Phylogeny of the Bifrenaria (Orchidaceae) Complex Based on Morphology and Sequence Data from Nuclear rDNA Internal Transcribed Spacers (ITS) and Chloroplast trnL‐trnF Region

2002 ◽  
Vol 163 (6) ◽  
pp. 1055-1066 ◽  
Author(s):  
Samantha Koehler ◽  
Norris H. Williams ◽  
W. Mark Whitten ◽  
Maria do Carmo E. do Amaral
Keyword(s):  
Sequence Data ◽  
Internal Transcribed Spacers ◽  
Nuclear Rdna

Phylogenetic relationships in the Mediterranean Helichrysum (Asteraceae, Gnaphalieae) based on nuclear rDNA ITS sequence data

2004 ◽  
Vol 17 (3) ◽  
pp. 241 ◽  
Author(s):  
M. Galbany-Casals ◽  
N. Garcia-Jacas ◽  
A. Susanna ◽  
L. Sáez ◽  
C. Benedí
Keyword(s):  
Sequence Data ◽  
Cladistic Analysis ◽  
Mediterranean Area ◽  
Internal Transcribed Spacers ◽  
Nuclear Rdna ◽  
Generic Delimitation ◽  
Rdna Its ◽  
The Mediterranean ◽  
Sectional Classification

The internal transcribed spacers ITS1 and ITS2 of the nuclear rDNA were sequenced for 41 Helichrysum species (Gnaphalieae), focusing on the Mediterranean group of species, together with eight representatives of other genera of the Gnaphalieae, in order to check the hypothesised monophyly of the Mediterranean Helichrysum group and the correspondence of the sequence data with its traditional sectional classification. The cladistic analysis of sequence data supports monophyly of the Mediterranean Helichrysum excluding H. frigidum and H. montelinasanum. The traditional classification of the Mediterranean species into two sections, Helichrysum and Virginea, is not supported, whereas a group constituted by species from the west Mediterranean area is shown as a moderately supported monophyletic clade in the strict consensus tree. Other results also show and confirm the complexity, still not satisfactorily resolved, of the Helichrysum generic delimitation: Pseudognaphalium luteoalbum appears merged in Helichrysum whereas Helichrysum dasyanthum appears more related to Anaxeton laeve than to any Helichrysum species.

Genetic characterisation and taxonomy of species of Anisakis (Nematoda:Anisakidae) parasitic in Australian marine mammals

2012 ◽  
Vol 26 (2) ◽  
pp. 204 ◽  
Author(s):  
Shokoofeh Shamsi ◽  
Robin Gasser ◽  
Ian Beveridge
Keyword(s):  
Marine Mammals ◽  
Sequence Data ◽  
Internal Transcribed Spacers ◽  
Nuclear Rdna ◽  
Delphinus Delphis ◽  
The World ◽  
Morphological Approach ◽  
First Time ◽  
Kogia Sima ◽  
Anisakid Nematodes

Three species of Anisakis from Australian marine mammals, including Anisakis brevispiculata, A. simplex C and A. pegreffii, are described and characterised genetically on the basis of sequence data for the first and second internal transcribed spacers (ITS-1 and ITS-2) of nuclear rDNA. Parasite specimens were collected from Delphinus delphis, Tursiops truntatus and Kogia sima in Australia. A. brevispiculata is reported for the first time in Australia. However, analyses of sequence data suggests that A. brevispiculata in Australia is genetically distinct from specimens considered to represent the same species from other parts of the world. Fourth larval and adult stages of A. pegreffii were found in dolphins. Assigning larvae to A. pegreffii was based on the ITS-1 and ITS-2 sequences. A description of these larvae also is provided. Furthermore, fourth-stage larvae of A. simplex C were found in Kogia sima. Alignments of ITS-1 and ITS-2 sequences for members of A. simplex sensu lato revealed that nucleotide differences in ITS-1 can be used to differentiate among members of A. simplex sensu lato. This study reinforces the use of a combined molecular and morphological approach for the specific identification of anisakid nematodes.

scholarly journals The Evolution of Life Modes in Stictidaceae, with Three Novel Taxa

2021 ◽  
Vol 7 (2) ◽  
pp. 105
Author(s):  
Vinodhini Thiyagaraja ◽  
Robert Lücking ◽  
Damien Ertz ◽  
Samantha C. Karunarathna ◽  
Dhanushka N. Wanasinghe ◽  
...  
Keyword(s):  
New Species ◽  
Large Scale ◽  
Sequence Data ◽  
Large Subunit ◽  
Monte Carlo Sampling ◽  
Small Subunit ◽  
Sensu Stricto ◽  
Internal Transcribed Spacers ◽  
Character State ◽  
Phenotypic Data

