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35 results for “cpDNA”
Data from: Insights into the genetic relationships and breeding patterns of the African tea germplasm based on nSSR markers and cpDNA sequences
Africa is one of the key centers of global tea production. Understanding the genetic diversity and relationships of cultivars of African tea is important for future targeted breeding efforts for new crop cultivars, specialty tea processing, and to guide germplasm conservation efforts. Despite the economic importance of tea in Africa, no research work has been done so far on its genetic diversity at a continental scale. Twenty-three nSSRs and three plastid DNA regions were used to investigate the genetic diversity, relationships, and breeding patterns of tea accessions collected from eight countries of Africa. A total of 280 African tea accessions generated 297 alleles with a mean of 12.91 alleles per locus and a genetic diversity (HS) estimate of 0.652. A STRUCTURE analysis suggested two main genetic groups of African tea accessions which corresponded well with the two tea types Camellia sinensis var. sinensis and C. sinensis var. assamica, respectively, as well as an admixed "mosaic" group whose individuals were defined as hybrids of F2 and BC generation with a high proportion of C. sinensis var. assamica being maternal parents. Accessions known to be C. sinensis var. assamica further separated into two groups representing the two major tea breeding centers corresponding to southern Africa (Tea Research Foundation of Central Africa, TRFCA), and East Africa (Tea Research Foundation of Kenya, TRFK). Tea accessions were shared among countries. African tea has relatively lower genetic diversity. C. sinensis var. assamica is the main tea type under cultivation and contributes more in tea breeding improvements in Africa. International germplasm exchange and movement among countries within Africa was confirmed. The clustering into two main breeding centers, TRFCA, and TRFK, suggested that some traits of C. sinensis var. assamica and their associated genes possibly underwent selection during geographic differentiation or local breeding preferences. This study represents the first step toward effective utilization of differently inherited molecular markers for exploring the breeding status of African tea. The findings here will be important for planning the exploration, utilization, and conservation of tea germplasm for future breeding efforts in Africa.
Data from: Phylogenetic relationships of Iranian Allium sect. Allium (Amaryllidaceae, Allioideae) as inferred from nrDNA ITS, cpDNA rps16 and trnL–F sequences
Allium is a particularly species rich (more than 800 species) and economically important genus, with numerous taxonomic problems at all levels of classification. In this study, we try to uncover the phylogenetic relationships in the common leek (A. ampeloprasum) based on selected samples of this species and its putative relatives in sect. Allium from Iran. The silica-dried leaf samples of 56 accessions representing 23 species of Allium were sequenced for this study, 53 sequences of nrDNA ITS, 35 sequences of plastid rps16 and 52 sequences of trnL-F were generated and several accessions were extracted from GenBank in order to cover all recognized main lineages in the genus. Maximum Parsimony and Bayesian Inference generated similar trees, but the placement of A. ampeloprasum and its relatives differs slightly in the nuclear versus plastid datasets. In the nrITS tree A. ampeloprasum is retrieved in a highly supported clade with A. iranicum, while in the combined plastid tree A. ampeloprasum formed a highly supported clade with A. vineale. This supports the hypothesis of a possible hybrid origin of A. ampeloprasum. Allium iranicum formed a clade in the plastid tree, but was resolved as paraphyletic in the nrITS tree, probably due to presence of multiple non-concerted copies of nrITS. Close relationships are suggested between following species: A. aznavense and A. wendelboi with A. talyschense, A. erubescens and A. rotundum with A. scorodoprasum, and A. abbasii with A. phanerantherum.
