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373 results for “Chloroplast”
Data from: Intraspecific haplotype diversity in Cherleria sedoides L. (Caryophyllaceae) is best explained by chloroplast capture from an extinct species
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Rhizophora complete chloroplast genome sequences
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Chloroplast haplotypes and main haplotypes of nrITS clones of Gentiana crassicaulis
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Data from: Reticulate evolution, ancient chloroplast haplotypes, and rapid radiation of the Australian plant genus Adenanthos (Proteaceae)
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data from "The chloroplast land plant phylogeny: analyses employing better-fitting tree- and site-heterogeneous composition models"
<p>The nucleotide, codon-degenerate and protein concatenated alignments of 83 chloroplast genes, with the respective character sets, in nexus format.</p>
Figure 3 from: Maurin KJL (2020) A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S–26S repeat region sequences. PhytoKeys 155: 15-32. https://doi.org/10.3897/phytokeys.155.53460
Figure 3 Undated 18S–26S nuclear DNA repeat region BEAST 2 phylogeny of Pennantia, under the Birth-Death model. The tree was rooted to make P. cunninghamii sister to the other species of Pennantia, in accordance with the chloroplast DNA tree and the ITS tree of Keeling et al. (2004). Node posterior probability is shown next to the corresponding node. The sequences downloaded from GenBank have their accession number in round brackets; the others were generated from the samples used in this study.
Supplementary material 2 from: Maurin KJL (2020) A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S–26S repeat region sequences. PhytoKeys 155: 15-32. https://doi.org/10.3897/phytokeys.155.53460
BEAST2 and RAxML files
Figure 2 from: Maurin KJL (2020) A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S–26S repeat region sequences. PhytoKeys 155: 15-32. https://doi.org/10.3897/phytokeys.155.53460
Figure 2 Dated chloroplast DNA BEAST 2 phylogeny of Pennantia, under the Birth-Death model. Mean node age and 95% HPD (in My) is given in the table embedded in the figure under the corresponding letter code. 95% HPD is also represented by blue bars. All node posterior probabilities are equal to 1 except if indicated otherwise. The calibrated nodes (see text) are indicated by red dots.
Supplementary material 1 from: Maurin KJL (2020) A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S–26S repeat region sequences. PhytoKeys 155: 15-32. https://doi.org/10.3897/phytokeys.155.53460
Figs S1–S5; Tables S1–S3
Figure 1 from: Maurin KJL (2020) A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S–26S repeat region sequences. PhytoKeys 155: 15-32. https://doi.org/10.3897/phytokeys.155.53460
Figure 1 General distribution of the four Pennantia species. TKI = Three Kings Islands. Generated in QGIS 3.0.1 from Google Satellite data obtained through the XYZ Tiles tool (https://mt1.google.com/vt/lyrs=s&x={x}&y={y}&z={z}).
Evolution of Rosaceae chloroplast genomes highlights unique Cerasus diversification and independent origins of fruit cherry
<p>Rosaceae plants comprise numerous fruit crops with huge economic values. The lack of genomic characteristics has largely blocked our understanding about the Rosaceae gene and plastome evolution. Here, we analyzed 121 Rosaceae chloroplast (cp) genomes of 51 taxa from 19 genera, predominantly including the Cerasus plants and their relatives. To our knowledge, we generated the first comprehensive map of genomic variation across Rosaceae plastomes. Protein-coding genes of Rosaceae plastomes were characterized with high proportion (over 50%) of synonymous variants and InDels with multiple triplets. Four photosynthesis-related genes were under Darwin selection, which are unique in woody fruit trees of Rosaceae. We detected considerable variations in genome size among Rosaceae plastomes and observed trivial and obvious structural variation in the examined cp genomes of tribes Pyrodae and Amygdaleae. Phylogenomic analyses and molecular dating highlighted the independent evolution of true cherry, dwarf cherry and relatives. Our findings strongly support to taxonomically treat the monophyletic true cherry group as a separate genus excluding dwarf cherry. High levels of genomic differentiation and distinct phylogenetic relationships implied independent origins and domestication between fruit cherries, particularly between cultivated Cerasus psuedocerasus and Cerasus avium. We further proposed an evolutionary model to elucidate multiple genomic introgression events among true cherries occurring since ~15 Mya. Well-resolved maternal phylogeny suggested that the cultivated C. pseudocerasus might be originated from Longmenshan Fault zone, the eastern edge of Himalaya-Hengduan Mountains, where they have subjected to frequent genomic introgression between its presumed wild ancestors and other close relatives. In conclusion, comparative analyses of plastomes and chloroplast genes detected diverse evolutionary behaviors and divergent adaptive selection in Rosaceae. We provide robust evidences for the independent origins and domestication of fruit cherries.</p>
