Molecular phylogeny of Acacia subgenus Phyllodineae (Mimosoideae : Leguminosae) based on DNA sequences of the internal transcribed spacer region

2003 ◽  
Vol 16 (1) ◽  
pp. 19 ◽  
Author(s):  
Daniel J. Murphy ◽  
Joseph T. Miller ◽  
Randall J. Bayer ◽  
Pauline Y. Ladiges
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Internal Transcribed Spacer Region ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Dna Repeat ◽  
Outgroup Taxon

The largest monophyletic group within Acacia is subgenus Phyllodineae, with more than 950 predominately Australian species, the majority characterised by adult foliage consisting of phyllodes. Molecular sequence data from the internal transcribed spacers (ITS) of the nuclear ribosomal DNA repeat were used to investigate the monophyly of seven sections within the subgenus. A nested PCR approach was used to amplify the ITS region. Fifty-one species representative of all sections were sequenced together with one outgroup taxon Lysiloma divaricata (Ingeae).Phylogenetic parsimony analysis suggested that there are two main clades within Phyllodineae but that only one section, Lycopodiifoliae, is apparently monophyletic. In one of the main clades, Lycopodifoliae is related to some taxa in sections Alatae and Pulchellae and some members of section Phyllodineae. In the second main clade, sections Juliflorae, Plurinerves and Botrycephalae cluster with other members of section Phyllodineae. The two sections that are characterised by bipinnate foliage, Botrycephalae and Pulchellae, are nested within phyllodinous clades, indicating that at least two separate reversals to bipinnate leaves have occurred. Botrycephalae is paraphyletic with respect to taxa from section Phyllodineae that have single-nerved phyllodes and racemose inflorescences.

A re-evaluation of North American Tephroseris and Sinosenecio (Asteraceae: Senecioneae) based on molecular and micromorphological data

2001 ◽  
Vol 79 (10) ◽  
pp. 1195-1201 ◽  
Author(s):  
J L Golden ◽  
Y D Kim ◽  
J F Bain
Keyword(s):  
North America ◽  
North American ◽  
Sequence Data ◽  
Its Region ◽  
Nuclear Ribosomal Dna ◽  
Related Genus ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Island Endemic ◽  
Queen Charlotte Island

The recent transfer of the Queen Charlotte island endemic, Senecio newcombei Greene (Senecioneae: Asteraceae), to the Asiatic genus Sinosenecio extends the biogeographic range of Sinosenecio to North America and introduces a large amphi-Beringian gap in the distribution of the genus. However, the closely related genus Tephroseris includes a number of North American species with distributions in the vicinity of S. newcombei. We provide molecular sequence data from the ITS region of nuclear ribosomal DNA and micromorphological data from anther endothecial cells that indicate S. newcombei is closely related to North American Tephroseris species. However, the overall relationship between Sinosenecio and Tephroseris remains unresolved, so that transfer of S. newcombei to Tephroseris is not proposed.Key words: Tephroseris, Sinosenecio, phylogeny, ITS, anther endothecial cells.

scholarly journals Neotypification of Pleurocapsa fuliginosa and epitypification of P. minor (Pleurocapsales): resolving a polyphyletic cyanobacterial genus

Phytotaxa ◽  
2019 ◽  
Vol 392 (4) ◽  
pp. 245 ◽  
Author(s):  
SERGEI SHALYGIN ◽  
KATHERINE J. KAVULIC ◽  
NICOLE PIETRASIAK ◽  
MARKÉTA BOHUNICKÁ ◽  
MELISSA A. VACCARINO ◽  
...  
Keyword(s):  
Sequence Data ◽  
Its Region ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Rock Face ◽  
Sister Clade ◽  
Alpha Level ◽  
Single Well ◽  
Definition Of ◽  
Cyanobacterial Genus

Strains with complete morphological match to Pleurocapsa fuliginosa and P. minor were isolated from Oahu, with another strain matching P. minor isolated from a wet rock face in Utah. Phylogenetically these baeocyte and pseudofilament producing strains fell in a single well-supported clade among a number of pleurocapsalean strains.  They were sister to a clade of baeocyte-producing strains that lack the ability to form psuedofilaments and likely belong in an as-yet-to-be-described genus. Strains putatively named Pleurocapsa are scattered throughout the Pleurocapsales and Chroococcales, indicating a need for clear definition of the genus so that revisionary work and alpha-level taxonomy can move forward. To satisfy this need, P. fuliginosa HA4302-MV1 and P. minor HA4230-MV1 were chosen as neotype and epitype, respectively, establishing the genus based on molecular sequence data. In addition to the distinctive morphology of the genus, all Pleurocapsa species for which 16S-23S ITS regions are available have an unusually long, branched D5 helix at the termination of the ITS region. The sister clade of strains that lack the ability to form pseudofilaments also possess an unusually long and branched D5 helix as well, suggesting that this feature of the ITS region may be a family-level synapomorphy.

