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373 results for “Chloroplast”
Data from: Phylogeographical patterns of an alpine plant, Rhodiola dumulosa (Crassulaceae), inferred from chloroplast DNA sequences
The phylogeographical patterns of Rhodiola dumulosa, an alpine plant species restrictedly growing in the crevices of rock piles, were investigated based on 4 fragments of the chloroplast genome. To cover the full distribution of R. dumulosa in China, 19 populations from 3 major disjunct distribution areas (northern, central, and northwestern China) were sampled. A total of 5881bp (after alignment) of chloroplast DNA (cpDNA) from 100 individuals were sequenced. The combined cpDNA data set yielded 36 haplotypes. The total genetic diversity of R. dumulosa was remarkably high (H T = 0.981). The interpopulation genetic differentiation was significantly large (F ST = 0.8537, P < 0.001), possibly due to the long-term isolation of the natural populations. N ST was significantly larger than G ST (P < 0.001), indicating the presence of phylogeographical structure among the R. dumulosa populations. We propose 2 migration steps to explain the current distribution of R. dumulosa in China. First, this species migrated from refugia in the Qinghai-Tibetan Plateau to northern areas via the intervening highlands when temperatures increased; second, the highland populations migrated toward the mountaintops when temperatures increased further because R. dumulosa is adapted to cold environments. During the second migration step, the common ancestral haplotypes may have been gradually lost.
Data from: Distinctive architecture of the chloroplast genome in the chlorodendrophycean green algae Scherffelia dub and Tetraselmis sp. CCMP 881
The Chlorodendrophyceae is a small class of green algae belonging to the core Chlorophyta, an assemblage that also comprises the Pedinophyceae, Trebouxiophyceae, Ulvophyceae and Chlorophyceae. Here we describe for the first time the chloroplast genomes of chlorodendrophycean algae (Scherffelia dubia, 137,161 bp; Tetraselmis sp. CCMP 881, 100,264 bp). Characterized by a very small single-copy (SSC) region devoid of any gene and an unusually large inverted repeat (IR), the quadripartite structures of the Scherffelia and Tetraselmis genomes are unique among all core chlorophytes examined thus far. The lack of genes in the SSC region is offset by the rich and atypical gene complement of the IR, which includes genes from the SSC and large single-copy regions of prasinophyte and streptophyte chloroplast genomes having retained an ancestral quadripartite structure. Remarkably, seven of the atypical IR-encoded genes have also been observed in the IRs of pedinophycean and trebouxiophycean chloroplast genomes, suggesting that they were already present in the IR of the common ancestor of all core chlorophytes. Considering that the relationships among the main lineages of the core Chlorophyta are still unresolved, we evaluated the impact of including the Chlorodendrophyceae in chloroplast phylogenomic analyses. The trees we inferred using data sets of 79 and 108 genes from 71 chlorophytes indicate that the Chlorodendrophyceae is a deep-diverging lineage of the core Chlorophyta, although the placement of this class relative to the Pedinophyceae remains ambiguous. Interestingly, some of our phylogenomic trees together with our comparative analysis of gene order data support the monophyly of the Trebouxiophyceae, thus offering further evidence that the previously observed affiliation between the Chlorellales and Pedinophyceae is the result of systematic errors in phylogenetic reconstruction.
