Nuclear Ribosomal ITS Research Articles

Morphological and molecular evidence for a new species of Russula subgen. Compactae from Pakistan

A new species of Russula has been collected from Punjab and Khyber pakhtunkhwa provinces, Pakistan. Russula punjabensis sp. nov. is characterized by grayish purple to grayish red pileus with brittle central region, white lamellae with brown striations, becoming brown at maturity, a rhizoidal base, small (7.48 × 6.64 µm) subglobose to broadly ellipsoid basidiospores as compared to R. acrifolia (7.7 µm), small (34.80 × 4.35 µm) cylindrical to narrowly fusiform pileocystidia and presence of clamp connections in pileipellis. Phylogenetic analysis based on nuclear ribosomal ITS & LSU nucleotide sequences confirm its novelty.

Persistence Over Millennia Through Extreme Clonal Longevity: Phylogenomic Insight Into History of One of the World's Rarest Plant Species

ABSTRACTAimThe evolutionary history of European alpine plant species with medium to large geographical ranges is relatively well explored. Here, we investigate the genetic structure and diversity of an extremely narrow endemic and one of the world's rarest plants.LocationEastern Carpathians, Romania.TaxonAndryala laevitomentosa (Asteraceae), an evolutionarily isolated herb species with a worldwide range limited to five micropopulations distributed along a 1.8 km long mountain ridge.MethodsWe used three plastid loci, nuclear ribosomal ITS and genome‐wide, mostly nuclear 26,272 Single‐Nucleotide Polymorphism (SNPs) obtained from RAD‐seq data. We assessed haplotype and genotype diversity, dated the resulting phylogeographic structure, quantified seed production and inferred vegetative propagation.ResultsMaternally inherited plastid markers and nuclear genomic data revealed a concordant pattern: (i) limited genetic diversity, with seven cpDNA haplotypes and 11 RAD‐seq multilocus genotypes; (ii) a strong geographic structure corresponding to spatially isolated genets (clones). The species is likely of early Pleistocene origin (c. 2 Mya), and the estimated age of individual clones varied from c. 24 to 64 Kya. The average seed set assessed over 3 years was only 0.4%. However, the species reproduces veg by axillary and adventitious rosettes formed on rhizomes and roots, respectively.Main ConclusionsThe strong trade‐off between sexual and vegetative reproduction explains not only a deep and ancient phylogeographic structure but also the rarity of the species. Its survival depends almost entirely on vegetative reproduction. The genets of A. laevitomentosa are amongst the oldest clones ever documented in angiosperms. The persistence of these clones in situ for tens of thousands of years suggests an exceptional ability of this species to adapt to major climatic oscillations throughout the Pleistocene and Holocene and challenge our perception of the extent of resilience in plants.

A new species of Hypericum section Olympia (Hypericaceae) from Central Greece

Hypericum intricatum, discovered in an ophiolitic area near the city of Domokos, Central Greece, is here described and illustrated as a species new to science. It belongs to section Olympia, as indicated by nuclear ribosomal ITS phylogeny, congruent with several but not all key morphological characters of this taxon. The sole known population of the new species is critically small and restricted to a floristically noteworthy spot accompanied by other rare and threatened serpentine-specialist species.

The genus Peniophora (Russulales, Basidiomycota) from Patagonia revisited

The identity of Peniophora specimens from Patagonia is examined based on morphological, cultural, and biological features as well as phylogenetic analyses of nuclear ribosomal ITS and 28S sequences. Three new species are described from Patagonia: Peniophora patagonica, P. pitrae, and P. revoluta. In total, five species are known in the area, growing on endemic trees in Southern Argentina. Peniophora cinerea and P. rufomarginata are excluded from the Patagonian records, and the presence of P. incarnata and P. lycii is confirmed by molecular methods. A key to Peniophora species from Patagonia is presented.

