nrDNA Sequences Research Articles

New insights into the phylogenetic relationships within the Lauraceae from mitogenomes

BackgroundThe family Lauraceae is subdivided into six main lineages: Caryodaphnopsideae, Cassytheae, Cryptocaryeae, Hypodaphnideae, Laureae, and Neocinnamomeae. However, phylogenetic relationships among these lineages have been debatable due to incongruence between trees constructed using nuclear ribosomal DNA (nrDNA) sequences and chloroplast (cp) genomes. As with cp DNA, the mitochondrial (mt) DNA of most flowering plants is maternally inherited, so the phylogenetic relationships recovered with mt genomes are expected to be consistent with that from cp genomes, rather than nrDNA sequences.ResultsThe mitogenome of Machilus yunnanensis, with a length of 735,392 bp, has a very different genome size and gene linear order from previously published magnoliid mitogenomes. Phylogenomic reconstructions based on 41 mt genes from 92 Lauraceae mitogenomes resulted in highly supported relationships: sisterhood of the Laureae and a group containing Neocinnamomeae and Caryodaphnopsideae, with Cassytheae being the next sister group, followed by Cryptocaryeae. However, we found significant incongruence among the mitochondrial, chloroplast, and nuclear phylogenies, especially for the species within the Caryodaphnopsideae and Neocinnamomeae lineages. Time-calibrated phylogenetic analyses showed that the split between Caryodaphnopsideae and Neocinnamomeae dated to the later Eocene, around 38.5 Ma, Laureae originated in the Late Cretaceous, around 84.9 Ma, Cassytheae originated in the mid-Cretaceous around 102 Ma, and Cryptocaryeae originated in the Early Cretaceous around 116 Ma. From the Late Cretaceous to the Paleocene, net diversification rates significantly increased across extant clades of major lineages, and both speciation rates and net diversification rates continued steady growth towards the present.ConclusionsThe topology obtained here for the first time shows that mt genes can be used to support relationships among lineages of Lauraceae. Our results highlight that both Caryodaphnopsideae and Neocinnamomeae lineages are younger than previously thought, likely first diversifying in the Eocene, and species in the other extant lineages of Lauraceae dates in a long-time span from the Early Cretaceous to the Eocene, and the climate of a period of about 90 million years was relatively warm, while the extant species of Lauraceae then continuously diversified with global cooling from the Eocene to the present day.

Diversity and Antifungal Susceptibilities of Yeasts from Mangroves in Hong Kong, China-A One Health Aspect.

While mangrove ecosystems are rich in biodiversity, they are increasingly impacted by climate change and urban pollutants. The current study provides first insights into the emergence of potentially pathogenic yeasts in Hong Kong's mangroves. Sediment and water samples were collected from ten urban and rural mangroves sites. Initial CHROMagarTM Candida Plus screening, representing the first application of this differential medium for water and soil samples collected from a non-clinical environment, enabled the rapid, preliminary phenotypic identification of yeast isolates from mangroves. Subsequent molecular profiling (ITS and/or 28S nrDNA sequencing) and antifungal drug susceptibility tests were conducted to further elucidate yeast diversity and drug resistance. A diversity of yeasts, including 45 isolates of 18 distinct species across 13 genera/clades, was isolated from sediments and waters from Hong Kong mangroves. Molecular profiling revealed a dominance of the Candida/Lodderomyces clade (44.4%), a group of notorious opportunistic pathogens. The findings also reveal a rich biodiversity of non-Candida/Lodderomyces yeasts in mangroves, including the first reported presence of Apiotrichum domesticum and Crinitomyces flavificans. A potentially novel Yamadazyma species was also discovered. Remarkably, 14.3% of the ubiquitous Candida parapsilosis isolates displayed resistance to multiple antifungal drugs, suggesting that mangroves may be reservoirs of multi-drug resistance. Wildlife, especially migratory birds, may disseminate these hidden threats. With significant knowledge gaps regarding the environmental origins, drug resistance, and public health impacts of pathogenic yeasts, urgent surveillance is needed from a One Health perspective. This study provides an early warning that unrestrained urbanization can unleash resistant pathogens from coastal ecosystems globally. It underscores the necessity for enhanced surveillance studies and interdisciplinary collaboration between clinicians, ornithologists, and environmental microbiologists to effectively monitor and manage this environmental health risk, ensuring the maintenance of 'One Health'.

