scholarly journals Phylogeny and classification of Eucalyptus subgenus Eudesmia (Myrtaceae) based on nuclear ribosomal DNA, chloroplast DNA and morphology

2009 ◽  
Vol 22 (3) ◽  
pp. 158 ◽  
Author(s):  
Adele K. Gibbs ◽  
Frank Udovicic ◽  
Andrew N. Drinnan ◽  
Pauline Y. Ladiges
Keyword(s):  
Chloroplast Dna ◽  
Intergenic Spacer ◽  
Morphological Characters ◽  
Nuclear Ribosomal Dna ◽  
Maximum Parsimony Analysis ◽  
Taxonomic Rank ◽  
Intergenic Spacer Region ◽  
Main Clade ◽  
Rdna Sequences ◽  
South Wales

Phylogenetic analysis of Eucalyptus subgenus Eudesmia is presented on the basis of the following three datasets: sequences of the internal transcribed spacer (ITS) and the external transcribed spacer (ETS) regions from nuclear rDNA, sequences of the psbA–trnH intergenic spacer region from chloroplast DNA, and morphological characters, including stamen bundling, operculum development, seeds and trichomes. Studies of floral development were essential for understanding the morphology of mature flowers and interpretation of synapomorphy and homoplasy. A summary phylogeny was constructed from a maximum parsimony analysis of those nodes coded as characters that had support in the molecular trees together with morphological characters. A revised infra-subgeneric classification is presented on the basis of the summary phylogeny, and compared with classifications of Hill and Johnson (1998) and Brooker (2000). Differences relate to relationships between clades and taxonomic rank (sections, series and subseries) and valid names of Brooker (2000) are conserved where possible. One main clade of 14 species (section Limbatae), many of mallee growth form, was found in all analyses; this clade is distributed in the South-West of Western Australia and adjacent Interzone and desert areas. A second main clade (section Complanatae) occurs in the northern and eastern tropical and subtropical regions of Australia, including Kimberley, Arnhem, Queensland and New South Wales. This section includes E. tetrodonta, previously treated as an isolated taxon in a monotypic section; however, this species is related to E. baileyana, E. similis, E. lirata and series Miniatae. The hypothesised phylogeny provides a framework for further analyses of biogeography and ecology, including functional traits.

Revisiting phylogenetic relationships in Phoradendreae (Viscaceae): utility of the trnL-F region of chloroplast DNA and presence of a homoplasious inversion in the intergenic spacer

Botany ◽  
2017 ◽  
Vol 95 (3) ◽  
pp. 247-258 ◽  
Author(s):  
Vanessa E.T.M. Ashworth
Keyword(s):  
Chloroplast Dna ◽  
Phylogenetic Relationships ◽  
Nucleotide Substitution ◽  
Strong Support ◽  
Intergenic Spacer ◽  
Nuclear Ribosomal Dna ◽  
Morphological Data ◽  
Maximum Parsimony Analysis ◽  
Tropical Species ◽  
F Region

The utility of the trnL-F region of the chloroplast DNA for inferring relationships in 26 taxa in the mistletoe tribe Phoradendreae (Viscaceae) was compared with that of sequences from three regions of the nuclear ribosomal DNA (nrDNA). Chloroplast- and nuclear-inferred phylogenies generally were congruent based on maximum parsimony analysis of nucleotide substitution data. Results suggested that the intron and intergenic spacer of the chloroplast partition were not sufficiently variable to resolve phylogenetic relationships among either close relatives or more distantly related species. The distribution of insertions and deletions generally supported the phylogeny inferred from nucleotide substitution data. However, presence or absence of a 59-nucleotide inversion in the trnL-F intergenic spacer of eight Phoradendron species showed no agreement with the topology inferred from molecular and morphological data. Combined analyses of the nuclear partitions and the chloroplast region (with the homoplasious inversion inserted in reverse orientation) provided strong support for P. californicum as sister to a clade uniting North American species and not as sister to a clade comprising more tropical species. Consistent with results from previous studies using nrDNA, a lineage in the Phoradendron leucarpum complex (comprising subsp. leucarpum and macrophyllum) was strongly supported, but subspecies tomentosum was not confidently placed.

scholarly journals Intraspecific Variation in Cannabis sativa L. Based on Intergenic Spacer Region of Chloroplast DNA.