Ostropales sensu lato is a large group comprising both lichenized and non-lichenized fungi, with several lineages expressing optional lichenization where individuals of the same fungal species exhibit either saprotrophic or lichenized lifestyles depending on the substrate (bark or wood). Greatly variable phenotypic characteristics and large-scale phylogenies have led to frequent changes in the taxonomic circumscription of this order. Ostropales sensu lato is currently split into Graphidales, Gyalectales, Odontotrematales, Ostropales sensu stricto, and Thelenellales. Ostropales sensu stricto is now confined to the family Stictidaceae, which includes a large number of species that are poorly known, since they usually have small fruiting bodies that are rarely collected, and thus, their taxonomy remains partly unresolved. Here, we introduce a new genus Ostropomyces to accommodate a novel lineage related to Ostropa, which is composed of two new species, as well as a new species of Sphaeropezia, S. shangrilaensis. Maximum likelihood and Bayesian inference analyses of mitochondrial small subunit spacers (mtSSU), large subunit nuclear rDNA (LSU), and internal transcribed spacers (ITS) sequence data, together with phenotypic data documented by detailed morphological and anatomical analyses, support the taxonomic affinity of the new taxa in Stictidaceae. Ancestral character state analysis did not resolve the ancestral nutritional status of Stictidaceae with confidence using Bayes traits, but a saprotrophic ancestor was indicated as most likely in a Bayesian binary Markov Chain Monte Carlo sampling (MCMC) approach. Frequent switching in nutritional modes between lineages suggests that lifestyle transition played an important role in the evolution of this family.

scholarly journals First Report of Leptosphaeria biglobosa (Blackleg) on Brassica oleracea (Cabbage) in Mexico

Plant Disease ◽  
2010 ◽  
Vol 94 (6) ◽  
pp. 791-791 ◽  
Author(s):  
A. Dilmaghani ◽  
M. H. Balesdent ◽  
T. Rouxel ◽  
O. Moreno-Rico
Keyword(s):  
Brassica Oleracea ◽  
Sequence Data ◽  
Leptosphaeria Maculans ◽  
The United States ◽  
Internal Transcribed Spacers ◽  
First Report ◽  
5.8S Rdna ◽  
Single Location ◽  
Leptosphaeria Biglobosa ◽  
Β Tubulin

Broccoli (Brassica oleracea var. italica), cauliflower (B. oleracea var. botrytis), and cabbage (B. oleracea var. capitata) have been grown in central Mexico since 1970, with 21,000 ha cropped in 2001. In contrast, areas grown with oilseed rape (B. napus) are very limited in Mexico (<8,000 ha). Blackleg, a destructive disease of B. napus in most parts of the world, was first observed in Mexico in Zacatecas and Aguascalientes in 1988 on B. oleracea, causing as much as 70% yield loss. A species complex of two closely related Dothideomycete species, Leptosphaeria maculans and L. biglobosa, is associated with this disease of crucifers (1), but leaf symptoms on susceptible plants are different, with L. maculans typically causing >15-mm pale gray lesions with numerous pycnidia, whereas L. biglobosa causes dark and smaller lesions only containing a few pycnidia. Having a similar epidemiology, both species can be present on the same plants at the same time, and symptom confusion can occur as a function of the physiological condition of the plant or expression of plant resistance responses. A total of 209 isolates from symptomatic B. oleracea leaves were collected from three fields in central states of Mexico (58 to 71 isolates per location). All leaves showed similar symptoms, including a 10- to 15-mm tissue collapse with an occasional dark margin. Cotyledons of seven B. napus differentials were inoculated with conidia of all the isolates as described by Dilmaghani et al. (1). Two hundred isolates caused tissue collapse typical of L. maculans. However, nine obtained from white cabbage in a single location in Aguascalientes caused <5-mm dark lesions. When inoculated onto cotyledons of three B. oleracea genotypes commonly grown in Mexico (cvs. Domador, Monaco, and Iron Man), the nine isolates caused a range of symptoms characterized by tissue collapse (maximum 10 to 15 mm), showing the presence of patches of black necrotic spots within the collapse. The occasional presence of a few pycnidia allowed us to reisolate the fungus for molecular identification. ITS1-5.8S-ITS2, (internal transcribed spacers and 5.8S rDNA), actin, and β-tubulin sequences were obtained as described previously (4). Multiple gene genealogies based on these sequence data showed two subclades of L. biglobosa: L. biglobosa ‘occiaustralensis’ (one isolate; ITS [AM410082], actin [AM410084], and β-tubulin [AM410083]) and L. biglobosa ‘canadensis’ (eight isolates; ITS [AJ550868], actin [AY748956], and β-tubulin [AY749004]) (3,4), which were previously described on B. napus in the United States, Canada, and Chile. To our knowledge, this is the first report of L. biglobosa in Mexico. Previously, this species has only been reported once on B. oleracea without discrimination into subclades (2). In the Aguascalientes sampling, 24% of the isolates were L. biglobosa, similar to Canadian locations where this species is still common as compared with L. maculans (1). The large proportion of sampled L. biglobosa ‘canadensis’, highlights the prevalence of this subclade throughout the American continent (1). References: (1) A. Dilmaghani et al. Plant Pathol. 58:1044, 2009. (2) E. Koch et al. Mol. Plant-Microbe Interact. 4:341, 1991. (3) E. Mendes-Pereira et al. Mycol Res. 107:1287, 2003. (4) L. Vincenot et al. Phytopathology 98:321, 2008.