Conserved Plastid Genomes of Pourthiaea Trees: Comparative Analyses and Phylogenetic Relationship

The genus Pourthiaea Decne., a deciduous woody group with high ornamental value, belongs to the family Rosaceae. Here, we reported newly sequenced plastid genome sequences of Pourthiaea beauverdiana (C. K. Schneid.) Hatus., Pourthiaea parvifolia E. Pritz., Pourthiaea villosa (Thunb.) Decne., and Photinia glomerata Rehder & E. H. Wilson. The plastomes of these three Pourthiaea species shared the typical quadripartite structures, ranging in size from 159,903 bp (P. parvifolia) to 160,090 bp (P. beauverdiana). The three Pourthiaea plastomes contained a pair of inverted repeat regions (26,394–26,399 bp), separated by a small single-copy region (19,304–19,322 bp) and a large single-copy region (87,811–87,973 bp). A total of 113 unique genes were predicted for the three Pourthiaea plastomes, including four ribosomal RNA genes, 30 transfer RNA genes, and 79 protein-coding genes. Analyses of inverted repeat/single-copy boundary, mVISTA, nucleotide diversity, and genetic distance showed that the plastomes of 13 Pourthiaea species (including 10 published plastomes) are highly conserved. The number of simple sequence repeats and long repeat sequences is similar among 13 Pourthiaea species. The three non-coding regions (trnT-GGU-psbD, trnR-UCU-atpA, and trnH-GUG-psbA) were the most divergent. Only one plastid protein-coding gene, rbcL, was under positive selection. Phylogenetic analyses based on 78 shared plastid protein-coding sequences and 29 nrDNA sequences strongly supported the monophyly of Pourthiaea. As for the relationship with other genera in our phylogenies, Pourthiaea was sister to Malus in plastome phylogenies, while it was sister to the remaining genera in nrDNA phylogenies. Furthermore, significant cytonuclear discordance likely stems from hybridization events within Pourthiaea, reflecting complex evolutionary dynamics within the genus. Our study provides valuable genetic insights for further phylogenetic, taxonomic, and species delimitation studies in Pourthiaea, as well as essential support for horticultural improvement and conservation of the germplasm resources.

Rediscovery of the rare Cladochroa chnoosporiformis Skottsberg from the Falkland Islands and its merger with Utriculidium durvillei Skottsberg

Abstract The Subantarctic brown alga Cladochroa chnoosporiformis had been collected only on one occasion by Carl Skottsberg in 1907 from Port Philomel, West Falkland, Falkland Islands, resulting in its formal taxonomic description. Due to the lack of reports since then, doubts remained about its existence and identity. Within the framework of this study, Cladochroa was rediscovered 106 years after its original description at its type locality, confirming its existence and the morphological features described by Skottsberg. The re-collection enabled molecular studies on field material and isolated cultures. Sequences of nrDNA, rbcL, and 5′-COI suggest that C. chnoosporiformis is conspecific with Utriculidium durvillei, which has nomenclatural priority. However, the morphologies of C. chnoosporiformis and U. durvillei are significantly different. Utriculidium may be the gametophyte generation of Cladochroa, or hitherto unknown factors cause highly different morphologies without alternating generations.

Morphological and Molecular Characterization of the Pathogen Associated with Infected Leaf and Fruits of Tomato

This investigation describes the morpho-molecular characterization of the pathogen associated with infected leaf and fruits of tomato (Solanum lycopersicum L.). The fungal pathogen was identified based on their cultural morphology, microscopic features and analysis of Internal Transcribed Spacer (ITS) region sequences of nuclear ribosomal DNA (nrDNA). Cultural morphology including colour of the young and mature colony, growth pattern, concentric rings etc. and microscopic features including shape and size of microconidia, macroconidia, phialide, shape of apical and basal cells of macroconidia, septation in conidia, inter-septal distance and formation of chlamydospores corroborated the identity with the pathogenic fungi Fusarium oxysporum. The phylogenetic analysis based ITS regions sequences of nrDNA of the fungal isolate showed 100% identity with Fusarium oxysporum. Thus the ITS of nrDNA sequences validated the morphological data. Pathogenicity test also reconfirmed the identity of the test isolate of Fusarium oxysporum. The Chittagong Univ. J. B. Sci.,Vol. 10(1 &2):31-40, 2020.

