ITS Region Of Nuclear Ribosomal DNA Research Articles

Ganoderma gibbosum newly recorded from Pakistan

Ganoderma gibbosum is a new record for Pakistan, identified by morphological and molecular data. DNA sequence analysis of ribosomal 5.8S rRNA gene including the flanking nuclear ribosomal DNA-ITS regions confirmed the Pakistani specimens as G. gibbosum. Morphologically, the specimens are characterized by their non-laccate sessile basidiomata, truncate, short fine minute inter walled pillars, elongated basidiospores (7.5– 10.2 × 4.6–5.9 μm), and greyish to greyish-brown dull pileal surface.

On the identity of Goodyera rosulacea (Orchidaceae: Orchidoideae: Cranichideae: Goodyerinae)

Morphological studies based on the protologues, observations of herbarium specimens and field surveys suggest that Goodyera rosulacea is a synonym of G. brachystegia. According to genetic studies, accessions of G. rosulacea and G. brachystegia form a single clade in the phylogenetic trees obtained from analyses of the nuclear ribosomal DNA ITS region and four plastid regions (accD-psaI, matK, trnK-rps16 and trnL-F). This phylogenetic evidence further underpins the conclusion that the two names refer to one and the same species.

Molecular Phylogeny of <I>Chuquiraga</I> (Asteraceae-Barnadesioideae): Infrageneric Classification and Generic Affinities

Abstract— Chuquiraga is a genus of evergreen shrubs endemic to the arid and semiarid regions of the Andes and southern South America. The genus has been classified into two sections based on its variation in leaf morphology: Chuquiraga and Acanthophylla. Within section Chuquiraga, two series, Chuquiraga and Parviflorae, have been recognized based on variation in size of flower heads. The objectives of this study were to test this classification and to assess the monophyly of Chuquiraga and its intergeneric relationships with the closely related genera Doniophyton and Duseniella. The phylogenetic relationships of 24 of the 27 species and/or subspecies of Chuquiraga (19 of its 22 recognized species), plus 14 species representing seven of the remaining eight genera of Barnadesioideae, and two species of non-barnadesioid Asteraceae were inferred using sequence data from the chloroplast DNA psbA-trnH, rps16-trnK, trnL-rpl32, and/or nuclear ribosomal DNA ITS regions. The plastid and nuclear data sets were analy...

Two new species of Lactarius associated with Alnus acuminata subsp. arguta in Mexico

In pure stands of Alnus acuminata subsp. arguta trees from Sierra Norte de Puebla (central Mexico) two undescribed ectomycorrhizal species of Lactarius were discovered. Distinction of the two new species is based on morphological characters and supported with phylogenetic analyses of the nuclear ribosomal DNA ITS region and part of the gene that encodes for the second largest subunit of RNA polymerase II (rpb2). The phylogenies inferred recovered the two species in different clades strongly supported by posterior probabilities and bootstrap values. The new Lactarius species are recognized as part of the assemblage of ectomycorrhizal fungi associated with Alnus acuminata. Information about these taxa includes the morphological variation achieved along 16 monitories 2010–2013. Descriptions are provided. They are accompanied by photos including SEM photomicrographs of basidiospores and information on differences between them and other related taxa from Europe and the United States.

한국산 피막이속(Hydrocotyle L.) 식물의 분자계통학적 연구

Phylogenetic analyses were conducted to evaluate relationships of 5 taxa of Korean Hydrocotyle, H. spp. found in the Ulleung island including one outgroup (Centella asiatica). The molecular phylogenetic methods based on nuclear ribosomal DNA ITS region and cpDNA trnH-psbA region. Centella asiatica was used outgroup for analysis. As the result, genus Korean Hydrocotyle were grouped by 94% bootstrap value. Korean Hydrocotyle was grouped by four clades; Clade Ⅰ-H. maritima, H. sibthorpides and H. yabei clade Clade Ⅱ- H. nepalensis clade clade Ⅲ- H. ramiflora clade clade Ⅳ- H. spp. clade. H. maritima, H. sibthorpides and H. yabei was not distinguished, seperately. H. spp. was distinctly distinguished other Korean Hydrocotyle.

