Molecular systematics of Apiaceae subfamily Apioideae: phylogenetic analyses of nuclear ribosomal DNA internal transcribed spacer and Plastid rpoC1 intron sequences

1998 ◽  
Vol 85 (4) ◽  
pp. 563-591 ◽  
Author(s):  
Stephen R. Downie ◽  
Seemanti Ramanath ◽  
Deborah S. Katz-Downie ◽  
Esmeralda Llanas
Keyword(s):  
Molecular Systematics ◽  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Nuclear Ribosomal Dna

Phylogenetic analyses of Nematoctonus and Hohenbuehelia (Pleurotaceae)

2007 ◽  
Vol 85 (8) ◽  
pp. 762-773 ◽  
Author(s):  
Alexandra T.E. Koziak ◽  
Kei Chin Cheng ◽  
R. Greg Thorn
Keyword(s):  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Nuclear Ribosomal Dna ◽  
Monophyletic Clade ◽  
Parasitoid Species ◽  
Internal Transcribed Spacer Region ◽  
Species Limits ◽  
Additional Gene

Hohenbuehelia (Agaricales, Pleurotaceae) and Nematoctonus (Hyphomycetes) are the names for the sexual and asexual stages of a genus of nematode-destroying fungi (Basidiomycota). We obtained partial sequences of nuclear ribosomal DNA, including the internal transcribed spacer region and the 5′ end of the large subunit, of 37 isolates of Hohenbuehelia and Nematoctonus representing 13 of the 16 described species in Nematoctonus. Phylogenetic analyses support Hohenbuehelia–Nematoctonus as a monophyletic clade of the Pleurotaceae, within which the species were placed in five main subclades. Exclusively predatory species ( Nematoctonus brevisporus Thorn & G.L. Barron, Nematoctonus campylosporus Drechsler, Nematoctonus robustus F.R. Jones, and Nematoctonus sp. UAMH 5317) appear to be basal. In these species, adhesive knobs to capture prey are produced on their hyphae but not on their conidia. A single mycelial individual may feed on many nematodes. From these have arisen both exclusively parasitoid species ( Nematoctonus cylindrosporus Thorn & G.L. Barron, Nematoctonus leiosporus Drechsler, Nematoctonus leptosporus Drechsler, Nematoctonus pachysporus Drechsler, Nematoctonus tylosporus Drechsler), and species that we call intermediate predators ( Nematoctonus angustatus Thorn & G.L. Barron, Nematoctonus concurrens Drechsler, Nematoctonus geogenius Thorn & GL. Barron, Nematoctonus hamatus Thorn & G.L. Barron, and Nematoctonus subreniformis Thorn & G.L. Barron). Exclusively parasitoid species have conidia that germinate to form sticky knobs that attach to passing nematodes but lack adhesive knobs on the hyphae. Each mycelial individual feeds on only one nematode. Intermediate predators have adhesive knobs both on hyphae and on germinated conidia and can act in both predatory and parasitoid modes. Most morphospecies are resolved as monophyletic, but sequences of additional gene regions are required to clarify species limits within the N. angustatus – N. geogenius group.

Russula darjeelingensis, a new species from Eastern Himalaya, India

Phytotaxa ◽  
2018 ◽  
Vol 358 (1) ◽  
pp. 83 ◽  
Author(s):  
SOUMITRA PALOI ◽  
KANAD DAS ◽  
KRISHNENDU ACHARYA
Keyword(s):  
New Species ◽  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Nuclear Ribosomal Dna ◽  
Eastern Himalaya ◽  
Morphological Description ◽  
Molecular Phylogenetic ◽  
Internal Transcribed Spacer Sequences ◽  
A New Species

Russula darjeelingensis is characterized by its small sized white pileus with a tall and narrow stipe, white spore print, basidiospores with amyloid suprahilar spot and a pileipellis containing encrusted pileocystidia and absence of primordial hyphae. The combination of all these characters and molecular phylogenetic analyses of internal transcribed spacer sequences of nuclear ribosomal DNA confirmed it as a new species in genus Russula Pers., subg. Russula Romagn. emend. sect. Polychromae (Maire) Sarnari subsect. Paraintegrinae Sarnari. A comprehensive morphological description, illustrations, and comparisons with morphologically similar and phylogenetically related species are provided in the present study.

Multiple independent losses of the plastid rpoC1 intron in Medicago (Fabaceae) as inferred from phylogenetic analyses of nuclear ribosomal DNA internal transcribed spacer sequences

1998 ◽  
Vol 76 (5) ◽  
pp. 791-803 ◽  
Author(s):  
Stephen R Downie ◽  
Deborah S Katz-Downie ◽  
Erica J Rogers ◽  
Heidi L Zujewski ◽  
Ernest Small
Keyword(s):  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Nuclear Ribosomal Dna ◽  
Comprehensive Treatment ◽  
Likelihood Methods ◽  
Maximum Likelihood Methods ◽  
Intron Content ◽  
Internal Transcribed Spacer Sequences ◽  
Polymerase Chain

