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15 results for “rps16”
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.
FIGURE 1. Percentage Potentially Informative Character values for all 11 chloroplast regions. For the regions rps16 in A new genus and a major temperate bamboo lineage of the Arundinarieae (Poaceae: Bambusoideae) from Sri Lanka based on a multi-locus plastid phylogeny
FIGURE 1. Percentage Potentially Informative Character values for all 11 chloroplast regions. For the regions rps16–trnQ, trnC– rpoB, trnD–trnT, trnT–trnL and ndhF 3' the PIC values include the outgroups. For the regions psbD-trnT, psbJ-petA and ycf6- psbM the PIC values include only the ingroup species.
FIGURE. Maximum clade credibility tree of a post-burnin Bayesian analysis (100 million generations), based on nuclear (agt1, ETS, g3pdh, phyC, rpb2) and plastid (atpB–rbcL, matK, rps16, ycf1 pos. 1113-2103, ycf1 pos. 4492-5440) data. Above the branches, Bayesian posterior probabilities (PP) and maximum-likelihood bootstrap support (BS) are shown (PP/BS). The scale bar below the tree shows the branch length for 0.004 substitutions per nucleotide position. Capital letters at the branches are referred to in the tree description. in Re-evaluation of the Amazonian Hylaeaicum (Bromeliaceae: Bromelioideae) based on neglected morphological traits and molecular evidence
FIGURE. Maximum clade credibility tree of a post-burnin Bayesian analysis (100 million generations), based on nuclear (agt1, ETS, g3pdh, phyC, rpb2) and plastid (atpB–rbcL, matK, rps16, ycf1 pos. 1113-2103, ycf1 pos. 4492-5440) data. Above the branches, Bayesian posterior probabilities (PP) and maximum-likelihood bootstrap support (BS) are shown (PP/BS). The scale bar below the tree shows the branch length for 0.004 substitutions per nucleotide position. Capital letters at the branches are referred to in the tree description.
FIGURE 4 in Phylogeny and taxonomy of Meeboldia, Sinodielsia and their relatives (Apiaceae: Apioideae) inferred from nrDNA ITS, plastid DNA intron (rpl16 and rps16) sequences and morphological characters
FIGURE 4. Mericarp morphology of Meeboldia yunnanensis, S. microloba, S. thibetica, Tongoloa zhongdianensis and Hymenidium apiolens (a–c, d–f, g–i, j–l and m–o). Fruit views are dorsal side, commissural side and transverse section for each row from left to right. Scale bars are 1 mm. Terminologies followed Kljuykov et al. (2004). cv = commissural vittae; lr = lateral rib; mar = marginal rib; mer = median rib; vv = vallecular vittae.
FIGURE 1 in Phylogeny and taxonomy of Meeboldia, Sinodielsia and their relatives (Apiaceae: Apioideae) inferred from nrDNA ITS, plastid DNA intron (rpl16 and rps16) sequences and morphological characters
FIGURE 1. Phylogenetic tree of Acronema clade (A) and Sinodielsia clade (B) derived from Bayesian inference analysis using the ITS dataset. The numbers above and below the nodes are BI-PP and ML-BS presented as percentages, respectively (> 50%). Those nodes not occurring in the ML tree are indicated by pound symbols (#). The names of the clades follow the study of Downie et al. (2010).
FIGURE 6 in Phylogeny and taxonomy of Meeboldia, Sinodielsia and their relatives (Apiaceae: Apioideae) inferred from nrDNA ITS, plastid DNA intron (rpl16 and rps16) sequences and morphological characters
FIGURE 6. Habit and morphology of Sinodielsia microloba. a. Habit. b. Compound umbels. c. Flowers. d. Cauline leaf. e. Bracts. f. Bracteoles. g. Basal leaves. h. Root. i. Fruits.
FIGURE 3 in Phylogeny and taxonomy of Meeboldia, Sinodielsia and their relatives (Apiaceae: Apioideae) inferred from nrDNA ITS, plastid DNA intron (rpl16 and rps16) sequences and morphological characters
FIGURE 3. Specimen and fruits of Meeboldia achilleifolia. a. Specimen of M. achilleifolia (From herbarium BM, barcode BM000622295, Wallich 568 (Natural History Museum 2014)). b. Attachment on the specimen with note "Meeboldia 3402 Type of Meeboldia". c. Morphology of fruits in the attachment. d. Fruits drawing of M. achilleifolia from previous research (Pu & Peng 2005).
