A molecular estimate of the phylogeny of Styphelieae (Ericaceae)

2003 ◽  
Vol 16 (5) ◽  
pp. 581 ◽  
Author(s):  
Christopher J. Quinn ◽  
Darren M. Crayn ◽  
Margaret M. Heslewood ◽  
Elizabeth A. Brown ◽  
Paul A. Gadek
Keyword(s):  
Chloroplast Genome ◽  
Sequence Data ◽  
Intergenic Spacer ◽  
New Genera ◽  
Taxonomic Sampling ◽  
Jackknife Support

Parsimony analyses of sequence data derived from two regions of the chloroplast genome, matK and the atpB-rbcL intergenic spacer, separately and together, are reported for Styphelieae. Taxonomic sampling includes representatives of all currently accepted genera apart from the two non-Australian monotypics, Cyathopsis Brongn. & Gris and Decatoca F.Muell., and of all subgenera or informal infrageneric groups except for Trochocarpa subgenus Pseudocyathodes Sleumer. A well resolved estimate of the phylogeny of the tribe is obtained, with high levels of jackknife support for terminal groupings. The results provide support for the current concepts of Acrotriche R.Br., Androstoma Hook.f., Croninia J.M.Powell, Cyathodes Labill. sensu Weiller, Leptecophylla C.M.Weiller, Leucopogon R.Br. sensu Taaffe et al., Pentachondra R.Br., Planocarpa C.M.Weiller and Trochocarpa R.Br., but the following genera appear paraphyletic: Astroloma R.Br., Brachyloma Sond., Cyathodes sensu Labill., Leucopogon R.Br. sensu lato, Lissanthe R.Br., Monotoca R.Br. and Styphelia Sm. (sensu Bentham). Several robust clades are identified as potential new genera but formalisation of nomenclatural changes is left, pending morphological analyses of the various clades to identify synapomorphies with which to characterise generic groupings. The general approach to be adopted in this endeavour is discussed, with narrower generic concepts being favoured as more informative and less disruptive of the existing nomenclature.

Two new genera and twelve new species of Graphidaceae from Puerto Rico: a case for higher endemism of lichenized fungi in islands of the Caribbean?

Phytotaxa ◽  
2014 ◽  
Vol 189 (1) ◽  
pp. 186 ◽  
Author(s):  
JOEL A. MERCADO-DÍAZ ◽  
ROBERT LÜCKING ◽  
SITTIPORN PARNMEN
Keyword(s):  
Puerto Rico ◽  
New Species ◽  
Sequence Data ◽  
New Combination ◽  
New Genera ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Biodiversity Knowledge ◽  
Three New Species ◽  
High Level

Two new genera and twelve new species of Graphidaceae are described from Puerto Rico. The two new genera, Borinquenotrema and Paratopeliopsis, are based on a combination of molecular sequence data and phenotype characters. Borinquenotrema, with the single new species B. soredicarpum, features rounded ascomata developing beneath and persistently covered with soralia and with an internal anatomy reminescent of Carbacanthographis; it is close to the  tribe Ocellularieae. Paratopeliopsis, including the single new species P. caraibica, resembles a miniature Topeliopsis but differs in the distinctly farinose thallus and the small, brown ascospores; it is not closely related to the latter genus but belongs in tribe Thelotremateae. The other ten new species belong in the genera Acanthotrema, Clandestinotrema, Compositrema, Fissurina, Ocellularia, and Thalloloma. Acanthotrema alboisidiatum is closely related to A. brasilianum but differs in the short, white isidia resembling insect eggs. Clandestinotrema portoricense has a unique ascospore type with a longitudinal septum only in the proximal cell. Compositrema borinquense resembles a species of Stegobolus but belongs in Compositrema based on sequence data, and is characterized by ascomata with a unique columella composed of thick, irregularly radiating strands. The second new species in this genus, C. isidiofarinosum, differs by its ecorticate, farinose thallus with scattered, corticate isidia and by its small ascomata with inconspicuous columella. The three new species of Fissurina all have 3-septate ascospores and are otherwise characterized by an isidiate thallus and stellate, orange-yellow lirellae (F. aurantiacostellata), a verrucose thallus strongly encrusted with calcium oxalate crystals and white, irregularly branched lirellae (F. crystallifera), and myriotremoid ascomata arranged in short lines (F. monilifera). Ocellularia portoricensis belongs in the core group of Ocellularia and differs from O. cavata in the white medulla and the larger ascospores becoming brown, whereas O. vulcanisorediata produces prominent soralia and immersed ascomata with apically carbonized excipulum and columella and small, transversely septate, hyaline ascospores; it is closely related to O. conformalis. Finally, Thalloloma rubromarginatum resembles T. haemographum in the brownish lirellae with bright red margin but differs from that and other species in the corticate thallus and the norstictic acid chemistry. The new combination Ampliotrema rimosum (Hale) Mercado-Díaz, Lücking & Parnmen is also proposed. Considering the current biodiversity knowledge on this family, the high level of endemism observed in other groups of organisms in the island, and the relatively high number of Graphidaceae described, it is highly likely that at least some of these new taxa are endemic to the island. This view is further supported by the unique features of several of the new species, representing novel characters in the corresponding genera.

