Phylogenetic position of Arabis arenicola and generic limits of Aphragmus and Eutrema (Brassicaceae) based on sequences of nuclear ribosomal DNA

2006 ◽  
Vol 84 (2) ◽  
pp. 269-281 ◽  
Author(s):  
Suzanne I. Warwick ◽  
Ihsan A. Al-Shehbaz ◽  
Connie A. Sauder
Keyword(s):  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its Region ◽  
Molecular Data ◽  
The Other ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Position ◽  
New Combinations ◽  
Arabidopsis Lyrata ◽  
Relationship Of

Sequence data from the nuclear ribosomal internal transcribed spacer (ITS) region of 45 taxa were used to determine the phylogenetic relationship of Arabis arenicola to Arabis , Arabidopsis , Braya , and Eutrema , and that of Eutrema to the purportedly related genera Aphragmus , Lignariella , Neomartinella , Platycraspedum , Taphrospermum , and Thellungiella . Arabis arenicola was originally described as Eutrema in 1830, transferred to Arabis in 1898, and has remained in Arabis to the present, even though it is morphologically more similar to Arabidopsis, Braya, and Eutrema. Sequence data were obtained from representative taxa of Arabis, Arabidopsis, and related Boechera and Catolobus, Braya and Neotorularia, and Eutrema, Aphragmus, Lignariella, Neomartinella, Platycraspedum, Taphrospermum, and Thellungiella. The five Arabis arenicola accessions examined had ITS sequences that were identical to each other and to four Arabidopsis lyrata accessions. In both maximum parsimony and maximum likelihood analyses, Arabis arenicola fell within the Arabidopsis clade and was closely aligned with Arabidopsis lyrata. Two of six purportedly related genera were not closely related to Eutrema. Both analyses placed Lignariella within a separate well-supported clade with Aphragmus, while the other four genera, Neomartinella, Platycraspedum, Taphrospermum, and Thellungiella, fell within a well-supported clade with Eutrema. Morphology and molecular data strongly suggest transferring Arabis arenicola to Arabidopsis, expanding Aphragmus to include Lignariella, and expanding Eutrema to include Neomartinella, Platycraspedum, Taphrospermum, and Thellungiella. New combinations in Arabidopsis and Aphragmus are proposed.

Higher-level relationships among the eucalypts are resolved by ITS-sequence data

2002 ◽  
Vol 15 (1) ◽  
pp. 49 ◽  
Author(s):  
Dorothy A. Steane ◽  
Dean Nicolle ◽  
Gay E. McKinnon ◽  
René E. Vaillancourt ◽  
Brad M. Potts
Keyword(s):  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its Region ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Its Sequence ◽  
Phylogenetic Groups ◽  
Single Section ◽  
Western Australian ◽  
Genus Eucalyptus

This expanded survey of ITS sequences represents the largest analysis of molecular data ever attempted on Eucalyptus. Sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA were included in an analysis of 90 species of Eucalyptus s.s. and 28 species representing eight other genera (Allosyncarpia, Angophora, Arillastrum, Corymbia, Eucalyptopsis, Stockwellia, Lophostemon and Metrosideros). The results of the study indicate that Angophora and Corymbia form a well-supported clade that is highly differentiated from Eucalyptus s.s. Corymbia species are divided between two clades, one of which may be the sister to Angophora. Allosyncarpia, Arillastrum, Eucalyptopsis and ‘Stockwellia’ are also highly differentiated from Eucalyptus s.s. If the genus Eucalyptus is to be expanded to include Angophora and Corymbia(sensu Brooker 2000), ITS data suggest that Allosyncarpia, Eucalyptopsis, ‘Stockwellia’ and potentially Arillastrum should also be included in Eucalyptus s.l. The ITS data suggest that subg. Symphyomyrtus is paraphyletic and that subg. Minutifructus should be included within it. Within subg.Symphyomyrtus, only sect. Maidenaria appears to be monophyletic. Sections Adnataria and Dumaria are probably monophyletic; sections Exsertaria and Latoangulatae are very close and probably should be combined in a single section. Section Bisectae is polyphyletic and is divided into two distinct lineages. The phylogenetic groups depicted by ITS data are consistent with the frequency of natural inter-specific hybridisations as well as data from controlled crosses within subgenus Symphyomyrtus. The ITS data illustrate that subg. Idiogenes and western Australian monocalypts are early evolutionary lines relative to E. diversifolia, E. rubiginosa (monotypic subg. Primitiva) and the eastern monocalypts and that subg. Primitiva should be sunk into subg. Eucalyptus. Subgenus Eudesmia may be monophyletic, grouping with subgenera Idiogenes and Eucalyptus. Further work is required to confirm the phylogenetic positions of the monotypic subgenera Alveolata, Cruciformes, Acerosae and Cuboidea.