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.

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.

scholarly journals Molecular phylogeny based on its sequences of nrDNA of some species belonging to dodder (Cuscuta L.) genus from various ecological sites of Turkey

2020 ◽  
Vol 48 (3) ◽  
pp. 1332-1340
Author(s):  
Ilhan KAYA ◽  
Ibrahim DEMIR ◽  
Mustafa USTA ◽  
Hikmet M. SIPAHIOĞLU
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Sequence Data ◽  
Its Sequences ◽  
Nuclear Ribosomal Dna ◽  
Universal Primers ◽  
Morphological Examination ◽  
Internal Transcribed Spacer Region ◽  
Tissue Samples ◽  
Geographical Regions

Nuclear ribosomal DNA (nrDNA) sequence data of the Cuscuta genus, which have been considered as one of the most popular sequences for phylogenetic inference in plants, have been studied from a phylogenetic perspective in agricultural and non-agricultural lands of Turkey. The samples of Cuscuta spp. were collected from different geographical regions of Turkey between the years of 2013-2015. Some other species, not available locally, were taken from the herbarium samples of some research units. In order to study the phylogenetic relations of collected species, DNA isolations were made from body tissue samples. Conserved regions on ribosomal DNA (rDNA) were amplified by universal primers via PCR method and cloned into a proper cloning vector. The cloned DNA fragments were sequenced and analysed by web-based and computer programs. DNA sequences of certain species were recorded to the National Center for Biotechnology Information (NCBI) database. Based on the morphological examination and molecular analyses of fresh and the herbarium specimen, 8 species were identified. The identified species were C. hyalina (Gene bank accession no. KY020420), C. monogyna (KY020421), C. europaea (KY020422), C. palaestina (KY020423), C. approximata (KY020424), C. kurdica (KY020427), C. kotschyana (KY020430) and C. babylonica (KY020431). The ITS (Internal Transcribed Spacer) region contains several indels in identified Cuscuta species with the length varying from 668 to 730 bp. Sequence divergence ranges from 1.00% to 8.00% within Cuscuta spp. Based on our findings, the ITS sequences provided phylogenetically informative results in combination with the secondary structures.

Phylogeny of Sisymbrium (Brassicaceae) based on ITS sequences of nuclear ribosomal DNA

2002 ◽  
Vol 80 (9) ◽  
pp. 1002-1017 ◽  
Author(s):  
Suzanne I Warwick ◽  
Ihsan A Al-Shehbaz ◽  
Robert A Price ◽  
Connie Sauder
Keyword(s):  
Ribosomal Dna ◽  
New World ◽  
Sequence Data ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Maximum Parsimony Analysis ◽  
Rrna Gene ◽  
Old World ◽  
5.8S Rrna Gene

The genus Sisymbrium as currently circumscribed includes about 94 species disjunctly distributed in the Old (41 spp.) and the New World (53 spp.). Sisymbrium has been variously delimited, with several segregate genera proposed (subtribe Sisymbriinae) primarily for the new World taxa, including Schoenocrambe, Coelophragmus, and Mostacillastrum. Using sequence data from the internal transcribed spacers of nuclear ribosomal DNA and the 5.8S rRNA gene (collectively, ITS region), we examined the evolutionary relationships of Old and New World Sisymbrium species with its segregate genera and the validity of O.E. Schulz's classical sectional treatment of Sisymbrium. Sequence data were obtained from 33 Sisymbrium species, representing all 14 sections and two Sisymbrium species formerly assigned to segregate genera Coelophragmus and Mostacillastrum (subtribe Sisymbriinae), and two putative Sisymbrium species currently assigned to Neotorularia. Sequence data were also obtained from 26 taxa from segregate or related genera includingSchoenocrambe, Werdermannia (subtribe Sisymbriinae), eight genera in the Thelypodieae, Sibara (tribe Arabideae) and Pringlea (tribe Pringleeae), four members of the tribe Brassiceae, and three other Neotorularia species. Results from maximum parsimony analysis showed a polyphyletic origin for Sisymbrium and did not correspond well to Schulz's sectional classification. Sisymbrium species were split into three major clades: Old World Sisymbrium (including Neotorularia aculeolata, Neotorularia afghanica, and the type species of Schoenocrambe, Schoenocrambe linifolia, the sole New World member of this Old World clade); New World Sisymbrium (along with the remaining New World taxa) and designated as the New World Thelypodieae alliance; and the tribe Brassiceae ( including Sisymbrium supinum and Sisymbrium thellungii).Key words: Sisymbrium, Schoenocrambe, ITS, Thelypodieae, taxonomy, Brassicaceae.

