Nuclear Ribosomal ITS Sequences Research Articles

Liparis bomiensis (Orchidaceae, Epidendroideae, Malaxideae), a new species from Xizang, China

Liparis bomiensis, a new species of Orchidaceae from Bomi County, Linzhi, Xizang, China, is described and illustrated on morphological characters and molecular systematics. It is morphologically similar to L. rostrata with 2 thick projections at base of column, but differs from it by having purple and rhombic lip about 15 mm long, sepals and petals more than 15 mm long. Molecular phylogenetic results based on nuclear ribosomal ITS and plastid matK sequences showed that L. bomiensis is sister to L. glossula, but differs from it by having 2 thick nipple-like projections at base of column, two leaves, bracts triangular, column strongly curved. A detailed morphological description and photographic plates are provided for this new species.  

Luisia brachyota (Orchidaceae; Epidendroideae) a new species from China: evidence based on morphological and molecular data

We have described and illustrated a new species, Luisia brachyota (Epidendroideae, Orchidaceae), from south Yunnan, China. Morphological comparisons indicated the new species is similar to L. filiformis and L. cordata, but differs from L. brachyota inflorescences 3-or 5-flowered, lip shorter than petals, hypochile thickly fleshy, epichile cordate adaxially with 7 or 9 papillate longitudinal ridges. Molecular analysis based on the nuclear ribosomal ITS and plastid sequences (matK, rbcL, and trnL-trnF) shows that it is a new species.  

Antifungal Potential of Cladosporium sp. (Endophytic fungi) Associated with Olea europaea L. Leaves

In the leaves of Olea europaea L. Olive trees an endophytic fungus was discovered. Cladosporium sp. was identified to be the fungus based on its morphological characteristics and nuclear ribosomal DNA ITS sequence analysis and was registered in NCBI as the Cladosporium genus has been registered under the number (0P939922.1) The species was not specified, and it was considered of unknown species after comparing it to global isolates. In comparison to olive leaf extract, Cladosporium sp. including total flavonoid, total phenolic, total terpenoid, and total saponins, Which were 121.9%, 198.1%, 89.13%, and 29.87 % respectively compared to its content in olive leaf extract, which was 61.54 %, 67.88 % , 17.1%, and 20.19% respectively. The Cladosporium sp. extract inhibited the growth of 27 isolates belonging to different species of candida which were Candida albicans , C. lypolitica , C. tropicalis , C. sphaerica , C. krusei , C. guilliermondii , C. parapsilosis , C. norvegicus , C. glabrata , and C. kefyr , the inhibition effects increased with increasing concentration to reach the highest level to suppress fungal growth when concentrated 30 mg/ml. This proves the antifungal potential of endophytic fungi in the future.

Isolation and Characterization of Novel Huperzine-Producing Endophytic Fungi from Lycopodiaceae Species.

Huperzine A (HupA) is an important drug for treating Alzheimer's disease (AD) and is primarily extracted from the Huperzia serrata (Lycopodiaceae). Failures in the chemical synthesis of Hup and in vitro culture have put H. serrata in danger of extinction, and there is a need for an extensive investigation of Hup from alternative perspectives. The aim of this study is to identify endophytic fungi that produce high Hup or simultaneously produce many types of Hup and have high genetic stability derived from other Lycopodiaceae species as a source of materials for natural Hup production. In this work, Hup-producing endophytic fungi were isolated from three species: Lycopodium clavatum, Phlegmariurus squarrosus, and P. phlegmaria. Of these, L. clavatum and P. squarrosus were confirmed as novel sources of Hup-producing fungi. Based on morphological characteristics and nuclear ribosomal DNA ITS sequences, four endophytic fungi Colletotrichum siamense THG1-17, Epicoccum sorghinum THG01-18, Phoma sp. TKH3-2, and Phyllosticta sp. THG2-27 were firstly isolated from these Lycopodiaceae plants, which were capable of simultaneously producing both HupA and HupB, as evidenced by high-performance liquid chromatography analysis. The four strains showed stability in Hup yield over 50 generations of culture with an in vitro storage period of 3 months. These isolated fungi will provide a new source of materials for further research to develop drugs containing HupA as well as HupB for AD treatment in the future.