Comparison among the chloroplast genomes of five species of Chamaerhodos (Rosaceae: Potentilleae): phylogenetic implications
<p><em>Chamaerhodos</em> is a small genus with ca 7–8 species with a disjunct distribution in Asia and western North America. Due to limited sampling of species and genes in previous studies, little is known about the phylogenetic relationships among the species. Moreover, chloroplast genomic resources for <em>Chamaerhodos</em> have been limited. Herein, we conducted a comparative analysis of the complete chloroplast (cp) genomes of five <em>Chamaerhodos</em> species. The five cp genomes had a typical quadripartite structure with high conservation of gene content and gene order. These five cp genomes encoded an identical set of 129 genes, including 84 protein-coding genes, 37 tRNA genes and eight rRNA genes. Comparison of the boundaries between the IRs and single copy regions revealed only very slight boundary differences and the five cp genomes showed only little sequence divergence. Seven regions (<em>trnR-UCU-atpA</em>,<em> trnS-GCU- trnG-UCC</em>, <em>TrnG-GCC-trnfM-CAU</em>, <em>trnL-UAA</em> intron, <em>trnH-GUG-psbA</em>, <em>trnF-GAA- ndhJ</em>, <em>matK-5′-trnK-UUU</em>) were identified as excellent candidate markers. A total of 117, 108, 116, 117 and 118 perfect SSRs were detected in the cp genomes of <em>Ch. altaica</em>, <em>Ch. canescens</em>, <em>Ch. erecta</em>, <em>Ch. sabulosa</em> and <em>Ch. trifida</em>, respectively. A phylogenetic analysis support the monophyly of <em>Chamaerhodos</em> and place it as part of the Fragariinae clade sister to the clade of <em>Dasiphora</em>, <em>Drymocallis</em> and <em>Potaninia</em>. Within <em>Chamaerhodos</em>, <em>Ch. canescens</em> was inferred sister to a clade containing the other four species. The detailed characterization of the <em>Chamaerhodos</em> chloroplast genomes sets the foundation for further studies on the genus and its close relatives in the economically important Rosaceae.</p>
Characterization of the complete chloroplast genome of the medicinal herb Veronica polita Fr. (Lamiales: Plantaginaceae)
<p><em>Veronica polita</em> Fr. (synonym: <em>Veronica didyma</em> Ten.), an annual herbaceous species with high medicinal values, is originally from Southwest Asia but has been naturalized widely in many regions of the world. In this study, the complete chloroplast genome of <em>V. polita</em> was determined to be 150,191 bp long with a typical quadripartite structure. It encodes a panel of 114 genes with 18 of them being completely or partially duplicated and 19 of them possessing one or two introns. The phylogenetic analysis appeared to support the tribal-level taxonomy of the family Plantaginaceae, and revealed that <em>V. polita</em> was most closely related to the congener <em>V. persica</em>.</p>
The complete chloroplast genome of Pedicularis rudis Maxim. (Lamiales: Orobanchaceae), a perennial herb endemic to China
<p><em>Pedicularis rudis</em> Maxim. is a species of perennial herb endemic to China. In this study, the complete chloroplast genome of <em>P. rudis</em> was determined to be 151,443 bp long with a typical quadripartite structure, comprising two inverted repeat regions (IRa and IRb, 25,719 bp each), a large single-copy (LSC) region (83,119 bp) and a small single-copy (SSC) region (16,886 bp). It encodes a panel of 110 genes with 19 of them being completely or partially duplicated and 18 of them possessing one or two introns. Phylogenetic analysis revealed that <em>P. rudis</em> was most closely related to the congener <em>P. shansiensis</em>.</p>
Molecular systematics of the tribe Physarieae (Brassicaceae) based on the nuclear ITS, LUMINIDEPENDENS, and chloroplast ndhF: Sequence alignments, trees, and supplemental figures
