 12.3 to 27.6 µm (average 17.3 µm). The oospores were mostly spherical, either plerotic or aplerotic, 11.8 to 22.3 µm wide (average 18.9 µm), with occasional projections. The antheridia were rod-shaped and curved, with one end attached to the oogonia. Amplification of the sequences of internal transcribed spacer (ITS) regions and cytochrome c oxidase subunit I (COI) were conducted using the primers ITS1/ITS4 (White et al. 1990) and OomCoxI-Levlo/OomCoxI-Levup (Robideau et al. 2011), respectively. The sequencing results revealed identical ITS and COI sequences in all 16 isolates. BLASTn analysis of the 969-bp ITS sequence ON202808 showed 99.38-99.59% similarity (965/971bp, 967/971bp) with the KJ162353 and AY598701 sequences from Globisporangium spinosum isolates, while the 700-bp COI sequence ON075783 showed 100% and 99.41% identity (680/680bp, 676/680bp) with the GenBank sequences HQ708835 and HQ708832, respectively, from G. spinosum. Phylogenetic analysis also showed that the obtained isolate (termed MA16) clustered with isolates from G. spinosum on the same evolutionary branch. For pathogenicity testing, four-month-old healthy Jinyan (A. chinensis) plants grown in sterilized media were transferred to sterile petri dishes covered with wet filter paper, and their roots were inoculated with a 5-mm-wide disk of MA16 when cultivated on PDA medium for 5 days. Miliang-1 (A. deliciosa) and Hongyang (A. chinensis) plants were treated similarly. The control groups each included three plants that were inoculated with non-colonized PDA. The plants were kept at 25 °C with a 12-/12-h light/dark cycle for 10 days when the inoculated plants exhibited root rot symptoms similar to those seen in the field, together with rotting and browning of the leaves. The control plants appeared healthy with no symptoms. After re-isolated from infected tissues, the pathogen was verified to be G. spinosum according to its ITS sequence, thus fulfilling the Koch's postulates. Recently, Pythium spinosum has been classified as G. spinosum according to whole-genome sequencing and phylogenomic analysis (Nguyen et al. 2022). Based on the morphological features and pathogenicity results, MA16 was identified as G. spinosum (van der Plaats-Niterink 1981; Huo et al. 2023). This report appears to be the first description of kiwifruit root rots caused by G. spinosum in China, and its identification will assist the development of strategies to counteract the disease.

Chromosome-level genome assemblies of Cutaneotrichosporon spp. (Trichosporonales, Basidiomycota) reveal imbalanced evolution between nucleotide sequences and chromosome synteny

BackgroundSince DNA information was first used in taxonomy, barcode sequences such as the internal transcribed spacer (ITS) region have greatly aided fungal identification; however, a barcode sequence alone is often insufficient. Thus, multi-gene- or whole-genome-based methods were developed. We previously isolated Basidiomycota yeasts classified in the Trichosporonales. Some strains were described as Cutaneotrichosporon cavernicola and C. spelunceum, whereas strain HIS471 remained unidentified. We analysed the genomes of these strains to elucidate their taxonomic relationship and genetic diversity.ResultsThe long-read-based assembly resulted in chromosome-level draft genomes consisting of seven chromosomes and one mitochondrial genome. The genome of strain HIS471 has more than ten chromosome inversions or translocations compared to the type strain of C. cavernicola despite sharing identical ITS barcode sequences and displaying an average nucleotide identity (ANI) above 93%. Also, the chromosome synteny between C. cavernicola and the related species, C. spelunceum, showed significant rearrangements, whereas the ITS sequence identity exceeds 98.6% and the ANI is approximately 82%. Our results indicate that the relative evolutionary rates of barcode sequences, whole-genome nucleotide sequences, and chromosome synteny in Cutaneotrichosporon significantly differ from those in the model yeast Saccharomyces.ConclusionsOur results revealed that the relative evolutionary rates of nucleotide sequences and chromosome synteny are different among fungal clades, likely because different clades have diverse mutation/repair rates and distinct selection pressures on their genomic sequences and syntenic structures. Because diverse syntenic structures can be a barrier to meiotic recombination and may lead to speciation, the non-linear relationships between nucleotide and synteny diversification indicate that sequence-level distances at the barcode or whole-genome level are not sufficient for delineating species boundaries.

