scholarly journals Phylogeny of Aconitum Subgenus Aconitum in Europe

2020 ◽  
Vol 89 (3) ◽  
Author(s):  
Piotr Boroń ◽  
Ada Wróblewska ◽  
Bogusław Binkiewicz ◽  
Józef Mitka
Keyword(s):  
Sierra Nevada ◽  
Intergenic Spacer ◽  
Its Region ◽  
Sister Group ◽  
Genetic Stock ◽  
Maritime Alps ◽  
Quaternary Period ◽  
Massif Central ◽  
Phylogenetic Relations ◽  
Nuclear Its

<p>Phylogenetic relations within <em>Aconitum </em>subgen. <em>Aconitum </em>(Ranunculaceae) in Europe are still unclear. To infer the phylogeny of the nuclear (ITS) region and chloroplast intergenic spacer <em>trn</em>L<sup>(UAG)</sup>-<em>ndh</em>F of the chloroplast DNA (cpDNA), we analyzed 64 accessions within this taxon, 58 from Europe and six from the Caucasus Mts. Nuclear ITS sequences were identical in 51 European and two Caucasian accessions, whereas the remaining sequences were unique. cpDNA sequences could be categorized into five haplotypes, i.e., <em>A–E</em>, including a European-Caucasian <em>Aconitum </em>haplotype <em>B</em>. Ten cpDNA sequences were unique. A 5-bp indel distinguished the diploids from the tetraploids. None of the extant European diploids were basal to the tetraploid local group. A phylogenetic tree based on combined ITS and cpDNA sequences (bayesian inference, maximum likelihood, minimal parsimony) placed <em>Aconitum</em><em> </em><em>burnatii </em>(Maritime Alps, Massif Central) and <em>A. nevadense </em>(Sierra Nevada, Pyrenees) in a sister group to all other European species. A Bayesian relaxed clock model estimated the earliest split of the Caucasian species during the Late Miocene [ca. 7 million years ago (Mya)], and the divergence of <em>A. burnatii </em>and <em>A. nevadense </em>from the European genetic stock during the Miocene/Pliocene (ca. 4.4 Mya). Diploids in Europe are likely to be descendants of the Miocene European-Caucasian flora linked with the ancient Asian (arctiotertiary) genetic stock. The origins of the tetraploids remain unclear, and it is possible that some tetraploids originated from local, now extinct diploids. Both the diploids and tetraploids underwent rapid differentiation in the Late Pliocene – Quaternary period.</p>

scholarly journals Molecular identification of poisonous mushrooms using nuclear ITS region and peptide toxins: a retrospective study on fatal cases in Thailand

2016 ◽  
Vol 41 (1) ◽  
pp. 65-76 ◽  
Author(s):  
Sittiporn Parnmen ◽  
Sujitra Sikaphan ◽  
Siriwan Leudang ◽  
Thitiya Boonpratuang ◽  
Achariya Rangsiruji ◽  
...  
Keyword(s):  
Retrospective Study ◽  
Molecular Identification ◽  
Its Region ◽  
Nuclear Its ◽  
Peptide Toxins ◽  
Poisonous Mushrooms

Phylogenetic relations of European shrubby taxa of the genusUsnea

2011 ◽  
Vol 43 (5) ◽  
pp. 427-444 ◽  
Author(s):  
Lauri SAAG ◽  
Tiiu TÕRRA ◽  
Andres SAAG ◽  
Ruth DEL-PRADO ◽  
Tiina RANDLANE
Keyword(s):  
Maximum Parsimony ◽  
Chemical Separation ◽  
Molecular Data ◽  
Beta Tubulin ◽  
Phylogenetic Relations ◽  
Branch Lengths ◽  
Nuclear Its ◽  
Molecular Characters