<p>Physarieae is a small tribe of herbaceous annual and woody perennial mustards that are mostly endemic to North America, with its members including a large amount of variation in floral, fruit and chromosomal variation. Building on a previous study of Physarieae based on morphology and <i>ndhF</i> plastid DNA, we reconstructed the evolutionary history of the tribe using new sequence data from two nuclear markers, and compared the new topologies against previously published cpDNA-based phylogenetic hypotheses. The novel analyses included ca. 420 new sequences of ITS and <i>LUMINIDEPENDENS</i> (<i>LD</i>) markers for 39 and 47 species, respectively, with sampling accounting for all seven genera of Physarieae, including nomenclatural type species, and 11 outgroup taxa. Maximum parsimony, maximum likelihood, and Bayesian analyses showed that these additional markers were largely consistent with the previous <i>ndh</i>F data that supported the monophyly of Physarieae and resolved two major clades within the tribe, i.e. DDNLS (<i>Dithyrea</i>, <i>Dimorphocarpa</i>, <i>Nerisyrenia</i>, <i>Lyrocarpa</i>, and <i>Synthlipsis</i>) and PP (<i>Paysonia</i> and <i>Physaria</i>). New analyses also increased internal resolution for some closely related species and lineages within both clades. The monophyly<i> </i>of <i>Dithyrea</i> and the sister relationship of <i>Paysonia</i> to <i>Physaria</i> was consistent in all trees, with the sister relationship of <i>Nerisyrenia </i>to <i>Lyrocarpa </i>supported by <i>ndhF</i> and <i>ITS</i>, and the positions of <i>Dimorphocarpa</i> and <i>Synthlipsis</i> shifted within the DDNLS Clade depending on the employed data set. Finally, using the strong, new phylogenetic framework of combined cpDNA + nDNA data, we discussed standing hypotheses of trichome evolution in the tribe suggested by <i>ndhF</i>.</p>
Figure 3 from: Linh NN, Hang PLB, Hue HTT, Ha NH, Hanh HH, Ton ND, Hien LTT (2022) Species discrimination of novel chloroplast DNA barcodes and their application for identification of Panax (Aralioideae, Araliaceae). PhytoKeys 188: 1-18. https://doi.org/10.3897/phytokeys.188.75937
Figure 3 Successful identification rates among analyzed barcodes by Best Match and Best Close Match function.
Figure 2 from: Linh NN, Hang PLB, Hue HTT, Ha NH, Hanh HH, Ton ND, Hien LTT (2022) Species discrimination of novel chloroplast DNA barcodes and their application for identification of Panax (Aralioideae, Araliaceae). PhytoKeys 188: 1-18. https://doi.org/10.3897/phytokeys.188.75937
Figure 2 Percent relative abundance in distribution of intra/interspecific K2P pairwise distances estimated for markers.
Figure 5 from: Linh NN, Hang PLB, Hue HTT, Ha NH, Hanh HH, Ton ND, Hien LTT (2022) Species discrimination of novel chloroplast DNA barcodes and their application for identification of Panax (Aralioideae, Araliaceae). PhytoKeys 188: 1-18. https://doi.org/10.3897/phytokeys.188.75937
Figure 5 Percentage of variable sites, mean pairwise distances, and correct classification percentages of all markers and combinations
Figure 4 from: Linh NN, Hang PLB, Hue HTT, Ha NH, Hanh HH, Ton ND, Hien LTT (2022) Species discrimination of novel chloroplast DNA barcodes and their application for identification of Panax (Aralioideae, Araliaceae). PhytoKeys 188: 1-18. https://doi.org/10.3897/phytokeys.188.75937
Figure 4 Results of mPTP species delimitation analysis for several markers based on ML trees A Species delimitation for marker trnQ-rps16B Species delimitation for the combination of markers 1+3+4. Bootstrap values are displayed on the branches. The red branches represent supported species delimitations. Sequences highlighted in orange originate from this study.
Figure 1 from: Linh NN, Hang PLB, Hue HTT, Ha NH, Hanh HH, Ton ND, Hien LTT (2022) Species discrimination of novel chloroplast DNA barcodes and their application for identification of Panax (Aralioideae, Araliaceae). PhytoKeys 188: 1-18. https://doi.org/10.3897/phytokeys.188.75937
Figure 1 Distribution of Panax in Vietnam and sample locations. P. vietnamensis (green) collected in Quang Nam and Kon Tum Provinces. P. vietnamensis var. fuscidiscus (brown) collected in Lai Chau Province. Panax sp. Puxailaileng (pink) collected in Nghe An Province. P. bipinnatifidus (blue) and P. stipuleanatus (yellow) collected in Lao Cai Province. The natural distribution of P. vietnamensis, P. vietnamensis var. fuscidiscus, and Panax sp. are marked as green, brown, and pink, respectively. The wild habitat for P. bipinnatifidus and P. stipuleanatus is shown in yellow, and the purple area represents the distribution region of P. vietnamensis var. langbiangensis (not included in this study).
