ITS Dataset Research Articles

Hypomyces pseudolactifluorum sp. nov. (Hypocreales: Hypocreaceae) on Russula sp. from Yunnan, PR China.

BackgroundHypomyces is a large genus of fungicolous fungi, parasitising the fruiting bodies of Agaricales, Boletales, Helotiales, Pezizales and Polyporales. Hypomyces currently comprises of 147 species widely distributed in Australia, China, France, Germany, Italy, Japan, North America, Sri Lanka, Thailand and UK. Amongst them, 28 species have been recorded in China.New informationHypomyces pseudolactifluorum sp. nov., growing on the fruiting bodies of Russula sp. in subsect. Lactarioideae and collected from Yunnan, China, is described with illustrations and molecular phylogenetic data (combined ITS, LSU, TEF1-α and RPB2 sequence dataset). The new species is characterised by semi-immersed to immersed perithecia and fusiform, apiculate and verrucose ascospores. We also review the species diversity of the genus Hypomyces in China.

Comparative genome analysis proposes three new Aureobasidium species isolated from grape juice.

Aureobasidium pullulans is the most abundant and ubiquitous species within the genus and is also considered a core component of the grape juice microflora. So far, a small number of other Aureobasidium species have been reported, that in contrast to A. pullulans, appear far more constrained to specific habitats. It is unknown whether grape juice is a reservoir of novel Aureobasidium species, overlooked in the course of conventional morphological and meta-barcoding analyses. In this study, eight isolates from grape juice taxonomically classified as Aureobasidium through ITS sequencing were subjected to whole-genome phylogenetic, synteny and nucleotide identity analyses, which revealed three isolates to likely represent newly discovered Aureobasidium species. Analyses of ITS and metagenomic sequencing datasets show that these species can be present in grape juice samples from different locations and vintages. Functional annotation revealed the Aureobasidium isolates possess the genetic potential to support growth on the surface of plants and grapes. However, the loss of several genes associated with tolerance to diverse environmental stresses suggest a more constrained ecological range than A. pullulans.

A new genus of Bambusicolaceae (Pleosporales) on Corylus avellana (Fagales) from Italy.

BackgroundIn this study, we introduce Corylicola gen. nov. in the family of Bambusicolaceae (Pleosporales), to accommodate Corylicola italica sp. nov. The new species was isolated from dead branches of Corylus avellana (common hazel) in Italy. The discovery of this new genus with both sexual and asexual characters will contribute to expand the knowledge and taxonomic framework of Bambusicolaceae.New informationCorylicola gen. nov. has similar morphological characters compared to other genera of Bambusicolaceae. These are solitary, scattered, globose to subglobose and ostiolate ascomata; anastomosing and branching pseudoparaphyses; cylindrical asci with a well-developed ocular chamber and short furcate pedicel; and single-septate ascospores. The coelomycetous asexual morph of Corylicola has holoblastic, phialidic conidiogenous cells and light brown conidia analogous to other members in the family. Corylicola differs from the other genera of Bambusicolaceae in having yellowish-brown ascospore masses at the top of the ascomatal neck. Detailed morphological illustrations with comprehensive descriptions for the new taxa are provided, as well as a key to the genera of Bambusicolaceae. Maximum Likelihood analysis and Bayesian Inference of a combined SSU, LSU, ITS, RPB2 and TEF1 sequence dataset confirms the placement of this genus as a distinct lineage in Bambusicolaceae.

<p><strong><em>Lepiota cholistanensis </em></strong><strong>a new species of <em>Lepiota</em> (Agaricaceae: Basidiomycota) from Cholistan desert, Pakistan</strong></p>

Lepiota cholistanensis was collected from an unusual locality of Cholistan desert, an unexplored area of Pakistan. This species is characterized by having small basidiomata provided with slightly uplifted brown squamules on pileus surface. Stipe color changes to brown on handling or bruising. Compact hymeniderm pileus covering containing variable shaped pileus elements varies from sub-globose to broadly clavate, long and narrowly clavate, and sphaeropedunculate having cylindrical ante-terminal elements and cheilocystidia are cylindrical to narrowly clavate. Basidiospores are sub-globose, broadly ellipsoid to vaguely oval shaped, olivaceous green, binucleate and non-dextrinoid. The phylogenetic analyses were performed using ITS and LSU datasets. Our newly described taxon grouped well in section Cristatae during the phylogenetic analyses.