scholarly journals When forms meet genes: revision of the scleractinian genera Micromussa and Homophyllia (Lobophylliidae) with a description of two new species and one new genus

2016 ◽  
Vol 85 (4) ◽  
pp. 387-422 ◽  
Author(s):  
Roberto Arrigoni ◽  
Francesca Benzoni ◽  
Danwei Huang ◽  
Hironobu Fukami ◽  
Chaolun Allen Chen ◽  
...  
Keyword(s):  
New Genus ◽  
Nuclear Dna ◽  
New Caledonia ◽  
Sequence Data ◽  
Intergenic Spacer ◽  
Taxonomic Revision ◽  
Its Region ◽  
Distinct Species ◽  
Morphological Data ◽  
Eastern Australia

The scleractinian family Lobophylliidae is undergoing a major taxonomic revision thanks to the combination of molecular and morphological data. In this study, we investigate the evolutionary relationships and the macro- and micromorphology of six nominal coral species belonging to two of the nine molecular clades of the Lobophylliidae, clades A and B, and of Symphyllia wilsoni, a lobophylliid species analyzed from a molecular point of view for the first time. Sequence data from mitochondrial DNA (COI and the intergenic spacer between COI and l-rRNA), and nuclear DNA (histone H3 and ITS region) are used to generate robust molecular phylogenies and a median-joining haplotype network. Molecular results are strongly in agreement with detailed observations of gross- and fine-scale morphology of skeletons, leading to the formal revision of the genera Micromussa and Homophyllia and the description of two newly discovered zooxanthellate shallow-water species, Micromussa pacifica sp. nov. Benzoni & Arrigoni and Micromussa indiana sp. nov. Benzoni & Arrigoni, and a new genus, Australophyllia gen. nov. Benzoni & Arrigoni. In particular, Acanthastrea lordhowensis and Montastraea multipunctata are moved into Micromussa, A. hillae is synonymized with A. bowerbanki and is transferred to Homophyllia, and a revised diagnosis for both genera is provided. Micromussa pacifica sp. nov. is described from the Gambier Islands with its distribution spanning New Caledonia and eastern Australia. Despite a superficial resemblance with Homophyllia australis, it has distinctive macroand micromorphological septal features. Micromussa indiana sp. nov., previously identified as M. amakusensis, is here described from the Gulf of Aden and the southern Red Sea as a distinct species that is genetically separated from M. amakusensis and is morphologically distinct from the latter due to its smaller corallite size and lower number of septa. Finally, molecular trees show that S. wilsoni is closely related, but molecularly separated from clades A and B, and, also based on a unique combination of corallite and sub-corallite characters, the species is moved into Australophyllia gen. nov. These findings confirm the need for using both genetic and morphological datasets for the ongoing taxonomic revision of scleractinian corals.

scholarly journals Four new endemic genera of Rubiaceae (Pavetteae) from Madagascar represent multiple radiations into drylands

PhytoKeys ◽  
2018 ◽  
Vol 99 ◽  
pp. 1-66 ◽  
Author(s):  
Petra De Block ◽  
Franck Rakotonasolo ◽  
Salvator Ntore ◽  
Sylvain G. Razafimandimbison ◽  
Steven Janssens
Keyword(s):  
Sequence Data ◽  
Single Species ◽  
Dry Forest ◽  
New Combination ◽  
Phylogenetic Study ◽  
New Genera ◽  
Unique Combination ◽  
Generic Level ◽  
Plant Groups ◽  
Endemic Genera