FIGURE 5 in Phylogeny and taxonomy of Meeboldia, Sinodielsia and their relatives (Apiaceae: Apioideae) inferred from nrDNA ITS, plastid DNA intron (rpl16 and rps16) sequences and morphological characters
FIGURE 5. Diagnostic morphological characters of Meeboldia yunnanensis from Kunming, Yunnan. a. Habit. b–c. Compound umbels. d. Basal leaf. e. Root. f. Fruits.
FIGURE 2 in Phylogeny and taxonomy of Meeboldia, Sinodielsia and their relatives (Apiaceae: Apioideae) inferred from nrDNA ITS, plastid DNA intron (rpl16 and rps16) sequences and morphological characters
FIGURE 2. Phylogenetic tree of Meeboldia, Sinodielsia and their relatives derived from Bayesian inference analysis using concatenated rpl16 and rps16 introns dataset. The numbers above and below the nodes are BI-PP and ML-BS presented as percentages, respectively (> 50%). Those nodes not occurring in the ML tree are indicated by pound symbols (#). The names of the clades follow the study of Downie et al. (2010).
FIGURE 7 in Phylogeny and taxonomy of Meeboldia, Sinodielsia and their relatives (Apiaceae: Apioideae) inferred from nrDNA ITS, plastid DNA intron (rpl16 and rps16) sequences and morphological characters
FIGURE 7. Terminal leaflets of basal leaves, from 3 populations of Meeboldia yunnanensis and 1 population of Sinodielsia delavayi. Scale bars are 10 mm. P1. Population of M. yunnanensis from Kunming. P2. Population of S. delavayi from Baisha River, Eryuan. P3. Population of M. yunnanensis from Haba village, Zhongdian. P4. Population of M. yunnanensis from Tiger Leaping Gorge, Zhongdian.
Data from: Phylogenetic relationships of Iranian Allium sect. Allium (Amaryllidaceae, Allioideae) as inferred from nrDNA ITS, cpDNA rps16 and trnL–F sequences
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Data from: Plastid genome sequences of legumes reveal parallel inversions and multiple losses of rps16 in papilionoids
To date, publicly available plastid genomes of legumes have for the most part been limited to the subfamily Papilionoideae. Here we report 13 new plastid genomes of legumes spanning all three subfamilies. The genomes representing Caesalpinioideae and Mimosoideae are highly conserved in gene content and gene order, similar to the ancestral angiosperm genome organization. Genomes within the Papilionoideae, however, have reduced sizes due to deletions in nine intergenic spacers primarily in the large single copy region. Our study also indicates that rps16 has been independently lost at least five times in legumes, with additional gene and intron losses scattered among the papilionoids. Additionally, genera from two distinct lineages within the papilionoids, Lupinus and Robinia, have a parallel inversion of 36 kb and 39 kb, respectively. This parallel inversion is novel as it appears to be caused by a 29 bp repeat within two trnS genes. This repeat is present in all available legume plastid genomes indicating that there is the potential for this inversion to be present in more species. This case of a homoplasious inversion is also evidence that some inversion events may not be reliable phylogenetic markers.
Data from: Plastid genome sequences of legumes reveal parallel inversions and multiple losses of rps16 in papilionoids
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The Bayesian trees of the nuclear gene DMC1 and the chloroplast gene rps16 sequences
<p>Some plants with low fertility are morphologically intermediate between <i>Roegneria stricta</i><i> </i>and<i> Roegneria</i> <i>turczaninovii</i>, and were suspected to be natural hybrids between these species. In this study, karyotype analysis showed that natural hybrids and its putative parents were tetraploids (2n = 4x = 28). Meiotic pairing in natural hybrids is more irregular than its putative parents. Results of genomic <i>in situ</i> hybridization and fluorescence <i>in situ</i> hybridization indicate that natural hybrids contain the same genome as its putative parents. The nuclear gene DNA meiotic recombinase 1 (<i>DMC</i>1) and the chloroplast gene <i>rps</i>16 of natural hybrids and its putative parents were analyzed for evidence of hybridization. The results from molecular data supported by morphology and cytology demonstrated that the plants represent natural hybrids between <i>R. stricta</i><i> </i>and<i> R.</i> <i>turczaninovii</i>. The study is important understanding species evolution in the genus since it demonstrates for the first time the existence of populations of natural homoploid hybrids in <i>Roegneria. </i>The study also reports for the first time that the composition of the genomic formula of <i>R.</i> <i>turczaninovii </i>is <b>StY</b>, confirming that the current taxonomic status is correct.</p> <p> </p>
The Bayesian trees of the nuclear gene DMC1 and the chloroplast gene rps16 sequences
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