<p><strong><em>Triseptata sexualis </em></strong><strong>gen. et sp. nov. in <em>Latoruaceae</em> (Pleosporales)</strong></p>

A survey of lignicolous terrestrial ascomycetes conducted in Thailand yielded a number of novel species. In this paper, we report on a terrestrial collection of a taxon from dead branches of an unidentified plant. Triseptata gen. et sp. nov. is characterized by immersed, uni- to multi-loculate ascomata, filamentous pseudoparaphyses, bitunicate, fissitunicate, cylindrical-clavate asci and 3-septate, light brown spores, with asymmetrical ends, in its sexual form. In culture, it produced hyphomycetous, globose to subglobose, multi-septate and darkly pigmented conidia-like structures. Phylogenetic analysis of a combined LSU, ITS and SSU dataset shows Triseptata to be a well-separated lineage from all genera in Latoruaceae. Based on multigene phylogeny, Triseptata gen. nov. is introduced to accommodate a single new species Triseptata sexualis and placed in Latoruaceae. Illustrations, descriptions and notes are provided for the new genus and species.

Patellariopsidaceae Fam. Nov. With Sexual-Asexual Connection and a New Host Record for Cheirospora botryospora (Vibrisseaceae, Ascomycota)

Helotiales is a polyphyletic order of Ascomycetes. The paucity of relevant molecular data and unclear connections of sexual and asexual morphs present challenges in resolving taxa within this order. In the present study, Patellariopsidaceae fam. nov., the asexual morph of Patellariopsis atrovinosa, and a new record of Cheirospora botryospora (Vibrisseaceae) on Fagus sylvatica (Fagaceae) from Italy are discussed based on morphology and molecular phylogeny. Phylogenetic analyses based on a combined sequence dataset of LSU and ITS were used to infer the phylogenetic relationships within the Helotiales. The results of this research provide a solid base to the taxonomy and phylogeny of Helotiales.

First Report of the Sexual Morph of Pseudofusicoccum adansoniae Pavlic, T.I.Burgess & M.J.Wingf. on Para Rubber

Pseudofusicoccum adansoniae Pavlic, T.I.Burgess & M.J.Wingf. and P. ardesiacum Pavlic, T.I.Burgess & M.J.Wingf. were collected from branches and twigs of Hevea brasiliensis Muell. Arg. in Phayao Province, northern Thailand. Pseudofusicoccum Mohali, Slippers & M.J.Wingf. is known only by its asexual morph. Here, we report the sexual morph of P. adansoniae based on phylogenetic analyses of a combined ITS, LSU, TEF1 and β-tubulin dataset. The sexual morph is characterized by immersed, uniloculate ascomata, cylindric-clavate asci with a long pedicel, a well-developed ocular chamber and short clavate, hyaline, aseptate ascospores, surrounded by a mucilaginous sheath. Descriptions, illustrations and molecular data are provided for the taxa.

<p><strong>Species Delimitation In <em>Rhabdosciadium </em>(Apiaceae): Morphological and Molecular</strong></p>

Rhabdosciadium is a distinct and small Apiaceae genus represented by only 8 species worldwide, 5 of which are distributed in Turkey and 3 occur in Iran. They all are narrow endemic, rare mountain species. The genus is characterized by single-fruited umbellules, linear-cylindrical fruits, parennial, glabrous, and junciform habit, reduced cauline leaves, and fibrous collar at the base of the stem. Till present time, there has been no detailed information available on molecular phylogeny and genetic structure of these species in the country. Therefore, the present study was conducted with the aim to investigate species delimitation by both morphological and molecular data and to reveal genetic diversity and population structure in these three Rhabdosciadium species. For this study, 98 randomly collected plants from 15 geographical populations in Rhabdosciadium species were used. We encountered extensive within species genetic and morphological diversity. ISSR molecular markers could delimit the studied species. STRUCTURE analysis revealed the occurrence gene flow between these species. The Mantel test showed correlation between genetic distance and geographical distance of the populations studied. Phylogenetic tree was constructed based on ITS data set which separated out-groups from the studied species. Genetic affinity of the studied species have been discussed.

