Nuclear Ribosomal ITS Sequences Research Articles

Liparis wenshanensis, a new orchid species from China: Evidence from morphological and molecular analyses

A new orchid species, Liparis wenshanensis, discovered in Yunnan, China is described and illustrated in this study based on morphological and molecular analyses. A detailed comparison between the newly discovered orchid and other members of the genus, Liparis, was conducted. The new plant is characterized by the combination of the following features: a long rachis with 45 to 55 flowers; white sepals, petals and column; a greenish lip with a purplish center; strongly recurved and revolute dorsal sepals and petals; strongly recurved, oblong lateral sepals; a cordate lip that is strongly deflexed below the middle, with a two-lobed apex and a two-lobed callus at the base; an arcuate column with a lamella extending along the center almost to the stigma, and with a pair of broad wings toward the apex. These features distinguish the new orchid from all other known species of Liparis. We proceeded to a phylogenetic analysis to ascertain the systematic position of this enigmatic species. Molecular analyses based on nuclear ribosomal ITS and plastid matK DNA sequence data supports the recognition of L. wenshanensis as a distinct species.

Generic boundaries of Leucochrysum and Waitzia (Asteraceae: Gnaphalieae)

The Australasian clade of Gnaphalieae (Asteraceae) is an ecologically diverse group of species whose generic limits and phylogenetic relationships are still partly unresolved. Previous studies including hybridisation trials, morphological characterisation and preliminary phylogenetic analyses within the Gnaphalieae have suggested that two genera, namely, Waitzia and Leucochrysum, require further investigation into their generic boundaries. To explore the phylogenetic relationships of both genera, the present study used a combination of morphological and molecular approaches. The character traits of herbarium specimens from 14 species and six infraspecific taxa of Waitzia, Leucochrysum and Anemocarpa were examined. Chloroplast (psbA–trnH) and nuclear ribosomal ITS and ETS sequences were generated for phylogenetic analysis. Our findings support Waitzia in its current circumscription as a monophyletic group, whereas Leucochrysum was found to be polyphyletic. Leucochrysum fitzgibbonii was found to be the sister group of Waitzia and shares characters of the involucral bracts, indumentum and growth habit with that genus. The species is formally transferred to the genus Waitzia as W. fitzgibbonii.

Sinalliaria, a new genus of Brassicaceae from eastern China, based on morphological and molecular data

Sinalliaria is described here as a new genus of the family Brassicaceae from eastern China, based on the morphological characters and molecular sequences. Sinalliaria differs from the related genus Orychophragmus in having basal leaves petiolate, simple or rarely with 1‒3 lateral lobes (not pinnatisect); cauline leaves petiolate, cordate at base (not sessile, auriculate or amplexicaul at base); petals obovate to narrowly obovate, claw inconspicuous (not broadly obovate, with a claw as along as sepal); siliques truncate (not long-beaked) at apex. The microscopic characters of seed testa also show significant differences between Sinalliaria and Orychophragmus. Phylogenetic evidence from DNA sequences of nuclear ribosomal ITS and plastid region trnL-trnF indicates that Sinalliaria is a distinct group related to Orychophragmus and Raphanus, but these three genera do not form a clade. The new genus Sinalliaria is endemic to eastern China and has only one species and one variety. The new combinations, S. limprichtiana (Pax) X. F. Jin, Y. Y. Zhou & H. W. Zhang and S. limprichtiana var. grandifolia (Z. X. An) X. F. Jin, Y. Y. Zhou & H. W. Zhang are proposed here.

Goodyera malipoensis (Cranichideae, Orchidaceae), a new species from China: Evidence from morphological and molecular analyses

In this study, we describe a new orchid species, Goodyera malipoensis, from Yunnan, China. We have performed morphological and molecular analyses on this new species. A detailed comparison between the newly discovered orchid and other members of Goodyera was conducted. The new plant is characterized by having a dense brownish green pubescence on the peduncle. Its ovate-lanceolate petal is unique in Goodyera genus. The hypochile is deeply concave-saccate, and inside there are two papillose rows on each side. These features distinguish the new orchid from all other known species of Goodyera. The molecular study based on nuclear ribosomal ITS sequence data and morphological differences support G. malipoensis as a distinct species.