Nuclear ribosomal DNA-ITS region based molecular markers to distinguish botanical entities traded as ‘Vidari’

‘Vidari’ is an Ayurvedic herbal drug used as aphrodisiac and galactagogue. It is also used in the preparation of Chyavanaprash, an Ayurvedic Nutraceutical. Ayurvedic Pharmacopeia of India correlates tubers of Pueraria tuberosa (Roxb. ex Willd.) DC (Fabaceae) as ‘Vidari’ and Ipomoea mauritiana Jacq. (Convolvulaceae) as Kshiravidari, used as a substitute for Vidari in some parts of India. Tubers of Adenia hondala (Gaertn.) de Wilde (Passifloraceae) and pith of Cycas circinalis L. (Cycadaceae) are also traded in the name of Vidari, creating issues of botanical authenticity of the raw drug.DNA markers to distinguish the botanical entities traded as ‘Vidari’ were developed by amplifying and sequencing the complete nuclear ribosomal DNA – internal transcribed spacer (ITS) region (ITS1, 5.8S rRNA and ITS2) from the genomic DNA, using universal primers. Genetic variation in the rDNA-ITS region was identified and exploited to develop species-specific markers. These markers are efficient and reliable in distinguishing P. tuberosa, I. mauritiana, A. hondala and C. circinalis and can be used as molecular pharmacognostic tools.

Phylogenetic relationships of the Aurantioideae (Rutaceae) based on the nuclear ribosomal DNA ITS region and three noncoding chloroplast DNA regions, atpB-rbcL spacer, rps16, and trnL-trnF

The tribes and subtribes of Aurantioideae, an economically important subfamily of the Rutaceae, have a controversial taxonomic history because a phylogenetic framework has been lacking. In order to construct an evolutionary history and evaluate the most recent classification system [Swingle and Reece 1967. The botany of Citrus and its wild relatives, in: The Citrus Industry, vol. 1, History, World Distribution, Botany, and Varieties. University of California, Berkeley, pp. 190–430], one nuclear and three noncoding chloroplast genes were sequenced and analyzed phylogenetically along with selected non-molecular characters. Taxa representing tribes Citreae and Clauseneae and their six subtribes were sampled. In all analyses Aurantioideae is monophyletic. The majority-rule consensus tree from the combined analysis indicates that the two tribes are not monophyletic. The combined topology is not congruent with the widely used classification of Aurantioideae by Swingle and Reece (1967). The tribes and subtribes are in need of revision.

Phylogenetic Relationships of Gunnera based on Nuclear Ribosomal DNA ITS Region, rbcL and rps16 Intron Sequences

Abstract A previous analysis of two chloroplast gene regions, rbcL and the rps16 intron, showed a clear phylogenetic pattern in Gunnera. However, these regions were not informative enough to completely resolve the phylogeny. In this study the nuclear ITS region was sequenced for 24 specimens representing 22 species of Gunnera. 223 characters out of 819 were informative and supported the same monophyletic groups as the chloroplast gene regions. Because of its greater information content, the ITS region identified additional well-supported clades. In an analysis based on the three gene regions together, 272 characters out of 3154 were informative. The results show that the South American annual, G. herteri is sister to all other species. The African G. perpensa is well-supported as sister to the remaining species, which form two well-defined clades, one with the Malayan G. macrophylla as sister to subgenus Milligania from New Zealand and Tasmania. In the other clade, the South American subgenus Misandra is ...

Candida aurissp. nov., a novel ascomycetous yeast isolated from the external ear canal of an inpatient in a Japanese hospital

A single strain of a novel ascomycetous yeast species belonging to the genus Candida was isolated from the external ear canal of an inpatient in a Japanese hospital. Analyses of the 26S rDNA D1/D2 domain, nuclear ribosomal DNA ITS region sequences, and chemotaxonomic studies indicated that this strain represents a new species with a close phylogenetic relationship to Candida ruelliae and Candida haemulonii in the Metschnikowiaceae clade. This strain grew well at 40 degrees C, but showed slow and weak growth at 42 degrees C. The taxonomic description of Candida auris sp. nov. is proposed (type strain JCM15448T= CBS10913T= DSM21092T).