Four New Members of Foliicolous Green Algae Within the Watanabea Clade (Trebouxiophyceae, Chlorophyta) from China

Members of the Watanabea clade of Trebouxiophyceae are genetically diverse and widely distributed in all kinds of habitats, especially in most terrestrial habitats. Ten new strains of terrestrial algae isolated from the tropical rainforest in China, and four published strains were investigated in this study. Morphological observation and molecular phylogenetic analyses based on the 18S, ITS, rbcL, and tufA genes were used to identify the new strains. Four previously described species were reinvestigated to supplement molecular data and autospores' morphological photographs. The phylogenetic analyses based on 18S only, the concatenated dataset of 18S and ITS, as well as the concatenated dataset of rbcL and tufA, showed the same phylogenetic positions and relationships of these new strains. According to the phylogenetic analysis and morphological comparisons results, we described these 10 strains as four new members within the Watanabea clade, Polulichloris yunnanensis sp. nov., Polulichloris ovale sp. nov., Massjukichlorella orientale sp. nov., and Massjukichlorella minus sp. nov., and two known species, Massjukichlorella epiphytica, and Mysteriochloris nanningensis. Additionally, we provide strong evidence proving that Phyllosiphon, Mysteriochloris, Polulichloris, and Desertella all reproduce through unequal sized autospores.

Two new species of Fuscoporia (Hymenochaetales, Basidiomycota) from southern China based on morphological characters and molecular evidence.

Fuscoporia (Hymenochaetaceae) is characterized by annual to perennial, resupinate to pileate basidiocarps, a dimitic hyphal system, presence of hymenial setae, and hyaline, thin-walled, smooth basidiospores. Phylogenetic analyses based on the nLSU and a combined ITS, nLSU and RPB2 datasets of 18 species of Fuscoporia revealed two new lineages that are equated to two new species; Fuscoporia ramulicolasp. nov. grouped together with F. ferrea, F. punctatiformis, F. subferrea and F. yunnanensis with a strong support; Fuscoporia acutimarginatasp. nov. formed a strongly supported lineage distinct from other species. The individual morphological characters of the new species and their related species are discussed. A key to Chinese species of Fuscoporia is provided.

Phylogeography and population dynamics of an endemic oak (Quercus fabri Hance) in subtropical China revealed by molecular data and ecological niche modeling

High numbers of endemic plants exist in subtropical China, but there have been few investigations of the phylogeography and dynamic history for endemic tree species in this region. In this study, we explored the phylogeographic pattern of Quercus fabri, an endemic oak species in subtropical China, to assess the effects of past geographical and climatic changes on the evolutionary history of this deciduous species using three chloroplast DNA (cpDNA) fragments and the internal transcribed spacer region (ITS) and ecological niche modeling (ENM). The cpDNA fragments differentiated three phylogeographical groups among Q. fabri populations. A BEAST-derived chronogram based on the cpDNA haplotypes indicated that the initial divergence of Q. fabri probably occurred during the late Miocene (12.33 Ma), whereas haplotype divergence time could date back to the late Pliocene to early Pleistocene. ENM showed that the suitable areas contracted during the last glacial maximum (LGM) and expanded in the warm period during the Pleistocene. Consistently, both the cpDNA and ITS datasets suggested that population expansion occurred after the LGM period (ca. 13–14 kyr) for Q. fabri. Demographical analyses based on multiple genetic datasets and a coalescent-based method also suggested a shrinkage–expansion trend for the effective population sizes of Q. fabri during the glacial–interglacial periods in the Quaternary. Our results suggest that the Neogene and Pleistocene were important periods for triggering species differentiation and intraspecific diversification in Q. fabri, thereby providing insights into the effects of environmental changes in the Quaternary on the population dynamics of endemic tree species in subtropical China.

Molecular strategies for identification and characterization of some wild edible mushrooms of Nagaland, India.

