Hairpins create minute inversions in non-coding regions of chloroplast DNA

1996 ◽  
Vol 30 (3) ◽  
pp. 259-262 ◽  
Author(s):  
Scot A. Kelchner ◽  
J. F. Wendel
Keyword(s):  
Chloroplast Dna ◽  
Coding Regions

Molecular polymorphism of cytoplasmic DNA in Ficus carica L.: Insights from non-coding regions of chloroplast DNA

2010 ◽  
Vol 125 (3) ◽  
pp. 512-517 ◽  
Author(s):  
Ghada Baraket ◽  
Ahmed Ben Abdelkrim ◽  
Olfa Saddoud ◽  
Khaled Chatti ◽  
Messaoud Mars ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Ficus Carica ◽  
Molecular Polymorphism ◽  
Coding Regions ◽  
Cytoplasmic Dna

Hairpins involving both inverted and direct repeats are associated with homoplasious indels in non-coding chloroplast DNA of Taraxacum (Lactuceae: Asteraceae)

Genome ◽  
2000 ◽  
Vol 43 (4) ◽  
pp. 634-641 ◽  
Author(s):  
T HM Mes ◽  
P Kuperus ◽  
J Kirschner ◽  
J Stepanek ◽  
P Oosterveld ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Chloroplast Genome ◽  
Hot Spot ◽  
Phylogenetic Signal ◽  
Direct Repeats ◽  
Nucleotide Substitutions ◽  
Replication Slippage ◽  
Coding Regions ◽  
Chloroplast Genomes ◽  
Structural Mutations

Sequence variation in 2.2 kb of non-coding regions of the chloroplast genome of eight dandelions (Taraxacum: Lactuceae) from Asia and Europe is interpreted in the light of the phylogenetic signal of base substitutions vs. indels (insertions-deletions). The four non-coding regions displayed a total of approximately 30 structural mutations of which 9 are potentially phylogenetically informative. Insertions, deletions, and an inversion were found that involved consecutive stretches of up to 172 bases. When compared to phylogenetic relationships of the chloroplast genomes based on nucleotide substitutions only, many homoplasious indels (33%) were detected that differed considerably in length and did not comprise simple sequence repeats typically associated with replication slippage. Though many indels in the intergenic spacers were associated with direct repeats, frequently, the variable stretches participated in inverted repeat stabilized hairpins. In each intergenic spacer or intron examined, nucleotide stretches ranging from 30 to 60 bp were able to fold into stabilized secondary structures. When these indels were homoplasious, they always ranked among the most stabilized hairpins in the non-coding regions. The association of higher order structures that involve both classes of repeats and parallel structural mutations in hot spot regions of the chloroplast genome can be used to differentiate among mutations that differ in phylogenetic reliability.Key words: Taraxacum, indel, non-coding chloroplast DNA, hairpin, evolution.

scholarly journals Molecular polymorphism in Pistacia vera L. using non-coding regions of chloroplast DNA

2016 ◽  
Vol 14 (1) ◽  
pp. 31-37 ◽  
Author(s):  
Majid Talebi ◽  
Mohammad Akbari ◽  
Maryam Zamani ◽  
Badraldin Ebrahim Sayed-Tabatabaei
Keyword(s):  
Chloroplast Dna ◽  
Pistacia Vera ◽  
Molecular Polymorphism ◽  
Coding Regions

Universal primers for amplification of three non-coding regions of chloroplast DNA

1991 ◽  
Vol 17 (5) ◽  
pp. 1105-1109 ◽  
Author(s):  
Pierre Taberlet ◽  
Ludovic Gielly ◽  
Guy Pautou ◽  
Jean Bouvet
Keyword(s):  
Chloroplast Dna ◽  
Universal Primers ◽  
Coding Regions

scholarly journals Molecular phylogeny of Dipterocarp Species Using Nucleotide Sequences of Two Non-coding Regions in Chloroplast DNA.

Tropics ◽  
1998 ◽  
Vol 7 (3/4) ◽  
pp. 195-207 ◽  
Author(s):  
Koichi KAMIYA ◽  
Ko HARADA ◽  
Kazuhiko OGINO ◽  
Tadashi KAJITA ◽  
Tsuneyuki YAMAZAKI ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Chloroplast Dna ◽  
Nucleotide Sequences ◽  
Coding Regions

Points of rearrangements between plastid chromosomes: location of protein coding regions on broad bean chloroplast DNA

1987 ◽  
Vol 11 (4) ◽  
pp. 265-274 ◽  
Author(s):  
Christine Michalowski ◽  
Karin D. Breunig ◽  
Hans J. Bohnert
Keyword(s):  
Chloroplast Dna ◽  
Broad Bean ◽  
Protein Coding ◽  
Coding Regions
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