Genetic differentiation and admixture among Festuca idahoensis, F. roemeri, and F. ovina detected in AFLP, ITS, and chloroplast DNA

Botany ◽  
2008 ◽  
Vol 86 (4) ◽  
pp. 422-434 ◽  
Author(s):  
Thomas A. Jones ◽  
Steven R. Larson ◽  
Barbara L. Wilson
Keyword(s):  
Chloroplast Dna ◽  
Genetic Relatedness ◽  
Sequence Divergence ◽  
Natural Source ◽  
Nuclear Ribosomal Dna ◽  
Genetic Admixture ◽  
Festuca Rubra ◽  
Model Based Clustering ◽  
Intergenic Sequences ◽  
Festuca Idahoensis

North American forms of the Festuca ovina L. complex, Festuca idahoensis Elmer and Festuca roemeri (Pavlick) E.B. Alexeev, are distributed broadly east and narrowly west of the Cascade Mountains, respectively. The psbA-trnH and rps16-trnK chloroplast DNA intergenic sequences, 18S-5.8S-26S nuclear ribosomal DNA internal transcribed spacer (ITS) sequences, and six AFLP primer combinations were used to investigate genetic relatedness and differences among 327 plant samples from 24 F. idahoensis and 33 F. roemeri natural-source germplasm accessions, two multiple-origin F. idahoensis × F. roemeri cultivars, one apparently admixed F. ovina × F. idahoensis accession, four naturalized populations or cultivars of Eurasian-source F. ovina s. l., and several Festuca arizonica Vasey, Festuca occidentalis Hooker, and Festuca rubra L. reference accessions. The AFLP profiles of individual plants were unique, but distance-based and Bayesian model-based clustering separated AFLP genotypes into groups corresponding to taxa. Approximately 15.9% of the AFLP variation was apportioned between F. idahoensis and F. roemeri, with the remaining 61.2% and 22.9% variation maintained within and among natural-source accessions, respectively. Genetic admixture between F. idahoensis, F. roemeri, and F. ovina was detectable and DNA sequence divergence was very low in the chloroplast and ITS regions. These three taxa are genetically differentiated, but capable of hybridization.

scholarly journals Phylogeography of Prunus armeniaca L. revealed by chloroplast DNA and nuclear ribosomal sequences

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wen-Wen Li ◽  
Li-Qiang Liu ◽  
Qiu-Ping Zhang ◽  
Wei-Quan Zhou ◽  
Guo-Quan Fan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Chloroplast Dna ◽  
Population Expansion ◽  
Prunus Armeniaca ◽  
River Valley ◽  
Nuclear Ribosomal Dna ◽  
Glacial Refugium ◽  
Ili River Valley ◽  
Wild Apricot

AbstractTo clarify the phytogeography of Prunus armeniaca L., two chloroplast DNA fragments (trnL-trnF and ycf1) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to assess genetic variation across 12 P. armeniaca populations. The results of cpDNA and ITS sequence data analysis showed a high the level of genetic diversity (cpDNA: HT = 0.499; ITS: HT = 0.876) and a low level of genetic differentiation (cpDNA: FST = 0.1628; ITS: FST = 0.0297) in P. armeniaca. Analysis of molecular variance (AMOVA) revealed that most of the genetic variation in P. armeniaca occurred among individuals within populations. The value of interpopulation differentiation (NST) was significantly higher than the number of substitution types (GST), indicating genealogical structure in P. armeniaca. P. armeniaca shared genotypes with related species and may be associated with them through continuous and extensive gene flow. The haplotypes/genotypes of cultivated apricot populations in Xinjiang, North China, and foreign apricot populations were mixed with large numbers of haplotypes/genotypes of wild apricot populations from the Ili River Valley. The wild apricot populations in the Ili River Valley contained the ancestral haplotypes/genotypes with the highest genetic diversity and were located in an area considered a potential glacial refugium for P. armeniaca. Since population expansion occurred 16.53 kyr ago, the area has provided a suitable climate for the population and protected the genetic diversity of P. armeniaca.