Isolated, neglected, and likely threatened: a new species of Magoniella (Polygonaceae) from the seasonally dry tropical forests of Northern Colombia and Venezuela revealed from nuclear, plastid, and morphological data.

Seasonally tropical dry forests (SDTFs) in the American tropics are a highly diverse yet poorly understood and endangered ecosystem scattered from Northern Mexico to Southern Argentina. One floristic element of the STDFs is the genus Magoniella (Polygonaceae), which includes two liana species, M. laurifolia and M. obidensis, which have winged fruits and are distributed from Costa Rica to Southern Brazil. In a field expedition to the SDTFs of the Colombian Caribbean in 2015, morphologically distinctive individuals of Magoniella were found. In this study, we investigated the species boundaries within Magoniella and determined the phylogenetic position of these morphologically distinctive individuals in the tribe Triplaridae. We compiled morphological trait data across 19 specimens of both species and produced newly sequenced nuclear-plastid DNA data for M. obidensis. Morphometric analyses revealed significant differences in fruit length and perianth size among individuals from the Colombian Caribbean compared to M. obidensis and bract length when compared to M. laurifolia. Maximum likelihood analysis of non-conflicting nuclear and plastid datasets placed the Colombian Caribbean individuals as sister to M. obidensis with maximum statistical support. Additionally, pairwise sequence comparisons of the nuclear ribosomal ITS and the lfy2i loci consistently showed 15-point mutations (10 transitions, five transversions) and six 2 bp-long substitutions that differ between M. obidensis and the Colombian Caribbean individuals. Our morphological and molecular evidence thus suggests that the Colombian Caribbean individuals of Magoniella represent a divergent population from M. laurifolia and M. obidensis, which we describe and illustrate as a new species, M. chersina. Additionally, we provide nomenclatural updates for M. laurifolia and M. obidensis. This study highlights the power of combining morphological and molecular evidence in documenting and naming plant diversity.

Molecular phylogeny and morphology reveal two new species of Conocybe (Bolbitiaceae, Agaricales) from southwest China

ABSTRACT Conocybe commonly occur as saprobes, are distributed in tropical, subtropical, and temperate zones worldwide. In the present study, two new species in Conocybe section Conocybe, viz. Conocybe qujingensis and Conocybe qujinguniversitatis, are proposed based on morphological investigations and phylogenetic analyses. Molecular analyses based on sequence data from the nuclear ribosomal ITS loci support the taxonomic position of the two new species in the genus Conocybe. We also provide illustrations, line drawings, comparisons with closely related taxa, and descriptions of the new taxa.

Calanthe yingjiangensis (Epidendroideae; Orchidaceae), a new species from China: evidence from morphological and molecular data

A new species of Orchidaceae, Calanthe yingjiangensis, is described from Yingjiang (Yunnan, China) based on morphology and molecular phylogenetics. This new species is like C. puberula, but it differs from the latter in its midlob of lip with an elliptic yellow spot near the base of the column and four purple veins, triangular lateral lip lobs that is much smaller than middle lobe and twisted lateral sepals. Molecular phylogenetic analyses based on three plastid DNA makers (rbcL, matK and trnL-trnF) and nuclear ribosomal ITS support C. yingjiangensis as sister to C. puberula in Calanthe section Vernae.

A tough nutlet to crack: Resolving the phylogeny of Thesium (Thesiaceae), the largest genus in Santalales