The taxonomic positions and phylogenetic relationships of six Pavetteae species endemic to Madagascar were tested with a phylogenetic study of the Afro-Madagascan representatives of the tribe Pavetteae based on sequence data from six markersrps16,trnT-F,petD,accD-psa1,PIand ITS. The six species were resolved into four well-supported and morphologically distinct clades which we here formally recognise at generic level. The new genera are the monospecificExallospermaandPseudocoptosperma, each with a single species, andHelictospermaandTulearia, each with two species. Each genus is characterised by one or more autapomorphies or by a unique combination of plesiomorphic characters. Mostly, the distinguishing characters are found in fruit and seed;Exallospermadiffers from all other Pavetteae genera by the fruit consisting of two stony pyrenes, each with a single laterally flattened seed with irregularly distributed ridges on the surface;Helictospermais unique by its single spherical seed rolled-in on itself in the shape of a giant pill-millipede.Pseudocoptospermais characterised by the combination of three ovules pendulous from a small placenta and triangular stipules with a strongly developed awn, whereasTuleariais characterised by robust sericeous flowers, small leaves, uni- or pauciflorous inflorescences and fruits with two pyrenes, each with a single ruminate seed.The four new genera show marked adaptations to the dry habitats in which they grow. They represent multiple radiations into drylands and highlight the importance of the dry forest and scrub vegetation in western, southern and northern Madagascar for plant biodiversity. The description of the four new genera shows that the tribe Pavetteae exhibits the same pattern as many plant groups in Madagascar, which are characterised by a high proportion of endemic genera comprising a single or a few species.In the four new genera, five new species are described and one new combination is made:ExallospermalongifloraDe Block;Helictospermamalacophylla(Drake) De Block,HelictospermapoissonianaDe Block,PseudocoptospermamenabenseCapuron ex De Block;TuleariacapsaintemariensisDe Block andTuleariasplendidaDe Block.

scholarly journals Characterization of Race-Specific Interactions Among Isolates of Verticillium dahliae Pathogenic on Lettuce

2006 ◽  
Vol 96 (12) ◽  
pp. 1380-1387 ◽  
Author(s):  
Gary E. Vallad ◽  
Qing-Ming Qin ◽  
Rebecca Grube ◽  
Ryan J. Hayes ◽  
Krishna V. Subbarao
Keyword(s):  
Verticillium Dahliae ◽  
Field Experiments ◽  
Sequence Data ◽  
Intergenic Spacer ◽  
Distinct Subgroup ◽  
Race 1 ◽  
Race 2 ◽  
The 1960S ◽  
Significant Disease

Verticillium wilt, caused by Verticillium dahliae, poses a major threat to lettuce (Lactuca sativa) production in California. Incorporation of resistance into commercial lettuce cultivars offers the least expensive technique of sustaining production in infested areas. To test the breadth of the resistance identified in field experiments, a pair of susceptible (‘Salinas’ and ‘Sniper’) and resistant (‘La Brillante’ and ‘Little Gem’) lettuce cultivars were used as differentials and individually inoculated with 29 isolates of V. dahliae and two isolates of V. albo-atrum from several hosts, including lettuce, in replicated greenhouse experiments. The reactions of the four cultivars were determined based on the disease severity at maturity. None of the V. albo-atrum isolates or V. dahliae isolates from cruciferous hosts caused significant disease on lettuce. Both Salinas and Sniper were susceptible to many isolates of V. dahliae (21 of 23) from noncruciferous hosts, and the isolates varied in their overall virulence. However, of these, only three isolates caused significant disease on the resistant cvs. La Brillante and Little Gem. These three isolates also were distinct from the other V. dahliae isolates based on sequence data from the intergenic spacer (IGS) region of the nuclear ribosomal RNA gene, suggesting that they form a phylogenetically distinct subgroup that differs in virulence toward specific lettuce genotypes. Accordingly, isolates of V. dahliae virulent on all tested cultivars, including the resistant La Brillante and Little Gem, were designated as race 2, whereas those virulent only on the susceptible Salinas and Sniper were designated as race 1. Although a range of virulence among isolates has been described in other hosts, this is the first description of distinct virulence phenotypes in V. dahliae since a similar race structure was described in tomato in the 1960s.

scholarly journals Studies on diversity of soil microfungi in the Hornsund area, Spitsbergen

2013 ◽  
Vol 34 (1) ◽  
pp. 39-54 ◽  
Author(s):  
Siti Hafizah Hafizah ◽  
Siti Aisyah Alias ◽  
Hii Yii Siang ◽  
Jerzy Smykla ◽  
Ka−Lai Pang ◽  
...  
Keyword(s):  
Sequence Data ◽  
Intergenic Spacer ◽  
High Arctic ◽  
Soil Samples ◽  
Potato Dextrose Agar ◽  
Species Level ◽  
Thermal Growth ◽  
Geomyces Pannorum ◽  
Soil Microfungi

