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46 results for “Plastid genome”
Phylogenetic relationships of Tilia (Malvaceae) inferred from multiple nuclear loci and plastid genomes
<p class="MsoNormal"><em><span>Premise of research.</span></em><strong><span> </span></strong><em><span>Tilia</span></em><span> is a<strong> </strong>Eurasian-eastern North American disjunct plant genus with great economic and ecological importance. However, a robust phylogeny has not been established with a comprehensive taxon sampling and a large amount of data. </span></p> <p class="MsoNormal"><em><span>Methodology</span></em><span>. We obtained DNA sequences of plastomes and multiple nuclear loci using the anchored hybrid enrichment technique and next generation sequencing technology. Orthologous nuclear loci were inferred using tree-based methods. Phylogenetic analyses were performed using maximum parsimony, Bayesian, and coalescence-based species tree methods. Parentages of polyploids were inferred from the nuclear and plastid phylogenies. </span></p> <p class="MsoNormal"><em><span>Pivotal results</span></em><span>. <em>Craigia yunnanensis</em> is sister to <em>Tilia</em>, within which <em>T.</em> <em>endochrysea</em> endemic to southern China is the earliest lineage diverging followed by the European species <em>T. platyphyllos</em>. The European <em>T. cordata</em> and eastern Asian <em>T. amurensis</em> and <em>T. kiusiana </em>form a clade, while the North American <em>T. americana</em> is most closely related to the eastern and western Asian species complex including <em>T. chingiana</em>, <em>T. mandshurica</em>, <em>T. oliver</em>, and western Asian <em>T. tomentosa</em>. Significant incongruence exists between nuclear and plastid phylogenies.</span></p> <p class="MsoNormal"><em><span>Conclusions</span></em><span>. Our phylogenetic results<em> </em>suggest that there are six distinctive lineages or species complexes in the genus including 1) T. <em>endochrysea</em>, 2) <em>T. platyphyllos</em>, 3) <em>T. kiusiana</em>, 4) <em>T. cordata </em>and<em> T. amurensis</em>, 5) <em>T. chingiana</em>, <em>T. miqueliana</em>, <em>T. oliveri</em>, and 6) <em>T. tomentosa</em>, and <em>T. americana</em>. They may be divided into two sections (<em>Trichophilyra</em> and <em>Tilia</em>) and three subsections (<em>Tilia</em>, <em>Lindnera</em>, and <em>Trabeculares</em>). The prevalent incongruence between nuclear and plastid confirms the importance of ancient hybridization and introgression in the evolutionary history of the genus. Polyploid species in Eurasia and their corresponding diploid parental lineages may have formed a hybrid swarm in the region.</span></p>
Osmanthus plastid genome sequence for: Plastid genomes reveal evolutionary shifts in elevational range and flowering time of Osmanthus (Oleaceae)
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Data from: Correlation between sequence divergence and polymorphism reveals similar evolutionary mechanisms acting across multiple timescales in a rapidly evolving plastid genome
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Data from: Rapid diversification rates in Amazonian Chrysobalanaceae inferred from plastid genome phylogenetics
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Dissection for floral micromorphology and plastid genome of valuable medicinal borages Arnebia and Lithospermum (Boraginaceae)
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Plastid genome evolution in subtribe Gentianinae (Gentianaceae)
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Phylogenetic relationships of Tilia (Malvaceae) inferred from multiple nuclear loci and plastid genomes
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Data from: From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes
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Plastid genome random walks
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Data from: Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure
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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: Organellar phylogenomics inform systematics in the green algal family Hydrodictyaceae (Chlorophyceae) and provide clues to the complex evolutionary history of plastid genomes in the green algal Tree of Life.
Premise of the study: Phylogenomic analyses across the green algae are resolving relationships at the class, order and family levels, and highlighting dynamic patterns of evolution in organellar genomes. Here we present a within-family phylogenomic study to resolve genera and species relationships in the family Hydrodictyaceae (Chlorophyceae), for which poor resolution in previous phylogenetic studies, along with divergent morphological traits, have precluded taxonomic revisions. Methods: Complete plastome sequences and mitochondrial protein-coding gene sequences were acquired from representatives of the Hydrodictyaceae using Next-Generation sequencing methods. Plastomes were characterized and gene order and content were compared with plastomes spanning the Sphaeropleales. Single-gene and concatenated-gene phylogenetic analyses of plastid and mitochondrial genes were performed. Key results: The Hydrodictyaceae contain the largest sphaeroplealean plastomes thus far fully sequenced. Conservation of plastome gene order within Hydrodictyaceae is striking compared with more dynamic patterns revealed across Sphaeropleales. Phylogenetic analyses resolve Hydrodictyon sister to a monophyletic Pediastrum, though the morphologically distinct P. angulosum and P. duplex continue to be polyphyletic. Analyses of plastid data supported the neochloridacean genus Chlorotetraëdron as sister to Hydrodictyaceae, while conflicting signal was found in the mitochondrial data. Conclusions: A phylogenomic approach resolved within-family relationships not obtainable with previous phylogenetic analyses. Denser taxon sampling across Sphaeropleales is necessary to capture patterns in plastome evolution, and further taxa and studies are needed to fully resolve sister lineage to Hydrodictyaceae and polyphyly of Pediastrum angulosum and P. duplex.
