nrDNA ITS Sequences Research Articles

Scorzonera ahmet-duranii sp. nov. (Asteraceae) from southwest Anatolia, and its phylogenetic position

Scorzonera ahmet-duranii S. Makbul & Coskuncelebi sp. nov. (Asteraceae) is described and illustrated as a new species endemic to Turkey. It is morphologically similar to S. semicana DC., but differs by its rootstock, deeply undulating basal leaves and glabrous achenes. Additionally, the size and micro-morphological properties of achenes and some anatomical traits of the leaf and stem are helpful in distinguishing these closely related taxa. A phylogenetic analysis based on nrDNA ITS sequence data showed that S. semicana is the sister species of the new taxon presented in this study.

<p class="HeadingRunIn"><strong><em>Navarretia furnissii</em> (Polemoniaceae), a new diploid species from the intermountain western United States distinguished from tetraploid <em>Navarretia saximontana</em></strong></p>

Morphological and DNA-based characters distinguish a new diploid species centered in the Intermountain Region of the western United States, Navarretia furnissii, from N. saximontana, which is tetraploid. The two species are reciprocally monophyletic in analyses of chloroplast DNA sequences and nrDNA ITS sequences. Navarretia furnissii, presently known from Utah, Idaho, Wyoming, Montana, and Colorado, is distinguished morphologically from N. saximontana by a smaller corolla, greater frequency of pronged calyx lobes, and fewer seeds. A key to Navarretia of the Intermountain Region is presented.

Taxonomic Status and Genetic Variation of Korean Endemic Plants, Eranthis byunsanensis and Eranthis pungdoensis (Ranunculaceae) based on nrDNA ITS and cpDNA Sequences

To reappraise the taxonomic status of two Korean endemic plants, Eranthis byunsanensis and Eranthis pungdoensis, we analyzed five taxa of that genus plus three out-group genera (Cimicifuga, Anemonopsis, and Anemone). In all, 52 representative accessions were examined for nrDNA (ITS) and 43 accessions for cpDNA (trnH–psbA, rps16, trnL, and trnLF). In the ITS region, all of the aligned sequences from E. byunsanensis had the same ribotype as from E. pungdoensis. For the ITS phylogeny, E. pungdoensis could not be distinguished from E. byunsanensis. However, the clade of E. byunsanensis, including E. pungdoensis, was separated from Eranthis pinnatifida of Japan, which has a distinct ribotype and forms a sister group. In our cpDNA analysis, E. byunsanensis showed paraphyly, and the clade of E. pungdoensis was nested within the E. byunsanensis clade. Haplotypes of each population of E. byunsanensis were highly variable, and TCS analysis of that species implied that the Jeju population is ancestral. Moreover, the cp-group of E. pungdoensis was separated from the other cp-groups by five substitutions and five indels. Therefore, based on these DNA data and TCS analysis, we advise that the taxonomic status of E. pungdoensis be treated as E. byunsanensis B. Sun var. pungdoensis (B.U. Oh) S.H. Yeau, C.S. Lee & N.S. Lee, stat. nov.

A new Scorzonera (Asteraceae) species from South Anatolia, Turkey, and its taxonomic position based on molecular data

Scorzonera zorkunensis Coskuncelebi & S.Makbul (Asteraceae) is described and illustrated from Turkey. It grows on serpentine in alpine steppe vegetation together with several endemic Scorzonera L. species in southern Anatolia at altitudes of 2075-2100 m. It is morphologically similar to S. pisidica Hub.-Mor., but it differs in its habit and stem and leaf pubescence. Additionally, the size and micromorphological characters of the achenes and some anatomical traits of the leaves, stems, and roots are helpful in distinguishing these closely related taxa. The phylogenetic analyses based on nrDNA ITS sequence data indicate that S. pisidica is a sister species of the new taxon.

Resolving the Diaporthe species occurring on soybean in Croatia.