Phylogenetic incongruence in an Asiatic species complex of the genus Caryodaphnopsis (Lauraceae)

BackgroundCaryodaphnopsis, a group of tropical trees (ca. 20 spp.) in the family Lauraceae, has an amphi-Pacific disjunct distribution: ten species are distributed in Southeast Asia, while eight species are restricted to tropical rainforests in South America. Previously, phylogenetic analyses using two nuclear markers resolved the relationships among the five species from Latin America. However, the phylogenetic relationships between the species in Asia remain poorly known.ResultsHere, we first determined the complete mitochondrial genome (mitogenome), plastome, and the nuclear ribosomal cistron (nrDNA) sequences of C. henryi with lengths of 1,168,029 bp, 154,938 bp, and 6495 bp, respectively. We found 2233 repeats and 368 potential SSRs in the mitogenome of C. henryi and 50 homologous DNA fragments between its mitogenome and plastome. Gene synteny analysis revealed a mass of rearrangements in the mitogenomes of Magnolia biondii, Hernandia nymphaeifolia, and C. henryi and only six conserved clustered genes among them. In order to reconstruct relationships for the ten Caryodaphnopsis species in Asia, we created three datasets: one for the mitogenome (coding genes and ten intergenic regions), another for the plastome (whole genome), and the other for the nuclear ribosomal cistron. All of the 22 Caryodaphnopsis individuals were divided into four, five, and six different clades in the phylogenies based on mitogenome, plastome, and nrDNA datasets, respectively.ConclusionsThe study showed phylogenetic conflicts within and between nuclear and organellar genome data of Caryodaphnopsis species. The sympatric Caryodaphnopsis species in Hekou and Malipo SW China may be related to the incomplete lineage sorting, chloroplast capture, and/or hybridization, which mixed the species as a complex in their evolutionary history.

Molecular and morphological evidence supports the resurrection of Chrysospleniumguangxiense H.G.Ye & Gui C.Zhang (Saxifragaceae).

Chrysospleniumguangxiense H.G.Ye & Gui C.Zhang was first described as a new species in 1994 but later synonymized in the Flora of China treatment with C.glossophyllum H.Hara. Plastid genomes and nrDNA sequences were used to infer the phylogenetic relationships of selected taxa in Chrysosplenium. Our phylogenetic analyses revealed that C.guangxiense belongs to sect. Alternifolia, is closely related to Chrysospleniumhydrocotylifolium H.Lév. & Vaniot but distant from C.glossophyllum. Morphologically, C.guangxiense could be easily distinguished from C.glossophyllum by having robust rhizomes, basal leaves with a long cuneate base and fewer teeth in the margin, curled sepal margins, and red, larger seeds. It could also be easily distinguished from C.hydrocotylifolium by possessing long elliptic leaves and a long cuneate leaf base. Along with the phylogenetic studies, the complete plastid genome of C.guangxiense was also reported. The plastid genome was 154,004 bp in length and comprised two inverted repeats (IRs) of 28,120 bp, separated by a large single-copy of 80,646 bp and a small single-copy of 17,118 bp. A total of 111 functional genes were discovered, comprising 78 protein-coding genes, 29 tRNA genes, and four rRNA genes. Based on assessment of morphological and molecular data Chrysospleniumguangxiense H.G.Ye & Gui C.Zhang is resurrected from C.glossophyllum H.Hara at species level. A global conservation assessment classifies C.guangxiense as Vulnerable (VU).