First Report of Heterodera zeae Koshy, Swarup & Sethi, 1971 (corn cyst Nematode) Infecting Corn (Zea mays) in Spain.

Heterodera zeae Koshy, Swarup & Sethi, 1971 (corn cyst nematode) is an important disease of corn in several areas of the world, including India, Nepal, Pakistan, Egypt, USA, Greece and Portugal (Subbotin et al., 2010). It is a sedentary semi-endoparasite feeding on corn roots and other Poaceae plants and has been associated with significant yield losses in corn (Subbotin et al., 2010). During autumn 2022 a plant-parasitic nematode survey performed in corn at central-western area of Spain (Talavera de la Reina, Toledo), revealed a commercial field with stunted plants. Nematodes were extracted from soil by centrifugal-flotation method (Coolen, 1979). Corn roots inspection detected infections by immature and mature cysts, and soil revealed also mature live cysts and second-stage juveniles (J2s) with a population density of 1010 eggs and J2s/500 cm3 soil (including eggs from cysts). J2s and cysts were processed to pure glycerine using De Grisse's (1969) method. DNA was isolated from single live fresh J2s specimens for amplifying and sequencing of cytochrome c oxidase subunit II (COII) mitochondrial region using the primer pair species-specific H.Gly-COIIF_inFOR/P116F-1R (Riepsamen et al., 2011); D2 and D3 expansion domains of the 28S rRNA were amplified using the D2A/D3B primers (De Ley et al. 1999); internal transcribed spacer (ITS) region using primers TW81/AB28 (Subbotin et al., 2001); and cytochrome c oxidase subunit 1 (COI) gene was amplified using the primers JB3/JB5 (Bowles et al., 1992). Brown cysts were lemon-shaped with a protruding vulval cone with fenestra ambifenestrate, bullae prominent below underbridge and characteristically arranged in finger-like bullae (Fig. 1). J2 with slightly offset lip region (3-5 annuli), stylet strong with rounded stylet knobs, lateral field with four lines, and tail short and tapering conically. Measurements of cysts (n=10) included body length 559 (432-688) µm, body width 450 (340-522) µm, fenestral length 40 (36-43) µm, semifenestral width 19 (17-21) µm, and vulval slit 40 (35-44) µm. J2 measurements (n=10) included body length 477 (420-536) µm, stylet length 21 (20-22) µm, tail length 51 (47-56) µm, and tail hyaline region 23 (20-26) µm. Morphology and morphometrics of cysts and J2, fit with original description and others from several countries (Subbotin et al., 2010). Two J2s individuals were sequenced for COII region (OQ509010-OQ509011) showing 97.1-98.1% similarity with H. zeae from USA (HM462012). Six almost identical 28S rRNA sequences from J2s (OQ449649-OQ449654) were 99.2-99.4% similar to 28S rRNA sequences of H. zeae from Greece, Afghanistan and USA (GU145612, JN583885, DQ328695). Four identical ITS DNA fragments from J2s (OQ449655-OQ449658) were 97.0-97.8% similar to ITS sequences of H. zeae from Greece, and China (GU145616, MW785771, OP692770). Finally, six COI sequences of 400 bp obtained for J2s (OQ449699-OQ449704) were under 87% similarity to several COI sequences of Heterodera spp. in NCBI, being a new molecular barcoding for identifying this species. On the basis of these results, the cyst nematodes isolated from the corn plants from the central-western area of Spain (Talavera de la Reina, Toledo) were confirmed as H. zeae and up to our knowledge it is the first report in Spain. This is a well-known pest of corn, causing important losses in this crop (Subbotin et al., 2010) and it was previously regulated as a quarantine nematode in the Mediterranean region (EPPO).

Diddensiella parasantjacobensis f.a., sp. nov., a yeast species from forest habitats.