AbstractThis study focuses on EuropeanUsneaspecies with sorediate shrubby thalli, with the aim to evaluate the morphological and chemical separation of species in the light of molecular data. Twenty-twoUsneaspecies, including widely distributed taxa such asU. diplotypus, U. fulvoreagens, U. glabrescens, U. lapponica, U. subfloridana, U. substerilisandU. wasmuthii, were included in the study using Bayesian and maximum parsimony analyses of nuclear ITS and beta-tubulin sequences. The analyses showed that: 1) most taxa that are morphologically well delimited are also distinct by means of molecular characters, 2) shrubby taxa in the sectionUsneathat are difficult to determine by traditional characters form a group of closely related but still genetically distinct entities, exceptU. diplotypusandU. substeriliswhich appear to be polyphyletic. The branch lengths differed largely between two parts of the ITS tree (sectionsUsneaandCeratinae).Usnea intermediais proposed as the sexually reproducing counterpart for the sorediateU. lapponica. Additionally, some new chemotypes ofUsneaspecies were determined.

Two new species of Protonemura Kempny, 1898 (Plecoptera: Nemouridae) from Southern France

Zootaxa ◽  
2021 ◽  
Vol 5061 (3) ◽  
pp. 432-450
Author(s):  
GILLES VINÇON ◽  
BERTRAND LAUNAY ◽  
JEAN-PAUL G. REDING
Keyword(s):  
New Species ◽  
Maritime Alps ◽  
Massif Central ◽  
Southern France ◽  
Ecological Preferences ◽  
Two New Species ◽  
Southern Flank

Two new species of Protonemura Kempny, 1898, P. lupina sp. n., from the Castellane Prealps and the southern Mercantour region in the French Maritime Alps, and P. alexidis sp. n., from the southern flank of the Massif Central, are described, illustrated, and compared to their closest relative species P. risi (Jacobson & Bianchi, 1905) and P. spinulosa (Navás, 1921). Information on distribution and ecological preferences of these new species is provided.  

scholarly journals Dissection for Floral Micromorphology and Plastid Genome of Valuable Medicinal Borages Arnebia and Lithospermum (Boraginaceae)

2020 ◽  
Vol 11 ◽  
Author(s):  
Inkyu Park ◽  
Sungyu Yang ◽  
Jun-Ho Song ◽  
Byeong Cheol Moon
Keyword(s):  
General Structure ◽  
Intergenic Spacer ◽  
Sister Group ◽  
Rrna Genes ◽  
Trna Genes ◽  
Evolutionary Analysis ◽  
Arnebia Euchroma ◽  
Floral Micromorphology ◽  
Close Relationship ◽  
Cell Patterns

The genera Arnebia and Lithospermum (Lithospermeae-Boraginaceae) comprise 25–30 and 50–60 species, respectively. Some of them are economically valuable, as their roots frequently contain a purple-red dye used in the cosmetic industry. Furthermore, dried roots of Arnebia euchroma, A. guttata, and Lithospermum erythrorhizon, which have been designated Lithospermi Radix, are used as traditional Korean herbal medicine. This study is the first report on the floral micromorphology and complete chloroplast (cp) genome sequences of A. guttata (including A. tibetana), A. euchroma, and L. erythrorhizon. We reveal great diversity in floral epidermal cell patterns, gynoecium, and structure of trichomes. The cp genomes were 149,361–150,465 bp in length, with conserved quadripartite structures. In total, 112 genes were identified, including 78 protein-coding regions, 30 tRNA genes, and four rRNA genes. Gene order, content, and orientation were highly conserved and were consistent with the general structure of angiosperm cp genomes. Comparison of the four cp genomes revealed locally divergent regions, mainly within intergenic spacer regions (atpH-atpI, petN-psbM, rbcL-psaI, ycf4-cemA, ndhF-rpl32, and ndhC-trnV-UAC). To facilitate species identification, we developed molecular markers psaA- ycf3 (PSY), trnI-CAU- ycf2 (TCY), and ndhC-trnV-UAC (NCTV) based on divergence hotspots. High-resolution phylogenetic analysis revealed clear clustering and a close relationship of Arnebia to its Lithospermum sister group, which was supported by strong bootstrap values and posterior probabilities. Overall, gynoecium characteristics and genetic distance of cp genomes suggest that A. tibetana, might be recognized as an independent species rather than a synonym of A. guttata. The present morphological and cp genomic results provide useful information for future studies, such as taxonomic, phylogenetic, and evolutionary analysis of Boraginaceae.