Plastome evolution in the genus Sium (Apiaceae, Oenantheae) inferred from phylogenomic and comparative analyses

BackgroundSium L. (Apiaceae) is a small genus distributed primarily in Eurasia, with one species also occurring in North America. Recently, its circumscription has been revised to include 10 species, however, the phylogenetic relationships within its two inclusive clades were poorly supported or collapsed in previous studies based on nuclear ribosomal DNA ITS or cpDNA sequences. To identify molecular markers suitable for future intraspecific phylogeographic and population genetic studies, and to evaluate the efficacy of plastome in resolving the phylogenetic relationships of the genus, the complete chloroplast (cp) genomes of six Sium species were sequenced.ResultsThe Sium plastomes exhibited typical quadripartite structures of Apiaceae and most other higher plant plastid DNAs, and were relatively conserved in their size (153,029–155,006 bp), gene arrangement and content (with 114 unique genes). A total of 61–67 SSRs, along with 12 highly divergent regions (trnQ, trnG-atpA, trnE-trnT, rps4-trnT, accD-psbI, rpl16, ycf1-ndhF, ndhF-rpl32, rpl32-trnL, ndhE-ndhG, ycf1a and ycf1b) were discovered in the plastomes. No significant IR length variation was detected showing that plastome evolution was conserved within this genus. Phylogenomic analysis based on whole chloroplast genome sequences produced a highly resolved phylogenetic tree, in which the monophyly of Sium, as well as the sister relationship of its two inclusive clades were strongly supported.ConclusionsThe plastome sequences could greatly improve phylogenetic resolution, and will provide genomic resources and potential markers useful for future studies of the genus.

Accidental cultivation of the European truffle Tuber brumale in North American truffle orchards.

Tuber brumale is a European edible truffle species that is often viewed as a contaminant in truffle orchards, as it visually resembles more valuable black truffles such as T. melanosporum, but differs in aroma and flavor and sells for a much lower price. Although T. brumale is not native to or intentionally cultivated in North America, it was reported to have been accidently introduced into British Columbia in 2014 and North Carolina in 2020. However, in winter of 2021, various truffle orchards in eastern North America produced truffles that differed from the anticipated harvest of T. melanosporum. Molecular analysis of these specimens confirmed T. brumale truffle fruiting bodies from ten orchards distributed across six eastern USA states. Phylogenetic analysis of nuclear ribosomal ITS and 28S DNA sequences indicated that all samples belong to the T. brumale A1 haplogroup, the genetic subgroup of T. brumale that is more common in western Europe. This pattern of widespread fruiting of T. brumale in North American truffle orchards is likely the result of T. brumale being introduced in the initial inoculation of trees used as hosts in T. melanosporum truffle cultivation. We review other examples of introduced non-target truffle species and strategies for limiting their impact on truffle cultivation.

Phylogenetic analysis of Ziziphora (Lamiaceae) using nuclear (nrITS) and plastid (trnL-F) DNA: suggestions for new arrangements and status changes

In this study, Ziziphora taxa grown in Turkey along with those grown in different parts of the world were analyzed with respect to morphological revision and molecular systematic analyses using nuclear ribosomal ITS (nrITS) sequences and the chloroplast (trnL-F) sequences. Both nrITS and trnL-F sequences clearly suggested Ziziphora was a monophyletic genus. Morphological revision mostly confirmed the previous systematic position of the taxa examined, while for some taxa, morphological uncertainties combined with DNA sequence data suggested rearrangements and new taxa. With this respect, some of the unidentified Z. clenopodioides specimens were suggested as potentially 2 new subspecies while the status of Z. clenopodioides subsp. filicaulis was suggested to change from subspecies to species. Interestingly, four Z. tenuior ecotypes from the eastern, central and southern parts of Turkey displayed different nrITS sequences and hence they were suggested as four different new subspecies of Z. tenuior. This is the first report presenting a revised status of Ziziphora L. taxa in Turkey based on molecular systematic analysis, with respect to its related members in different parts of the world.

Leaf morphology, genetic analysis and low temperature requirement for flowering of Verbascum blattaria

AbstractVerbascum blattaria L., commonly known as moth mullein, naturalized in the USA that produces white or yellow flowers could be considered as a potential ornamental plant. However, genetic characterization using molecular markers and leaf morphology, colourimetric analysis and flowering of V. blattaria influenced by low temperature treatments was not investigated to evaluate as a potential horticultural and landscape plant use. The basal leaves developed during the rosette-growth stage were oblanceolate with an obtuse leaf apex and incisions at the margin. Leaves produced on the stem during the reproductive development were ovate or lanceolate with an obtuse or acute leaf apex. Regardless of the colour of the petiole and leaf blade during the rosette-growth stage, there were no differences in the sequences of nuclear ribosomal ITS and chloroplast interspacer. All plants produced creamy white flowers with a purplish base corolla. All leaves formed during the vegetative and reproductive development were glabrous. Numerous stalked glandular trichomes were observed in the sepal, pedicel and bracts. Seeds started to germinate in 10 days at 25°C and reached the plateau in 30 days after sowing. The earliest flowering occurred in 131 days when the plants received 20 days of low temperature treatment (CD) (20 CD), producing 76 flowers, the highest number compared to the number of flowers produced by plants that received 0, 40 and 60 CD. Plants that received 20 CD exhibited early flowering, probably because of the early transition from vegetative growth to reproductive development, as judged by the short stem to the first flower.