Diaporthe (anamorph = Phomopsis) species are plant pathogens and endophytes on a wide range of hosts including economically important crops. At least four Diaporthe taxa occur on soybean and they are responsible for serious diseases and significant yield losses. Although several studies have extensively described the culture and morphological characters of these pathogens, their taxonomy has not been fully resolved. Diaporthe and Phomopsis isolates were obtained from soybean and other plant hosts throughout Croatia. Phylogenetic relationships were determined through analyses of partial translation elongation factor 1-alpha (EF1-α) gene and ITS nrDNA sequence data. By combining morphological and molecular data, four species could be distinguished on soybeans in Croatia. Diaporthe phaseolorum is described in this study and its synonyms are discussed. Diaporthe phaseolorum var. caulivora is raised to species status and the name Diaporthe caulivora is introduced to accommodate it. A species previously known as Phomopsis sp. 9 from earlier studies on sunflower, grapevine, rooibos and hydrangea is reported for the first time on soybean, and is formally described as Diaporthe novem. The well-known soybean pathogen Phomopsis longicolla was also collected in the present study and was transferred to Diaporthe longicolla comb. nov. The presence of these species on herbaceous hosts raises once more the relevance of weeds as reservoirs for pathogens of economically important plants.

A comparative study of Neogymnomyces virgineus, a new keratinolytic species from dung, and its relationships with the Onygenales

Isolations of onygenalean fungi were made recently from different dung samples from Italy. A striking snow-white species with gymnothecial ascomata, developed in damp chamber on dormouse dung collected in a cave, was subjected to keratinolytic tests and morphological, cultural, and phylogenetic studies. The keratinolytic ability of this species, associated with a Chrysosporium anamorph and a sexual state of appendiculate reticuloperidia and oblate ascospores, allows it to be accomodated in Onygenaceae. White ascomata, blunt or subcapitate peridial appendages, pitted ascospores, and tuberculate conidia suggest it to be a new Neogymnomyces, and this was confirmed by parsimony analyses of LSU and ITS nrDNA sequences. Following recent phylogenetic analyses, the morphological and physiological features of order Onygenales and its families are re–examined and discussed. After the introduction of a new species, Neogymnomyces is reviewed and compared with all other genera in Onygenaceae. The Chrysosporium imperfect state of Neogymnomyces virgineus is described and compared to the anamorph of N. demonbreunii. It is also compared to the atypical Chrysosporium merdarium and to several other Chrysosporium species with echinulate to verrucose–tuberculate conidia, isolated from guano, dung, and nitrogen–rich soils in caves. The onygenalean fungi isolated from any kind of dung are discussed and their facultative coprophily ascribed to variable faecal contents of keratin or other degradable substances. A key to the families and genera of the Onygenales is provided.

Bupleurum candollei var. paucefulcrans comb. nov. (Apiaceae) from Guizhou, China: comparison of allied species based on morphology, anatomy and molecular data

The new combination, Bupleurum candollei Wallich ex de Candolle var. paucefulcrans (C. Y. Wu) X. J. He & C. B. Wang, is proposed. The status of this taxon, endemic to Guizhou, China, has been confused since it was first described in 1963. Morphological and anatomical evidence, based primarily on bractlet number and length, umbel number and length, fruit size and shape, and stem structure indicated that B. hamiltonii N. P. Balakrishnan var. paucefulcrans C. Y. Wu is more closely related to B. candollei than to B. hamiltonii. To evaluate the credibility of the morphological similarity, the phylogenetic relationship of B. candollei var. candollei, B. hamiltonii var. hamiltonii and B. candollei var. paucefulcrans were inferred by Bayesian analysis of nrDNA ITS sequences. The molecular analysis is fully congruent with the morphological data and supports the transfer of the variety to B. candollei.