Simulation of the evolution of codon usage in cpDNA
<p>The codon usage of the Angiosperm <i>psbA</i> gene is atypical for flowering plant chloroplast genes but similar to the codon usage observed in highly expressed plastid genes from some other Plantae, particularly Chlorobionta, lineages. The pattern of codon bias in these genes is suggestive of selection for a set of translationally optimal codons but the degree of bias towards these optimal codons is much weaker in the flowering plant <i>psbA</i> gene than in high expression plastid genes from lineages such as certain green algal groups. Two scenarios have been proposed to explain these observations. One is that the flowering plant <i>psbA</i> gene is currently under weak selective constraints for translation efficiency, the other is that there are no current selective constraints and we are observing the remnants of an ancestral codon adaptation that is decaying under mutational pressure. We test these two models using simulations studies that incorporate the context-dependent mutational properties of plant chloroplast DNA. We first reconstruct ancestral sequences and then simulate their evolution in the absence of selection on codon usage by using mutation dynamics estimated from intergenic regions. The results show that <i>psbA</i> has a significantly higher level of codon adaptation than expected while other chloroplast genes are within the range predicted by the simulations. These results suggest that there have been selective constraints on the codon usage of the flowering plant <i>psbA</i> gene during Angiosperm evolution.</p>
SSR and cpDNA marker dataset genetic integrity of M.sylvestris in Saxony, Germany
<p><i>Malus sylvestris</i> (Mill.) is the only indigenous wild apple species in Central Europe. Agriculture, forestry and urbanization increasingly endanger <i>Malus sylvestris </i>natural habitats. In addition, the risks of cross-hybridization associated with increase in the cultivation of the domesticated apple <i>Malus ×domestica</i> (Borkh.), threatens the genetic integrity of <i>M. sylvestris</i>.</p> <p>The present study investigated the number of hybrids, genetic diversity and genetic structure of 292 putative <i>M. sylvestris</i> that originate from five different natural <i>M. sylvestris</i> populations in Saxony, Germany. All samples were genetically analyzed using nine nuclear microsatellite markers (ncSSR) and four maternally inherited chloroplast markers (cpDNA) along with 56 apple cultivars commonly cultivated in Saxony.</p> <p>Eighty-seven percent of the wild apple accessions were identified as pure <i>M. sylvestris</i>. The cpDNA analysis showed six private haplotypes for <i>M. sylvestris,</i> whereas three haplotypes were present in <i>M. sylvestris </i>and<i> M. ×domestica.</i> The analysis of molecular variance (AMOVA) resulted in a moderate (ncSSR) and great (cpDNA) variation among pure <i>M. sylvestris</i> and <i>M. ×domestica </i>individuals indicating a low gene flow between both species. The genetic diversity within the pure <i>M. sylvestris</i> populations was high with a weak genetic structure between the <i>M. sylvestris</i> populations indicating an unrestricted genetic exchange between these <i>M. sylvestris</i> populations.</p> <p>The clear distinguishing of <i>M. sylvestris</i> and <i>M. ×domestica</i> confirms our expectation of the existence of pure <i>M. sylvestris </i>accessions<i> </i>in this area and supports the argument for the implementation of preservation measures to protect the <i>M. sylvestris </i>populations in<i> </i>Saxony. </p>
FIGURE 1 in Systematic position of Rivina humilis var. humilis, R. humilis var. bracteata and R. bengalensis based on nrDNA ITS and cpDNA rbcL & trnH-psbA sequence data
FIGURE 1. Best ML tree retrieved after analysing 43 taxa of family Phytolaccaceae. The best fit model of evolution GTR+G+I. The tree rooted at Hilleria latifolia (Lee et al. 2013).
FIGURE 3. A–E in Systematic position of Rivina humilis var. humilis, R. humilis var. bracteata and R. bengalensis based on nrDNA ITS and cpDNA rbcL & trnH-psbA sequence data
FIGURE 3. A–E: Rivina humilis L.var. bracteata; A) Habit (inset flowers); B) Infructescence; C) Bract; D) Fruit; E) Seed; F–J: Rivina humilis L. var. humilis; F) Habit (inset flower); G) Infructescence; H) Bract; I) Fruit; J) Seed; K–O: Rivina bengalensis S. C. Srivastava et T. K. Paul; K) Habit (inset flowers); L) Infructescence; M) Bract; N) Fruit; O) Seed.
FIGURE 1 in A partial cpDNA trnL sequence from the extinct legume Streblorrhiza speciosa confirms its placement in the tribe Coluteae (Fabaceae)
FIGURE 1. Bayesian maximum clade credibility tree showing the relationship of Streblorrhiza to other members of the tribe Coluteae. Posterior probability values are indicated above the branches.