Nagaland has a rich macro fungal flora but not many works has been carried out till today. Present investigation deals with molecular characterization and phylogenetic analysis of six popular wild edible mushrooms (WEMs) species of Nagaland, India viz., Lentinula edodes, Lentinus squarrosulus, L. sajor-caju, L. tigrinus, Schizophyllum commune, Termitomyces heimii and one variety of L. squarrosulus based on molecular markers (ITS, 18S rRNA and 28S rRNA genes) data. The use of DNA markers for identification of mushrooms is highly desirable and practical because it is reliable and quick. This approach could resolve successfully the identity and interrelationship of six WEM species with respect to their infrageneric groups. The high CI values of the mushrooms species indicated the low homoplasy nature. The ITS and 28S rRNA data sets were found to be more informative then the 18S rRNA datasets. The molecular data generated for each mushroom species in the present investigation will help in correct identification and conservation of these widely consumed WEM of the region. Additionally assessment of bioactive molecules indicates that studied species are rich in pro-health bioactive compounds. The study hence throws light on the potential and importance of mushrooms especially the edible mushrooms as an economically valuable crop.

First Report of Shoot Dieback on Apple Caused by Diaporthe nobilis in China

In May 2017, apple trees (Malus pumila Mill.) with shoot dieback were observed in Laiyang (36.97°N, 120.71°E), Shandong Province, China. Disease symptoms included twig and shoot dieback and black necrotic lesions. In the later stage, numerous black pycnidia were observed on the surface of necrotic bark. Small pieces (4 to 5 mm) of necrotic tissues from different apple trees were disinfected for 1 min in 75% ethanol, rinsed thrice with sterile distilled water, and plated onto potato dextrose agar (PDA) with 0.05% lactic acid at 25°C. Eight isolates were obtained, and colonies from all isolates were white. Abundant pycnidia developed on PDA for 3 weeks at 25°C, which produced α-conidia measuring 6.2 to 8.9 × 2.2 to 3.2 μm and β-conidia measuring 18.5 to 27.6 × 1.1 to 2.0 μm (n = 50). α-Conidia were one-celled, hyaline, fusiform, and biguttulate, whereas β-conidia were one-celled, hyaline, and filiform. To identify these isolates to species, total DNA was extracted from the monoconidial isolates. The internal transcribed spacer region (ITS), a partial sequence of β-tubulin gene (TUB), translation elongation factor 1-α gene (TEF1), and calmodulin (CAL) were amplified and sequenced using primers ITS1/ITS4 (White et al. 1990), Bt2a/Bt2b (Glass and Donaldson 1995), EF1-728F/EF1-986R, and CAL-228F/CAL-737R (Carbone and Kohn 1999), respectively. The sequences (GenBank accession nos. MK522125 for ITS, MK540236 for TUB, MK540238 for TEF1, and MK540240 for CAL) were aligned using BLASTn in GenBank, showing 99.4 to 100% with the sequences of ITS (KC343147), TUB (KC344120), TEF1 (KC343872), and CAL (KC343388) from the ex-epitype strain of Diaporthe nobilis complex (Gomes et al. 2013). The identity of the isolates was proved by maximum likelihood and Bayesian inference with a combined dataset of ITS, TUB, TEF1, and CAL sequences. The isolates were nested within the clade that includes D. nobilis with 98% bootstrap support and 1.0 Bayesian inference. The pathogenicity of three isolates (SDAp1, SDAp2, and SDAp3) was evaluated on 2-year-old shoots using a wound-inoculation method on living apple trees (cv. ‘Fuji’). Fifteen shoots were wounded (3 mm diameter, 2 mm deep) with a scalpel by cutting into the bark and inoculated with 10 μl of spore suspension (10⁶ α-conidia/ml). Wounds were then sealed with Parafilm. The same number of wounded shoots was inoculated with sterile water as a control. The pathogenicity test was conducted three times independently. Necrotic lesions (2.8 ± 0.5 cm in length) developed around the inoculation points after 3 weeks of inoculation. No disease symptoms developed on the control shoots. The pathogen was successfully reisolated from 93.3% of the inoculated shoots. In China, D. nobilis has been reported as a new pathogen of postharvest rot of blueberry (Yu et al. 2018) and shoot canker of chestnut (Zhang et al. 2018). To our knowledge, this is the first report of D. nobilis causing shoot dieback on apple in China. This report is important for the new research aiming at management of apple shoot disease.