Six conspecific yeast strains, representing an undescribed species, were isolated from rotten wood collected in different locations in Hungary and Germany and an additional one from fungal fruiting body in Taiwan. The seven strains share identical nucleotide sequences in the D1/D2 domain of the nuclear large subunit (LSU) rRNA gene. The Hungarian and Taiwanese isolates share identical internal transcribed spacer (ITS) sequences as well, while the two German isolates differ from them merely by three substitutions and four indels in this region. The investigated strains are very closely related to Diddensiella santjacobensis. Along their LSU D1/D2 domain they differ only by one substitution from the type strain of D. santjacobensis. However, in the ITS region of Hungarian and Taiwanese strains we detected 3.5 % divergence (nine substitutions and nine indels) between the undescribed species and D. santjacobensis, while the German strains differed by 13 substitutions and nine indels from D. santjacobensis. This ITS sequence divergence has raised the possibility that the strains investigated in this study may represent a different species from D. santjacobensis. This hypothesis was supported by comparisons of partial translation elongation factor 1-α (EF-1α) and cytochrome oxidase II (COX II) gene sequences. While no difference and 1-2 substitutions among the partial EF-1α and COX II gene sequences of the strains of the undescribed species, respectively, were detected; the undescribed species differ by about 4 % (36 substitutions) and 10 % (50-51 substitutions) from D. santjacobensis in these regions. Parsimony network analysis of the partial COX II gene sequences also separated the investigated strains from the type strain of D. santjacobensis. In this paper we propose Diddensiella parasantjacobensis f.a., sp. nov. (holotype: NCAIM Y.02121; isotypes: CBS 17819, DSM 114156) to accommodate the above-noted strains.

Morphotypes of Ciborinia camelliae Kohn infecting camellias in Italy

Ciborinia camelliae Kohn is the causal agent of camellia flower blight. The pathogen infects only flowers of camellias, causing serious damage to the plant. Seventy-one strains were collected from six Italian regions and were characterized at the phenotypic and genetic level. Morphotypes were identified based on their phenotypic differences in culture media. The Italian population consisted of eleven morphotypes. Internal transcribed spacer (ITS) regions of twenty-two isolates belonging to the different morphotypes were sequenced. All morphotypes have identical ITS sequences. The closest match of the ITS with the strain ICMP 19812 of Ciborinia camelliae from New Zealand (Massey University Arboretum, Palmerston North, 100% sequence identity), and the morphological features confirmed the presence of a variable population of C. camelliae in six different Italian regions.

Vegetative Growth and Molecular Identification of <i>Fusarium equiseti</i> Isolated from Wilt Disease of <i>Centella asiatica</i> L. in Bangladesh

Centella asiatica (L.) is commonly known as Thankuni plant and has ethnobotanical importance in Bangladesh. Present experiment was conceded to investigate the wilt disease of C. asiatica, vegetative growth and molecular characterization of pathogenic fungi. Pathogenic fungus, Fusarium equiseti was identified as a causal agent of wilt disease in C. asiatica. The effect of culture media on the mycelial growth of F. equiseti showed the highest (89.25 mm) on potato dextrose agar (PDA) medium followed by carrot agar (CA) medium and the lowest growth (40.25 mm) was measured in HA medium. The optimal temperature and pH for mycelial growth of F. equiseti were 30°C and 7, respectively. The genetic variation of the selected species of fungi, the internal transcribed spacer (ITS) region was amplified using ITS4 and ITS5 primers and sequenced. The PCR product of the ITS region of F. equiseti was 535 bp. Phylogenetic tree of thirty-seven strains of Fusarium sp. based on the nucleotide sequences of the ITS region using the neighbor-joining method with 1000 bootstrapping indicated that 98% - 100% identity with MN886590.1 JUF0046 (F. equiseti). ITS sequences are generally constant, or show little variation within species, but vary between species in a genus. The ITS region is relatively short and can be easily amplified by PCR using universal single primer pairs. Genetic distance exhibited high level of similarity with identical ITS sequences. To date, no published research articles are found on the molecular identification of F. equiseti, the causal agent of fusarium wilt disease of C. asiatica in Bangladesh.