Data from: Chloroplast phylogenomics resolves key relationships in ferns
Studies on chloroplast genomes of ferns and lycophytes are relatively few in comparison with those on seed plants. Although a basic phylogenetic framework of extant ferns is available, relationships among a few key nodes remain unresolved or poorly supported. The primary objective of this study is to explore the phylogenetic utility of large chloroplast gene data in resolving difficult deep nodes in ferns. We sequenced the chloroplast genomes from Cyrtomium devexiscapulae (eupolypod I) and Woodwardia unigemmata (eupolypod II), and constructed the phylogeny of ferns based on both 48 genes and 64 genes. The trees based on 48 genes and 64 genes are identical in topology, differing only in support values for four nodes, three of which showed higher support values for the 48-gene dataset. Equisetum was resolved as the sister to the clade of Psilotales-Ophioglossales, and the clade of Equisetales-Psilotales-Ophioglossales was sister to the clade of the leptosporangiate and marattioid ferns. The sister-relationship between the tree fern clade and polypods was supported by 82%, and 100%, bootstrap values in the 64-gene and the 48-gene trees, respectively. In polypod ferns, Pteridaceae was sister to the clade of Dennstaedtiaceae and eupolypods with a high support value, and the relationship of Dennstaedtiaceae-eupolypods was strongly supported. With recent parallel advances in the phylogenetics of ferns using nuclear data, chloroplast phylogenomics shows great potential in providing a framework for testing the impact of reticulate evolution in the early evolution of ferns.
Data from: Plastome mutations and recombination events in barley chloroplast mutator seedlings
The barley chloroplast mutator (cpm) is an allele of a nuclear gene that when homozygous induces several types of cytoplasmically inherited chlorophyll deficiencies. In this work, a plastome TILLING (Targeting Induced Local Lesions in Genomes) strategy based on mismatch digestion was used on families that carried the cpm genotype through many generations. Extensive scanning of 33 plastome genes and a few intergenic regions was conducted. Numerous polymorphisms were detected on both genic and intergenic regions. The detected polymorphisms can be accounted for by at least 61 independent mutational events. The vast majority of the polymorphisms originated in substitutions and small indels (insertions/deletions) in microsatellites. The rpl23 and the rps16 genes were the most polymorphic. Interestingly, the variation observed in the rpl23 gene consisted of several combinations of five different one nucleotide polymorphisms. Besides, four large indels that have direct repeats at both ends were also observed, which appear to be originated from recombinational events. The cpm mutation spectrum suggests that the CPM gene product is probably involved in plastome mismatch repair. The numerous subtle molecular changes that were localized in a wide range of plastome sites show the cpm as a valuable source of plastome variability for plant research and/or plant breeding. Moreover, the cpm mutant appears to be as an interesting experimental material for investigating the mechanisms responsible for maintaining the stability of plant organelles DNA.
Data from: Congruent deep relationships in the grape family (Vitaceae) based on sequences of chloroplast genomes and mitochondrial genes via genome skimming
Vitaceae is well-known for having one of the most economically important fruits, i.e., the grape (Vitis vinifera). The deep phylogeny of the grape family was not resolved until a recent phylogenomic analysis of 417 nuclear genes from transcriptome data. However, it has been reported extensively that topologies based on nuclear and organellar genes may be incongruent due to differences in their evolutionary histories. Therefore, it is important to reconstruct a backbone phylogeny of the grape family using plastomes and mitochondrial genes. In this study, next-generation sequencing data sets of 27 species were obtained using genome skimming with total DNAs from silica-gel preserved tissue samples on an Illumina HiSeq 2500 instrument. Plastomes were assembled using the combination of de novo and reference genome (of V. vinifera) methods. Sixteen mitochondrial genes were also obtained via genome skimming using the reference genome of V. vinifera. Extensive phylogenetic analyses were performed using maximum likelihood and Bayesian methods. The topology based on either plastome data or mitochondrial genes is congruent with the one using hundreds of nuclear genes, indicating that the grape family did not exhibit significant reticulation at the deep level. The results showcase the power of genome skimming in capturing extensive phylogenetic data: especially from chloroplast and mitochondrial DNAs.