FIGURE 7 in Indocalamus chongzhouensis (Poaceae: Bambusoideae), a new synonym of I. emeiensis: evidence from morphology and complete chloroplast genome data
FIGURE 7. Geographical distribution of Indocalamus emeiensis (red pentacles).
Data from: Whole chloroplast genome and gene locus phylogenies reveal the taxonomic placement and relationship of Tripidium (Panicoideae: Andropogoneae) to sugarcane
Background: For over 50 years, attempts have been made to introgress agronomically useful traits from Erianthus sect. Ripidium (Tripidium) species into sugarcane based on both genera being part of the 'Saccharum Complex', an interbreeding group of species believed to be involved in the origins of sugarcane. However, recent low copy number gene studies indicate that Tripidium and Saccharum are more divergent than previously thought. The extent of genus Tripidium has not been fully explored and many species that should be included in Tripidium are still classified as Saccharum. Moreover, Tripidium is currently defined as incertae sedis within the Andropogoneae, though it has been suggested that members of this genus are related to the Germainiinae. Results: Eight newly-sequenced chloroplasts from potential Tripidium species were combined in a phylogenetic study with 46 members of the Panicoideae, including seven Saccharum accessions, two Miscanthidium and three Miscanthus species. A robust chloroplast phylogeny was generated and comparison with a gene locus phylogeny clearly places a monophyletic Tripidium clade outside the bounds of the Saccharinae. A key to the currently identified Tripidium species is presented. Conclusion: For the first time, we have undertaken a large-scale whole plastid study of eight newly assembled Tripidium accessions and a gene locus study of five Tripidium accessions. Our findings show that Tripidium and Saccharum are eight million years divergent, last sharing a common ancestor 12 million years ago. We demonstrate that four species should be removed from Saccharum/Erianthus and included in genus Tripidium. In a genome context, we show that Tripidium evolved from a common ancestor with and extended Germainiinae clade formed from Germainia, Eriochrysis, Apocopis, Pogonatherum and Imperata. We re-define the 'Saccharum complex' to a group of genera that can interbreed in the wild and extend the Saccharinae to include Sarga along with Sorghastrum, Microstegium vimineum and Polytrias (but excluding Sorghum). Monophyly of genus Tripidium is confirmed and the genus is expanded to include Tripidium arundinaceum, Tripidium procerum, Tripidium kanashiroi and Tripidium rufipilum. As a consequence, these species are excluded from genus Saccharum. Moreover, we demonstrate that genus Tripidium is distinct from the Germainiinae.
Supplementary material 1 from: Fu L-F, Xiong C, Monro AK, Fan Q, Chen Z-X, Wen F, Xin Z-B, Wei Y-G, Liao W-B (2022) Pilea danxiaensis (Urticaceae), a new species in the Danxia landform from Guangdong, China including a description of the entire chloroplast genome. PhytoKeys 204: 109-119. https://doi.org/10.3897/phytokeys.204.86857
Appendix S1
Figure 8 from: Saarela JM, Bull RD, Paradis MJ, Ebata SN, Peterson PM, Soreng RJ, Paszko B (2017) Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1). PhytoKeys 87: 1-139. https://doi.org/10.3897/phytokeys.87.12774
Figure 8 - A portion (part of Agrostidinae p.p.) of the maximum likelihood phylogram inferred from ITS+ETS data. ML bootstrap support (left) and BI poster probabilities (right) are recorded along branches. A dash indicates bootstrap support <50%. No support is shown for branches with bootstrap support <50% and posterior probability <.5. The shaded area of the smaller tree on the upper left indicates the location in the overall tree of the portion shown. Placements of samples with asterisks (***) are incongruent in nrDNA and plastid trees. Two indels in ETS are mapped onto the phylogram.