FIGURE 6. Chamaesium paradoxum. A in Phylogeny of Chinese Chamaesium (Apiaceae: Apioideae) inferred from ITS, cpDNA and morphological characters
FIGURE 6. Chamaesium paradoxum. A. cross section of mericarp; B. blade of basal leaves; C. habit; D. fruiting umbellet with bracteoles; E. dorsal view of mericarp. [A, C, D and E from GXL1509270101; B from GXL1509270102].
FIGURE 1. Bayesian 50 in Phylogeny of Chinese Chamaesium (Apiaceae: Apioideae) inferred from ITS, cpDNA and morphological characters
FIGURE 1. Bayesian 50% majority-rule consensus tree of Chamaesium and its related genus inferred from ITS(B) and plastid rpl16+rps16+trnT-trnL(A) using a GTR+G nucleotide substitution model. Values on the branches indicate its support (Bayesian posterior probability/ parsimony bootstrap). Short line denotes no support value. The tree is rooted with Bupleurum. The names of the clades identified are those of Zhou et al. (2008, 2009) and Downie et al. (2010).
FIGURE 5. Chamaesium mallaeanum. A in Phylogeny of Chinese Chamaesium (Apiaceae: Apioideae) inferred from ITS, cpDNA and morphological characters
FIGURE 5. Chamaesium mallaeanum. A. cross section of mericarp; B. blade of basal leaves; C. habit; D. fruiting umbellet with bracteoles; E. dorsal view of mericarp. [A, D and E from GXL1509010101; B from GXL1509010102, C from GXL1509010103].
FIGURE 9. Chamaesium wolffianum. A in Phylogeny of Chinese Chamaesium (Apiaceae: Apioideae) inferred from ITS, cpDNA and morphological characters
FIGURE 9. Chamaesium wolffianum. A. cross section of mericarp; B. blade of basal leaves; C. habit; D. fruiting umbel; E. dorsal view of mericarps. [A, B, D, E from GXL1608200101; C from GXL1608200102].
FIGURE 2. Bayesian 50 in Phylogeny of Chinese Chamaesium (Apiaceae: Apioideae) inferred from ITS, cpDNA and morphological characters
FIGURE 2. Bayesian 50% majority-rule consensus tree of Chamaesium and its related genus inferred from combined ITS and plastid rpl16+rps16+trnT-trnL using a GTR+G nucleotide substitution model. Values on the branches indicate its support (Bayesian posterior probability/ parsimony bootstrap). The tree is rooted with Bupleurum. The names of the clades identified are those of Zhou et al. (2008, 2009) and Downie et al. (2010).
FIGURE 8. Chamaesium viridiflorum. A in Phylogeny of Chinese Chamaesium (Apiaceae: Apioideae) inferred from ITS, cpDNA and morphological characters
FIGURE 8. Chamaesium viridiflorum. A. cross section of mericarp; B. segment of basal leaf; C. habit; D. flowering umbellet with bracteoles; E. dorsal view of mericarps. [A, B, D, E from GXL1507150101; C from GXL1507150102].
FIGURE 7. Chamaesium thalictrifolium. A in Phylogeny of Chinese Chamaesium (Apiaceae: Apioideae) inferred from ITS, cpDNA and morphological characters
FIGURE 7. Chamaesium thalictrifolium. A. cross section of mericarp; B. segments of basal leaf; C. habit; D. fruiting umbel with bracts; E. dorsal view of mericarp. [A, B, D and E from GXL1509180101; C from GXL1509180102].
FIGURE 4. Chamaesium delavayi. A in Phylogeny of Chinese Chamaesium (Apiaceae: Apioideae) inferred from ITS, cpDNA and morphological characters
FIGURE 4. Chamaesium delavayi. A. cross section of mericarp; B. blade of basal leaf; C. habit; D. fruiting umbel; E. dorsal view of mericarps. [A, C and E from GXL1507100101; B, D from GXL1507100102].