Two new species of Entoloma (Entolomataceae) from Khyber Pakhtunkhwa, Pakistan

Cedar towering forests of Kumrat Valley, Khyber Pakhtunkhwa, Pakistan were visited on several occasions to collect mushrooms and this resulted in the discovery of two novel species of Entoloma. Entoloma kumraticus is characterized by bluish-brown, centrally depressed pileus, serrulate lamellar edge, bluish-violet fibrillose stipe, dense clusters of cheilocystidia, and presence of abundant grayish-brown intracellular pigments in the terminal cells of pileipellis, and cheilocystidia. Entoloma dirensis is characterized by brownish olive to dull violet, finely fibrillose striate pileus with a violet-blue margin, slightly twisted violet-blue stipe, and blackish-brown lamellar edge, with groups of cheilocystidia which are often septate. The new species are presented based on the morphological and molecular study. Entoloma kumraticus and E. dirensis formed distinct phylogenetic lineages based on the sequences of nuclear ribosomal ITS and LSU gene regions. A key to the Pakistani species in sect. Cyanula is also provided.

Resources of Iranian agarics (Basidiomycota) with an outlook on their antioxidant potential.

Agaric fungi are an important group of macromycetes with diverse ecological and functional properties, yet are poorly studied in many parts of the world. Here, we comprehensively analyzed 558 agaric species in Iran to reveal their resources of edible and poisonous species as well as their ecological guilds and luminescence potential. We also made a thorough survey of the antioxidant activity of the species. Phylogenetic relationships were reconstructed based on nuclear ribosomal LSU and ITS sequences. Our results reveal that agarics of Iran comprise about 189 edible, 128 poisonous, 254 soil saprotrophic, 172 ectomycorrhizal, 146 wood-inhabiting, 18 leaf/litter-inhabiting, 9 parasitic, and 19 luminescent species. Twenty percent of the Iranian agaric species possess antioxidant activity, phylogenetically distributed in four orders and 21 agaric families. About 5% of the antioxidant species can be considered strong antioxidants, many of which are also edible and could be utilized to develop functional foods. This is the first study combining phylogeny and antioxidant potential of agaric mushrooms in a large scale, and the obtained results would guide the selection of agaric taxa to be examined in the future for taxonomic revisions, biotechnological applications, and applied phylogeny studies.

Phylogenetic analysis of some fungi species in West Kazakhstan based on nuclear ribosomal DNA ITS sequences

In this study, phylogenetic analysis of some fungal species distributed in West Kazakhstan was performed based on ITS sequences. All of the mushroom samples were collected from different regions of West Kazakhstan and brought to the laboratory. Total genomic DNA was extracted using a GeneMark commercial kit. ITS1 and ITS4 primers were used for the amplification of the ITS region in PCR analyses. The resulting DNA sequences were then edited using BioEdit and FinchTV. For phylogenetic analysis used MEGA 6.0 program. As a result of the study, ITS sequences ranged from 532 to 715 nucleotides, while the divergence values of the sequences differed between 0.000 and 0.468. The maximum likelihood tree constructed using ITS sequences consists of two clades. According to the phylogenetic analysis results obtained using other fungal species, ITS results were found to be a good indicator for the differentiation of fungal genera.

Phylogenomic insight into dysploidy, speciation, and plastome evolution of a small Mediterranean genus Reichardia (Cichorieae; Asteraceae)

Reichardia Roth is a small Mediterranean genus comprising ten homogeneous species with basic chromosome numbers of 7, 8, and 9. To assess the plastid genome evolution and differentiation of Reichardia species, we assembled the complete plastome sequences of seven Reichardia and two Launaea species and conducted various phylogenomic analyses comparatively with nuclear ribosomal DNA ITS sequences. Reichardia and Launaea plastomes were highly conserved in gene content and order, containing 130 genes. Plastid phylogenomic reconstruction strongly suggested that Reichardia was a sister to Launaea, and its common ancestor initially diverged into two major lineages: the first containing species with n = 8 chromosomes exclusively, and the other with n = 9, 8, and 7 chromosomes. Although the ancestral Reichardia karyotype was suggested to most likely be n = 9 from ancestral chromosome number reconstruction, the pattern of descending dysploidy indicated by the phylogenetic trees based on nuclear ribosomal DNA ITS was less evident in the trees based on the plastome. Possible reasons for these findings are discussed.