Plastid DNA sequence data help to clarify phylogenetic relationships and reticulate evolution inLycoris(Amaryllidaceae)

The temperate East Asian genus Lycoris is a well known lineage of ornamental geophytes consisting of at least 20 species, some of which are thought to be of natural hybrid origin. Previous genetic studies have supported this hypothesis, but these have relied solely on the use of karyology and/or nuclear ribosomal ITS sequences. No plastid DNA data have been available to address interspecific relationships within Lycoris until now. In this study, 500 individuals from 29 populations representing 16 of the 20 published Lycoris spp. were sampled, and DNA sequences were generated for two plastid markers (trnS-trnfM and trnC-ycf6). From these data we inferred phylogenetic relationships among the sampled taxa at the species and population levels using concatenated phylogenetic methods. A well resolved and strongly supported phylogenetic reconstruction for Lycoris was obtained. Although the plastid DNA topology differs from that derived previously using ITS, both genomes produce trees that cluster Lycoris spp. into three clades. One of these, containing polyploid taxa such as L. albiflora, L. caldwellii, L. straminea and L. houdyshelii, shows strong evidence of reticulation, and we discuss the identity of potential parents of these allopolyploids. In contrast, we offer evidence that challenges the hypothesis that triploid individuals of L. radiata are the result of hybridization. Instead, they appear to be autotriploids that have arisen in more than one location. By comparing the phylogenetic results obtained using nuclear genomic data to those from the plastid genome, a much clearer picture of the role that hybridization and reticulation have played in the evolution of Lycoris is emerging.

Exploring Phylogenetic Relationships within a Broadly Distributed Northern Hemisphere Group of Semi-Aquatic <I>Iris</I> Species (Iridaceae)

Three series, Prismaticae, Tripetalae, and Laevigatae, in Iris subgenus Limniris comprise a clade of nine species with an affinity for wetland environments. Prior work has failed to resolve phylogenetic relationships among these taxa. We used maximum likelihood and Bayesian inference methods to analyze plastid and nuclear ribosomal ITS sequence data to infer a robust phylogeny for this circumboreal group. Our analyses recovered clades that do not reflect current series circumscriptions and show that species from Tripetalae and Laevigatae comprise one clade. Species relationships also do not reflect geographic proximity, as Asian and North American species do not assort into regional clades. This finding suggests that multiple exchanges between Asia and North America are required to explain current distributions and refutes the hypothesis that Asian taxa are the earliest diverging lineage within the clade.

Liparis funingensis (Orchidaceae; Epidendroideae; Malaxidae), a new species from Yunnan, China: evidence from morphology and DNA

A new orchid species, Liparis funingensis, from Yunnan, China, is described and illustrated in this study based on morphological and molecular analyses. A detailed comparison between the newly discovered orchid and other members of Liparis was performed. This new plant is characterized by an obovate lip and is trilobed. The sidelobes are semiorbicular and fleshy, and the midlobe is short and bilobed with triangular lobes. The disc has a deeply bilobed basal callus and two longitudinal lamellae from the base extending to above the middle. There are four pollinia in two pairs, with each pair exhibiting long caudicles without a viscidium. The rostellum also has a bursa synovialis. These features distinguish this new orchid from all other known species of Liparis. A phylogenetic analysis was subsequently performed to determine the systematic position of this enigmatic species. A molecular study based on nuclear ribosomal ITS and plastid matK DNA sequence data indicates that L. funingensis is a member of L. layardii subclade.

미세구조학적 형질 및 핵 리보솜 DNA의 ITS 염기서열에 의한 긴병꽃풀속(꿀풀과)의 계통분류학적 연구

미세구조학적 형질 및 핵 리보솜 DNA의 ITS 염기서열에 의한 긴병꽃풀속(꿀풀과)의 계통분류학적 연구

Molecular phylogeny of Daucus (Apiaceae): Evidence from nuclear ribosomal DNA ITS sequences

The Apiaceae genus Daucus consists of approximately 25 species (including carrots) which are characterized by the presence of bracts in pedunculate umbels, dorsally compressed mericarps, hairs on primary ridges, and uniseriately arranged spines on the secondary ridges of the fruit. Taxonomically, Daucus has been considered to be one of the most problematic genera in the Apiaceae due to the highly variable fruit morphology. Despite taxonomic controversy and economic importance of the genus, no rigorously constructed estimate of phylogenetic relationships exists. To examine generic limit and relationships among species of Daucus and its putatively related taxa, phylogenetic analyses of characters derived from nuclear ribosomal DNA ITS sequences were conducted. Two major clades emerged within Daucus, but neither of them have been previously recognized using morphological characters. The phylogeny also provides taxonomic status of recently reported new species of Daucus, D. arcanus and D. conchitae.