Phylogenetic relationships of the monogenomic species of the wheat tribe, Triticeae (Poaceae), inferred from nuclear rDNA (internal transcribed spacer) sequences

Genome ◽  
1995 ◽  
Vol 38 (2) ◽  
pp. 211-223 ◽  
Author(s):  
C. Hsiao ◽  
N. J. Chatterton ◽  
K. H. Asay ◽  
K. B. Jensen
Keyword(s):  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Parallel Evolution ◽  
Diploid Species ◽  
Its Region ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
The Arctic ◽  
Cytogenetic Evidence

Phylogenetic relationships of 30 diploid species of Triticeae (Poaceae) representing 19 genomes were estimated from the sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. The ITS sequence phylogeny indicated that: (i) each genome group of species is monophyletic, concordant with cytogenetic evidence; (ii) Hordeum (I) and Critesion (H) are basal; (iii) Australopyrum (W) is closely related to Agropyron (P); (iv) Peridictyon (G), Heteranthelium (Q), and Dasypyrum (V) are closely related to Pseudoroegneria (S); (v) most of the annuals, Triticum s.l. (A, B, D), Crithopsis (K), Taeniatherum (T), Eremopyrum (F), Henrardia (O), Secale (R), and two perennials, Thinopyrum (J) and Lophopyrum (E), all of Mediterranean origin, are a monophyletic group. However, phylogenetic trees based on morphology group these Mediteranean species with various perennial lineages of the Arctic-temperate region. The molecular data and biogeography of the tribe suggest that the Mediterranean lineage is derived from the Arctic-temperate lineage and that the two lineages have evolved in parallel. Extensive morphological parallelism apparently obscures the true genealogical history of the tribe when only morphology is considered.Key words: Poaceae, Triticeae, rDNA sequence, molecular phylogeny, parallel evolution.

Peucedanum huangshanense (Apiaceae), a new species from Anhui, China

Phytotaxa ◽  
2020 ◽  
Vol 430 (1) ◽  
pp. 17-24
Author(s):  
SHAN-SHAN CHU ◽  
DE-QUN WANG ◽  
HUA-SHENG PENG ◽  
LU-QI HUANG
Keyword(s):  
New Species ◽  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Its Region ◽  
Distinct Species ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Position ◽  
A New Species

Peucedanum huangshanense, a new species discovered in Anhui, China, is illustrated and described. Detailed morphological comparisons have showed that it is similar to P. praeruptorum but differs from the latter by having larger compound umbels (5–14 cm across), rays up to 25, and long-ovoid mericarps with lateral ribs narrowly winged. To explore the phylogenetic position of this species, nuclear ribosomal DNA internal transcribed spacer (ITS) region was sequenced for P. huangshanense and P. praeruptorum collected in different places. The morphological and molecular evidences support the hypothesis that P. huangshanense is a new distinct species.

scholarly journals A novel Arabidopsis phyllosphere resident Protomyces species and a re-examination of genus Protomyces based on genome sequence data

IMA Fungus ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Kai Wang ◽  
Timo Sipilä ◽  
Kirk Overmyer
Keyword(s):  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Host Plants ◽  
Sequence Data ◽  
Nuclear Gene ◽  
Molecular Data ◽  
Rapid Identification ◽  
Nuclear Ribosomal Dna ◽  
Species Relationships ◽  
Internal Transcribed Spacer Sequences

AbstractProtomyces is an understudied genus of yeast-like fungi currently defined as phytopathogens of only Umbelliferae and Compositae. Species relationships and boundaries remain controversial and molecular data are lacking. Of the 82 named Protomyces, we found few recent studies and six available cultures. We previously isolated Protomyces strains from wild Arabidopsis thaliana, a member of Brassicaceae, a family distant from accepted Protomyces hosts. We previously sequenced the genomes of all available Protomyces species, and P. arabidopsidicola sp. nov. strain C29, from Arabidopsis. Phylogenomics suggests this new species occupied a unique position in the genus. Genomic, morphological, and physiological characteristics distinguished P. arabidopsidicola sp. nov. from other Protomyces. Nuclear gene phylogenetic marker analysis suggests actin1 gene DNA sequences could be used with nuclear ribosomal DNA internal transcribed spacer sequences for rapid identification of Protomyces species. Previous studies demonstrated P. arabidopsidicola sp. nov. could persist on the Arabidopsis phyllosphere and Protomyces sequences were discovered on Arabidopsis at multiple sites in different countries. We conclude that the strain C29 represents a novel Protomyces species and propose the name of P. arabidopsidicola sp. nov. Consequently, we propose that Protomyces is not strictly associated only with the previously recognized host plants.