<p><strong><em>Tremateia murispora sp. nov.</em></strong><strong> (<em>Didymosphaeriaceae</em>, Pleosporales) from Guizhou, China</strong></p>

An Ascomycetous species was found from decaying woody stems in Guizhou, China. Morphologically, the fungus can be assigned well in Tremateia in having immersed ascomata, cellular pseudoparaphyses and muriform ascospores, but it differs from other species in having the 3–7 transverse septa ascospores surrounded by a gelatinous sheath. Phylogenetic analyses based on a concatenated dataset of ITS, LSU, SSUand TEF1-α sequence data indicated that the fungus belongs to the genus Tremateia, Didymosphaeriaceae, four taxa formed a monophyletic clade and represent the genus Tremateia with well supported. The new collection formed a distinct lineage and can be recognized as a new species. Therefore, a new species Tremateia murispora is introduced with detailed description and illustration, the notes on its morphologically and phylogenetically related taxa is provided.

Aster dianchuanensis (Asteraceae, Astereae), a new species from Yunnan and Sichuan, China

Aster dianchuanensis J.W.Xiao & W.P.Li (Asteraceae, Astereae), a new species from Yunnan and Sichuan, China, is described and illustrated with photographs. Morphological data and a phylogenetic analysis based on a combined ITS, ETS and trnL-F dataset, suggest that A. dianchuanensis is a distinct species closely related to A. tongolensis. The new species differs from the latter by its few-branched stems (vs simple in A. tongolensis), basal rosette and lower cauline leaves marcescent at anthesis (vs present at anthesis), larger middle cauline leaves (3 – 5.8 × 0.7 cm – 1.2 vs 1 – 4 × 0.2 – 0.9 cm), capitula 2 – 5 in lax corymbiform inflorescence (vs solitary capitula), 3 – 4 (5 –)-seriate phyllaries (vs 2- or 3-seriate), unequal (rarely equal) disc floret lobes (vs equal, or rarely unequal).

Phylogenetic placement, floral anatomy, and morphological characterization of the North African pastoral halophyte Atriplexmollis Desf. (Amaranthaceae)

Atriplex mollis Desf. (Amaranthaceae), a North African endemic halophytic species, is further described in this study. Phylogenetic analysis based on a combined dataset of ITS and ETS rDNA and atpB-rbcL and trnK cpDNA showed that A. mollis is closely related to the Malta- and Gozo-endemic Cremnophyton lanfrancoi Brullo & Pavone. Given this close phylogenetic relationship, A. mollis is also considered among the oldest species of Atriplex, together with C. lanfrancoi. Molecular data also suggest that A. mollis in North Africa, C. lanfrancoi on Malta Island, and Atriplex cana Ledeb.in Eurasian semideserts constitute a separate clade within the tribe Atripliceae. As an 18-month-old shrub, A. mollis can reach a mean height of 44.06 ± 8.09 cm with a leaf area around 1.24 ± 0.15 cm2, and can produce seeds in order of 113.08 ± 28.52 g plant?1. The anatomy of A. mollis shows the presence of male and female developed flowers. Hermaphroditic flowers that may lead to the appearance of male flowers with underdeveloped female organs were rarely found. Three main shapes of ovule (campylotropous, amphitropous, and orthotropous) were found in A. mollis.