A Remarkable New Species of Liparis (Orchidaceae) from China and Its Phylogenetic Implications

In the present study, we formally describe Liparis pingxiangensis as a new species from Guangxi, China on the basis of morphological and molecular phylogenetic analyses. It is easily distinguished from closely related species by strongly curved column without column wings, and broadly rhombic-elliptic lip with 2 uncinate calli at the base. In particular, it differs most markedly from its congeners in possessing two pollinia attached by long and prominent caudicles (not stipes), to a distinct sticky disc. This type of pollinarium, as far as we know, is not found in any other species of Liparis, and is also unique among the orchids with waxy pollinia. We then proceeded to a phylogenetic analysis to ascertain the systematic position of this enigmatic species. Molecular study based on nuclear ribosomal ITS and plastid matK DNA sequence data supports L. pingxiangensis as a distinct species, which forms an independent lineage sister to L. nervosa and its allies (93% BS, 1.00 BPP). In the light of previous work, the findings have important implications for a better understanding of the well-supported pattern mainly based on vegetative features in Malaxideae.

An Endophytic Sanguinarine-Producing Fungus from Macleaya cordata, Fusarium proliferatum BLH51

Fermentation processes using sanguinarine-producing fungi other than Macleaya cordata may be an alternative way to produce sanguinarine (SA), which is a quaternary benzo[c]phenanthridine alkaloid possessing antibacterial, anthelmintic, and anti-inflammatory properties. In this study, a SA-producing endophytic fungus strain BLH51 was isolated from the leaves of M. cordata grown in the Dabie Mountain, China. Strain BLH51 produced SA when grown in potato dextrose liquid medium. The amount of SA produced by this endophytic fungus was quantified to be 178 μg/L by HPLC, substantially lower than that produced by the host tissue. The fungal SA--which was analyzed by thin layer chromatography and high-performance liquid chromatography--was shown to be identical to authentic SA. Strain BLH51 was identified as Fusarium proliferatum based on the morphological characteristics and nuclear ribosomal DNA ITS sequence analysis. To the best of our knowledge, this is the first report concerning the isolation and identification of endophytic SA-producing fungi from the host plant, which further proved that endophytic fungi are valuable reservoirs of bioactive compounds.

Phylogenetic position and taxonomy of the enigmatic Orobanche krylowii (Orobanchaceae), a predominatly Asian species newly found in Albania (SE Europe)

We report on the occurrence of Orobanche krylowii in the Alpet Shqiptare (Prokletije, Albanian Alps) mountain range in northern Albania (Balkan Peninsula). The species was previously known only from eastern-most Europe (Volga-Kama River in Russia), more than 2500 km away, and from adjacent Siberia and Central Asia. We used morphological evidence as well as nuclear ribosomal ITS sequences to show that the Albanian population indeed belongs to O. krylowii and that its closest relative is the European O. lycoctoni, but not O. elatior as assumed in the past. Both Orobanche krylowii and O. lycoctoni parasitize Ranunculaceae (Thalictrum spp. and Aconitum lycoctonum, respectively). We provide an identification key and a taxonomic treatment for O. krylowii, and suggest the IUCN category CE (critically endangered) for the highly disjunct Albanian population.

Systematic position of Cyathocline Cass. (Asteraceae): evidences from molecular, cytological and morphological data

Cyathocline, a small genus, has been treated as a member of subtribe Grangeinae of tribe Astereae (Asteraceae), but has been neglected in molecular phylogenetic analyses of Astereae. Plastid trnL-F and nuclear ribosomal DNA ITS sequences were used to carry out phylogenetic analyses of Cyathocline (represented by C. purpurea) through maximum parsimony and Bayesian analyses. In addition, its karyotype, morphology and micromorphology were also investigated. The results show that in our three phylogenetic trees, C. purpurea is deeply nested within the Blumea clade and/or the Inulinae clade, and is closest to Blumea balsamifera (Inuleae, Inulinae). C. purpurea is similar to Blumea in chromosome size bimodality and to Inulinae in one single large oxalate crystal within each cell of the cypsela epidermis, which, together with molecular evidences, suggests strongly that Cyathocline should be transferred from Astereae to Inuleae subtribe Inulinae. Although C. purpurea has many anomalous features, its most characters still are within a wide range of morphological variations of Blumea. DNA data and the karyotypic character support to merge C. purpurea into Blumea. As a result, the new combination Blumea purpurea (O. Kuntze) W.P. Li was made.