AbstractWith over 350 species, Thesium is the largest genus in Santalales. It is found on all continents except Antarctica; however, its highest diversity is in the Cape Floristic Region of South Africa where approximately half the species occur. Thesium samples of ca. 590 collections from throughout its entire geographic range were obtained and nuclear ribosomal ITS sequenced from 396 accessions representing 196 named taxa and 30 currently unnamed taxa for a total of ca. 230 species. In addition, two chloroplast genome spacers (trnDT, trnLF) were sequenced from 269 and 315 accessions, respectively. Maximum parsimony, maximum likelihood and Bayesian methods were employed to generate gene trees and infer phylogenies. The value of the morphological characters traditionally used in the taxonomy of the genus and previous infrageneric classifications are discussed. Broad scale relationships were generally congruent among the ITS and the chloroplast trees. For example, both the nuclear and chloroplast trees support the presence of Eurasian and African clades. In contrast, major incongruence was detected between nuclear and chloroplast trees for a number of taxa including the recently described T. nautimontanum that is sister to the entire African clade on the ITS tree. Although the causes of this incongruence are currently unknown, a novel form of chloroplast capture is hypothesized. A hypothesis of the biogeographical history of the genus based on our molecular phylogeny is presented.

Reappraisal of the Identity of Batrachium pekinense (Ranunculaceae) and Its Implication for Biodiversity Conservation and Management

Because of human-induced habitat deterioration and climate change, a large number of species are threatened and even endangered. Batrachium pekinense Liang Liu, a perennial aquatic plant endemic to Beijing, was synonymized as a widely distributed species in Northern China, B. bungei Steudel, but it was later listed in the national key protected wild plants in China. Taxonomic uncertainty should be clarified especially when related species may be allocated with a limited conservation budget. In this study, we reappraised the identity of B. pekinense based on results from molecular phylogenetic analysis and 15-year field observations. Our result shows that 77% of the 65 individuals collected from various sites share identical sequences in both the nuclear ribosomal ITS and the plastid psbA-trnH markers, all samples of the two species consist of one monophyletic clade with strong support, and continuous morphological variations on the key distinguishing character, the leaf shape, are observed in the field. Integrative evidence from both our and the others’ studies supports the same identity for B. pekinense and B. bungei. Hence, we suggest excluding B. pekinense from the list of national key protected wild plants of China in its next update and advocate the integrative evidence-based taxonomy and systematics for biodiversity conservation and management.

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.

Gastorchilus pseudodresslerii (Orchidaceae; Vandeae), a new species from China: evidence from morphological and DNA analysis

Gastrochilus pseudodresslerii (Aeridinae), a new species from Maguan County, Yunnan Province, China, is described and illustrated. Morphological comparisons indicated that this new species is similar to G. dresslerii, but differs by its longer and broadly lanceolate to oblong leaves, larger and elliptic dorsal sepal, longer and elliptic petals, subcupular hypochile, and narrowed toward apex of column. Phylogenetic analysis based on nuclear ribosomal ITS and four plastid sequences (atpI, matK, psbA and trnL-F) indicated that G. pseudodresslerii is also closely related to G. formosanus and G. raraensis, but can be easily distinguished from these two species based on its leaves, epichile and hypochile.

Millennial-scale variations in Arctic sea ice are recorded in sedimentary ancient DNA of the microalga Polarella glacialis

Sea ice is a critical component of the Earth’s Climate System and a unique habitat. Sea-ice changes prior to the satellite era are poorly documented, and proxy methods are needed to constrain its past variability. Here, we demonstrate the potential of sedimentary DNA from Polarella glacialis, a sea-ice microalga, for tracing past sea-ice conditions. We quantified P. glacialis DNA (targeting the nuclear ribosomal ITS1 region) in Arctic marine and fjord surface sediments and a sediment core from northern Baffin Bay spanning 12,000 years. Sea ice and sediment trap samples confirmed that cysts of P. glacialis are common in first-year sea ice and sinking particulate matter following sea-ice melt. Its detection is more efficient with our molecular approach than standard micropaleontological methods. Given that the species inhabits coastal and marine environments in the Arctic and Antarctic, P. glacialis DNA has the potential to become a useful tool for circum-polar sea-ice reconstructions.