scholarly journals Diversification of the North American shrub genusCeanothus(Rhamnaceae): conflicting phylogenies from nuclear ribosomal DNA and chloroplast DNA

2000 ◽  
Vol 87 (1) ◽  
pp. 108-123 ◽  
Author(s):  
Terry M. Hardig ◽  
Pamela S. Soltis ◽  
Douglas E. Soltis
Keyword(s):  
Chloroplast Dna ◽  
Ribosomal Dna ◽  
North American ◽  
Nuclear Ribosomal Dna ◽  
The North

scholarly journals Foeniculum sanguineum Triano & A. Pujadas (Apiaceae) new species from the South-Western Mediterranean Region

2017 ◽  
Vol 40 ◽  
pp. 71
Author(s):  
Antonio J. Pujadas Salvà ◽  
Enrique Triano Muñoz ◽  
Josefa Anaya ◽  
Manuel Grande ◽  
César Raposo ◽  
...  
Keyword(s):  
New Species ◽  
Mediterranean Region ◽  
Phylogenetic Analyses ◽  
Diploid Species ◽  
Sequence Divergence ◽  
Western Mediterranean ◽  
Nuclear Ribosomal Dna ◽  
Rbcl Gene ◽  
The South ◽  
Foeniculum Vulgare

English. Foeniculum sanguineum Triano & A. Pujadas, sp. nov., from the south western Mediterranean Region (Spain & Morocco) is described. Its characterization and a comparative study with the related species Foeniculum vulgare Mill., has been carried out through morphological, cytological, chemical and molecular analysis. F. sanguineum is distinguished primarily for its red petals, pink pollen in fresh, and red stylopod. It is a diploid species (2n= 22). A high proportion of limonene and piperitenone oxide (absent in F. vulgare) has been found in the essential oil composition of the dry fruits of F. sanguineum and a high amount (about 50 %) of α-phellandrene in its roots and stems. Phylogenetic analyses were performed using the internal transcribed spacer sequences of nuclear ribosomal DNA (ITS) and the chloroplast rbcL gene sequences. ITS analysis supports the existence of the new species, while revealing sequence divergence both at the intraspecific and at the interspecific levels. A Single-nucleotide-polymorphism (SNP) sequence divergence found in the slow evolving chloroplast gene provided additional support for the novel species characterization, for which the name Foeniculum sanguineum is proposed.Español.  Se describe Foeniculum sanguineum Triano & A. Pujadas, sp. nov., del suroeste de la Región Mediterránea (España y Marruecos). Para su caracterización se ha realizado el análisis morfológico, citológico, fitoquímico y molecular. Se ha llevado a cabo el studio comparativo con Foeniculum vulgare Mill. La nueva especie F. sanguineum se distingue principalmente por sus pétalos rojos, polen rosado en fresco y por su estilopodio rojo. Es una especie diploide (2n= 22). Se ha encontrado una alta proporción de óxido de limoneno y piperitenona (ausente en F. vulgare) en la composición de aceite esencial de los frutos secos de F. sanguineum y una elevada cantidad (aproximadamente 50%) de α-felandreno en sus raíces y tallos. El análisis filogenético se realizó utilizando las secuencias del espaciador transcrito interno de ADN ribosomal nuclear (ITS) y las secuencias del gen cloroplástico rbcL. El análisis ITS apoya la existencia de la nueva especie, al tiempo que revela la divergencia de secuencias tanto a nivel intraespecífico como a nivel interespecífico. La divergencia de secuencia encontrada en el gen cloroplástico, aunque reducida a un nucleótido, proporcionó apoyo adicional para la caracterización de la nueva especie, para la que se propone el nombre de Foeniculum sanguineum.