scholarly journals Phylogenetics of Taxus Using the Internal Transcribed Spacers of Nuclear Ribosomal DNA and Plastid trnL-F Regions

Horticulturae ◽  
2020 ◽  
Vol 6 (1) ◽  
pp. 19
Author(s):  
Patricia Coughlan ◽  
James C. Carolan ◽  
Ingrid L. I. Hook ◽  
Lisa Kilmartin ◽  
Trevor R. Hodkinson
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Intergenic Spacer ◽  
Its Region ◽  
Single Species ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Trnl Intron ◽  
Group Status ◽  
Haplotype Networks

Taxus is a genus of trees and shrubs with high value in horticulture and medicine as a source of the anticancer drug paclitaxel. The taxonomy of the group is complex due to the lack of diagnostic morphological characters and the high degree of similarity among species. Taxus has a wide global geographic distribution and some taxonomists recognize only a single species with geographically defined subgroups, whereas others have described several species. To address these differences in taxonomic circumscription, phylogenetic analyses were conducted on DNA sequences using Maximum Likelihood, Bayesian Inference and TCS haplotype networks on single and combined gene regions obtained for the nuclear ribosomal ITS region and the plastid trnL intron and trnL-F intergenic spacer. Evidence is presented for the sister group status of Pseudotaxus to Taxus and the inclusion of Amentotaxus, Austrotaxus, Cephalotaxus and Torreya within Taxaceae. Results are consistent with the taxonomic recognition of nine species: T. baccata, T. brevifolia, T. canadensis, T. cuspidata, T. floridana, T. fuana, T. globosa, T. sumatrana and T. wallichiana, but evidence is found for less species distinction and considerable reticulation within the T. baccata, T. canadensis and T. cuspidata group. We compare the results to known taxonomy, biogeography, present new leaf anatomical data and discuss the origins of the hybrids T. ×media and T. ×hunnewelliana.

Biatora Britannica sp. Nov. and the Occurrence of Biatora Efflorescens in the British Isles

2001 ◽  
Vol 33 (3) ◽  
pp. 181-187 ◽  
Author(s):  
Christian Printzen ◽  
H. Thorsten Lumbsch ◽  
Alan Orange
Keyword(s):  
Its Region ◽  
Molecular Data ◽  
Sister Taxon ◽  
British Isles ◽  
Close Relationship ◽  
Nuclear Its ◽  
Relationship Of

AbstractBiatora Britannica sp. nov is described from Wales. The species is the sorediate sister taxon of the Madeiran Biatora hertelii. The close relationship is supported by the presence of the hymenial pigment Hertelii-green, which is hitherto known only from these two species. Molecular data from the nuclear ITS-region of 14 Bratora¯ species renders further support for the close relationship of both species. Sterile, sorediate material from the British Isles earlier referred to B. efflorescens may in fact belong to B. britannica.

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.

Molecular systematics of Australian Podolepis (Asteraceae: Gnaphalieae): evidence from DNA sequences of the nuclear ITS region and the chloroplast matK gene

2000 ◽  
Vol 13 (5) ◽  
pp. 709 ◽  
Author(s):  
N. Konishi ◽  
K. Watanabe ◽  
K. Kosuge
Keyword(s):  
Dna Sequences ◽  
Its Region ◽  
Chromosomal Evolution ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Base Number ◽  
Monophyletic Clade ◽  
Matk Gene ◽  
Nuclear Its ◽  
Generic Relationships