A new species of Brassica (Brassicaceae) from Bolkar Mountains (Türkiye) with morphological and molecular evidence

Brassica huseyin-duralii from Niğde province in the Central Anatolian region of Türkiye is described and illustrated here as a new species of the tribe Brassiceae. It resembles B. repanda but differs from that species by its combination of woody caudex, leaf structure, and rosette and stem leaf shapes. It is also similar to B. elongata, from which it differs by its stem length, basal and stem leaf shapes and hair types, number of flowers, siliqua position and its width. This classification is also supported by phylogenetic analyses of nuclear ribosomal ITS data with B. huseyin-duralii and B. elongata constituting a monophyletic clade. The diagnosis, description, distribution and habitat of a new species, its distribution map and diagnostic key to Turkish Brassica species, are given; a Turkish name and IUCN Red List category are suggested.

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.

Jurinea stenocarpa (Asteraceae, Cardueae), a new species from the north‐west of Iran

Jurinea stenocarpa, is described as a new species based on morphological characters. This species is a mountainous Irano‐Turanian element distributed in the north‐west of Iran, –the Azarbaijan region. Specimens of this species were collected from Aqdagh (type location) and Talesh Mountains in Ardabil Province, Pir‐Saqqa Mountain in Eastern Azarbaijan Province. The taxonomic position of the new species is assessed using sequence data from the nuclear ribosomal ITS region, and the findings are discussed based on a morphological background as well. The new species is morphologically close to its sympatric species, J. heterophylla by having linear‐lanceolate simple and more or less entire leaves, but differs mostly in the form of inflorescence and shape and status of phyllaries. The new species also has similarities to its allopatric species J. monocephala, mainly by having semi‐globose involucre and scapose stems, but differs in plant indumentum, the shape of phyllaries and features of achenes and size of pappus rays. Description, photos and a distribution map for the new species and closely related species are presented.

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.

Taxonomy and phylogeny of some geophilic Umbelliferae - Apioideae genera based on anatomical, morphological and molecular data

The paper provides an overview of the concordance between molecular (nuclear ribosomal DNA ITS) and morphological data in the group of geophilic Umbelliferae of Middle Asia, which includes the genera Elwendia, Elaeosticta, Hyalolaena, Galagania, Oedibasis, Mogoltavia and Gongylotaxis. In general, a good consistency of data of different types can be observed. At the same time, at some levels of the taxonomic hierarchy, the consistency between morphological and molecular data looks much higher than at others. The identification of the group of geophilic Umbelliferae agrees much better with molecular data than the boundaries between genera within it and the proposed intrageneric groupings. Some observed cases of inconsistency, such as the position of Hyalolaena melanorrhiza among the species of the genus Elaeosticta and the polyphyly of the genera Hyalolaena and Oedibasis, are rather difficult to explain from a morphological point of view, only from a biogeography.

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.

Rapid cryptic divergence of the Anastrepha fraterculus complex in the Late Pleistocene: a phylogeographical–ecological approach

Abstract The Anastrepha fraterculus complex (AF complex) is a complex of fruit fly species consisting of eight morphotypes distributed across the Americas. In this study, landscape genetics, phylogeographical inferences and coalescence simulations were used to unveil the evolutionary history of the AF complex. Nuclear ribosomal ITS1 sequences from 331 samples distributed in 10 American countries throughout 32 ecoregions and seven biomes were analysed. Results showed high levels of diversity, intraspecific divergence and structuring associated with the different morphotypes of the complex. The analysis of gene flow and genetic diversity showed a clear geographical and environmental pattern. The morphotype–environment association suggested that the cryptic divergence process has involved local adaptation as a mechanism to withstand harsh, novel or variable conditions. The analysis showed a rapid divergence between morphotypes. Haplotypes have been diverging for ~27 000 years before the present, probably enhanced by environmental changes during the Last Glacial Maximum. Diversity estimators and neutrality tests revealed that populations have been experiencing a recent linear growth, starting in the Early Holocene (~11 500 years before the present). The Bayesian phylogeographical and ecological clustering approach detected five spatially separated and ecologically differentiated clusters. Additionally, equatorial Amazonia was indicated to be the most probable ancestral centre of origin for the AF complex.

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.