Substantial intraspecific genome size variation in golden-brown algae and its phenotypic consequences.

While nuclear DNA content variation and its phenotypic consequences have been well described for animals, vascular plants and macroalgae, much less about this topic is known regarding unicellular algae and protists in general. The dearth of data is especially pronounced when it comes to intraspecific genome size variation. This study attempts to investigate the extent of intraspecific variability in genome size and its adaptive consequences in a microalgal species. Propidium iodide flow cytometry was used to estimate the absolute genome size of 131 strains (isolates) of the golden-brown alga Synura petersenii (Chrysophyceae, Stramenopiles), identified by identical internal transcribed spacer (ITS) rDNA barcodes. Cell size, growth rate and genomic GC content were further assessed on a sub-set of strains. Geographic location of 67 sampling sites across the Northern hemisphere was used to extract climatic database data and to evaluate the ecogeographical distribution of genome size diversity. Genome size ranged continuously from 0.97 to 2.02 pg of DNA across the investigated strains. The genome size was positively associated with cell size and negatively associated with growth rate. Bioclim variables were not correlated with genome size variation. No clear trends in the geographical distribution of strains of a particular genome size were detected, and strains of different genome size occasionally coexisted at the same locality. Genomic GC content was significantly associated only with genome size via a quadratic relationship. Genome size variability in S. petersenii was probably triggered by an evolutionary mechanism operating via gradual changes in genome size accompanied by changes in genomic GC content, such as, for example, proliferation of transposable elements. The variation was reflected in cell size and relative growth rate, possibly with adaptive consequences.

Use of Internal Transcribed Spacer Sequence Polymorphisms as a Method for Trichomonas vaginalis Genotyping.

Trichomonas vaginalis is the most common non-viral, sexually transmitted pathogen with a worldwide distribution. The aim of the present study was to design a new genotyping tool for T. vaginalis isolates using internal transcribed spacer (ITS) sequences. First, a total of 20 cryopreserved T. vaginalis isolates were thawed and genomic DNA was isolated from fresh cultures. A polymerase chain reaction (PCR) was performed to amplify the ITS regions and the amplicons were sequenced. These sequences were aligned with others from Genbank and polymorphisms were detected. At last, each ITS sequence was given a different sequence type. More than 99% homology was observed among sequences. Of 20 isolates, five had identical ITS sequence to reference (L29561) defined as ITST1. Moreover, 13 had A58 deletion (ITST10), one had C203T mutation (ITST2), and one had both A58 deletion and C203T mutation (ITST11). ITS typing of T. vaginalis sequences on Genbank revealed a total of 11 ITS types with the predominance of ITST1 (44.4%) globally. ITS typing seems to be an applicable and useful tool for a better understanding of molecular epidemiology as well as for the dissemination of T. vaginalis clones.

Genetic diversity of Bulgarian representatives of genus Carduus L. (Asteraceae) as revealed by variability in sequences of internal transcribed spacers region

ABSTRACTThe biodiversity of genus Carduus in Bulgaria is grossly under-studied with modern methods, which leads to unclear status of species and hampers the assessment of their habitats and conservation status. In this study, we used the variability of internal transcribed spacers (ITS) to investigate the biodiversity of Carduus species collected from different floristic regions of Bulgaria. Thirty-three samples were processed. Among the studied species, C. acanthoides exhibited the highest ITS variability (eight single nucleotide polymorphisms were found). High ITS variability was also found in C. crispus and C. hamulosus, demonstrating that some of the local Carduus species possesses unique genetic diversity, which can serve as source for future divergence of new forms and subspecies. For each species, unique nucleotides suitable as molecular taxonomy markers were identified. However, C. nutans and C. thoermeri displayed completely identical ITS sequences, which is in agreement with all ITS sequences of these species collected elsewhere in the world and deposited in the NCBI database. After careful analyses of both molecular and morphological data, we propose to restore C. nutans and C. thoermeri as one species with two subspecies. Namely, Carduus nutans subsp. nutans and Carduus nutans subsp. thoermeri. We recommend diameter of capitulum, length of peduncle, width of peduncle and width of bract as diagnostic features of taxonomic significance for distinguishing the two subspecies.