Callistosporium luteo-olivaceum (Callistosporiaceae: Basidiomycota), an agaric fungi new to Türkiye

Callistosporium luteo-olivaceum collected from Mediterranean region of Türkiye is identified based on morphological characters and combined dataset of nuclear ribosomal ITS and LSU sequences. Callistosporium luteo-olivaceum is new to the country’s mycobiota and it is the first report of this species from the relict endemic Liquidambar orientalis forest. Description of the species based on macro and micromorphological characters, colour photograph from its natural habitat and line-drawings of microscopic features are presented.

Phylogenetic inferences using nuclear ribosomal ITS and chloroplast sequences provide insights into the biogeographic origins, diversification timescales and trait evolution of Rubus in the Japanese Archipelago

Phylogenetic inferences using nuclear ribosomal ITS and chloroplast sequences provide insights into the biogeographic origins, diversification timescales and trait evolution of Rubus in the Japanese Archipelago

A Remarkable New Species of Euphorbia section Helioscopia (Euphorbia subgenus Esula, Euphorbiaceae) from Jiufeng Mountains in Fujian Province, Eastern China

Abstract— Euphorbia xiangxiui, a new species of Euphorbiaceae from Eastern China, supported by morphological and molecular evidence, is illustrated and described here. It can be distinguished from its closest relatives by the combination of several characters, including taller stature (up to 1.6 m), leaves of 5‐18 × 0.6‐3 cm in size, color of primary involucral leaves and cyathophylls changing from pink to rose, fading to green after fruiting, and four to six reniform-rounded concave glands. The molecular phylogenetic analysis, based on combined nuclear ribosomal ITS and plastid ndhF sequences, further supports that E. xiangxiui should be placed in the East Asian Clade of Euphorbia subg. Esula sect. Helioscopia.

A new genus of Lythraceae emerges from rocky outcrops of the Atlantic Forest in Brazil

Abstract Recent collections of Lythraceae from an isolated mountain range in eastern Brazil were found to possess a unique morphology including spurless, weakly actinomorphic floral tubes, two deep red petals, a stipitate ovary and irregularly circumscissile dehiscence of a thickened capsule, characters typically applied to taxon recognition at the generic level. Genomic DNA was extracted from herbarium specimens or silica-dried leaf tissue and subjected to Illumina sequencing, and a phylogenetic analysis was performed based on a combination of plastid trnL-trnF and rpl16 and nuclear ribosomal ITS sequences. Sequences of 22 genera of Lythraceae, including 74 Cuphea spp. representing all recognized sections of the genus and three Pleurophora spp., were included in the analysis; Ludwigia octovalvis (Onagraceae) was used to root the trees. A maximum-likelihood tree was reconstructed based on the concatenated matrix. Strong morphological evidence was found to recognize a new genus and species in Lythraceae: Gyrosphragma latipetala sp. nov., gen. nov. The same characteristics also occur in a little-known species, Cuphea santos-limae, which we transfer to Gyrosphragma. Molecular phylogenetic analysis confirms Gyrosphragma as a monophyletic genus, sister to Cuphea; together these genera form a clade with Pleurophora. The new genus, supported by morphological and molecular evidence, adds new features and extends knowledge on the ecological and geographical diversity within Lythraceae.

Huchimingia, a new genus segregated from Millettia (Leguminosae, Millettieae) based on morphological and molecular evidence

Millettia Wight & Arn. is a heterogeneous genus within the tribe Millettieae (Leguminosae) and has long been used as a repository to accommodate all undistinctive species of the tribe with elastically dehiscent pods. Millettia sect. Podocarpae Dunn is representative of the heterogeneous genus. This section includes five Asian species that have a unique combination of characters that distinguishes them from all other species of the genus, including the deciduous tree habit, conspicuous buds covered with scales, pseudoracemes or pseudopanicles with very indistinct brachyblasts, two flowers per brachyblast, conspicuous large bracts, ebracteolate calyx, well-developed hypanthium, stipitate ovary, and flat, stipitate and dehiscent pods. Our molecular phylogeny based on plastid matK and nuclear ribosomal ITS sequences also suggested the section is clearly monophyletic, separate from other congeneric species, and is most closely related to Antheroporum Gagnep. with inflated, vacuous pods and Ohashia X.Y. Zhu & R.P. Zhang with indehiscent flat pods. Therefore, we propose a new genus, Huchimingia Z.Q. Song & Shi J. Li, to accommodate this distinct section.