Abstract We assessed culturable soil microfungal diversity in various habitats around Hornsund, Spitsbergen in the High Arctic, using potato dextrose agar (PDA) medium. Thermal growth classification of the fungi obtained was determined by incubating them in 4°C and 25°C, permitting separation of those with psychrophilic, psychrotolerant and mesophilic char− acteristics. In total, 68 fungal isolates were obtained from 12 soil samples, and grouped into 38 mycelial morphotypes. Intergenic spacer regions of these morphotypes were sequenced, and they represented 25 distinct taxonomic units, of which 21 showed sufficient similarity with available sequence data in NCBI to be identified to species level. Soil under ornithogenic influence showed the highest species diversity, including sequences assigned to Mortierella macrocystis, M. elongata, Mortierella sp., Cudoniella sp., Varicosporium elodeae, Beauveria bassiana, Geomyces pannorum, Penicillium sp. and Atradidymella muscivora. Fourteen taxa were classified as psychrophilic, seven mesophilic, and four psychrotolerant.

A phylogenetic study of Pimelea and Thecanthes (Thymelaeaceae): evidence from plastid and nuclear ribosomal DNA sequence data

2010 ◽  
Vol 23 (4) ◽  
pp. 270 ◽  
Author(s):  
M. Cynthia Motsi ◽  
Annah N. Moteetee ◽  
Angela J. Beaumont ◽  
Barbara L. Rye ◽  
Martyn P. Powell ◽  
...  
Keyword(s):  
Sequence Data ◽  
Intergenic Spacer ◽  
Taxonomic Status ◽  
Molecular Study ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Study ◽  
Rps16 Intron ◽  
Dna Sequence Data ◽  
Close Relationship ◽  
Nuclear Its

A comprehensive molecular study, using sequence data from nuclear ITS rDNA and plastid rbcL and matK exons, rps16 intron, and the trnL-F intronic and intergenic spacer, was used to assess the taxonomic status of Thecanthes Wikstr., and to evaluate the relationships within Pimelea Banks & Sol. ex Gaertn. and Thecanthes (Thymelaeaceae). Both genera are Australasian and they constitute the subtribe Pimeleinae, which is characterised by a reduction to two stamens. Previous studies indicated a close relationship among Pimelea, Thecanthes and Gnidia L. species from tropical Africa. We conclude that Pimelea and Thecanthes form a strongly supported clade, with Thecanthes possibly included within Pimelea, although we await further data before formally proposing a series of new taxonomic combinations.

scholarly journals Sequence diversity of two chloroplast genes: rps4 and tRNAGly (UCC), in the liverwort Marchantia polymorpha, an emerging plant model system

2018 ◽  
Vol 87 (1) ◽  
Author(s):  
Hanna Kijak ◽  
Weronika Łodyga ◽  
Ireneusz J. Odrzykoski
Keyword(s):  
Chloroplast Genome ◽  
Sequence Variation ◽  
Sequence Divergence ◽  
Intergenic Spacer ◽  
Marchantia Polymorpha ◽  
Homologous Sequences ◽  
Clonal Lines ◽  
Suspension Line ◽  
Marchantia Paleacea ◽  
Almost All

<p>The primary purpose of this study is to evaluate the sequence variation for two regions of chloroplast DNA in a collection of 27 taxonomically well-annotated clonal lines of <em>Marchantia polymorpha</em> sensu lato derived from European populations. We attempted to develop molecular markers so as to identify three taxa usually recognized as subspecies. We sequenced two regions: the <em>rps4</em> gene along with the <em>rps4-trnT</em> intergenic spacer and an intron of the tRNA<sup>Gly</sup> (UCC) gene. Samples of <em>Marchantia paleacea</em> ssp. <em>diptera</em> from Japan were used for comparative purposes.</p><p>Three haplotypes (MA, MB, and MC) were identified for the species, and almost all sequence divergence between subspecies was found to occur at the level of 0.0023–0.0032 substitutions per site. The sequence divergence between <em>M. polymorpha</em> and <em>M. paleacea</em> was tenfold greater (0.0331–0.0340). We did not detect any differences between <em>M. paleacea</em> and homologous sequences from the reference chloroplast genome of <em>M. polymorpha</em> obtained from the GeneBank (NC_001319). It was confirmed that the cell suspension line A-18 used for the sequencing of the full chloroplast genome in 1986 was incorrectly taxonomically annotated.</p>

scholarly journals Characterizing the ribosomal tandem repeat and its utility as a DNA barcode in lichen-forming fungi