Genetic Bottlenecks for Two Populations of Ceratocystis fimbriata on Sweet Potato and Pomegranate in China.

Chinese isolates of Ceratocystis fimbriata from sweet potato (Ipomoea batatas) and pomegranate (Punica granatum) were genetically compared with a worldwide collection of isolates from a variety of hosts. Isolates from black-rotted storage roots of sweet potato in China, Japan, Australasia, and the United States had identical internal transcribed spacer (ITS) ribosomal DNA (rDNA) sequences and only minor variation in microsatellite alleles. Sequences of their mating type genes were most similar to those of isolates from various hosts in Ecuador, a center of diversity for sweet potato. Isolates from Colocasia esculenta (taro) and pomegranate from Yunnan and Sichuan had only one ITS rDNA sequence (haplotype ITS5). This haplotype, sequences of mating type genes, and microsatellite alleles linked these isolates to isolates from Eucalyptus stumps in South China and diseased Eucalyptus trees in Brazil, supporting the hypothesis that the pomegranate population originated from Brazil via cuttings of Eucalyptus. Isolates from sweet potato and pomegranate in China were interfertile with tester strains of C. fimbriata, confirming that the causes of the two epidemics in China belong to a single biological species. However, other isolates from Eucalyptus stumps were intersterile with the tester strains and had ITS rDNA sequences typical of the Asian species, C. cercfabiensis.

Cyst-theca relationship and phylogenetic positions of Scrippsiella plana sp. nov. and S. spinifera (Peridiniales, Dinophyceae)

Species belonging to the dinophyte genus Scrippsiella are frequently reported in marine waters, but information on their distribution in brackish environments is limited. Here we describe a new species, S. plana, through incubation of non-calcified cysts from sediments collected in the South China Sea and Caspian Sea. The vegetative cells consist of a conical epitheca and a rounded hypotheca with the plate formula of Po, X, 4′, 3a, 7′′, 5C+t, 5S, 5′′′, 2′′′′. It differs from other Scrippsiella species by its flattened body in dorsoventral view and a small first anterior intercalary (1a) plate (half the size of plate 3a). Scrippsiella plana strains from the South China Sea and Caspian Sea share identical internal transcribed spacer (ITS) sequences, and show phenotypic plasticity and local adaptation in growth rate at various salinities, consistent with the environments in which they originated. In addition, two strains of S. spinifera were obtained by incubating ellipsoid cysts with calcareous spines from sediments collected along the Turkish and Hawaiian coast. They also share identical ITS sequences and differ from Duboscquodinium collinii (a parasite of tintinnids) only at two base pair positions (in the ITS2 region). Molecular phylogeny based on ITS and large subunit ribosomal DNA (LSU rDNA) sequences revealed that S. plana was nested within the Calciodinellum (CAL) clade and S. spinifera within the S. trochoidea (STR) clade. The phylogenetic position of ‘Peridinium’ wisconsinense is reported for the first time, which supports multiple transitions of the Peridiniales to freshwater.

The infrageneric taxonomy ofChaerophyllum(Apiaceae) revisited: new evidence from nuclear ribosomal DNA ITS sequences and fruit anatomy