Morphological homoplasy and sectional polyphyly in Centaurea sect. Cynaroides and related taxa

Building natural classifications for genera with complex morphological variations such as Centaurea needs the support of molecular analysis and knowledge of morphological character diversification. Here we use parsimony and Bayesian analyses of nuclear ribosomal ITS sequences to gain insight into the sectional relationships and character evolution in Centaurea sections Chartolepis, Cheirolepis, Cynaroides, Grosheimia, Microlophus, Paraphysis, Phaeopappus, Plumosipappus, Pseudoserida, Pseudophaeopappus, Ptheracantha, Ptosimopappus, and Rhizocalathium, from Turkey. In particular, we increase sampling in Turkish endemic species of Centaurea sect. Cynaroides and related taxa. The new ITS sequences for 26 taxa from 48 locations are given. Sequences of 17 taxa are given here the first time. The phylogeny derived from ITS data provides a reasonably resolved and reasonably supported phylogenetic framework for the genus. Our analysis shows characters traditionally used in Centaurea taxonomy such as flower colour, appendage width, spine length, and pappus length evolved several times independently and show a lot of homoplasies. However, we can confirm the validity of character combinations for a reliable subgeneric classification of Centaurea.

Judge it by its shape: a pollinator-blind approach reveals convergence in petal shape and infers pollination modes in the genus Erythrina.

Pollinators are thought to exert selective pressures on plants, mediating the evolution of convergent floral shape often recognized as pollination syndromes. However, little is known about the accuracy of using petal shape for inferring convergence in pollination mode without a priori pollination information. Here we studied the genus Erythrina L. as a test case to assess whether ornithophyllous pollination modes (hummingbirds, passerines, sunbirds, or mixed pollination) can be inferred based on the evolutionary analysis of petal shape. We characterized the two-dimensional dissected shape of standard, keel, and wing petals from 106 Erythrina species using geometric morphometrics and reconstructed a phylogenetic tree of 83 Erythrina species based on plastid trnL-F and nuclear ribosomal ITS sequences. We then used two phylogenetic comparative methods based on Ornstein-Uhlenbeck models, SURFACE and l1OU, to infer distinct morphological groups using petal shape and identify instances of convergent evolution. The effectiveness of these methods was evaluated by comparing the groups inferred to known pollinators. We found significant petal shape differences between hummingbird- and passerine-pollinated Erythrina species. Our analyses also revealed that petal combinations generally provided better inferences of pollinator types than individual petals and that the method and optimization criterion can affect the results. We show that model-based approaches using petal shape can detect convergent evolution of floral shape and relatively accurately infer pollination modes in Erythrina. The inference power of the keel petals argues for a deeper investigation of their role in the pollination biology of Erythrina and other bird-pollinated legumes.

Response of balsam poplar to inoculation with Marssonina balsamiferae from Minnesota, USA

AbstractLeaf spots of poplar (Populus) species and hybrids in North America commonly are caused by three Drepanopeziza species (previously referred to by their asexual morph names in genus Marssonina). A fourth species, Marssonina balsamiferae, is known only from herbarium specimens and was described from balsam poplar (Populus balsamifera) leaves collected in 1966 in Manitoba, Canada. Balsam poplar leaves collected in 2014 in Minnesota, USA bore spots with acervuli and conidia consistent with those of M. balsamiferae, and isolates were obtained from these leaves. Conidial morphology and analysis of nuclear ribosomal ITS sequences distinguished the Minnesota strains from the very common leaf spot pathogen of poplars in the northcentral region of the USA, Drepanopeziza brunnea. Inoculation of rooted balsam poplar cuttings with conidia of M. balsamiferae strains from Minnesota resulted in necrotic leaf spots. Acervuli bearing conidia consistent with those of M. balsamiferae were observed on symptomatic leaves, and the fungus was reisolated from infected tissues. Contemporary recognition of existence and pathogenicity of M. balsamiferae, including presence in the USA, should prompt further investigation of its geographic distribution and relationships with hosts and related fungal species.