Data from: A chloroplast tree for Viburnum (Adoxaceae) and its implications for phylogenetic classification and character evolution
Premise of the study: Despite recent progress, significant uncertainties remain concerning relationships among early-branching lineages within Viburnum (Adoxaceae). This has prohibited a new classification, and has hindered studies of character evolution and the increasing use of Viburnum in addressing a wide range of ecological and evolutionary questions. We hoped to resolve these issues by sequencing whole plastid genomes for representative species and combining these with molecular data previously obtained from an expanded taxon sample. Methods: We performed paired-end Illumina sequencing of plastid genomes of 22 Viburnum species, and combined these data with a 10-gene dataset to infer phylogenetic relationships for 113 species. We used the results to devise a comprehensive phylogenetic classification and to analyze the evolution of eight morphological characters that vary among early-branching lineages. Key results: With greatly increased levels of confidence in most of the early branches, we propose a phylogenetic classification of Viburnum, providing formal phylogenetic definitions for 30 clades, including 13 with ICN names, eight with previously proposed informal names, and nine newly proposed names for major branches. Our parsimony reconstructions of bud structure, leaf margins, inflorescence form, ruminate endosperm, extrafloral nectaries, glandular trichomes, palisade anatomy, and pollen exine showed varying levels of homoplasy, but collectively provided morphological support for some, though not all, of the major clades. Conclusions: Our study demonstrates the value of next generation plastid sequencing, the ease of creating a formal phylogenetic classification, and the utility of such a system in describing patterns of character evolution.
Data from: Intra-individual polymorphism in chloroplasts from NGS data: where does it come from and how to handle it?
Next generation sequencing allows access to a large quantity of genomic data. In plants, several studies used whole chloroplast genome sequences for inferring phylogeography or phylogeny. Even though the chloroplast is a haploid organelle, NGS plastome data identified a non negligible number of intra-individual polymorphic SNPs. Such observations could have several causes such as sequencing errors, the presence of heteroplasmy or transfer of chloroplast sequences in the nuclear and mitochondrial genomes. The occurrence of allelic diversity has practical important impacts on the identification of diversity, the analysis of the chloroplast data and beyond that, significant evolutionary questions. In this study, we show that the observed intra-individual polymorphism of chloroplast sequence data is probably the result of plastid DNA transferred into the mitochondrial and/or the nuclear genomes. We further assess nine different bioinformatics pipelines' error rates for SNP and genotypes calling using SNPs identified in Sanger sequencing. Specific pipelines are adequate to deal with this issue, optimizing both specificity and sensitivity. Our results will allow a proper use of whole chloroplast NGS sequence and will allow a better handling of NGS chloroplast sequence diversity.
Data from: Chloroplast phylogenomic analyses resolve deep-level relationships of an intractable bamboo tribe Arundinarieae (Poaceae)
The temperate woody bamboos constitute a distinct tribe Arundinarieae (Poaceae: Bambusoideae) with high species diversity. Estimating phylogenetic relationships among the 11 major lineages of Arundinarieae has been particularly difficult, owing to a possible rapid radiation and the extremely low rate of sequence divergence. Here we explore the use of chloroplast genome sequencing for phylogenetic inference. We sampled 25 species (22 temperate bamboos and 3 outgroups) for the complete genome representing 8 major lineages of Arundinarieae in an attempt to resolve backbone relationships. Phylogenetic analyses of coding versus noncoding sequences, and of different regions of the genome (large and small single-copy, and inverted repeats regions) yielded no well-supported contradicting topologies but potential incongruence was found between the coding and noncoding sequences. The use of various data partitioning schemes in analysis of the complete sequences resulted in nearly identical topologies and node support values, although the partitioning schemes were decisively different from each other as to the fit to the data. Our full genomic data set substantially increased resolution along the backbone and provided strong support for most relationships despite the very short internodes and long branches in the tree. The inferred relationships were also robust to potential confounding factors (e.g., long-branch attraction) and received support from independent indels in the genome. We then added taxa from the three Arundinarieae lineages that were not included in the full-genome data set; each of these were sampled for >50% genome sequences. The resulting trees not only corroborated the reconstructed deep-level relationships but also largely resolved the phylogenetic placements of these three additional lineages. Furthermore, adding 129 additional taxa sampled for only 8 chloroplast loci to the combined data set yielded almost identical relationships, albeit with low support values. We believe that the inferred phylogeny is robust to taxon sampling. Having resolved the deep-level relationships of Arundinarieae, we illuminate how chloroplast phylogenomics can be used for elucidating difficult phylogeny at low taxonomic levels in intractable plant groups.