Phylogeny and evolutionary divergence times in Apterosperma and Euryodendron: Evidence of a Tertiary origin in south China

Abstract Apterosperma and Euryodendron, monotypic genera in Theaceae (sensu lato), are endemic and restrictedly distributed in south China. The two genera are not included in the major classification systems. However, their systematic position and origin have been subject to intense debate in the last decade. In this study, the phylogeny and divergence times of both Apterosperma and Euryodendron were inferred using combined dataset of chloroplast DNA trnL-F and atpB-rbcL non-coding sequences and nrDNA ITS sequences. The results from Bayesian inference, maximum parsimony, and maximum likelihood consistently showed that (i) Euryodendron is a valid genus, which is closer to Eurya than to Cleyera and (ii) Apterosperma is a genus of the tribe Theeae along with Tutcheria and Camellia. It was first reported that the divergence time of Apterosperma was 61.98 million years ago (mya), whereas that of Euryodendron 20.51 mya, indicating Tertiary origins in south China. The divergence of Apterosperma appears to be the result of increased ecological opportunity after Cretaceous/Tertiary extinction events and related with high temperatures and high humidity environments. By contrast, the origin of Euryodendron may be associated with historical mountain building events as well as the significant climate changes that established cooler temperatures prevailing until today.

The Caloplaca crenulatella species complex; its intricate taxonomy and description of a new species

AbstractThe Caloplaca crenulatella species complex is monophyletic, based on analysis of ITS nrDNA sequences. It is characterized mainly by its ascospores and a simplified thallus. Caloplaca aquensis, C. borysthenica, C. interfulgens, C. lactea, C. marmorata and C. tominii represent well-defined monophyletic lineages within it. Caloplaca diffusa, described here as a new species, is a well-supported lineage with a distinctive phenotype. Caloplaca crenulatella s. lat. and C. ferrarii s. lat. are heterogeneous taxa appearing in four and two places respectively within our tree. Caloplaca ochracea also belongs to the group, although it has different ascospore characters. Caloplaca gyalolechiaeformis and C. pseudocitrina are later synonyms of C. tominii. Arctic and North American sorediate specimens morphologically very close to C. tominii represent a separate lineage recently recognized as C. erichansenii. The North American Caloplaca nashii has a C. crenulatella-like phenotype but does not belong to the C. crenulatella complex. The identities of Caloplaca lacteoides and Caloplaca epigaea are not clear, but the latter may be a terricolous ecotype of one of the entities within C. crenulatella s. lat. A key to the European species of the group is provided.

Kuramosciadium (Umbelliferae): A New Genus from the Uzbekistanian Part of the Western Tian Shan Mountains

Abstract Kuramosciadium corydalifolium , a new genus and species of Umbelliferae (Apiaceae) from the Kurama Ridge (Western Tian Shan Mountains) in Uzbekistan is described and illustrated. The new taxon is not closely related to any other genus in the flora of Middle Asia or adjacent countries. The analyses of fruit morphology and anatomy and nrDNA ITS sequence data reveal a distant affinity to Ligusticum s. l. and Cnidium s. l. and their allies in the traditional family classifications. In particular, Kuramosciadium is most similar to Sphaenolobium, Paulita, and Seselopsis. The new genus differs from its morphologically closest relative, Sphaenolobium, in its monocarpic life-form, unbranched rootstock, bipinnate leaves with almost sessile segments, brownish (not light yellow) petals, distinctly unequal umbel rays, narrow mericarp commissure, and winged dorsal ribs of mericarps. Kuramosciadium corydalifolium appears to be a rare, narrowly endemic, and its natural populations need protection.