scholarly journals Status of Reseda pentagyna Abdallah & A.G. Miller (Resedaceae) inferred from combined nuclear ribosomal and chloroplast sequence data

2013 ◽  
Vol 20 (2) ◽  
pp. 233-238 ◽  
Author(s):  
M. Ajmal Ali ◽  
Fahad M. Al-Hemaid ◽  
Ritesh K. Choudhary ◽  
Joongku Lee ◽  
Soo-Yong Kim ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its Region ◽  
Nuclear Ribosomal Dna ◽  
Bootstrap Support ◽  
Local Alignment ◽  
Blast Search ◽  
The Status ◽  
Search Tool ◽  
Plant Taxon

The present study focuses on the status of Reseda pentagyna Abdallah & A.G. Miller (Resedaceae). The internal transcribed spacer (ITS) region of nuclear ribosomal DNA and chloroplast trnL-F gene of the questioned species were sequenced. The Basic Local Alignment Search Tool (BLAST) search showed maximum identity with R. stenostachya. The parsimony analysis of ITS, trnL-F and combined sequences data analyses revealed grouping of Reseda species consistent with established taxonomic sections of the genus, R. pentagyna showed proximity with R. stenostachya (100% bootstrap support), nested within the clade of section Reseda.DOI: http://dx.doi.org/10.3329/bjpt.v20i2.17397Bangladesh J. Plant Taxon. 20(2): 233-238, 2013

scholarly journals A comparison of populations of Armillaria hinnulea in New Zealand and Australia

2008 ◽  
Vol 61 ◽  
pp. 41-47 ◽  
Author(s):  
T.D. Ramsfield ◽  
M.W.P. Power ◽  
G.S. Ridley
Keyword(s):  
New Zealand ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its Region ◽  
The Other ◽  
Dna Sequence Data ◽  
Nothofagus Forests ◽  
Preliminary Study ◽  
Decaying Wood ◽  
The Relationship

Armillaria hinnulea has been recorded from the northwest quadrant of the South Island of New Zealand Tasmania and Australia In New Zealand A hinnulea is rare being restricted to decaying wood in South Island Nothofagus forests A preliminary study of the relationship between the populations of A hinnulea was performed using DNA sequence data from the internal transcribed spacer (ITS) region of the ribosomal DNA Two major ITS clades were observed each of which included representative sequences from Australian collections Within one ITS clade one Australian sequence was 100 identical with the New Zealand isolates while in the other ITS clade eight New Zealand isolates representing five locations were 100 identical but the Australian sequence differed by five base substitutions and was in a separate subclade These results suggest at least two introductions of A hinnulea have occurred one relatively recently and one in the more distant past

scholarly journals Four New Keratinophyton Species (Onygenaceae) From Europe

2020 ◽  
Author(s):  
Roman Labuda ◽  
Andreas Bernreiter ◽  
Doris Hochenauer ◽  
Christoph Schüller ◽  
Alena Kubatova
Keyword(s):  
Internal Transcribed Spacer ◽  
Large Subunit ◽  
Its Region ◽  
Soil Samples ◽  
The Other ◽  
Lsu Rdna ◽  
New Combinations ◽  
Internal Transcribed Spacer Region ◽  
Asexual Morphs ◽  
Terminal Cluster

Abstract Four new Keratinophyton species (Ascomycota: Pezizomycotina, Onygenales), K. gollerae, K. lemmensii, K. straussii and K. wagneri, isolated from soil samples originating from Europe (Austria, Italy and Slovakia) are described and illustrated. The new taxa are well supported by phylogenetic analysis of the internal transcribed spacer region (ITS) region, the nuclear large subunit (LSU) rDNA, and their phenotype. Within the Keratinophyton clade, K. lemmensii is clustered with K. durum, K. hubeiense, K. submersum and K. siglerae, while K. gollerae, K. straussii and K. wagneri are resolved in a separate terminal cluster along with K. minutisporosum. All four new species can be well distinguished from the other asexual taxa in the genus Keratinophyton based on phenotypical characteristics alone. Ten new combinations are proposed for all other Chrysosporium asexual morphs which are resolved in the monophyletic Keratinophyton clade.

scholarly journals (269) Taxonomic Relationship of Korean Native Aster, Based on Internal Transcribed Spacer (ITS) Sequences of Nuclear Ribosomal DNA

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 1017A-1017
Author(s):  
Su-Young Hong ◽  
Kwang-Soo Cho ◽  
Ki-Oug Yoo ◽  
Jong-Taek Suh ◽  
Dong-Lim Yoo
Keyword(s):  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Its Region ◽  
Sister Group ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Position ◽  
Its2 Region ◽  
Base Pairs ◽  
Total Length