2019 ◽  
Author(s):  
Michael Bradshaw ◽  
Felix Grewe ◽  
Anne Thomas ◽  
Cody H. Harrison ◽  
Hanna Lindgren ◽  
...  
Keyword(s):  
Species Complex ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Dna Barcode ◽  
Intergenic Spacer ◽  
Its Region ◽  
Nuclear Ribosomal Dna ◽  
Nucleotide Position ◽  
Ribosomal Operon ◽  
Intragenomic Variation

Abstract Background: Regions within the nuclear ribosomal operon are a major tool for inferring evolutionary relationships and investigating diversity in fungi. In spite of the prevalent use of ribosomal markers in fungal research, central features of nuclear ribosomal DNA (nrDNA) evolution are poorly characterized for fungi in general, including lichenized fungi. The internal transcribed spacer (ITS) region of the nrDNA has been adopted as the primary DNA barcode identification marker for fungi. However, little is known about intragenomic variation in the nrDNA in symbiotic fungi. In order to better understand evolution of nrDNA and the utility of the ITS region for barcode identification of lichen-forming fungal species, we generated nearly complete nuclear ribosomal operon sequences from nine species in the Rhizoplaca melanophthalma species complex using short reads from high-throughput sequencing. Results: We estimated copy numbers for the nrDNA operon, ranging from nine to 48 copies for members of thiscomplex, and found low levels of intragenomic variation in the standard barcode region (ITS). Monophyly of currently described species in this complex was supported in phylogenetic inferences based on the ITS, 28S, IGS, and some intronic regions; however, a phylogenetic inference based on the 18S provided much lower resolution. Phylogenetic analysis of concatenated ITS and intergenic spacer sequence data generated from 496 specimens collected worldwide revealed previously unrecognized lineages in the nrDNA phylogeny. Conclusions: The results from our study support the general assumption that the ITS region of the nrDNA is an effective barcoding marker for fungi. For the R. melanophthalma group, the limited amount of potential intragenomic variability in the ITS region did not correspond to fixed diagnostic nucleotide position characters separating taxa within this species complex. Previously unrecognized lineages inferred from ITS sequence data may represent undescribed species-level lineages or reflect uncharacterized aspects of nrDNA evolution in the R. melanophthalma species complex.

scholarly journals An Elegy to Rangaeris, Including a Description of Two New Genera in the Cyrtorchis–Tridactyle Clade (Orchidaceae, Angraecinae)

2020 ◽  
Vol 105 (3) ◽  
pp. 300-322
Author(s):  
João N. M. Farminhão ◽  
Tania D'haijère ◽  
Vincent Droissart ◽  
Landry Dumbo Isonga ◽  
Ling Dong ◽  
...  
Keyword(s):  
Conservation Status ◽  
Intergenic Spacer ◽  
Phylogenetic Position ◽  
Morphological Evidence ◽  
New Genera ◽  
Representative Sampling ◽  
Distribution Maps ◽  
Nuclear Its ◽  
Plastid Markers ◽  
Angraecoid Orchids

The phylogenetic position of Rangaeris (Schltr.) Summerh. has been one of the most problematic issues of angraecoid orchid taxonomy. A recently published phylogenetic tree with nearly comprehensive taxon sampling of African angraecoid orchids suggested that this genus was polyphyletic, as its species appear nested within different subclades of the Cyrtorchis–Tridactyle clade. However, the lack of DNA data for the generic type, R. muscicola (Rchb. f.) Summerh., and for the little-known species R. longicaudata (Rolfe) Summerh. and R. trilobata Summerh., has precluded an integrative reappraisal of the delimitation of this genus. Here we present the results of a new phylogenetic analysis of one nuclear (ITS) and five plastid markers (matK, rps16, trnC-petN intergenic spacer, trnL-trnF intergenic spacer, ycf1) for all six species of Rangaeris, including those recently transferred to Podangis Schltr. and Ypsilopus Summerh., together with a representative sampling of 14 other species of the genera Cyrtorchis Schltr., Listrostachys Rchb. f., Plectrelminthus Raf., Summerhayesia P. J. Cribb, Tridactyle Schltr., and Ypsilopus. Based on molecular and morphological evidence, R. muscicola is transferred to Podangis, where Rangaeris is reduced to the rank of section. In addition, R. longicaudata and R. trilobata are each moved to new monotypic genera, Planetangis Stévart & Farminhão and Aziza Farminhão & D’haijère, respectively. An identification key for all genera of the Cyrtorchis–Tridactyle clade is presented, together with one for the three species of recircumscribed Podangis. Finally, taxonomic accounts of the new genera are presented, including amended descriptions, illustrations, distribution maps, and preliminary conservation status assessments of their species.

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