Molecular Systematics of Cyperaceae Tribe Cariceae Based on Two Chloroplast DNA Regions: ndhF and trnL Intron-Intergenic Spacer

2000 ◽  
Vol 25 (3) ◽  
pp. 479 ◽  
Author(s):  
Alan C. Yen ◽  
Richard G. Olmstead
Keyword(s):  
Chloroplast Dna ◽  
Molecular Systematics ◽  
Intergenic Spacer ◽  
Trnl Intron ◽  
Chloroplast Dna Regions

Phylogenetic analysis of Australian Acacia (Leguminosae: Mimosoideae) by using sequence variations of an intron and two intergenic spacers of chloroplast DNA

2000 ◽  
Vol 13 (5) ◽  
pp. 745 ◽  
Author(s):  
Daniel J. Murphy ◽  
Frank Udovicic ◽  
Pauline Y. Ladiges
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Dna ◽  
Small Sample Size ◽  
Intergenic Spacer ◽  
Small Sample ◽  
Total Evidence ◽  
Trnl Intron ◽  
Intergenic Spacers ◽  
Sequence Variations ◽  
Jackknife Support

Three regions of chloroplast DNA are assessed for their utility for phylogenetic analysis of Acacia subgenus Phyllodineae: psbA–trnH intergenic spacer, the trnL intron and the trnL–trnF intergenic spacer. There are large differences in the lengths of the psbA–trnH spacer (155–440 bp) and trnL–trnF intergenic spacer (101–422 bp) regions, and large multi-residue indels were coded as multistate characters. Overall information content in these regions is relatively low, but the total evidence tree has 12 nodes resolved, five with jackknife support. By using Parkia timoriana as the outgroup, Acacia subgenus Acacia (A. farnesiana) is basal and Acacia subgenus Aculeiferum (A. senegal) is the sister taxon to subgenus Phyllodineae. Although based on a small sample size, within subgenus Phyllodineae, the results of this study have shown that section Alatae is not monophyletic, section Lycopodiifoliae is monophyletic and Botrycephalae is related to members of section Phyllodineae with racemose inflorescences.

Understanding taxonomic position of local endemic Agropyron deweyi (Poaceae) using morphological characters and sequences of nuclear and chloroplast DNA regions

Biologia ◽  
2015 ◽  
Vol 70 (10) ◽  
Author(s):  
Mesut S. Pinar ◽  
Ayten Dizkirici ◽  
Oktay Yigit
Keyword(s):  
Chloroplast Dna ◽  
Dna Sequences ◽  
Morphological Characters ◽  
Molecular Techniques ◽  
Taxonomic Position ◽  
Nuclear Ribosomal Dna ◽  
Trnl Intron ◽  
Internal Transcribed Spacer Region ◽  
Local Endemic ◽  
Chloroplast Dna Regions

AbstractIn this study, both morphological characters and molecular techniques were used to determine the taxonomic position of the local endemic Agropyron deweyi within the genus. Plant length, inflorescence type, flower, leaf, spike, spikelet, indumentum and lemma structures were studied as morphological characters. DNA sequences of the nuclear ribosomal DNA internal transcribed spacer region (nrDNA ITS) and four chloroplast DNA regions [trnT-trnL intergenic spacer (IGS), trnL intron, trnL-trnF IGS and matK gene] were analyzed as part of molecular investigations. The results demonstrated that no remarkable morphological differences exist among studied specimens of A. deweyi and A. cristatum complex. Based on 12 sequences of 4 Agropyron taxa produced from the current study and different numbers of sequences obtained from GenBank, our results support the conclusion that the taxonomic status of Agropyron deweyi is synonymous to that of the species A. cristatum. Sequence divergences were estimated using Kimura two-parameter model, and the phylogenetic analyses were performed using the maximum parsimony (MP) and maximum likelihood (ML) methods. No genetic variation was observed among samples of native A. deweyi and A. cristatum complex regardless of the analyzed region. Agropyron deweyi was especially very similar to A. cristatum subsp. pectinatum var. pectinatum in terms of morphological characters such as inflorescence rachis tough at maturity, spikelets with distinct gaps, indumentum glabrous, and lemma glabrous. Therefore, when all morphological and molecular results are taken into account, A. deweyi and A. cristatum subsp. pectinatum var. pectinatum should be considered as synonym.