MORPHOLOGICAL AND NRDNA-ITS SEQUENCES-BASED IDENTIFICATION AND DISTRIBUTION OF VOLVOPLUTEUS EARLEI IN PAKISTAN

Volvopluteus is represented by seven species distributed in America, Asia and Europe. They occur in the tropical regions growing as saprobes on wood debris and leaves, in grassy fields and forests. To explore the macrofungal diversity, different localities in Punjab were visited and collections were made. Among these several collections were found similar to Volvopluteus species. They were analyzed morphologically and phylogenetically using ITS sequences of nrDNA. Comparative analysis on the basis of morphological and anatomical features revealed that these collections represent V. earlei . Maximum likelihood phylogeny also showed the position of current sequences in a same clade with already known V. earlei sequences with 74% bootstrap value. Volvopluteus earlei is being described from different areas of Pakistan with variety of climatic conditions from warm semi-arid climate of Kasur, Lahore and Sheikhupura districts, humid subtropical climate of Sialkot district, in Punjab and warm semi-arid to humid subtropical climate of Swat district, Khyber Pakhtunkhwa. The occurrence of V. earlei in different climatic zones represents its wide distribution range and ecological amplitude in the country.

A new species of Odontarrhena (Brassicaceae) endemic to Greek ultramafics: From taxonomy to metal accumulation behavior

AbstractA new species of Odontarrhena (Brassicaceae) is described from Mount Vourinos in western Macedonia, Greece. The species is restricted to the ridge and the northern slopes of Mt. Vourinos above 1500 m a.s.l. and grows on stony slopes and dry rocky grassland on ultramafic soil with elevated trace metal concentrations. Based on morphological, karyological, and nrDNA sequences, the species is tetraploid with supernumerary B‐chromosomes (2n = 4× = 32 + 2B) and related to the Balkan endemic Odontarrhena decipiens. It differs from the latter mainly by the habit of subshrub with woody base and a denser indumentum of stellate trichomes, resulting in a white‐silvery color of the leaves and shoots. The presence of four degenerate positions in the ITS1 region was detected only in the new species from Mt. Vourinos. Shoot Ni concentrations determined by x‐ray fluorescence analysis and atomic absorption spectroscopy were largely variable (6200–18,700 μg g−1 dw), but always significantly higher than in roots. Hydroponic trials confirmed the typical features of Ni hyperaccumulating plants, such as growth stimulating effect at low metal doses and shoot metal concentration above the hyperaccumulation threshold. The new species of Odontarrhena is a Ni hyperaccumulator with substantial aboveground biomass production, making it a promising candidate for phytomining applications.

Skmer approach improves species discrimination in taxonomically problematic genus Schima (Theaceae)

Genome skimming has dramatically extended DNA barcoding from short DNA fragments to next generation barcodes in plants. However, conserved DNA barcoding markers, including complete plastid genome and nuclear ribosomal DNA (nrDNA) sequences, are inadequate for accurate species identification. Skmer, a recently proposed approach that estimates genetic distances among species based on unassembled genome skims, has been proposed to effectively improve species discrimination rate. In this study, we used Skmer to identify species based on genomic skims of 47 individuals representing 10 out of 13 species of Schima (Theaceae) from China. The unassembled reads identified six species, with a species identification rate of 60%, twice as high as previous efforts that used plastid genomes (27.27%). In addition, Skmer was able to identify Schima species with only 0.5× sequencing depth, as six species were well-supported with unassembled data sizes as small as 0.5 Gb. These findings demonstrate the potential for the Skmer approach in species identification, where nuclear genomic data plays a crucial role. For taxonomically difficult taxa such as Schima, which have diverged recently and have low levels of genetic variation, Skmer is a promising alternative to next generation barcodes.

Testing plastomes and nuclear ribosomal DNA sequences as the next-generation DNA barcodes for species identification and phylogenetic analysis in Acer