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. 

scholarly journals Proliferation of group II introns in the chloroplast genome of the green algaOedocladium carolinianum(Chlorophyceae)

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2627 ◽  
Author(s):  
Jean-Simon Brouard ◽  
Monique Turmel ◽  
Christian Otis ◽  
Claude Lemieux
Keyword(s):  
Chloroplast Genome ◽  
Gene Order ◽  
Binding Sites ◽  
Sequence Divergence ◽  
Hypothetical Protein ◽  
Group Ii Introns ◽  
Data Set ◽  
Secondary Structure Analysis ◽  
Intergenic Sequences ◽  
Group Ii

BackgroundThe chloroplast genome sustained extensive changes in architecture during the evolution of the Chlorophyceae, a morphologically and ecologically diverse class of green algae belonging to the Chlorophyta; however, the forces driving these changes are poorly understood. The five orders recognized in the Chlorophyceae form two major clades: the CS clade consisting of the Chlamydomonadales and Sphaeropleales, and the OCC clade consisting of the Oedogoniales, Chaetophorales, and Chaetopeltidales. In the OCC clade, considerable variations in chloroplast DNA (cpDNA) structure, size, gene order, and intron content have been observed. The large inverted repeat (IR), an ancestral feature characteristic of most green plants, is present inOedogonium cardiacum(Oedogoniales) but is lacking in the examined members of the Chaetophorales and Chaetopeltidales. Remarkably, theOedogonium35.5-kb IR houses genes that were putatively acquired through horizontal DNA transfer. To better understand the dynamics of chloroplast genome evolution in the Oedogoniales, we analyzed the cpDNA of a second representative of this order,Oedocladium carolinianum.MethodsTheOedocladiumcpDNA was sequenced and annotated. The evolutionary distances separatingOedocladiumandOedogoniumcpDNAs and two other pairs of chlorophycean cpDNAs were estimated using a 61-gene data set. Phylogenetic analysis of an alignment of group IIA introns from members of the OCC clade was performed. Secondary structures and insertion sites of oedogonialean group IIA introns were analyzed.ResultsThe 204,438-bpOedocladiumgenome is 7.9 kb larger than theOedogoniumgenome, but its repertoire of conserved genes is remarkably similar and gene order differs by only one reversal. Although the 23.7-kb IR is missing the putative foreign genes found inOedogonium, it contains sequences coding for a putative phage or bacterial DNA primase and a hypothetical protein. Intergenic sequences are 1.5-fold longer and dispersed repeats are more abundant, but a smaller fraction of theOedocladiumgenome is occupied by introns. Six additional group II introns are present, five of which lack ORFs and carry highly similar sequences to that of the ORF-less IIA intron shared withOedogonium. Secondary structure analysis of the group IIA introns disclosed marked differences in the exon-binding sites; however, each intron showed perfect or nearly perfect base pairing interactions with its target site.DiscussionOur results suggest that chloroplast genes rearrange more slowly in the Oedogoniales than in the Chaetophorales and raise questions as to what was the nature of the foreign coding sequences in the IR of the common ancestor of the Oedogoniales. They provide the first evidence for intragenomic proliferation of group IIA introns in the Viridiplantae, revealing that intron spread in theOedocladiumlineage likely occurred by retrohoming after sequence divergence of the exon-binding sites.

scholarly journals Population Genetic Analysis ofLobelia rhynchopetalumHemsl. (Campanulaceae) Using DNA Sequences fromITSand Eight Chloroplast DNA Regions

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Mulatu Geleta ◽  
Tomas Bryngelsson
Keyword(s):  
Chloroplast Dna ◽  
Dna Sequences ◽  
Population Genetic ◽  
Sequence Data ◽  
Gene Diversity ◽  
Nuclear Ribosomal Dna ◽  
Bootstrap Support ◽  
Population Genetic Analysis ◽  
Mountain Systems ◽  
Chloroplast Dna Regions

DNA sequence data from the internal transcribed spacer of nuclear ribosomal DNA and eight chloroplast DNA regions were used to investigate haplotypic variation and population genetic structure of the Afroalpine giant lobelia,Lobelia rhynchopetalum.The study was based on eight populations sampled from two mountain systems in Ethiopia. A total of 20 variable sites were obtained, which resulted in 13 unique haplotypes and an overall nucleotide diversity (ND) of 0.281 ± 0.15 and gene diversity (GD) of 0.85 ± 0.04. Analysis of molecular variance (AMOVA) revealed a highly significant variation (P<0.001) among populations (FST), and phylogenetic analysis revealed that populations from the two mountain systems formed their own distinct clade with >90% bootstrap support. Each population should be regarded as a significant unit for conservation of this species. The primers designed for this study can be applied to anyLobeliaand other closely related species for population genetics and phylogenetic studies.