Data from: SiSTL1, encoding a large subunit of ribonucleotide reductase, is crucial for plant growth, chloroplast biogenesis, and cell cycle progression in Setaria italica
The activity of ribonucleotide reductase (RNR), which catalyzes the transformation of four ribonucleoside diphosphates (NDPs) to their corresponding deoxyribonucleoside diphosphates (dNDPs), is the main determiner of the cellular concentration of dNTP pools and should be tightly coordinated with DNA synthesis and cell-cycle progression. Either constitutively increased or decreased RNR activity are indeed likely to interfere with DNA replication and lead to arrested cell cycle progression; however, the mechanisms underlying these disruptive effects in higher plants remain to be uncovered. In this study, we identified a RNR large subunit mutant, sistl1, in Setaria italica (foxtail millet), that exhibited growth retardation as well as striped leaf phenotype, i.e., irregularly reduced leaf vein distances and decreased chloroplast biogenesis. We determined that a Gly737 to Glu substitution occurrring in the C-terminus of the SiSTL1 protein slightly affected its optimal function, leading in turn to the reduced expression of genes variously involved in the assembly and activation of the DNA pre-replicative complex, elongation of replication forks and S phase entry. Our study provides new insight into how SiSTL1 regulates plant growth, chloroplast biogenesis, and cell cycle progression in Poaceae crops.
Data from: Chloroplast phylogenomic data from the green algal order Sphaeropleales (Chlorophyceae, Chlorophyta) reveal complex patterns of sequence evolution
Chloroplast sequence data are widely used to infer phylogenies of plants and algae. With the increasing availability of complete chloroplast genome sequences, the opportunity arises to resolve ancient divergences that were heretofore problematic. On the flip side, properly analyzing large multi-gene data sets can be a major challenge, as these data may be riddled with systematic biases and conflicting signals. Our study contributes new data from nine complete and four fragmentary chloroplast genome sequences across the green algal order Sphaeropleales. Our phylogenetic analyses of a 56-gene data set show that analyzing these data on a nucleotide level yields a well-supported phylogeny – yet one that is quite different from a corresponding amino acid analysis. We offer some possible explanations for this conflict through a range of analyses of modified data sets. In addition, we characterize the newly sequenced genomes in terms of their structure and content, thereby further contributing to the knowledge of chloroplast genome evolution.
Data from: Measuring CO2 and HCO3- permeabilities of isolated chloroplasts using a MIMS-18O approach
To support photosynthetic CO2 fixation by Rubisco, the chloroplast must be fed with inorganic carbon in the form of CO2 or bicarbonate. However, the mechanisms allowing the rapid passage of this gas and this charged molecule through the bounding membranes of the chloroplast envelope are not yet completely elucidated. We describe here a method allowing us to measure the permeability of these two molecules through the chloroplast envelope using a membrane inlet mass spectrometer and 18O-labelled inorganic carbon. We established that the internal stromal carbonic anhydrase activity is not limiting for this technique, and precisely measured the chloroplast surface area and permeability values for CO2 and bicarbonate. This was performed on chloroplasts from several plant species, with values ranging from 2.3 × 10–4 m s–1 to 8 × 10–4 m s–1 permeability for CO2 and 1 × 10–8 m s–1 for bicarbonate. We were able to apply our method to chloroplasts from an Arabidopsis aquaporin mutant, and this showed that CO2 permeability was reduced 50% in the mutant compared with the wild-type reference.
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