Figure 9 from: Saarela JM, Bull RD, Paradis MJ, Ebata SN, Peterson PM, Soreng RJ, Paszko B (2017) Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1). PhytoKeys 87: 1-139. https://doi.org/10.3897/phytokeys.87.12774
Figure 9 - A portion (part of Agrostidinae p.p., Anthoxanthinae, Brizinae, Calothecinae, Phalaridinae, Scolochloinae and Torreyochloinae) of the maximum likelihood phylogram inferred from ITS+ETS data. ML bootstrap support (left) and BI poster probabilities (right) are recorded along branches. A dash indicates bootstrap support <50%. No support is shown for branches with bootstrap support <50% and posterior probability <.5. The shaded area of the smaller tree on the left indicates the location in the overall tree of the portion shown. One indel in ETS is mapped onto the phylogram.
Figure 22 from: Saarela JM, Bull RD, Paradis MJ, Ebata SN, Peterson PM, Soreng RJ, Paszko B (2017) Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1). PhytoKeys 87: 1-139. https://doi.org/10.3897/phytokeys.87.12774
Figure 22 - A portion (part of Agrostidinae p.p.) of the maximum likelihood phylogram inferred from combined plastid data (atpF–atpH, psbK–psbI, psbA–rps19–trnH, matK, trnL–trnF). ML bootstrap support (left) and BI poster probabilities (right) are recorded along branches. A dash indicates bootstrap support <50%. No support is shown for branches with bootstrap support <50% and posterior probability <.5. The shaded area of the smaller tree on the left indicates the location in the overall tree of the portion shown. Placement of the sample with asterisks (***) is incongruent in nrDNA and plastid trees. One indel in psbK–psbI and one in atpF–atpH are mapped onto the phylogram.
Figure 24 from: Saarela JM, Bull RD, Paradis MJ, Ebata SN, Peterson PM, Soreng RJ, Paszko B (2017) Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1). PhytoKeys 87: 1-139. https://doi.org/10.3897/phytokeys.87.12774
Figure 24 - A portion (part of Agrostidinae p.p., Anthoxanthinae, Brizinae, Calothecinae, Phalaridinae and Torreyochloinae) of the maximum likelihood phylogram inferred from combined plastid data (atpF–atpH, psbK–psbI, psbA–rps19–trnH, matK, trnL–trnF). ML bootstrap support (left) and BI poster probabilities (right) are recorded along branches. A dash indicates posterior probability <.5. No support is shown for branches with bootstrap support <50% and posterior probability <.5. The shaded area of the smaller tree on the left indicates the location in the overall tree of the portion shown. Placements of samples with asterisks (***) are incongruent in nrDNA and plastid trees. An indel in psbK–psbI is mapped onto the phylogram.
Figure 21 from: Saarela JM, Bull RD, Paradis MJ, Ebata SN, Peterson PM, Soreng RJ, Paszko B (2017) Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1). PhytoKeys 87: 1-139. https://doi.org/10.3897/phytokeys.87.12774
Figure 21 - A portion (Koeleriinae clade B) of the maximum likelihood phylogram inferred from combined plastid data (atpF–atpH, psbK–psbI, psbA–rps19–trnH, matK, trnL–trnF). ML bootstrap support (left) and BI poster probabilities (right) are recorded along branches. A dash indicates bootstrap support <50%. No support is shown for branches with bootstrap support <50% and posterior probability <.5. The shaded area of the smaller tree on the bottom left indicates the location in the overall tree of the portion shown. Placements of samples with asterisks (***) are incongruent in nrDNA and plastid trees. An indel in psbK–psbI is mapped onto the phylogram.
Figure 2 from: Saarela JM, Bull RD, Paradis MJ, Ebata SN, Peterson PM, Soreng RJ, Paszko B (2017) Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1). PhytoKeys 87: 1-139. https://doi.org/10.3897/phytokeys.87.12774
Figure 2 - Overview of the maximum likelihood phylogram inferred from ITS data. Major clades in the complete tree are collapsed. The corresponding figures showing details of subsections of the tree are indicated. ML bootstrap support is recorded along branches. No support is shown for branches with bootstrap support <50%. The ML tree is presented in its entirety in Suppl. material 4.
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