Untangling a mess of worms: Species delimitations reveal morphological crypsis and variability in Southeast Asian semi-aquatic earthworms (Almidae, Glyphidrilus)

Semi-aquatic freshwater earthworms in the genus Glyphidrilus from Southeast Asia are characterized by both an extreme morphological crypsis among divergent phylogenetic lineages and a high morphological variability within the same phylogenetic lineages. The present study provides a new taxonomic framework for this problematic genus in SE Asia by integrating DNA sequence and morphological data. When single-locus and multilocus multispecies coalescent-based (MSC) species delimitation methods were applied to DNA sequence data, they usually yielded highly incongruent results compared to morphology-based species identifications. This suggested the presence of several cryptic species and high levels of intraspecific morphological variation. Applying reciprocal monophyly to the cytochrome c oxidase subunit 1 (COI) gene tree allowed us to propose the existence of 33 monophyletic species. Yet, often substantially more molecular operational taxonomic units (MOTUs) were obtained when species delimitation was based on COI and 16S rRNA sequences. In contrast, the ITS1 and ITS2 sequences suggested fewer MOTUs and did not recover most of the monophyletic species from the Mekong basin. However, several of these latter taxa were better supported when MSC species delimitation methods were applied to the combined mtDNA and ITS datasets. The ITS2 secondary structure retrieved one unnamed Mekong basin species that was not uncovered by the other methods when applied to ITS2 sequences. In conclusion, based on an integrative taxonomic workflow, 26 Glyphidrilus candidate species were retained and two remained to be confirmed. As such, this study provides evidence to suggest nine species new to science and to synonymize 12 nominal morphospecies. It also illustrates that the uncritical use of COI as a universal DNA barcode may overestimate species diversity because COI may be unable to distinguish between divergent conspecific lineages and different candidate species.

Molecular phylogeny of the genus Hylodesmum (Fabaceae)

The phylogenetic relationships of 12 Hylodesmum species and closely related genera were reconstructed using maximum parsimony, maximum likelihood, and Bayesian analyses based on two chloroplast DNA regions (rps16-trnQ and trnL-F) and one nuclear marker (internal transcribed spacer, ITS). All analyses yielded reliable relationships among the major lineages within Hylodesmum, suggesting that Hylodesmum is monophyletic. Neither the traditionally defined Desmodium sect. Podocarpium nor D. sect. Repanda within the genus was supported as being monophyletic based on the ITS analyses and the combined ITS and chloroplast dataset analyses. The phylogenetic topologies indicated that the three species included in D. sect. Repanda were separated into different clades, which suggested that D. sect. Repanda is paraphyletic. Generally, the clades retrieved by phylogenetic analyses within D. sect. Podocarpium were consistent with traditionally defined groups except for the American group. The molecular analysis provides information regarding the revision of the traditional taxonomic system of Hylodesmum and for the evaluation of the systematic positions of each species within the genus Hylodesmum.

Verruconis heveae, a novel species from Hevea brasiliensis in Thailand

Verruconis heveae, a new species accommodated in Sympoventuriaceae was isolated from dried latex on bark of a rubber tree (Hevea brasiliensis) collected from Phayao Province, Thailand. The comparison of its morphological characters distinguished V. heveae from other Verruconis species by having brown, woolly mycelium on the natural substrate and solitary, ellipsoidal to subglobose, 1–3 septate conidia. Phylogenetic analysis of a combined LSU and ITS dataset revealed a distinct lineage within Sympoventuriaceae.

Reinstatement of the corticioid genus Leifia (Hymenochaetales, Basidiomycota) with a new species L.brevispora from Hubei, Central China.

The monotypic genus Leifia was previously considered to be a later synonym of Odonticium. With the morphological and phylogenetic evidence provided by an additional four East Asian specimens, we propose to reinstate Leifia as an independent genus in Hymenochaetales. Leifia morphologically differs from Odonticium by its grandinioid hymenophore with hyphal strands, numerous thick-walled cystidia with an invaginated apical end and narrowly and thick-walled basidia. The phylogeny generated from the current data set of ITS and 28S regions indicates that Leifia forms a sister clade to Odonticium. Besides the generic type Leifiaflabelliradiata in the Leifia clade, two specimens, collected from Hubei, Central China, are newly introduced as Leifiabrevispora. This new species is the second species of Leifia and differs from the generic type by its shorter basidiospores and distribution in warm-temperate to subtropical areas in East Asia. The additional two specimens, collected from Da Lat, Viet Nam, differ morphologically, both from each other and from known species of Leifia, but more samples need to be examined before further taxonomic decisions can be made.