There are 25 species of aster in Korea. There is a controversy about the taxonomical classification of Aster. The genus Aster was classified into four genera, Aster, Gymnaster, Kalimeris, and Heteropappus, by morphological characters. In order to clarify the phylogenetic position of aster, the nucleotide sequence of the nuclear ribosomal DNA internal transcribed spacer (ITS) region was compared among 11 taxa in Korean native aster. The size of ITS1 and ITS2 ranged from 283 to 286 bp and from 251 to 257 bp, respectively. The size of 5.8S region was 164 bp in 11 taxa. The total length of ITS1, 5.8S and ITS2, A. tripolium was shown to be the shortest length, 701 bp; and A. scaber was shown to be the longest length, 706 bp. The G+C content of ITS1 ranged from 47.9% to 51.2% and ITS2 ranged from 52.2% to 55.1%. The range of each taxon was narrow. The total length of the character matrix was 708 characters. Among them, total indel showed 9; in the ITS1 region indel showed 6 it was 67%; and in the ITS2 region, indel showed 3. Most of the indels showed deletion or insertion of only one base pair, but in A. spathulifolius deleted two base pairs and in A. tripolium deleted five base pairs. But in A. yomena, A. hayatae, A. koraiensis, and A. hispidus, the indel was not detected. Phylogenetic trees did not even make a difference inter-genus, but A. yomena and A. koraiensis called genus Kalimeris and genus Gymnaster, respectively; these constituted a clade. A. hispidus called genus Heteropappus was placed as a sister group to the clade of A. ageratoides and A. glehni.

DISTINCTION BETWEEN CRINUM LATIFOLIUM AND CRINUM ASIATICUM (AMARYLLIDACEAE) USING MOLECULAR DATA

2020 ◽  
Vol 27 (03) ◽  
Author(s):  
VAN HONG THIEN ◽  
TRAN THỊ THU NGAN ◽  
LUU THAO NGUYEN ◽  
TRINH NGOC NAM
Keyword(s):  
Phylogenetic Tree ◽  
Dna Sequence ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Dna Sequence Data ◽  
Crinum Asiaticum ◽  
Molecular Makers

Crinum latifolium and C. asiaticum are the two species of genus Crinum, Amaryllidaceae family and they have highly medicinal values. Distinction between two species is challenging due to many similar morphological characteristics. In this study, we used molecular makers to distinguish the two species Crinum latifolium and C. asiaticum. The phylogenetic tree was constructed based on the DNA sequence data of the ITS (internal transcribed spacer) nuclear ribosomal DNA (nrDNA) sequences of Crinum latifolium and C. asiaticum. As a result, C. latifolium and C. asiaticum were sorted into two different groups in the phylogenetic tree. Therefore, C. latifolium and C. asiaticum were carried out to solve the taxonomic ambiguity.

scholarly journals Phylogenetic Relationship of Mangosteen (Garcinia mangostana) and Several Wild Relatives (Garcinia spp.) Revealed by ITS Sequence Data

2004 ◽  
Vol 129 (3) ◽  
pp. 368-373 ◽  
Author(s):  
Chinawat Yapwattanaphun ◽  
Suranant Subhadrabandhu ◽  
Chitose Honsho ◽  
Keizo Yonemori
Keyword(s):  
Sequence Data ◽  
Its Region ◽  
Wild Relatives ◽  
Nuclear Ribosomal Dna ◽  
Its Sequence ◽  
Nucleotide Position ◽  
Neighbor Joining ◽  
Garcinia Mangostana ◽  
Its Sequence Analysis ◽  
Relationship Of

The phylogenetic relationships among 17 Garcinia species including G. mangostana (mangosteen) were analyzed by comparing sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA). Both parsimonious and neighbor joining (NJ) analyses revealed that G. mangostana is closely related to G. malaccensis believed to be a progenitor of mangosteen. Another suspected progenitor of mangosteen, G. hombroniana, was more distant from G. mangostana than G. malaccensis phylogenetically. Garcinia hombroniana formed a cluster with G. rostrata, G, speciosa and G. sizygiifolia, and this cluster was connected with a cluster of G. mangostana and G. malaccensis. The ITS sequence analysis showed that G. atroviridis, G. cowa, G. dulcis, G. malaccensis, G. mangostana, G. rostrata and G. vilersiana have nucleotide additivity (two different nucleotides at the same nucleotide position) at several sites in the ITS region. The occurrence of these species might be related to hybridization with ancestors, but the genomic compositions, even chromosome numbers, of these species are still unknown.

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