The evolutionary history of Eryngium (Apiaceae, Saniculoideae): Rapid radiations, long distance dispersals, and hybridizations

Eryngium is the largest and arguably the most taxonomically complex genus in the family Apiaceae. Infrageneric relationships within Eryngium were inferred using sequence data from the chloroplast DNA trnQ– trnK 5′-exon and nuclear ribosomal DNA ITS regions to test previous hypotheses of subgeneric relationships, explain distribution patterns, reconstruct ancestral morphological features, and elucidate the evolutionary processes that gave rise to this speciose genus. In total, 157 accessions representing 118 species of Eryngium, 15 species of Sanicula (including the genus Hacquetia that was recently reduced to synonymy) and the monotypic Petagnaea were analyzed using maximum parsimony and Bayesian methods. Both separate and simultaneous analyses of plastid and nuclear data sets were carried out because of the prevalence of polyploids and hybrids within the genus. Eryngium is confirmed as monophyletic and is divided into two redefined subgenera: Eryngium subgenus Eryngium and E. subgenus Monocotyloidea. The first subgenus includes all examined species from the Old World (Africa, Europe, and Asia), except Eryngium tenue, E. viviparum, E. galioides, and E. corniculatum. Eryngium subgenus Monocotyloidea includes all examined species from the New World (North, Central and South America, and Australia; herein called the “New World sensu stricto” clade) plus the aforementioned Old World species that fall at the base of this clade. Most sectional and subgeneric divisions previously erected on the basis of morphology are not monophyletic. Within the “New World sensu stricto” group, six clades are well supported in analyses of plastid and combined plastid and nuclear data sets; the relationships among these clades, however, are unresolved. These clades are designated as “Mexican”, “Eastern USA”, “South American”, “North American monocotyledonous”, “South American monocotyledonous”, and “Pacific”. Members of each clade share similar geographical distributions and/or morphological or ecological traits. Evidence from branch lengths and low sequence divergence estimates suggests a rapid radiation at the base of each of these lineages. Conflict between chloroplast and nuclear data sets is weak, but the disagreements found are suggestive that hybrid speciation in Eryngium might have been a cause, but also a consequence, of the different rapid radiations observed. Dispersal-vicariance analysis indicates that Eryngium and its two subgenera originated from western Mediterranean ancestors and that the present-day distribution of the genus is explained by several dispersal events, including one trans-Atlantic dispersal. In general, these dispersals coincide with the polytomies observed, suggesting that they played key roles in the diversification of the genus. The evolution of Eryngium combines a history of long distance dispersals, rapid radiations, and hybridization, culminating in the taxonomic complexity observed today in the genus.

Chromones and indolinone alkaloids from Actaea asiatica Hara

1. Subject and sourceActaea asiatica Hara (Ranunculaceae), one of the eight species of genera Actaea, occurs mainly in the north tem-perate zones, e.g. China, North America, Korea, Russia and Siberia (Wang, 1979). The rhizomes of this plant werecollected in Luoping village, Suijiang county, Shaotong area, Yunnan province in July 2004. A voucher specimen(AA-04-0717) has been deposited in the Herbarium of Institute of Medicinal Plant Development, Chinese Academyof Medical Science and Peking Union Medical College. In a recent phylogenetic study of the genera Cimicifuga andActaea, Cimicifuga was transferred to Actaea based on the sequence of nuclear ribosomal DNA ITS region (Comptonet al., 1998).2. Previous workThe circumscriptionsof thegeneraActaea and Cimicifugahas long been debated. In the recent phylogenystudyofCimicifuga and Actaea, Cimicifuga has been transferred to Actaea based on the sequence of nuclear ribosomal DNAITS region (Compton et al., 1998).OurpreviousphytochemicalinvestigationonA.asiaticaresultedintheisolationof9,19-cycloartanetriterpenesap-onions and cinnamic acid derivatives, which are the major constituents of Cimicifuga plants (Gao et al, 2006a,b). Inour continuous study on the chemical constituents of A. asiatica, four furan chromones and two indolinone alkaloidswere obtained.

Natural hybridization origin of Rhododendron agastum (Ericaceae) in Yunnan, China: inferred from morphological and molecular evidence

The natural hybridization that occurs between two sympatric species of Rhododendron subgenus Hymenanthes in Yunnan, China, was investigated. The assumed parents, Rhododendron delavayi Franch. and R. decorum Franch., are morphologically distinct, and the putative hybrid species, R. agastum Balf. f. et W. W. Smith, has an intermediate morphology. We used the main morphological characters, sequences of the nuclear ribosomal DNA ITS region, and the chloroplast DNA trnL-F intronspacer to analyze the three species, and compared these morphological and molecular data with an artificial hybrid between R. decorum (female symbol) x R. delavayi (male symbol). From the results, we conclude that R. agastum is a natural hybrid between a female R. delavayi and a male R. decorum.