Phylogenetic affiliation of Choiromyces magnusii and C. venosus Tuberaceae Ascomycota) from Spain

The only two species of Choiromyces collected up to now in Spain, C. venosus and C. magnusii, were studied with both morphological and molecular methods. Phylogenetic inference of nrDNA ITS and LSU sequences showed that they should be considered independent species in the genus Choiromyces. Choiromyces venosus is a hypogeous fungus, infrequent but naturally present in the Iberian Peninsula, that is imported into Spain from central Europe without any indication of its origin or proper taxonomic identification. It is usually sold as highly-prized edible species of the genus Tuber such as T. magnatum. Choiromyces magnusii is a more frequent hypogeous fungus in Spain that is commercialized in spring on a local scale together with different species in the genus Terfezia. Additionally, the Australian species Reddellomyces westraliensis, which was introduced with Eucalyptus camaldulensis plantations, is cited here for the first time in Spain and Europe.

Phylogeny of <I>Discosia</I> and <I>Seimatosporium</I>, and introduction of <I>Adisciso</I> and <I>Immersidiscosia</I> genera nova

Discosia (teleomorph unknown) and Seimatosporium (teleomorph Discostroma) are saprobic or plant pathogenic, coelomycetous genera of so-called 'pestalotioid fungi' within the Amphisphaeriaceae (Xylariales). They share several morphological features and their generic circumscriptions appear unclear. We investigated the phylogenies of both genera on the basis of SSU, LSU and ITS nrDNA and β-tubulin gene sequences. Discosia was not monophyletic and was separated into two distinct lineages. Discosia eucalypti deviated from Discosia clade and was transferred to a new genus, Immersidiscosia, characterised by deeply immersed, pycnidioid conidiomata that are intraepidermal to subepidermal in origin, with a conidiomatal beak having periphyses. Subdividing Discosia into 'sections' was not considered phylogenetically significant at least for the three sections investigated (sect. Discosia, Laurina, and Strobilina). We recognised Seimatosporium s.l. as a monophyletic genus. An undescribed species belonging to Discosia with its associated teleomorph was collected on living leaves of Symplocos prunifolia from Yakushima Island, Japan. We have therefore established a new teleomorphic genus, Adisciso, for this new species, A. yakushimense. Discostroma tricellulare (anamorph: Seimatosporium azaleae), previously described from Rhododendron species, was transferred to Adisciso based on morphological and phylogenetic grounds. Adisciso is characterised by relatively small-sized ascomata without stromatic tissue, obclavate to broadly cylindrical asci with biseriate ascospores that have 2 transverse septa, and its Discosia anamorph. Based on these features, it can easily be distinguished from Discostroma, a similar genus within the Amphisphaeriaceae.

Variation in the nrDNA ITS sequences of some powdery mildew species: do routine molecular identification procedures hide valuable information?

During the past years, nrDNA ITS sequences have supported the identification of many powdery mildew fungi because comprehensive analyses showed that differences in these sequences have always correlated with the delimitation of different species and formae speciales of the Erysiphales. Published data, obtained using direct sequencing of the PCR products, suggested that even one to five nucleotide differences in the ITS sequences delimit different, albeit closely related, species, and/or indicate differences in host range patterns. Here we show that such differences in the ITS sequences can be detected even in a single sample of a powdery mildew fungus. We sequenced the ITS region in 17 samples, representing six powdery mildew species, both directly and after cloning the PCR products. Among these, samples of O. longipes exhibited two or three, samples of O. neolycopersici three or four, those of an Oidium sp. from Chelidonium majus up to seven, and a sample of another Oidium sp. from Passiflora caerulea two different ITS types determined after cloning. No ITS nucleotide polymorphisms were found in samples of O. lycopersici and Erysiphe aquilegiae. This suggests that some powdery mildew taxa are more variable at the ITS level than others. Thus, although the ITS sequences determined by direct sequencing represent robust data useful in delimitation and phylogenetic analysis of distinct species of the Erysiphales, these need to be used with precaution, and preferably determined after cloning, especially when dealing with closely related taxa at species and sub-species levels. With this method a hitherto undetected genetic diversity of powdery mildews can be revealed.