BackgroundAcer is a taxonomically intractable and speciose genus that contains over 150 species. It is challenging to distinguish Acer species only by morphological method due to their abundant variations. Plastome and nuclear ribosomal DNA (nrDNA) sequences are recommended as powerful next-generation DNA barcodes for species discrimination. However, their efficacies were still poorly studied. The current study will evaluate the application of plastome and nrDNA in species identification and perform phylogenetic analyses for Acer.ResultBased on a collection of 83 individuals representing 55 species (c. 55% of Chinese species) from 13 sections, our barcoding analyses demonstrated that plastomes exhibited the highest (90.47%) species discriminatory power among all plastid DNA markers, such as the standard plastid barcodes matK + rbcL + trnH-psbA (61.90%) and ycf1 (76.19%). And the nrDNA (80.95%) revealed higher species resolution than ITS (71.43%). Acer plastomes show abundant interspecific variations, however, species identification failure may be due to the incomplete lineage sorting (ILS) and chloroplast capture resulting from hybridization. We found that the usage of nrDNA contributed to identifying those species that were unidentified by plastomes, implying its capability to some extent to mitigate the impact of hybridization and ILS on species discrimination. However, combining plastome and nrDNA is not recommended given the cytonuclear conflict caused by potential hybridization. Our phylogenetic analysis covering 19 sections (95% sections of Acer) and 128 species (over 80% species of this genus) revealed pervasive inter- and intra-section cytonuclear discordances, hinting that hybridization has played an important role in the evolution of Acer.ConclusionPlastomes and nrDNA can significantly improve the species resolution in Acer. Our phylogenetic analysis uncovered the scope and depth of cytonuclear conflict in Acer, providing important insights into its evolution.

Revisiting the bicontinental allopolyploid origin of Australasian Lepidium species with amplicon sequencing of 15 nuclear genes

New Zealand is home to 16 endemic species of Lepidium (Brassicaceae), including two species considered to have become extinct since European colonisation and an additional species shared with Australia. Previous meiotic chromosome counts suggest at least some are high polyploids. A hybrid origin has been proposed for several of them, with African and American species implicated as parents. We generated amplicon sequence data for 15 genes derived from targeted enrichment data from a selection of species endemic to New Zealand, and of African, American, and Australian origin naturalised in New Zealand. These were analysed, along with publicly available genomic data from other Lepidium species. Our results are consistent with earlier work in supporting two main groups of endemic New Zealand Lepidium, corresponding to different dominant nrDNA sequences. Our data suggest that these two groups differ in ploidy (one octoploid, the ploidy of the other uncertain). The octoploid species combine four distinguishable subgenomes and the other species may be the products of allopolyploidisation between octoploid species and a diploid species closely related to, if not, L. africanum. Previously proposed links to American Lepidium are also supported, with at least two Australasian Lepidium subgenomes related to subgenomes present in American polyploid species. The affinities of two further subgenomes present in Australasian Lepidium remain to be determined, but they may also be of American origin. One New Zealand endemic species, L. naufragorum, displays sequences broadly consistent with it being the octodecaploid product of hybridisation between octoploid and decaploid New Zealand groups.

Phylogeny and Taxonomic Revision of the Genus Melanosciadium (Apiaceae), Based on Plastid Genomes and Morphological Evidence

Melanosciadium is considered a monotypic genus and is also endemic to the southwest of China. No detailed phylogenetic studies or plastid genomes have been identified in Melanosciadium. In this study, the plastid genome sequence and nrDNA sequence were used for the phylogenetic analysis of Melanosciadium and its related groups. Angelica tsinlingensis was previously considered a synonym of Hansenia forbesii. Similarly, Ligusticum angelicifolium was previously thought to be the genus Angelica or Ligusticopsis. Through field observations and morphological evidence, we believe that the two species are more similar to M. pimpinelloideum in leaves, umbel rays, and fruits. Meanwhile, we found a new species from Anhui Province (eastern China) that is similar to M. pimpinelloideum and have named it M. Jinzhaiensis. We sequenced and assembled the complete plastid genomes of these species and another three Angelica species. The genome comparison results show that M. pimpinelloideum, A. tsinlingensis, Ligusticum angelicifolium, and M. jinzhaiensis have similarities to each other in the plastid genome size, gene number, and length of the LSC and IR regions; the plastid genomes of these species are distinct from those of the Angelica species. In addition, we reconstruct the phylogenetic relationships using both plastid genome sequences and nrDNA sequences. The phylogenetic analysis revealed that A. tsinlingensis, M. pimpinelloideum, L. angelicifolium, and M. jinzhaiensis are closely related to each other and form a monophyletic group with strong support within the Selineae clade. Consequently, A. tsinlingensis and L. angelicifolium should be classified as members of the genus Melanosciadium, and suitable taxonomical treatments have been proposed. Meanwhile, a comprehensive description of the new species, M. jinzhaiensis, is presented, encompassing its habitat environment and detailed morphological traits.