The generic circumscription and intra-generic relationships of the genus Podolepis Labill., with various chromosome numbers from n = 12 to n = 3, were examined by sequences of the internal transcribed spacers (ITS) of nuclear ribosomal DNA and the matK gene of chloroplast DNA. The topology of the ITS tree for 17 species and the matK tree for 18 species of the genus Podolepis sensu Davis (1957) and Anderberg (1991) and 15 taxa from eight related genera (Anderberg 1989, 1991, 1994) are basically concordant. Except for P. georgei Diels andP. kendallii F.Muell., parsimony analyses support the monophyly of the genus Podolepis sensu Davis (1957) and Anderberg (1991). The genera of Asteridea Lindl. and Pterochaeta Steetz are sisters toPodolepis in the combined tree based on the ITS and matK sequences. Within the monophyletic clade of the genus Podolepis, three lineages are identified. The chromosome base number of x = 12 may be ancestral in the genus Podolepis. The dysploidal reduction in chromosome number from n = 12 to n = 10 and 9, from n = 12 to n = 8 and 7, and from n = 12 to n = 11 and 3 in three lineages, respectively, is the primary mode of chromosomal evolution in this genus. Total karyotypic length (= genome size) is much greater in perennials than in annuals within the genus Podolepis. The number of pappus bristles on outer female florets tends to decrease and they are absent in some annuals of this genus, while myxogenic cells on the pericarp become prominent.

A putative transposase gene in the 16S–23S rRNA intergenic spacer region of Mycoplasma imitans

Microbiology ◽  
2004 ◽  
Vol 150 (4) ◽  
pp. 1023-1029 ◽  
Author(s):  
Ryô Harasawa ◽  
David G. Pitcher ◽  
Ana S. Ramírez ◽  
Janet M. Bradbury
Keyword(s):  
Relative Size ◽  
Intergenic Spacer ◽  
Its Region ◽  
23S Rrna ◽  
Mycoplasma Species ◽  
Insertion Element ◽  
Transposase Gene ◽  
Intergenic Spacer Region ◽  
Pcr Products ◽  
Type Strains

Examination of the nucleotide sequences of the 16S–23S intergenic transcribed spacer (ITS) region of Mycoplasma imitans and Mycoplasma gallisepticum identified a putative transposase gene located only in the ITS of M. imitans, which can be used as a genetic marker to distinguish these two species. The relative size of the PCR products of the ITS region allowed a clear distinction to be made between strains of M. imitans and M. gallisepticum, both of which could be readily discriminated from the type strains of all the other recognized avian Mycoplasma species. In addition, the putative transposase gene assigned in the ITS of M. imitans was shown to include a sequence homologous to that of the P75 gene of M. gallisepticum. This is believed to be the first description of an insertion element in the rRNA operon region of a mycoplasma species.

Molecular phylogeny of the tribe Anthospermeae (Rubiaceae): Systematic and biogeographic implications

2001 ◽  
Vol 14 (2) ◽  
pp. 231 ◽  
Author(s):  
Cajsa L. Anderson ◽  
Johan H. E. Rova ◽  
Lennart Andersson
Keyword(s):  
Its Region ◽  
Plastid Dna ◽  
Sister Group ◽  
Nuclear Ribosomal Dna ◽  
Long Distance Dispersal ◽  
Long Distance ◽  
Ancestral Area ◽  
Nucleotide Sequence Variation ◽  
North Eastern ◽  
One Step

Phylogeny of the tribe Anthospermeae is estimated on the basis of nucleotide sequence variation in the ITS region (nuclear ribosomal DNA) and the rps16 intron (plastid DNA). It is concluded that it is dubious whether the tribe is monophyletic including Carpacoce. If Carpacoce does belong to the tribe, then it is the sister group of all other genera. There is no support for the traditional subdivision of the tribe into three subtribes. Anthospermum, Galopina, Nenax and Phyllis form one strongly supported subclade. Coprosma, Durringtonia, Leptostigma, Nertera, Normandia, Opercularia and Pomax form another subclade in all most parsimonious trees, but this subclade lacks jackknife support. Opercularia and Pomax, referred to the subtribe Operculariinae, form a basal grade of this second group. However, trees on which Operculariinae are monophyletic are only one step longer than the most parsimonious ones. Normandia is deeply nested within Coprosma. The subdivision of Coprosma into two subgenera is shown to be artificial. It is suggested that the ancestral area of Anthospermeae is Africa, and that the group was spread by long-distance dispersal to north-eastern Antarctica. It is further suggested that occurrences in Hawaii, Tristan da Cunha, and America are due to long-distance dispersal at a time much later than primary cladogenesis.

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