Major Lineages of the Genus Lilium (Liliaceae) Based on nrDNA ITS Sequences, with Special Emphasis on the Korean Species

We present most comprehensive phylogenetic analysis of 196 accessions of Lilium representing 83 species and 14 varieties of Lilium and three outgroup genera (Cardiocrinum, Notholirion, and Fritillaria) to investigate infrageneric relationships within Lilium as well as to determine the origin and evolution of Korean species of Lilium. We used the internal transcribed spacer sequences of nuclear ribosomal DNA and phylogenetic analysis using maximum parsimony and Bayesian inference identified several major lineages within Lilium. Only one section, Martagon, turned out to be monophyletic in the study. Three sections, Archelirion, Liriotypus, and Pseudolirium, are not monophyletic because two, one, and two species in each section were placed in other lineage, respectively. Two major lineages of section Leucolirion were confirmed in this study, and as several previous studies suggested, section Sinomartagon is highly polyphyletic. The origin of Lilium hansonii, a Korean endemic to Ullung Island, is perplexing given the fact that it has ribotype of Martagon, while its cpDNA haplotype is similar to Sinomartagon. The origin of another endemic, Lilium amabile, is equally elusive and additional phylogenetic and phylogeographic studies will shed light on their evolutions in Korea. We determined that Lilium callosum var. flavum originated from L. callosum in Southern Korea.

Patterns and processes in the genetic differentiation of the Brachionus calyciflorus complex, a passively dispersing freshwater zooplankton

Elucidating the evolutionary patterns and processes of extant species is an important objective of any research program that seeks to understand population divergence and, ultimately, speciation. The island-like nature and temporal fluctuation of limnetic habitats create opportunities for genetic differentiation in rotifers through space and time. To gain further understanding of spatio-temporal patterns of genetic differentiation in rotifers other than the well-studied Brachionus plicatilis complex in brackish water, a total of 318 nrDNA ITS sequences from the B. calyciflorus complex in freshwater were analysed using phylogenetic and phylogeographic methods. DNA taxonomy conducted by both the sequence divergence and the GMYC model suggested the occurrence of six potential cryptic species, supported also by reproductive isolation among the tested lineages. The significant genetic differentiation and non-significant correlation between geographic and genetic distances existed in the most abundant cryptic species, BcI-W and Bc-SW. The large proportion of genetic variability for cryptic species Bc-SW was due to differences between sampling localities within seasons, rather than between different seasons. Nested Clade Analysis suggested allopatric or past fragmentation, contiguous range expansion and long-distance colonization possibly coupled with subsequent fragmentation as the probable main forces shaping the present-day phylogeographic structure of the B. calyciflorus species complex.

English

The new species Myriophyllum jacobsii (previously recognised variously as M. crispatum, M. simulans, and M. variifolium) is described from southeast Queensland. This species is distinguished from these other taxa primarily by comparably extreme emergent leaf length and novelty in transitional leaves (basal leaves of the emergent stem with pinnae or teeth). This is supported by phylogenetic results based on nrDNA ITS and cpDNA matK-trnK sequence data. The species is also put in a phylogenetic context in relation to other closely related Australian species.