Evolutionary relationships among 65 Chaerophyllum spp. were inferred from nuclear ribosomal DNA internal transcribed spacer (ITS) sequence variation. Thirty-one species, represented by 158 mericarp samples, were analysed for fruit anatomical character variation, employing phylogenetic and phenetic methods to explore their congruence with infrageneric divisions based on molecular data. Phylogenetic trees inferred from molecular data using maximum likelihood (ML) and Bayesian inference (BI) methods corroborated the division of the genus into four sections: Chaerophyllum, Dasypetalon, Physocaulis and Chrysocarpum. From among the newly sequenced species, the Greek endemic C. heldreichii was grouped with section Chaerophyllum, whereas the highly variable Asian C. reflexum–C. villosum complex formed an early-branching paraphyletic assemblage in section Chrysocarpum. The recently described C. karsianum has an identical ITS sequence to C. bulbosum, whereas C. aksekiense was clearly separated from the morphologically similar C. macrospermum. Our study confirmed the postulated synonymy of several species on the basis of morphology, but also demonstrated distant relationships between some morphologically similar species. With the exception of the monotypic section Physocaulis, we were unable to find carpological traits matching sectional divisions. We hypothesize that fruit characters evolved rapidly as a result of diversification of members of the genus in different habitats. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178, 298–313.

Occurrence and ITS diversity of wood‐associatedBursaphelenchusnematodes in Scots pine forests in Switzerland

The quarantine pathogenBursaphelenchus xylophilus(pine wood nematode,PWN) represents a serious threat forPinusspecies in Europe. To exclude its presence in Switzerland, in 2010 and 2011 a countrywide survey was conducted in 102Pinus sylvestrisstands, chosen according to whether they contained dying or dead trees or were located in areas at risk ofPWNintroduction. In total, 285 trees (1–5 per site) were sampled. Nematodes were extracted from wood chips using a standard procedure, and identified to species by internal transcribed spacer (ITS) sequencing.Bursaphelenchusspecies were present in 34% of the trees, but noB. xylophiluswas identified, i.e.PWNis still not present in Switzerland. The nematodes found belonged to seven different species, withB. vallesianusthe most frequent species, followed byB. sexdentati,B. mucronatus kolymensisandB. eggersi. Three other species (B. borealis,B. pinophilus,B. poligraphi) were each only present in one or two trees. Three groups of sequences could not be assigned to a species because of the lack of matching reference sequences. The species composition found in Switzerland suggests co‐existence of southern and central EuropeanBursaphelenchusspecies. Intraspecific ITS variability differed considerably among the four most common species.Bursaphelenchus eggersi,B. mucronatus kolymensisandB. sexdentatihad several variable sites in the ITS region, resulting in multiple ITS genotypes in each species. In contrast, all 99B. vallesianusisolates had an identical ITS region. This could indicate a founder effect, and possibly thatB. vallesianusis not native to the Alpine region.

First Report of Foliar Blight Caused by Phytophthora capsici on Citrus reticulata Blanco cv. Nian Ju in Guangdong, China.

Citrus reticulata Blanco cv. Nian Ju, an important ornamental plant, is traditionally displayed during the Chinese Spring Festival because its golden fruits are a symbol of auspiciousness. In the spring of 2012, foliar blight was observed on 10 to 30% of the Nian Ju plants at four nurseries in Yangjiang, Guangdong Province, China. Initial symptoms appeared as brown to black foliar lesions, followed by expansion of spots into blight. Some young branches also had necrosis. During frequent rainfall and prolonged wet periods at 22°C to 30°C, white and dense mycelia and sporangia were observed on the infected seedlings. To isolate the causal organism, leaves and stems were cut into sections. Each section included some partial lesion and adjacent asymptomatic tissues. They were surface-disinfested in 1% sodium hypochlorite for 60 s, rinsed three times with sterile water, and placed on V8 juice agar (V8A) at 25°C. After 3 days, 10 isolates were obtained and purified by single-zoospore method. These isolates were identified to species level by sequencing the rRNA internal transcribed spacer (ITS) region. Four representative isolates had an identical ITS sequence (GenBank Accession No. KF750568), which had 99% homology with Phytophthora capsici sequences in GenBank. In addition, all recovered isolates were identical in morphological characteristics. They produced caducous, papillate, and ovoid to ellipsoid sporangia (Length × width = 46.2 ± 7.7 × 23.6 ± 11.3 μm), often with a tapered base. The average length of pedicels was 33.3 ± 4.5 μm. All isolates are A2 mating type. They produced gametangia when paired with an A1 tester of P. capsici isolated from pepper on V8A. Plerotic oospores were 25.3 ± 2.1 μm in diameter. Amphigynous antheridia were 13.6 ± 2.8 μm long and 11.2 ± 0.9 μm wide. Oogonia were 27.4 ± 3.2 μm in diameter. To determine the pathogenicity, three 3-year-old potted C. reticulata cv. Nian Ju plants were sprayed with 20 ml of zoospore suspension from one representative isolate at 105 per ml. Two control plants were sprayed with 20 ml distilled water. All plants were then maintained at 90% relative humidity at 25°C with a 12-h photoperiod. Symptoms similar to those observed in the nurseries developed on all inoculated plants but not on any control plants after 10 days. The pathogenicity test was repeated once and similar results were obtained. P. capsici was recovered from all inoculated plants and resultant isolates had identical morphology to that of the isolates used for inoculation. P. capsici has a relatively broad host range including pumpkins, cucumbers, peppers, beans, squashes, and spinach (1,2). To our knowledge, this is the first report of foliar blight of C. reticulata cv. Nian Ju caused by P. capsici. This study indicates that P. capsici is potentially an important pathogen of C. reticulata cv. Nian Ju plants and further investigations into its epidemiology and development of site-specific integrated management programs for this new disease are warranted.