FIGURE 1. A–B. Veltheimia capensis. A in Genetic diversity and species limits in Veltheimia (Asparagaceae: Scilloideae): insights from noncoding cpDNA sequence data
FIGURE 1. A–B. Veltheimia capensis. A. Flowering plant in situ. B. Plant in fruit, also showing the papery tunic at the exposed part of the bulb. C–F. Veltheimia bracteata. C. Yellow form in cultivation. D. Common colour form. E. Striated leaved form from Baviaanskloof. F. Whole plant showing the globose bulb and fleshy scales. Photographs: A, B: L. Mucina; C: J. Sampson; D: T. Dold; E: G. Schafer; F: N. Barker.
FIGURE 2 in Genetic diversity and species limits in Veltheimia (Asparagaceae: Scilloideae): insights from noncoding cpDNA sequence data
FIGURE 2. Specimen distribution of species of Veltheimia. Red dots = known localities of V. bracteata, blue triangles = known locations of V. capensis (based on data from the BODATSA database of the National Herbarium, South Africa, http://posa.sanbi.org/). The inserted frame shows the Bayesian Inference phylogeny of the combined chloroplast non-coding data set (numbers shown below the branches indicate Posterior Probability values, the number above the red branch is the parsimony Bootstrap Support value). The branch with the thick red line indicates the "bracteata clade". Numbers preceding sample names link to specimens listed in Table 1, and are also (where the locality is known) indicated on the map. The Median Joining Network (MJN) is shown overlaid on the distribution to indicate the location of the samples (and haplotypes) used in the MJN analysis. The numbers in parentheses next to the lines linking the haplotypes indicate the number of mutational differences between the haplotypes, and the solid black circle indicate an un-sampled or hypothesised missing haplotype.
Data from: Phylogeography of the arid shrub Atraphaxis frutescens (Polygonaceae) in northwestern China: evidence from cpDNA sequences
Climatic fluctuations during the Pleistocene are usually considered as a significant factor in shaping intraspecific genetic variation and influencing demographic histories. To well-understand these processes in desert northwest China, we selected arid adapted Atraphaxis frutescens as the study species. Two cpDNA regions (psbK-psbI, psbB-psbH) were sequenced in 272 individuals from 33 natural populations across the range of this shrub, and 10 haplotypes were identified. It was found to contain high levels of total gene diversity (H T = 0.858), and low levels of within-population diversity (H S = 0.092). Analysis of molecular variance (AMOVA) indicates that genetic differentiation primarily occurs among groups of populations. Based on BEAST (Bayesian Evolutionary Analysis Sampling Trees) analysis, we suggest that intraspecific differentiation of the species, resulting from isolated populations, accompanied enhanced desertification during the middle and late Pleistocene. The expansion of the Gurbantunggut and Kumtag deserts in this area appears to have triggered divergence among populations of the western, central, and eastern portions of the region and shaped genetic differentiation among them. Two possible independent glacial refugia were predicted, the Ili Valley and the northern Junggar Basin. Extensive development of arid habitats (desert margin and arid piedmont grassland) coupled with a more equable climate because the early Holocene are factors likely to have generated recent expansion of A. frutescens.
Context-dependent substitution matrices for coding regions of angiosperm cpDNA
<p>The dataset contains 4x4 substitution matrices generated from fourfold degenerate sites within coding regions of flowering plant chloroplast DNA. Substitution data was generated from multiple sets of 3 taxa sequence comparisons, one taxon serving as the outgroup to root the substitution. There is one matrix for each of the possible 192 tetranucleotide contexts consisting of the two bases immediately flanking the substitution on the 5' side and the two bases immediately flanking the substitution on the 3' side. These are count matrices but can be converted to Markov transition matrices. The analysis presented in the paper examines variation in substitution dynamics as a function of context.</p>
FIGURE 6. The maximum likehood tree generated using cpDNA trnL-F in A new species of Hedysarum (Fabaceae) from Turkey
FIGURE 6. The maximum likehood tree generated using cpDNA trnL-F sequences and outgroups sequences retrieved from NCBI (Bootstrap values are given above branches).
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