Halenia coreana (Gentianaceae), a new species from Korea: Evidence from morphological and molecular data

Phytotaxa ◽  
2019 ◽  
Vol 403 (2) ◽  
pp. 86
Author(s):  
SU-MIN HAN ◽  
HYOSIG WON ◽  
CHAE EUN LIM
Keyword(s):  
New Species ◽  
Sequence Data ◽  
Its Region ◽  
Molecular Data ◽  
Rbcl Gene ◽  
Species Status ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Morphological And Molecular Data ◽  
A New Species

A new species of Halenia (Gentianaceae) from Korea, H. coreana S.M.Han, H.Won & C.E.Lim, is recognized based on morphological and molecular data, and its description and illustration are provided. It is distinct from H. corniculata in having long, narrower and incurved spurs and attenuated leaf apex. Molecular sequence data of nuclear ribosomal ITS region, nuclear XDH gene, and chloroplast rbcL gene also strongly support its species status.

Rediscovery of the enigmatic Scutellaria xylorrhiza (Scutellarioideae; Lamiaceae)—a rare endemic species from Iran

Phytotaxa ◽  
2019 ◽  
Vol 394 (4) ◽  
pp. 267
Author(s):  
YASAMAN SALMAKI ◽  
JOCHEN MÜLLER
Keyword(s):  
Endemic Species ◽  
Sequence Data ◽  
Conservation Status ◽  
Nuclear Ribosomal Dna ◽  
Sequence Analyses ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Critically Endangered Species ◽  
Phylogenetic Placement ◽  
Rare Endemic

After more than 100 years since the first discovery, Scutellaria xylorrhiza, a critically endangered species listed in the Red List of Iranian plants had been presumed to be extinct. We rediscovered recently a population of this species in Sofeh Mountain South of Isfahan. Here, we perform the taxonomic history, phylogenetic placement and conservation status of this endemic species, and compare our findings with the description provided in the protologue and other references. Besides the updated description, notes on typification and new photographs of this species are presented. In addition, we compare S. xylorrhiza with other related Scutellaria species occurring in Iran and neighboring regions using molecular sequence data from the nuclear ribosomal DNA (Internal Transcribed Spacer). Our morphological and sequence analyses show that S. xylorrhiza is close to S. ariana.

scholarly journals A new species of Aspicilia (Megasporaceae), with a new lichenicolous Sagediopsis (Adelococcaceae), from the Falkland Islands

2021 ◽  
Vol 53 (4) ◽  
pp. 307-315
Author(s):  
Alan M. Fryday ◽  
Timothy B. Wheeler ◽  
Javier Etayo
Keyword(s):  
New Species ◽  
South America ◽  
Secondary Metabolite ◽  
Dna Sequences ◽  
Sequence Data ◽  
Falkland Islands ◽  
Molecular Sequence Data ◽  
Lichenicolous Fungi ◽  
Molecular Sequence ◽  
A New Species

AbstractThe new species Aspicilia malvinae is described from the Falkland Islands. It is the first species of Megasporaceae to be discovered on the islands and only the seventh to be reported from South America. It is distinguished from other species of Aspicilia by the unusual secondary metabolite chemistry (hypostictic acid) and molecular sequence data. The collections of the new species support two lichenicolous fungi: Endococcus propinquus s. lat., which is new to the Falkland Islands, and a new species of Sagediopsis with small perithecia and 3-septate ascospores c. 18–20 × 4–5 μm, which is described here as S. epimalvinae. A total of 60 new DNA sequences obtained from species of Megasporaceae (mostly Aspicilia) are also introduced.

Photobiont genetic variation in Flavocetraria nivalis from Poland (Parmeliaceae, lichenized Ascomycota)

2004 ◽  
Vol 36 (2) ◽  
pp. 125-131 ◽  
Author(s):  
Magdalena OPANOWICZ ◽  
Martin GRUBE
Keyword(s):  
Sequence Data ◽  
Its Region ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Algal Symbionts ◽  
Green Algal ◽  
Single Clade ◽  
Alpine Habitats ◽  
South Sweden ◽  
Nuclear Its

Molecular sequence data of the nuclear ITS region was used to investigate the diversity of photobionts in Polish samples of Flavocetraria nivalis. The samples came both from alpine habitats, as well as from lowland localities near the coast. All green algal symbionts were identified as members of the Trebouxia simplex aggregate. These were compared with those of additional samples from Flavocetraria nivalis collected in different parts of Europe and also with photobionts assigned to T. simplex from other lichens. Within the T. simplex aggregate, the Trebouxia ITS sequences from F. nivalis formed four clades. In the Polish lowland populations only a single clade of T. simplex was detected which also occurs in Polish mountains, south Sweden and Austria. A further clade of T. simplex is present in F. nivalis from Polish mountains and is also known from F. nivalis further north in Scandinavia and Greenland, as well as from other lichens in Sweden, the Austrian Alps, and Antarctica.

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