Wickerhamomyces arborarius f.a., sp. nov., an ascomycetous yeast species found in arboreal habitats on three different continents

Five strains representing a novel yeast species belonging to the genus Wickerhamomyces were independently isolated from Ecuador, Taiwan and the USA. One strain (CLQCA 10-161(T)) was isolated from the white flower of an unidentified plant species collected in the Maquipucuna cloud forest reserve, near Quito, in Ecuador. A second strain (GY7L12) was isolated from the leaf of a Chinese sumac or nutgall tree (Rhus chinensis 'roxburghiana') collected in the Taoyuan mountain area, Kachsiung, in Taiwan. Three additional strains (A543, A546 and A563) were isolated from two species of wood-boring beetle (Xyleborus glabratus and Xyleborinus saxeseni) collected near Clyo, Georgia, USA. Analysis of the D1/D2 domains of the LSU rRNA gene indicated that the novel species belongs to the genus Wickerhamomyces, and is most closely related to Wickerhamomyces sydowiorum, an insect-associated species predominantly found in South Africa. The North American and Taiwanese strains have identical internal transcribed spacer (ITS) sequences and can be distinguished from the Ecuadorian strain based on a single nucleotide substitution in the ITS1 region. The species name of Wickerhamomyces arborarius f.a., sp. nov. is proposed to accommodate these strains, with CLQCA 10-161(T) ( = CBS 12941(T) = NCYC 3743(T)) designated the type strain.

Morphology and phylogeny of Scrippsiella enormis sp. nov. and S. cf. spinifera (Peridiniales, Dinophyceae) from the China Sea

Gu H., Luo Z., Liu T. and Lan D. 2013. Morphology and phylogeny of Scrippsiella enormis sp. nov. and S. cf. spinifera (Peridiniales, Dinophyceae) from the China Sea. Phycologia 52: 182–190. DOI: 10.2216/12-036.1The genus Scrippsiella contains approximately 20 species that are widespread in coastal and oceanic areas. Classification of Scrippsiella traditionally relied on cyst morphology because the plate pattern was rather conserved. A new species, S. enormis sp. nov. was obtained by incubating a noncalcified cyst from sediments collected in the East China Sea. The vegetative cells consisted of a conical-convex epitheca and a round hypotheca with the plate formula of po, x, 4′, 3a, 7″, 6c (5c+t), 5s, 5‴, 2″″. It differed from other Scrippsiella species by possessing an asymmetrical 1′ and generating noncalcareous, spherical cysts with paratabulation. Phylogenetic analyses based on internal transcribed spacer (ITS) and 5.8S rDNA sequences revealed that S. enormis was nested within the Calciodinellum clade. In addition, two strains of S. cf. spinifera (strains SSFC02, SSFC03) were obtained by incubating calcareous cysts from sediments collected in the South China Sea. They shared identical ITS sequence and formed a sister clade of the S. trochoidea species complex, suggesting little phylogenetic significance of antapical spines in Scrippsiella.