Wax plants disentangled: A phylogeny of Hoya (Marsdenieae, Apocynaceae) inferred from nuclear and chloroplast DNA sequences

Hoya (Marsdenieae, Apocynaceae) includes at least 200 species distributed from India to the Pacific Islands. We here infer major species groups in the genus based on combined sequences from the chloroplast atpB-rbcL spacer, the trnL region, and nuclear ribosomal DNA ITS region for 42 taxa of Hoya and close relatives. To assess levels of ITS polymorphism, ITS sequences for a third of the accessions were obtained by cloning. Most ITS clones grouped by species, indicating that speciation in Hoya usually predates ITS duplication. One ITS sequence of H. carnosa, however, grouped with a sequence of the morphologically similar H. pubicalyx, pointing to recent hybridization or the persistence of paralogous copies through a speciation event. The topology resulting from the combined chloroplast and nuclear data recovers some morphology-based sections, such as Acanthostemma and Eriostemma, as well as a well-supported Australian/New Guinean clade. The combined data also suggest that morphological adaptations for ant-symbiosis evolved at least three times within Hoya.

Phylogenetics and Biogeography of Alnus (Betulaceae) Inferred from Sequences of Nuclear Ribosomal DNA ITS Region

Sequences of nuclear ribosomal DNA ITS region were used to estimate phylogenetic relationships of Alnus. We recognize three major clades in Alnus, including subgenera Alnobetula, Clethropsis, and Alnus; subgenus Alnobetula is sister to subgenera Clethropsis and Alnus. The eastern Asian subgenus or section Cremastogyne is embedded in the subgenus Alnus clade. Alnus nepalensis is part of subgenus Alnus, not subgenus Clethropsis. Alnus maritima is part of subgenus Clethropsis (excl. A. nepalensis). Long and short branching pattern, sessile winter bud, and 2‐yr phenology are plesiomorphies in Alnus, while 1‐yr floral phenology and fall blooming are derived features. The simple axillary female inflorescence has evolved more than once in Alnus. Central and South American species of Alnus are derived from migrants from eastern Asia via the Bering land bridge and western North America. In subgenus Clethropsis, A. formosana of eastern Asia is more closely related to eastern North American species than to the other Asian species, A. nitida. The low sequence divergence within both the A. incana and A. viridis species complexes indicates their recent history of diversification in the circumpolar areas.

Phylogenetic relationships within the ?core? Laureae ( Litsea complex, Lauraceae) inferred from sequences of the chloroplast gene mat K and nuclear ribosomal DNA ITS regions

A phylogenetic analysis of the ‘core’ Laureae (Litsea complex) was conducted using the chloroplast gene matK and nuclear ribosomal DNA ITS sequences to investigate generic relationships and boundaries within the complex. Despite low genetic divergence for matK, rooting of the tree with Sassafras resulted in Iteadaphne as the basal member of the complex and five resolved clades: a Neolitsea clade and then Laurus, Parasassafras, Litsea and Lindera clades in a large polytomy with unresolved Lindera sections plus Umbellularia. A combined analysis of the data (identical to the ITS results) provided a more resolved phylogeny of the Laureae, with four major lineages: the Laurus, Litsea, Lindera and Actinodaphne II clades. These clades also appear to reflect the importance of inflorescence structure and ontogeny within the Laureae, as well as data from cuticular micromorphology, but there was no support for traditional generic characters such as 2- versus 4- celled anthers. As a result, genera such as Actinodaphne, Litsea, Neolitsea and Lindera were polyphyletic in all analyses. Parasassafras was related to Sinosassafras by the matK data, but distant from it in the ITS and combined analyses.