THE PHYLOGENY OF TRIBE ZINGIBEREAE (ZINGIBERACEAE) BASED ON ITS (nrDNA) AND trnL–F (cpDNA) SEQUENCES

2003 ◽  
Vol 60 (3) ◽  
pp. 483-507 ◽  
Author(s):  
C. NGAMRIABSAKUL ◽  
M. F. NEWMAN ◽  
Q. C. B. CRONK
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Dna ◽  
Ribosomal Dna ◽  
Nuclear Ribosomal Dna ◽  
Its Nrdna ◽  
First Time

A phylogenetic analysis of the tribe Zingibereae (Zingiberaceae) was performed using nuclear ribosomal DNA (ITS1, 5.8S and ITS2) and chloroplast DNA (trnL (UAA) 5′ exon to trnF (GAA)). The tribe is monophyletic with two major clades, the Curcuma clade and the Hedychium clade. Paracautleya, sampled for the first time, comes out as predicted while Caulokaempferia comes out in a different position from that found in another recent study. The genera Boesenbergia and Curcuma are apparently not monophyletic.

scholarly journals Phylogeography of Prunus Armeniaca L. By Chloroplast DNA and Nuclear Ribosomal Sequences

2021 ◽  
Author(s):  
Wen-Wen Li ◽  
Li-Qiang Liu ◽  
Qiu-Ping Zhang ◽  
Wei-Quan Zhou ◽  
Guo-Quan Fan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Chloroplast Dna ◽  
Sequence Data ◽  
Population Expansion ◽  
Prunus Armeniaca ◽  
River Valley ◽  
Nuclear Ribosomal Dna ◽  
Ili River Valley ◽  
Wild Apricot

Abstract To clarify the phytogeography of Prunus armeniaca L., two chloroplast DNA fragments (trnL-trnF and ycf1) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to assess the genetic variation across 12 P. armeniaca populations. The results of cpDNA and ITS sequence data analysis showed that the level of genetic diversity in P. armeniaca was high (cpDNA: HT=0.499; ITS: HT=0.876), and the level of genetic differentiation was low (cpDNA: FST=0.1628; ITS: FST=0.0297). An analysis of molecular variance (AMOVA) revealed that most of the genetic variation in P. armeniaca occurred among individuals within populations. The value of interpopulation differentiation (NST) was significantly higher than the number of substitution types (GST), indicating a genealogical structure in P. armeniaca. P. armeniaca shared the same genotypes with related species and may be associated with them through continuous and extensive gene flow. The haplotypes/genotypes of cultivated apricot populations in Xinjiang, North China, and foreign apricot populations were mixed with large numbers of haplotypes/genotypes of wild apricot populations from the Ili River Valley. The wild apricot populations in the Ili River Valley contained the ancestral haplotypes/genotypes with the highest genetic diversity and were located in an area considered a potential glacial refugiume for P. armeniaca. Since population expansion occurred 16.53 kyr ago, the area has provided a suitable climate for the population and protected the genetic diversity of P. armeniaca.

Origin and phylogeny of Guinea yams as revealed by RFLP analysis of chloroplast DNA and nuclear ribosomal DNA

1992 ◽  
Vol 83-83 (6-7) ◽  
pp. 743-751 ◽  
Author(s):  
R. Terauchi ◽  
V. A. Chikaleke ◽  
G. Thottappilly ◽  
S. K. Hahn
Keyword(s):  
Chloroplast Dna ◽  
Ribosomal Dna ◽  
Rflp Analysis ◽  
Nuclear Ribosomal Dna ◽  
Guinea Yams
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