Taxonomy and phylogeny of theCaloplaca cerinagroup in Europe

AbstractUsing ITS nrDNA sequence data, theCaloplaca cerinagroup (Teloschistaceae) is defined here as a monophyletic, but internally richly branched lineage. The group is also characterized by a combination of morphological and anatomical characters. Its internal lineages are supported by phenotypic characters in addition to ecology and distribution. Within the largeC. cerinagroup, we have found at least 20 phylospecies in the temperate zone of the Northern Hemisphere. Two species complexes do not produce any vegetative diaspores: the polyphyletic, corticolousCaloplaca cerinas. lat. (six separated cryptic or semi-cryptic species) and the monophyleticC. stillicidiorums. lat. that grows mainly on plant debris, small shrubs and bryophytes and consists of at least four internal lineages. All lineages producing vegetative diaspores (soredia, blastidia, isidia or lobules) are phenotypically characteristic and represent fairly easily distinguishable species:C. chlorina,C. isidiigera,C. monacensis,C. subalpina,C. thracopontica,C. turkuensisandC. ulmorum. Only the North American sorediateC. pinicolapossibly represents an aggregate of species.Caloplaca sterilisis described as a new species. A key to the phenotypically distinguishable species is provided.Lectotypes are designated forC. albolutea,Caloplaca cerinaf.coronulataand forC. monacensis. The AustralianC. hannesherteliibelongs to this group, but this and other possible species from the Southern Hemisphere are not treated here in detail. Some species traditionally placed in theC. cerinagroup due to their similar morphology are excluded here on the basis of our phenotype examinations and molecular data.Caloplaca albolutea,C. mydalaeaandC. virescensare uncertain taxa and their identities still remain unclear.

Systematic status and phylogenetic relationships of the enigmatic Tanacetum paradoxum Bornm. (Asteraceae, Anthemideae): evidences from nrDNA ITS, micromorphological, and cytological data

In order to evaluate the phylogenetic relationships and taxonomic classification of the Iranian endemic Tanacetum paradoxum Bornm. (Asteraceae, Anthemideae), a molecular analysis based on nrDNA ITS sequences of 16 species of Tanacetum together with representatives of 27 genera of subtribes Artemisiinae and Handeliinae as well as a micromorphological study of achenes and pollen grains was performed. The chromosome number of 2n = 2x = 16 and the genome size of T. paradoxum (2C = 8.81 ± 0.19 pg) are reported here for the first time. Due to the well-supported close phylogenetic relationship of T. paradoxum to the species of the genus Artemisia (Bayesian inference, posterior probability PP = 1), which is supported by cytological (x = 8) and micromorphological features concerning the achene shape and pollen type, the combination Artemisia paradoxa (Bornm.) Sonboli is proposed.

Molecular phylogeny and divergence times estimates of Lilium section Liriotypus (Liliaceae) based on plastid and nuclear ribosomal ITS DNA sequence data

In the present study the phylogeny and the biogeography of the genus Lilium L. section Liriotypus Asch. et Graebn. were investigated and divergence times for the section Liriotypus were calculated. The study group covers Lilium species from Europe, the Italian and Balkan peninsulas, Anatolia, and the Caucasus. Plastid DNA sequence data (the trnC-petN intergenic spacer and petN gene) and nuclear DNA ITS sequence data were used to infer the phylogenetic history of the section Liriotypus. Molecular phylogenetic dating using the molecular clock hypothesis with sequences of nrDNA ITS region was used to calculate the time of diversification within the section Liriotypus and with other members of the genus Lilium. The phylogenetic reconstruction based on combined analysis of plastid and nrDNA ITS sequence data shows that all of the analysed species of section Liriotypus form a well-supported monophyletic clade. However, there are some incongruences between the analysis made by plastid DNA alone and with a combined dataset regarding the positions of L. monadelphum M.Bieb., L. szovitsianum Fisch. & Avé-Lall., L. ciliatum P.H.Davis, and L. akkusianum R.Gämperle. Our molecular dating analysis based on nrDNA ITS sequence data showed that members of the section Liriotypus were separated from the rest of the genus Lilium approximately 9 million years ago and within this section, speciation increased in the last 6 million years.

A phylogenetic analysis of Antrodia s.l. based on nrDNA ITS sequences, with emphasis on rhizomorphic European species

The rhizomorphic European species of Antrodia, belonging to the traditionally called Antrodia radiculosa group, are investigated. On the basis of morphological and molecular analysis, the genus Fibroporia is supported. Specimens from Central Europe previously ascribed to Antrodia radiculosa constitute a species of their own, and are herein described as Fibroporia bohemica. Moreover, a new combination, Fibroporia citrina, is proposed.