2000 ◽  
Vol 23 (6) ◽  
pp. 727-730 ◽  
Author(s):  
Mareshige KOHJYOUMA ◽  
I-Jung LEE ◽  
Osamu IIDA ◽  
Kogo KURIHARA ◽  
Kazuya YAMADA ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Intraspecific Variation ◽  
Cannabis Sativa ◽  
Intergenic Spacer ◽  
Intergenic Spacer Region

Incorrect sequencing and taxon misidentification: an example in the Trichinella genus

2010 ◽  
Vol 84 (3) ◽  
pp. 336-339 ◽  
Author(s):  
G. Marucci ◽  
G. La Rosa ◽  
E. Pozio
Keyword(s):  
Intergenic Spacer ◽  
Morphological Characters ◽  
Internal Transcribed Spacers ◽  
5S Rrna ◽  
Lsu Rdna ◽  
Intergenic Spacer Region ◽  
Reference Centre ◽  
Polymerase Chain ◽  
Taxon Identification ◽  
Selection Of

AbstractMolecular analyses such as polymerase chain reaction (PCR) and sequencing are very useful for taxon identification, especially when morphological characters useful for identifying taxa are lacking. However, the use of molecular tools can be the source of taxon misidentification if they are not correctly applied and the results are not critically evaluated and compared with the literature and GenBank data. We describe a case of misidentification of a taxon of the genus Trichinella due to sequencing mistakes, lack of reference material and selection of a single molecular marker. A Trichinella sp. isolate from an Iranian wild boar (Sus scrofa) was identified as belonging to the Nearctic species Trichinella murrelli, through the molecular analysis of the 5S rRNA intergenic spacer region. A successive molecular identification of the same isolate was performed by the International Trichinella Reference Centre in Rome, Italy, using the 5S rRNA intergenic spacer region, the LSU rDNA expansion segment five, and the internal transcribed spacers 1 and 2. According to these analyses, the Iranian isolate belonged to Trichinella britovi, a Palaearctic species already described in Iran.

scholarly journals Associations between nuclear loci and chloroplast DNA genotypes in wild barley.

Genetics ◽  
1992 ◽  
Vol 131 (1) ◽  
pp. 225-231
Author(s):  
M A Maroof ◽  
Q Zhang ◽  
D B Neale ◽  
R W Allard
Keyword(s):  
Chloroplast Dna ◽  
Linear Models ◽  
Wild Barley ◽  
Blot Hybridization ◽  
Intergenic Spacer ◽  
Southern Blot Hybridization ◽  
Gene Pools ◽  
Intergenic Spacer Region ◽  
Evolutionary Forces ◽  
Nuclear Loci

Abstract Associations among alleles at nine nuclear loci and three chloroplast DNA (cpDNA) genotypes were assessed in a sample of 247 accessions of the wild barley, Hordeum vulgare ssp. spontaneum. Alleles at two of the nine nuclear loci are marked by length variations in the intergenic spacer region of ribosomal DNA (rDNA), and those of the other seven loci are well characterized allozymes. The three chloroplast DNA (cpDNA) genotypes are marked by restriction fragment length polymorphisms resulting from three polymorphic restriction sites detected by Southern blot hybridization. The analyses were performed by dividing the nine nuclear loci into a series of two-locus subsets and constructing log-linear models to characterize associations between the subsets of two nuclear loci and the cpDNA genotypes. Statistically significant associations were detected between six of the nine nuclear loci and the cpDNA genotypes, either individually as pairwise correlations, or through interaction with another nuclear locus to form three-variate complexes. Although the sample size of the present study was inadequate for statistical evaluation of higher order interactions, the results suggest the existence of interactions in which more than two nuclear loci are involved in associations with cpDNA genotypes. The observed cytonuclear associations appear to result from interplay among a number of evolutionary forces including a mating system of predominant selfing, differentiation among gene pools of local populations, and adaptation of barley genotypes to specific environmental conditions.

scholarly journals The comparison between nuclear ribosomal DNA and chloroplast DNA in molecular systematic study of four sections of genus Dendrobium sw. (orchidaceae)

2016 ◽  
Vol 5 (03) ◽  
pp. 4944 ◽  
Author(s):  
Maryam Moudi* ◽  
Rusea Go
Keyword(s):  
Chloroplast Dna ◽  
Ribosomal Dna ◽  
Morphological Characters ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Study ◽  
Data Sets ◽  
Molecular Systematic ◽  
Resolution Level ◽  
Reliable Marker