Phylogenetic relationships of Empetraceae inferred from sequences of chloroplast gene matK and nuclear ribosomal DNA ITS region

We used sequences of nrDNA ITS and chloroplast gene matK to evaluate the monophyly of Empetrum and Corema and to examine phylogenetic relationships of the Empetraceae. Sequences of these two DNA markers were obtained for 11 plant samples, representing species of Empetrum from both the Southern and Northern Hemispheres, species and subspecies of Corema, and the monotypic Ceratiola. Sequences of four species of Rhododendron were used for rooting purposes. Our results show that species of Empetrum form a clade sister to the clade containing both Corema and Ceratiola. These two clades are strongly supported in both the matK and ITS trees, suggesting that Ceratiola is more closely related to Corema than to Empetrum, and is not of a hybrid origin between the ancestors of the latter two genera. In the matK tree, Corema conradii is more closely related to Ceratiola than to Corema album and C. album subsp. azoricum, whereas in the ITS tree, Ceratiola is allied with Corema album and C. album subsp. azoricum. This suggests that C. conradii might be a hybrid between ancestral populations of Ceratiola and C. album. The monophyly of Empetrum rejects the hypothesis of its independent origin in the two Hemispheres. Our trees also suggest the fact that the modern amphitropical distribution of Empetrum is the result of long distance dispersal, not of the vicarious events.

Botryosphaeria spp. isolated from apple and several deciduous fruit trees are divided into three groups based on the production of warts on twigs, size of conidia, and nucleotide sequences of nuclear ribosomal DNA ITS regions

We examined the phytopathological and biological characters ofBotryosphaeria spp. isolated from apples and other deciduous fruit trees, and determined the nucleotide sequences of their rDNA ITS regions. TheBotryosphaeria isolates from deciduous fruit trees can be divided into three groups based on their production of warts on twigs, size of the conidia, and nucleotide sequences of rDNA ITS 1, ITS 2 and 5.8S rDNA. Isolates ofBotryosphaeria in ITS group A produced conidia of intermediate size and showed warts on infected twigs prior to the development of ring rot on fruit. This group was common on deciduous fruit trees in Japan as a causal agent of ring rot and wart bark diseases of apples and pears; and it appears similar to theB. dothidea from the US that was isolated from apple exhibiting white rot. The ITS group BBotryosphaeria produced small conidia and induced shoot blight without wart development prior to the development of ring rot on fruit. This group was localized on pear, persimmon, and kiwi fruit in restricted areas of Japan. The ITS group CBotryosphaeria consisted ofB. obtusa, the causal agent of apple black rot in the US, which produced large dark brown conidia.

Intraspecific comparisons of Laetiporus sulphureus isolates from broadleaf and coniferous trees in Europe

Laetiporus sulphureus causes heart-rot in deciduous trees and conifers. European isolates were examined using nuclear DNA markers as well as somatic and sexual compatibility. Pairing tests for somatic compatibility with isolates from 20 different host individuals revealed that each tree is normally colonized by a different genet. The hyphae are multinucleate, basidiospores are binucleate, and conidia contain 2–6 nuclei. Basidiospore germination was erratic, and no clear mating pattern was observed. In one case all single spore isolates from the same basidioma were compatible with each other. Single spore isolates from coniferous and from broadleaf trees were incompatible. The nuclear ribosomal DNA ITS regions from six isolates of different origin revealed nucleotide distances of up to 14.6%. Phylogenetic analysis resulted in a single clade for all isolates. Within this clade, a subclade including only the isolates from gymnosperm hosts was present, indicating that these isolates were derived from ancestral lines from broadleaf hosts. While there is evidence that more than one species or ecotype is represented within the current definition of L. sulphureus , circumscription of additional taxa, and separations within this taxon, remain unclear.

Phylogeny of Actaea including Cimicifuga (Ranunculaceae) inferred from nrDNA ITS sequence variation

Abstract Phylogenetic analysis of the rapidly changing nuclear ribosomal DNA ITS region in all 23 taxa of Cimicifuga and in all five taxa of Actaea was performed. The phylogenetic affinities of Souliea were investigated. Eranthis and Anemonopsis were shown to be separated from the ingroup by a similar number of steps. A monophyletic clade including all studied species of Actaea, Cimicifuga and Souliea is strongly supported and within it a group consisting of all Actaea species and Cimicifuga racemosa is identified. A large but weakly supported clade consisting of only Eurasian species is divided into two subclades; one with taxa possessing yellow staminodia, the other with taxa possessing white staminodia. Three other well supported groups are indicated: one clade consisting of two North American species with long carpel stipes: C. americana and C. laciniata , another with three North American species with short carpel stipes: C. arizonica, C. elata and C. rubifolia , and a third with three eastern Asian species with caducous bracts: C. biternata, C. japonica and C. purpurea . Cimicifuga is paraphyletic at least with respect to Actaea and possibly also with respect to Souliea .