A previous polymerase chain reaction based survey for the occurrence of the intron in chloroplast gene rpoC1 revealed its absence in one of the eight species of Medicago (Fabaceae; Trifolieae) examined. We extend the survey of Medicago to include 65 of the 86 species, representing all 12 sections and seven of the eight subsections recognized in the most recent comprehensive treatment of the genus. Our results indicate that 17 species from five sections lack the intron and that three of these sections are heterogeneous with regard to intron content. DNA sequencing across the rpoC1 intron-exon boundary in three of these species reveals the precise excision of the intron from the gene. Phylogenies derived from nuclear ribosomal DNA internal transcribed spacer sequences, estimated using maximum parsimony and maximum likelihood methods, suggest that most of the previously recognized sections in Medicago are not monophyletic as currently circumscribed. Furthermore, these results suggest that the rpoC1 intron has been lost independently a minimum of three times during the evolution of the group. The occurrence of multiple independent intron losses severely reduces the utility of this character as a phylogenetic marker in Medicago.Key words: Medicago, Fabaceae, chloroplast DNA, rpoC1 intron, nuclear ribosomal DNA internal transcribed spacer (ITS) sequences.

scholarly journals Molecular phylogenetic analyses of internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA indicate monophyly of the genus Phytolacca L. (Phytolaccaceae)

2015 ◽  
Vol 22 (1) ◽  
pp. 1-8 ◽  
Author(s):  
M. Ajmal Ali ◽  
Joongku Lee ◽  
Soo-Yong Kim ◽  
Sang-Hong Park ◽  
Fahad M.A. Al-Hemaid
Keyword(s):  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Its Sequences ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Study ◽  
Molecular Evidence ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Plant Taxon

Relationships within the family Phytolaccaceae sensu lato were examined based on internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA (nrDNA). The study revealed Phytolacca L. as taxonomically the most difficult genus in the family with completely unknown phylogeny. Molecular evidence was used from nrDNA ITS sequences of about 90% of the species for maximum parsimony analyses, and the molecular phylogenetic analyses defined a monophyletic Phytolacca. This first molecular phylogenetic study of Phytolacca concludes that the relationships among the species within the genus do not show harmony with the generic classification based on morphology. These results set the stage for a more detailed phylogenetic analysis of Phytolacca.Bangladesh J. Plant Taxon. 22(1): 1­–8, 2015 (June)

MOLECULAR SYSTEMATICS OF TETRAPLASANDRA, MUNROIDENDRON AND REYNOLDSIA SANDWICENSIS (ARALIACEAE) AND THE EVOLUTION OF SUPERIOR OVARIES IN TETRAPLASANDRA

2001 ◽  
Vol 58 (2) ◽  
pp. 229-242 ◽  
Author(s):  
A. COSTELLO ◽  
T. J. MOTLEY
Keyword(s):  
Molecular Systematics ◽  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Monophyletic Group ◽  
Nuclear Ribosomal Dna ◽  
Data Sets ◽  
Parsimony Analysis ◽  
Distinct Genus ◽  
Single Genus ◽  
Systematic Relationships

Systematic relationships within the Hawaiian group Tetraplasandra A. Gray, Munroidendron Sherff and Reynoldsia sandwicensis A. Gray are investigated here based on parsimony analysis of nucleotide sequences from the internal transcribed spacer (ITS 1 and 2) regions and the non-transcribed spacer of 5S (5S-NTS) nuclear ribosomal DNA. Results indicate that Tetraplasandra, Munroidendron and Reynoldsia sandwicensis form a single monophyletic group, and that Reynoldsia A. Gray is paraphyletic. Both data sets support combining Reynoldsia sandwicensis with Munroidendron and treating it as distinct from Reynoldsia species outside Hawaii. Both data sets support two major clades: a Munroidendron/Reynoldsia sandwicensis clade and a Tetraplasandra clade, but they are discordant in relation to the monophyly of Tetraplasandra. 5S-NTS results support treating Tetraplasandra, Munroidendron and Reynoldsia sandwicensis as a single genus, whereas ITS results suggest that Tetraplasandra represents a distinct genus from Reynoldsia sandwicensis and Munroidendron. Tetraplasandra gymnocarpa (Hillebr.) Sherff is the only member of the Araliaceae with a completely superior ovary, and in T. kavaiensis (H. Mann) Sherff the ovary is partially superior. Together, they form a well-supported clade within the Hawaiian complex, confirming the hypothesis that in Tetraplasandra superior ovaries evolved in Hawaii from an epigynous ancestor.

Internal transcribed spacer sequences of nuclear ribosomal DNA resolving complex taxonomic history in the genus Vicia L.

2014 ◽  
Vol 61 (5) ◽  
pp. 909-925 ◽  
Author(s):  
Behrouz Shiran ◽  
Soghra Kiani ◽  
Deepmala Sehgal ◽  
Akram Hafizi ◽  
Tanvir ul-Hassan ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Nuclear Ribosomal Dna ◽  
Taxonomic History ◽  
Internal Transcribed Spacer Sequences

A new species of Chlorociboria (Helotiales, Ascomycota) on herbaceous stems from China

Phytotaxa ◽  
2017 ◽  
Vol 312 (1) ◽  
pp. 111
Author(s):  
HUAN-DI ZHENG ◽  
WEN-YING ZHUANG
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Central China ◽  
Nuclear Ribosomal Dna ◽  
Light Blue ◽  
Ectal Excipulum ◽  
A New Species

A new species, namely Chlorociboria herbicola, is discovered on herbaceous stems in central China. Morphologically, the new fungus is distinctive by the combination of light blue-green apothecia, rectangular cells in ectal excipulum, and elongate-ellipsoidal ascospores with rounded ends. Phylogenetic analyses of the internal transcribed spacer and large subunit of nuclear ribosomal DNA sequences confirm its ascription in Chlorociboria and distinction from the known species of the genus.

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