Data from: Evolutionary origin of highly repetitive plastid genomes within the clover genus (Trifolium)
Background: Some clover species, particularly Trifolium subterraneum, have previously been reported to have highly unusual plastomes, relative to closely related legumes, enlarged with many duplications, gene losses and the presence of DNA unique to Trifolium, which may represent horizontal transfer. In order to pinpoint the evolutionary origin of this phenomenon within the genus Trifolium, we sequenced and assembled the plastomes of eight additional Trifolium species widely sampled from across the genus. Results: The Trifolium plastomes fell into two groups: those of Trifolium boissieri, T. strictum and T. glanduliferum (representing subgenus Chronosemium and subg. Trifolium section Paramesus) were tractable, assembled readily and were not unusual in the general context of Fabeae plastomes. The other Trifolium species ("core Trifolium") proved refractory to assembly mainly because of numerous short duplications. These species form a single clade, which we call the "refractory clade" (comprising subg, Trifolium sections Lupinaster, Trifolium, Trichocephalum, Vesicastrum and Trifoliastrum). The characteristics of the refractory clade are the presence of numerous short duplications and 7-15% longer genomes than the tractable species. Molecular dating estimates that the origin of the most recent common ancestor (MRCA) of the refractory clade is approximately 13.1 million years ago (MYA). This is considerably younger than the estimated MRCA ages of Trifolium (c. 18.6 MYA) andTrifolium subg. Trifolium (16.1 MYA). Conclusions: We conclude that the unusual repetitive plastome type previously characterized in Trifolium subterraneum had a single origin within Trifolium and is characteristic of most (but not all) species of subgenus Trifolium. It appears that an ancestral plastome within Trifolium underwent an evolutionary change resulting in plastomes that either actively promoted, were permissive to, or were unable to control, duplications within the genome. The precise mechanism of this important change in the mode and tempo of plastome evolution deserves further investigation.
Plastid genome structure and phylogenomics of Nymphaeales: conserved gene order and new insights into relationships
<p>The plastid genomes of early-diverging angiosperms were among the first land plant plastomes investigated. Despite their importance to understanding angiosperm evolution, no investigation has so far compared gene content or gene synteny of these plastid genomes with a focus on the Nymphaeales. Here, we report an evaluation and comparison of gene content, gene synteny and inverted repeat length for a set of 15 plastid genomes of early-diverging angiosperms. Seven plastid genomes of the Nymphaeales were newly sequenced for this investigation. We compare gene order and inverted repeat (IR) length across all genomes, review the gene annotations of previously published genomes, generate a multi-gene alignment of 77 plastid-encoded genes and reconstruct the phylogenetic relationships of the taxa under study. Our results show that gene content and synteny are highly conserved across early-diverging angiosperms: All species analyzed display complete gene synteny when accounting for expansions and contractions of the IRs. This conservation was initially obscured by ambiguous and potentially incorrect gene annotations in previously published genomes. We also report the presence of intact open reading frames across all taxa analyzed. The multi-gene phylogeny displays maximum support for the families Cabombaceae and Hydatellaceae, but no support for a clade of all Nymphaeaceae. It further indicates that the genus <em>Victoria</em> is embedded within <em>Nymphaea</em>. Plastid genomes of <em>Trithuria</em> were found to deviate by numerous substitutions and length changes in the IRs. Phylogenetic analyses further indicate that a previously published plastome named <em>Nymphaea mexicana</em> falls into a clade of <em>N. odorata</em> and should be re-evaluated.</p>
Plastid genome evolution in leafless members of the orchid subfamily Orchidoideae, with a focus on Degranvillea dermaptera
<p><strong>Premise</strong>: Leafless, heterotrophic plants are prime examples of organismal modification, the genomic consequences of which have received considerable interest. In particular, plastid genomes (plastomes) are being sequenced at a high rate, allowing continual refinement of conceptual models of reductive evolution in heterotrophs. Yet, numerous sampling gaps exist, hindering the ability to conduct comprehensive phylogenomic analyses in these plants. </p><p><strong>Methods</strong>: We sequenced and analyzed the plastome of <i>Degranvillea dermaptera</i>, a rarely collected, leafless orchid species from South America about which little is known, including its phylogenetic affinities. </p><p><strong>Key Results</strong>: We revealed the most reduced plastome sequenced to date among the orchid subfamily Orchidoideae. <i>Degranvillea</i> has lost the majority of genes found in leafy autotrophic species, is structurally rearranged, and has similar gene content to the most reduced plastomes among the orchids. We found strong evidence for the placement of <i>Degranvillea</i> within the subtribe Spiranthinae using models that explicitly account for heterotachy, or lineage-specific evolutionary rate variation over time. We further found evidence of relaxed selection on several genes and correlations among substitution rates and several other "traits" of the plastome among leafless members of orchid subfamily Orchidoideae. </p><p><strong>Conclusions</strong>: Our findings advance knowledge on the phylogenetic relationships and paths of plastid genome evolution among the orchids, which have experienced more independent transitions to heterotrophy than any other plant family. This study demonstrates the importance of herbarium collections in comparative genomics of poorly known species of conservation concern. </p>
Sequencing of historical plastid genomes reveal exceptional genetic diversity in rye before the start of systematic breeding
<p>The files found in this repository are sequencing files of historical rye samples used for generating the analyses presented in the Komluski et al. manuscript. The metadata.csv contains sampling sites and taxon information for the respective sequence file.</p>
Fig. 2 in Plastid genome of Aster altaicus var. uchiyamae Kitam., an endanger species of Korean asterids
Fig. 2. The secondary structure of ψ-trnT_GGU of Aster altaicus var. uchiyamae and A. spathulifolius compared to that of normal trnT_ GGU gene. Variable sequences were marked in red.
Data from: Organellar phylogenomics inform systematics in the green algal family Hydrodictyaceae (Chlorophyceae) and provide clues to the complex evolutionary history of plastid genomes in the green algal Tree of Life.
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Data from: Genus-wide screening reveals four distinct types of structural plastid genome organization in Pelargonium (Geraniaceae)
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Data from: Comparative analysis of Begonia plastid genomes and their utility for species-level phylogenetics
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.