Phylogenetic placement of DethawiaMeum, and Rivasmartinezia (Apioideae, Apiaceae): Evidence from nuclear and plastid DNA sequences

The flora of Western Europe is rich in endemic species of Apiaceae, many of which have been poorly investigated and whose phylogenetic relationships are poorly known. To investigate relationships among three endemic European genera (Dethawia, Meum, and Rivasmartinezia gen. nov.) and to ascertain their higher-level phylogenetic placements within the subfamily Apioideae, we examined nuclear ribosomal DNA ITS sequences and the plastid trnL-trnF region. Phylogenies estimated using parsimony and Bayesian inference reveal that (1) the historically known “Conioselinum chinense” Clade (Conioselinum chinense; C. scopulorum; Ligusticum canadense; L. porteri; Meum athamanticum; Mutellina purpurea; and Trochiscanthes nodiflora) comprise a strongly supported monophyletic group (100% BS); (2) the genera Dethawia and Meum comprise a strongly supported monophyletic group also included in the “Conioselinum chinense” Clade; and finally (3) a new genus (Rivasmartinezia) with one species (R. vazquezii) from the Northwestern of the Iberian Peninsula, and placed in the basal position in the “Conioselinum chinense” Clade, is described for the family Apiaceae subfamily Apioideae.

A novel species in the genus Heveochlorella (Trebouxiophyceae, Chlorophyta) witnesses the evolution from an epiphytic into an endophytic lifestyle in tree-dwelling green algae

Roystonea regia is a popular landscape palm famous for its smoothly sculpted white trunk, but sometimes it is spoiled by epiphytic green algae inhabiting the bark. We identified a trebouxiophycean green alga as the single dominant species growing on the trunk of a royal palm in Hainan, China. Light and transmission electron microscopy showed adult cells to be spherical with a diameter of 6.4–13.7 μm, and to contain a single cup-shaped parietal chloroplast. Each chloroplast contained a pyrenoid of 1.4–2.1 μm in diameter. The pyrenoid was penetrated by radially arranged tubular invaginations surrounded by pyrenoglobuli, which is similar to Heveochlorella hainangensis. Phylogenetic analyses inferred from nuclear-encoded 18S rRNA sequences placed strain ITBB A3-8 in the Watanabea clade (Trebouxiophyceae, Chlorophyta), closely related to H. hainangensis. But strain ITBB A3-8 differs sufficiently from H. hainangensis in significant aspects of ultrastructure, physiology, and nuclear and plastid ribosomal RNA and ITS sequences to be treated as a novel species, H. roystonensis Shuai Ma, V. Huss, Xuepiao Sun & Jiaming Zhang, sp. nov. The growth of the epiphytic H. roystonensis seems to be promoted by air pollution in the city, while the endophytic H. hainangensis requires an organic carbon source for optimal growth. Thus in the genus Heveochlorella both an epiphytic and an endophytic lifestyle of tree-dwelling green algae can be observed.

Zhengyia shennongensis: A new bulbiliferous genus and species of the nettle family (Urticaceae) from central China exhibiting parallel evolution of the bulbil trait

AbstractZhengyia shennongensis is described here as a new genus and species of the nettle family (Urticaceae) from Hubei province, central China. The phylogenetic position of Z. shennongensis is determined using DNA sequences of nuclear ribosomal ITS and three plastid regions (rbcL, psbA–trnH, trnL–F). Zhengyia shennongensis is readily distinguished from the related genera Urtica, Hesperocnide, and Laportea in the tribe Urticeae by its seed (oblong–globose or subglobose and not compressed achenes, surface densely covered with nipple–shaped protuberances) and stipule morphology (large leaf–like stipules with auriculate and amplexicaulous base and united with stem). Phylogenetic evidence indicates that Zhengyia is a distinct group related to Urtica (including Hesperocnide) species and Laportea cuspidata in tribe Urticeae. The bulbiliferous species of the tribe (L. bulbifera, L. cuspidata, Z. shennongensis) do not form a clade. This result indicates that the bulbil trait evolved in parallel within Urticeae. Our findings highlight the importance of shady and moist habitats in promoting species diversification and the parallel evolution of morphological traits that are likely to be adaptive.