Molecular Identification and Characterization of Five Ganoderma Species from the Lower Volta River Basin of Ghana Based on Nuclear Ribosomal DNA (nrDNA) Sequences.

Ganoderma is a genus of biomedical fungus that is used in the development of numerous health products throughout the world. The Lower Volta River Basin of Ghana is an undulating land surface covered by extensive vegetation and water bodies and is rich in polypore mushrooms resembling various members of the Ganoderma genus. Despite the extensive biopharmaceutical benefits of Ganoderma spp., the isolates from the Lower Volta River Basin have not been properly characterized, thus limiting their use in the development of biotechnological products. In this study, Ganoderma spp. collected from the Lower Volta River Basin were genetically analyzed using the nuclear ribosomal sequences, the internal transcribed spacer 2 (ITS 2), the complete internal transcribed spacer (ITS), and the nuclear large subunit (nLSU). Blastn search and sequence analysis revealed that the sample we coded as Ganoderma LVRB-2 belongs to G. mbrekobenum, whereas Ganoderma LVRB-1, Ganoderma LVRB-14, and Ganoderma LVRB-16 belong to the species G. enigmaticum. Our analysis further demonstrates that Ganoderma LVRB-17 belongs to the species G. resinaceum. Thus, the five samples collected in the present study were positioned in three different distinct groups, namely G. mbrekobenum, G. enigmaticum, and G. resinaceum. The current data may serve as reference points for future studies.

Phylogeny and taxonomic review of Oreocomopsis with description of a new genus Oreocomoides (Apioideae, Apiaceae)

A revision of the genus Oreocomopsis was carried out based on the study of morphological, anatomical and molecular phylogenetic data based on ITS nrDNA sequences, of which the scope and composition were specified. The identity of O. xizangensis with the previously described O. dochenensis is shown; on the contrary, O. aromatica is singled out as an independent taxon. Ostericum scaberulum var. longiinvolucellatum is included in the genus Oreocomopsis as an independent species. Taxonomic features of the genus and differences from related genera are analysed. The species Oreocomopsis stelliphora has been assigned to the new genus Oreocomoides. The new genus Oreocomoides markedly differs from Oreocomopsis in many morphological characters, such as heterophyllous leaf blades: bipinnate in lower part and narrow-linear pinnate in upper part; bracts polymorphic, linear or pinnate with linear lobules; calyx teeth developed; petals with oval plate, at base with well-developed claw; pedicels rounded; mericarps ribs similar, narrowly-winged, slightly widened at the base.

Phylogenomic analysis of Bupleurum in Western Sichuan, China, including an overlooked new species

A comparative analysis of chloroplast (cp) genomes and 45s nuclear ribosomal DNA (nrDNA), and a phylogenomic study of six closely related species (including an overlooked new species) of genus Bupleurum from the western part of Sichuan Province in southwestern China were performed. The six species are similar morphologically and it is difficult to identify them; moreover, their genetic relationships remain unclear. It was found that the cp genomes of the six Bupleurum species were extremely similar, and they were highly homogeneous in terms of cp genome structure, genes and its arrangement. Intergenic spacer rpl32-trnL, petA-psbJ, trnK-rps16, and the coding gene ycf1 were considered highly variable. In phylogenetic trees constructed based on the complete cp genome, protein-coding sequences, nrDNA and ITS sequences, Chinese Bupleurum species all formed two major clades; among these trees, nrDNA tree had the best species resolution; the highly variable regions showed no advantage over other molecular markers. Among the six Bupleurum species, B. malconense, B. sichuanense were close relatives to B. chinense and B. yinchowense, B. chaishoui may also be a consanguinity, while B. microcephalum, B. wenchuanense, and the new species B. pseudochaishoui were closely related. At the end, the new species B. pseudochaishoui Z. Chao sp. nov. was described and illustrated, and a key to the six species was tabulated.