First Report of Flower Anthracnose Caused by Colletotrichum karstii in White Phalaenopsis Orchids in the United States.

In October 2010, a Colletotrichum species was isolated from white Phalaenopsis flowers growing in a greenhouse in San Francisco, CA. This Phalaenopsis is a common commercial orchid hybrid generated mostly likely from Phalaenopsis amabilis and P. aphrodite. The white petals showed anthracnose-like lesions where necrotic tissue is surrounded by a ring of green tissue. The green halo tissues around the necrotic tissue contain functional chloroplasts. One-centimeter disks were cut around the necrotic sites and surface-sterilized with 95% ethanol and 0.6% sodium hypochlorite. The disks were placed on potato dextrose agar (PDA) medium to establish cultures. Pure cultures were obtained by subculturing hyphal tips onto fresh PDA plates. The generated colonies had white aerial mycelia and orange conidial mass. The color of the reverse colony varies between colorless and pale orange. Microscopic observations identified the conidia as cylindrical, straight, and rounded at both ends. In addition, the conidia were approximately 15.0 to 18.0 μm long and 5.0 to 6.5 μm in diameter. These observed morphological features suggested that these isolates possessed the same characteristics as previously described for Colletotrichum karstii, a species considered as part of the C. boninense species complex (1). Four putative independent Colletotrichum isolates were recovered (DED9596, DED9597, DED9598, and DED9599). To confirm the Colletotrichum isolates as the causative pathogen, healthy white Phalaenopsis flowers (five total) in a whole plant were sprayed with a conidial suspension (approximately 1.2 × 106 conidia/ml) of the isolates and incubated at 20°C and 100% relative humidity with cycles of 16 h light and 8 h of darkness. Approximately 1 ml of conidial suspension solution was used for each flower. The plants were watered regularly and flowers were sprayed with sterile double-distilled water daily. As negative controls, five flowers in a whole plant were sprayed with water. Fifteen to twenty days after inoculation, lesions started to form on the petals sprayed with the putative Colletotrichum isolates. All controls remained healthy. The Colletotrichum-inoculated flowers remained alive and did not die as a result of the infection. This same experiment was repeated and the same results were obtained. DNA was extracted from the necrotic regions of the petals infected by the pure cultures of the four isolates and used to sequence the 18S rRNA ITS (internal transcribed spacer) region. All four isolates gave identical ITS sequences. Analysis of the obtained representative sequences (GenBank Accession No. JQ277352) suggested that the isolated pathogen as C. karstii. Using the published ITS data for the C. boninense species complex (1), a phylogenetic tree was generated via the maximum likelihood method. This created tree places the isolates in the same group as C. karstii. This type of C. karstii infection in Phalaenopsis orchid petals was not documented in the U.S. before, although it has been reported in China and Thailand (2). To our knowledge, this is the first report of infection and green island formation caused by C. karstii on orchid flower in the United States.

Species pattern and phylogenetic relationships ofTrichodermastrains in rice fields of Southern Caspian Sea, Iran

As a first step of a project aimed at the identification of potential biocontrol agents of Rhizoctonia solani, the rice sheath blight fungus, we surveyed the biodiversity of the genus Trichoderma based on sequence of the internal transcribed spacer (ITS) 1 and 2 of the ribosomal RNA gene cluster in paddy fields in Mazandaran province, Northern Iran. Amongst the six obtained species of Trichoderma, T. harzianum and T. virens proved to be the most frequent species in this habitat. Sequence alignment and phylogenetic analysis revealed that the T. harzianum isolates can be divided into 14 different ITS genotypes clustering in four groups. Our results are in agreement with previous molecular studies, which also revealed that T. harzianum is a complex species comprising more or less different ITS genotypes. T. virens was not as diverse as T. harzianum and three different genotypes were distinguished which constituted only one cluster. All T. atroviride and T. hamatum strains had identical ITS sequences.