Phylogenetic position ofKontumia(Polypodiaceae) inferred from four chloroplast DNA regions

2012 ◽  
pp. n/a-n/a
Author(s):  
Changkyun Kim ◽  
Hong-Guang Zha ◽  
Tao Deng ◽  
Hang Sun ◽  
Su-Gong Wu
Keyword(s):  
Chloroplast Dna ◽  
Phylogenetic Position ◽  
Chloroplast Dna Regions

scholarly journals Molecular variation in chloroplast DNA regions in ancestral species of wheat.

Genetics ◽  
1994 ◽  
Vol 137 (3) ◽  
pp. 883-889 ◽  
Author(s):  
N T Miyashita ◽  
N Mori ◽  
K Tsunewaki
Keyword(s):  
Chloroplast Dna ◽  
Restriction Enzymes ◽  
Triticum Dicoccoides ◽  
The Other ◽  
Major Type ◽  
Aegilops Speltoides ◽  
Triticum Timopheevi ◽  
Restriction Sites ◽  
D Values ◽  
Chloroplast Dna Regions

Abstract Restriction map variation in two 5-6-kb chloroplast DNA regions of five diploid Aegilops species in the section Sitopsis and two wild tetraploid wheats, Triticum dicoccoides and Triticum araraticum, was investigated with a battery of four-cutter restriction enzymes. A single accession each of Triticum durum, Triticum timopheevi and Triticum aestivum was included as a reference. More than 250 restriction sites were scored, of which only seven sites were found polymorphic in Aegilops speltoides. No restriction site polymorphisms were detected in all of the other diploid and tetraploid species. In addition, six insertion/deletion polymorphisms were detected, but they were mostly unique or species-specific. Estimated nucleotide diversity was 0.0006 for A. speltoides, and 0.0000 for all the other investigated species. In A. speltoides, none of Tajima's D values was significant, indicating no clear deviation from the neutrality of molecular polymorphisms. Significant non-random association was detected for three combinations out of 10 possible pairs between polymorphic restriction sites in A. speltoides. Phylogenetic relationship among all the plastotypes (plastid genotype) suggested the diphyletic origin of T. dicoccoides and T. araraticum. A plastotype of one A. speltoides accession was identical to the major type of T. araraticum (T. timopheevi inclusively). Three of the plastotypes found in the Sitopsis species are very similar, but not identical, to that of T. dicoccoides, T. durum and T. aestivum.

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 The trnL-F plastid DNA characters of three Poa pratensis (Kentucky bluegrass) varieties

2011 ◽  
Vol 51 (No. 2) ◽  
pp. 94-99 ◽  
Author(s):  
S.D. Stoneberg Holt ◽  
L. Horová ◽  
P. Bureš ◽  
J. Janeček ◽  
V. Černoch
Keyword(s):  
Poa Pratensis ◽  
Intergenic Spacer ◽  
Plastid Dna ◽  
Kentucky Bluegrass ◽  
Variety Identification ◽  
Trnl Intron ◽  
Major Band ◽  
F Region ◽  
Pcr Rflp

The characterization of crop cultivars (varieties) will come to depend increasingly on molecular characters in addition to traditional morphological and agronomic characters. Three cultivars of Kentucky bluegrass (Poa pratensis L.), developed by the Plant Breeding Station Hladké Životice (PBHŽ), were characterized using sequences and PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism) patterns from the non-coding plastid trnL-F region (trnL intron, 549 bp, and trnL-trnF intergenic spacer [IGS], 344 to 364 bp). These characters could be readily and repeatably determined not only for mature plants, but also for seedlings (less than 12 weeks old), which are difficult to distinguish morphologically. The method is quick and sensitive. When restricted with a combination of BsaJ I and Bsm I, cultivar Slezanka has one major band, Moravanka has two, and Harmonie has three. When restricted with Alu I, the heaviest band migrates most slowly for Slezanka. It is expected that many Kentucky bluegrass cultivars will share the same trnL-F sequence, so these characters alone are not sufficient for variety identification.

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