Authentication of Allium ulleungense, A. microdictyon and A. ochotense based on super-barcoding of plastid genome and 45S nrDNA.

Allium ulleungense (AU) and A. microdictyon (AM) are valuable medicinal and edible vegetables, referred to as mountain garlic in Korea. The identification of AU, AM and a neighboring species A. ochotense (AO) is difficult because of their morphological similarities. We collected samples from three species and 46 cultivated collections to understand the genetic diversity of these valuable Allium species. Among them, we sequenced six collections, including three species and three cultivating collections to obtain data from the plastid genome (plastome) and nuclear 45S ribosomal DNA (nrDNA) for super-barcoding. The AM and AO showed around 60 single nucleotide polymorphisms (SNPs) and 39 Insertion/Deletion (InDels) in the plastome but no variations in the nrDNA sequences. Conversely, the AU and AM showed more than 170 SNPs and 80 InDels in the plastomes, and 20 SNPs and 1 InDel were found in the 45S nrDNA sequences. Among the three cultivating collections, one TB collection was determined to be the AU type in both plastome and nrDNA sequences. However, the other two collections, JB and SA, showed the AM type plastome but were heterozygous in the 45S nrDNA sequences, indicating both AU and AM types (putative AM x AU hybrid). Ten molecular markers were developed based on sequence variations to identify these three species and assess their genetic diversity. A total of 49 collections were genotyped using the ten developed markers and classified into five groups: 14 AU, 22 AM, 1 AO, 3 putative AM x AU hybrids, and 9 putative AU x AM hybrid collections. Super-barcoding with plastomes and nrDNAs revealed the genetic diversity of the three Allium species and putative hybrids between species. The newly developed markers will facilitate species and hybrid identification, thereby benefiting marker-assisted molecular breeding of Allium species.

Acarospora americana (Acarosporaceae), a new species for Eurasia from the European part of Russia

A lichen species Acarospora americana H. Magn., new to Russia and Eurasia, was discovered on the territory of the Pavlovsk granite quarry in the Voronezh Region. A detailed description of morphological and anatomical features is given, chemotaxonomic analysis is carried out. A comparison is made with closely related species: A. fuscata (Ach.) Arnold and A. veronensis A. Massal. ITS nrDNA sequence is obtained.

PHYLOGENY OF <i>TRICHIA BRUNNEA</i> AND NEW NAMES IN THE GENUS <i>ARCYRIA</i> (<i>TRICHIALES</i>, <i>MYXOMYCETES</i>)

Recent phylogenetic studies indicate taxonomic uncertainty of some species in the genera Arcyria (Arcyriaceae) and Trichia (Trichiaceae). For example, a phylogenetic position of Trichia brunnea still is not resolved. We revised a taxonomic position of this species based on extensively sampled 18S nrDNA sequences, as well as a morphological analysis of sporocarps and spores. The nomenclatural history of T. brunnea is briefly presented and acomprehensive morphological description of the species is provided. In result, we support the transfer of T.brunnea to Arcyria. Because of the name Arcyria brunnea exists already, we propose a new name, A. brunneo-iridescens (= Trichia brunnea).

<i>SIDERA TIBETICA</i> (<i>HYMENOCHAETALES</i>, <i>BASIDIOMYCOTA</i>), A NEW SPECIES TO RUSSIA

The first findings of recently described polypore fungus Sidera tibetica are revealed in the Caspian lowland forests of the Samursky National Park in the Republic of Dagestan, Russia. Basidiomata collected on Pinus brutia var. eldarica were studied by both light microscopy and molecular methods. Detailed information on new localities and habitats of Sidera tibetica as well as the collection numbers of specimens deposited in the Mycological Herbarium of the Komarov Botanical Institute of RAS (LE) are provided. Two complete sequences of ITS1–5.8S–ITS2 nuclear ribosomal DNA for Caucasian specimens of S. tibetica have been obtained and submitted to the GenBank database. Newly generated sequences are formed a separate well-supported clade in the Maximum Likelihood phylogenetic analysis together with all available ITS nrDNA sequences of S. tibetica originated from Belarussian and Chinese collections including the reference sequence from a holotype.