Aspergillus affinis sp. nov., a novel ochratoxin A-producing Aspergillus species (section Circumdati) isolated from decomposing leaves

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 1007-1015 ◽  
Author(s):  
Domenico Davolos ◽  
Anna Maria Persiani ◽  
Biancamaria Pietrangeli ◽  
Alessandra Ricelli ◽  
Oriana Maggi
Keyword(s):  
Ochratoxin A ◽  
Dna Sequences ◽  
Sequence Data ◽  
Taxonomic Status ◽  
Internal Transcribed Spacers ◽  
Chain Gene ◽  
Protein Coding ◽  
5.8S Rdna ◽  
Rdna Gene ◽  
Molecular Phylogenetic

Two ochratoxin A (OTA)-producing Aspergillus isolates, recently collected from submerged riparian decomposing leaves in Italy, were found to have a similar morphology to Aspergillus cretensis (subgenus Circumdati, section Circumdati). However, marked differences emerged between these two novel isolates and A. cretensis as the former displayed different colony features and had larger vesicles, metulae, phialides and conidia, as well as a distinct sclerotial form and size. In order to determine the taxonomic status and to infer the evolutionary relationships of these two morphologically identical isolates, a molecular phylogenetic analysis was performed on all the officially recognized lineages in the section Circumdati. The DNA sequences and the deduced amino acid residues from the nuclear loci were analysed. Both rRNA and protein coding genes were assessed, which are widely used to differentiate taxa belonging to genus Aspergillus at various evolutionary levels. The 5.8S rDNA gene and internal transcribed spacers (ITS), the D1/D2 domains of the 28S rDNA gene, a region of the tubulin beta chain gene (benA) and part of the calmodulin gene (cmd) were amplified by PCR and then sequenced. The analysis of the rRNA regions and of the benA and cmd sequence data indicated that the two isogenic isolates belonged to a genetically distinct OTA-producing species of the genus Aspergillus. The isolates are proposed as representing a novel species, Aspergillus affinis sp. nov., with the type strain ATCC MYA-4773T ( = CBS 129190 = 417). Phylogenetically, A. affinis sp. nov. appeared to be very closely related to A. cretensis, from which it could be distinguished by means of a morphological trait analysis.

Molecular systematics of subtribe Banksiinae (Banksia and Dryandra; Proteaceae) Based on cpDNA and nrDNA sequence data: Implications for taxonomy and biogeography

1998 ◽  
Vol 11 (4) ◽  
pp. 321 ◽  
Author(s):  
Austin R. Mast
Keyword(s):  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Morphological Characters ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Base Substitution ◽  
Trnl Intron ◽  
Single Root ◽  
Cladistic Analyses ◽  
Molecular Characters

Despite considerable research interest in the subtribe Banksiinae (Banksia L.f. and Dryandra R.Br.), no strongly supported phylogenetic hypothesis for the relationship between the genera exists, nor have molecular characters been sampled for phylogenetic reconstruction at any level. In this study, DNA sequence characters were sampled from chloroplast DNA (cpDNA; the trnL intron, the trnL 3′ exon, and the spacer between the trnL 3′ exon and trnF) and nuclear ribosomal DNA (nrDNA; both internal transcribed spacers) of 18 species of Banksia and five of Dryandra, with six outgroup taxa from the subfamily Grevilleoideae. The molecular characters provided the opportunity to code taxa outside of Banksia for cladistic comparison with the genus—an opportunity not previously provided by morphological characters. Cladistic analyses, using parsimony, explored the effects of various weightings of transition to transversion events and base substitution to insertion and deletion events to determine which relationships in the cladograms were robust. The trnL/trnF and ITS characters strongly supported a paraphyletic Banksia with respect to a monophyletic Dryandra. The molecular results supported a single root for Thiele and Ladiges’(1996) unrooted morphological cladogram along the branch between the Isotylis to B. fuscolutea clade and the Grandes to B. tricuspis clade. George’s (1981) subgenus Banksia and section Banksia appeared dramatically non-monophyletic. The distribution of eastern taxa at derived positions on the molecular cladograms suggested considerable cladogenesis in the the genus prior to the formation of the Nullarbor Plain during the Tertiary.

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