A chloroplast DNA hairpin structure provides useful phylogenetic data within tribe Senecioneae (Asteraceae)

2006 ◽  
Vol 84 (5) ◽  
pp. 862-868 ◽  
Author(s):  
J.F. Bain ◽  
R.K. Jansen
Keyword(s):  
Chloroplast Dna ◽  
Intergenic Spacer ◽  
Hairpin Structure ◽  
Dna Hairpin ◽  
Phylogenetic Information ◽  
Phylogenetic Marker ◽  
Intergenic Spacer Region ◽  
Wide Range ◽  
Loop Regions ◽  
Taxonomic Groups

The distribution of an inversion associated with a small hairpin structure in the psbA–trnH intergenic spacer region of chloroplast DNA was surveyed to determine its phylogenetic utility within the tribe Senecioneae of the Asteraceae. Over 2000 sequences were examined from a wide range of angiosperms. Although the inversion is homoplasious in a number of taxonomic groups, including the Senecioneae, it still provides useful phylogenetic information, especially when point substitutions in both the stem and loop regions are scored along with the inversion. The presence of two nested inversions within the hairpin structure allows it to be treated as a partially ordered multistate character, adding to its potential utility as a phylogenetic marker.

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

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 Molecular Diversity of The Tidal Swamp Rice (Oryza sativa L.) Germplasm of The South Kalimantan, Indonesia

2018 ◽  
Author(s):  
Dindin H. Mursyidin ◽  
Purnomo Purnomo ◽  
Issirep Sumardi ◽  
Budi S. Daryono
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Phylogenetic Reconstruction ◽  
Intergenic Spacer ◽  
The South ◽  
Abiotic And Biotic Stresses ◽  
Intergenic Spacer Region ◽  
Biotic Stresses ◽  
Tidal Swamp ◽  
Wide Range

Tidal swamp rice has long been cultivated by the local people of the South Kalimantan, Indonesia. This germplasm possess some important traits for adapted to a wide range of abiotic and biotic stresses. In this study, a total of sixteen cultivars of this germplasm, consisting of fifteen of the South Kalimantan Province and one of Sumatera Island, Indonesia (an outgroup) were analyzed, phylogenetically based on the chloroplast trnL-F and nuclear intergenic spacer region (IGS). The results showed that this germplasm has a relatively more extraordinary genetic diversity than other local rice germplasm. In a nucleotide level, this germplasm showed a genetic diversity of 0.61 for nuclear IGS and 0.58 for trnL-F. The phylogenetic reconstruction also exhibited that this germplasm has the unique illustration of phylogenetic trees, particularly for the combined sequence datasets. Thus, the results of our study would provide useful information for further understanding of evolutionary relationships of this germplasm and facilitate the efficient utilization of valuable genes for genetic improvement, particularly in the tidal swamp areas.

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.

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.

Characterization of Fusarium spp. isolates by PCR-RFLP analysis of the intergenic spacer region of the rRNA gene (rDNA)

2006 ◽  
Vol 106 (3) ◽  
pp. 297-306 ◽  
Author(s):  
A. Llorens ◽  
M.J. Hinojo ◽  
R. Mateo ◽  
M.T. González-Jaén ◽  
F.M. Valle-Algarra ◽  
...  
Keyword(s):  
Intergenic Spacer ◽  
Rflp Analysis ◽  
Rrna Gene ◽  
Fusarium Spp ◽  
Intergenic Spacer Region ◽  
Pcr Rflp
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