Phylogenetic analysis of the genus Stachys sect. Eriostomum (Lamiaceae) in Turkey based on nuclear ribosomal ITS sequences

Morphological revision and phylogenetic analysis of Stachys L. sect. Eriostomum (Hoffmanns. & Link) Dumort. (Lamiaceae) based on nuclear ribosomal internal transcribed spacer (nrITS) sequences were conducted. Morphological analysis confirmed the previous arrangements of 3 subsections, i.e. Germanicae R.Bhattacharjee, Creticae R.Bhattacharjee, and Spectabiles R.Bhattacharjee, while suggesting some status changes and new records that were also confirmed by the phylogenetic analysis. The phylogenetic analysis suggested, however, some arrangements different from those indicated by morphology. Two subsections, i.e. Creticae and Germanicae-Spectabiles, instead of 3 were observed in the phylogenetic tree. The tree also suggested that 9 Stachys cretica L. subspecies form a polyphyletic rather than a monophyletic group. While at least 2 clades were clearly identified in the subsection Creticae, no meaningful clades in the subsection Germanicae-Spectabiles were detected in the tree. Flower colour and altitude were not represented by any difference in nrITS DNA sequence of the taxa examined, while 2 distant populations of Stachys spectabilis Choisy ex DC. differed in that respect. A potentially new species of Stachys was observed in the tree. The tree clearly displayed the monophyly of Eriostomum, while confirming the recently suggested new status (as a genus) of the subgenus Betonica (L.) R.Bhattacharjee.

Peltiera(Fabaceae), the coming and going of an “extinct” genus in Madagascar

Peltiera Du Puy & Labat is a Malagasy genus of two described species thought probably to be extinct at the time of its publication in 1997, when it was known only from a total of three pre-1950 collections. However, recent field work in east-central Madagascar has resulted in the discovery of still extant populations, and therefore it is now possible to reconsider the phylogenetic position and status of the genus and its two species. Phylogenetic analyses based on molecular (chloroplast trnK and nuclear ribosomal ITS sequences) and morphological data corroborate the close relationship between Peltiera and Ormocarpopsis R. Vig., a genus of six species, also endemic to Madagascar. Peltiera differs from Ormocarpopsis mainly by having articulated, dehiscent fruits, and the two genera together are, in turn, sister to the widespread but mainly African Ormocarpum P. Beauv. Morphological, distributional and habitat data gathered from the new collections show that only a single species of Peltiera can be recognized, and as this species shares important synapomorphies with all species of Ormocarpopsis, it is transferred to this genus as O. nitida, comb. nov. A distribution map and photographs of O. nitida comb. nov. are presented, and a conservation threat analysis of the species is provided. The name Ormocarpopsis is lectotypified and an amended description of the genus with its new circumscription is given.

Polyphyly of the Padus group of Prunus (Rosaceae) and the evolution of biogeographic disjunctions between eastern Asia and eastern North America

Prunus subgenus Padus is a group with a wide distribution in temperate eastern Asia and eastern North America with one species extending to Europe and one to Central America. Phylogenetic relationships of subgenus Padus were reconstructed using sequences of nuclear ribosomal ITS, and plastid ndhF gene, and rps16 intron and rpl16 intron. Prunus subgenus Padus is shown to be polyphyletic. Taxa of subgenus Padus and subgenus Laurocerasus are highly intermixed in both the ITS and the plastid trees. The results support two disjunctions between eastern North America and Eurasia within the Padus group. One disjunction is between Prunus virginiana of eastern North America and P. padus of Eurasia, estimated to have diverged at 2.99 (95% HPD 0.59-6.15)-4.1 (95% HPD 0.63-8.59) mya. The other disjunction is between P. serotina and its Asian relatives. The second disjunction may have occurred earlier than the former one, but the age estimate is difficult due to the unresolved phylogenetic position of the P. serotina complex.

A New Species ofLeymus(Poaceae, Triticeae) from China

A new species of Leymus Hochst. (Poaceae, Triticeae) from Inner Mongolia, China, L. pubens H. X. Xiao, is described, illustrated, and compared with its closest relatives. This species was initially identified as L. chinensis (Trin.) Tzvelev, but the upper surfaces of its leaf blades are spinulose, and the internode below the spike, upper half of the rachis, rachilla, and lemmas are sparsely puberulent. A key is provided for L. pubens and closely related species of Leymus. The identification of the new species is also supported by nuclear ribosomal ITS and chloroplast trnL-F sequence analyses.