Phylogenetic study of the four sections (Aporum, Crumenata, Strongyle, and Bolbidium) of genus Dendrobium (family Orchidaceae) was conducted using molecular data. Classifications based on morphological characters have not being able to clearly divide these four sections neither do they supported their monophyly origin. Therefore, deeper and detailed analysis especially using molecular data is required to ascertain their status. Molecular evidences were used to clarify their relations either to lump them into one section or reduce them into two. The study has been carried out for the 34 species of Dendrobium using Maximum Parsimony (MP). Three nucleotide sequences data sets from two distinct genomes chloroplast DNA genes (rbcL and matK) and nuclear ribosomal DNA (ITS) were used to construct cladograms. The results that obtained from the Internal Transcribed Spacer (ITS) gene showed that the nuclear genes are reliable marker for the phylogenetic study of Dendrobium compared to chloroplast DNA with low resolution level among sections. 

Variation in ribosomal DNA among isolates of the mycorrhizal fungus Cenococcum geophilum

1991 ◽  
Vol 69 (11) ◽  
pp. 2331-2343 ◽  
Author(s):  
Katherine F. Lobuglio ◽  
Scott O. Rogers ◽  
C. J. K. Wang
Keyword(s):  
Ribosomal Dna ◽  
Restriction Site ◽  
Mycorrhizal Fungus ◽  
Intergenic Spacer ◽  
Fungal Species ◽  
Nuclear Ribosomal Dna ◽  
Cenococcum Geophilum ◽  
Taxonomic Rank ◽  
Reference Isolate ◽  
Length Polymorphisms

Restriction fragment length polymorphisms in ribosomal DNA were used to assess the degree of variation among 71 Cenococcum geophilum isolates of both geographically distinct and similar origins. Southern hybridizations using cloned C. geophilum ribosomal DNA indicated extensive variation among isolates, greater than has been previously reported to occur within a fungal species. Most of the polymorphisms were located within the region from the intergenic spacer through internal transcribed spacer 1. Restriction-site and length polymorphisms also occurred within the 5.8S through 26S genic region. Sixteen size categories of length mutations, six restriction-site additions, and four restriction-site deletions were observed compared with a reference isolate. HindIII-digested DNAs displayed fewer polymorphisms in the mitochondrial 24S ribosomal RNA gene (and flanking regions) than in nuclear ribosomal DNA. UPGMA cluster analysis of shared nuclear ribosomal DNA patterns indicated 32 unique phenotypes and grouped C. geophilum isolates into a broad range of clusters ranging from 100 to 44% similarity. The amount of ribosomal DNA variation demonstrated in this study indicates that C. geophilum is either an extremely heterogenous species or a fungal complex representing a broader taxonomic rank than presently considered. Key words: Cenococcum geophilum, ribosomal DNA, restriction polymorphisms.

Regional Differences in Plant Development, Water Relations, and Chloroplast DNA of Hard Maples

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 456d-456
Author(s):  
Rolston St. Hilaire ◽  
William R. Graves
Keyword(s):  
Chloroplast Dna ◽  
Water Relations ◽  
Plant Development ◽  
Regional Differences ◽  
Intergenic Spacer ◽  
Principal Component ◽  
Western Region ◽  
Intergenic Spacer Region ◽  
Geographical Regions ◽  
Leaf Osmotic Potential

Principal component analysis of foliar traits of hard maples (Acer saccharum Marsh. and Acer nigrum Michx. f.) near 43°N latitude clustered data into two populations composed of trees from different geographical regions. Seedlings from these two regions, and a third, geographically intermediate region, were grown in a greenhouse for 2 years with two irrigation frequencies to assess regional differences in plant development and water relations. Leaves from the most western region (west of 93°W longitude) had the highest specific mass (5.97 mg/cm2), trichome frequency (531/cm2), and stomate frequency (628/cm2). Across regions, plants irrigated frequently had more stomates (596/cm2) than plants irrigated sparsely (483/cm2). Traits similar across regions but higher with frequent irrigation included surface area and mass of lamina, shoot-to-root ratio, the ratio of lamina area to stem xylem diameter, and leaf water potential. Sparse irrigation caused a comparatively large decrease in stomatal conductance of plants from the most western region, and pressure-volume analysis showed no regional or irrigation effects on leaf osmotic potential at full turgor. Identical banding patterns resulted when Hinf I digested the PCR-amplified trnL-trnF intergenic spacer region of chloroplast DNA from each region; work with the rpL16 and ndhA introns is proceeding. Trichome frequency on abaxial leaf surfaces, which differs regionally both in nature and in controlled environments, is the most consistent character we have measured for discerning populations.

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