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72 results for “plastome”
Data from the article "Plastome sequencing of South American Podocarpus species reveals low rearrangement rates despite ancient Gondwanan disjunctions"
<p>Input data, intermediate and final analysis output files associated to the manuscript "Plastome sequencing of South American <em>Podocarpus </em>species reveals low rearrangement rates despite ancient Gondwanan disjunctions"</p> <p>We sequenced the plastomes of four South American species of <em>Podocarpus</em> from Patagonia, southern Yungas, and Brazilian subtropical forests: <em>P. nubigenus, P. parlatorei, P. salignus </em>and <em>P. selowii</em>. We compared their plastomes to those published from Brazil, Africa, New Zealand, and Southeast Asia, along with representatives from other genera within Podocarpaceae as outgroups. The four newly sequenced plastomes ranged in size between 133,791 bp and 133,991 bp. Gene content and order among chloroplasts from South American, African and Asian <em>Podocarpus</em> were conserved and different from the plastome of <em>P. totara</em>, from New Zealand. Most genes showed substitution patterns consistent with a conservative selective regime. Phylogenies inferred from either complete sequences or protein coding regions were mostly congruent with previous studies, but showed earlier branching of <em>P. salignus</em>, <em>P. totara</em> and <em>P. sellowii</em>.</p>
The chloroplast genomes of Sanicula (Apiaceae): plastome structure, comparative analyses, and phylogenetic relationships
<p><em>Sanicula</em> (Apiaceae subfamily Saniculoideae) is a taxonomically difficult genus of medicinal value. Its distribution center is in China, where there are 18 species (11 of which are endemic). To provide plastid genome resources, whole chloroplast genomes of five <em>Sanicula</em> species (<em>S. flavovirens</em>, <em>S. giraldii</em>, <em>S. lamelligera</em>, <em>S. odorata</em>, and <em>S. rubriflora</em>) were sequenced and compared to the previously published <em>S. orthacantha</em> plastome. These genomes exhibit a typical quadripartite structure. All contain 129 different genes, including 84 protein-coding, 37 tRNA, and 8 rRNA genes. Loci <em>rpl2</em>, <em>matK</em>, <em>psbA</em>, and <em>ycf1</em> are the most variable. Results of maximum likelihood analysis of 90 whole plastome sequences from Apioideae and Saniculoideae and the outgroup <em>Hydrocotyle</em> (Araliaceae) reveal sectional relationships in <em>Sanicula</em> different from the traditional classification system, support the monophyly of Apioideae and its sister group relationship to Saniculoideae, and show concordant topologies to nrDNA ITS and other plastome-based phylogenies. <em>Sanicula orthacantha</em> and <em>S. chinensis</em> form a clade sister group to <em>S. lamelligera</em> and <em>S. odorata</em>, consecutively. These four species comprise a clade sister group to the clade of <em>S. rubriflora</em> and <em>S. flavovirens</em>, with this entire group sister to <em>S. giraldii</em>. The plastid genome resources provided herein will be important for future systematic, evolutionary, phylogenomic, and population-level studies of <em>Sanicula</em>.</p>
Linked collectors and determiners for: Refining the phylogeny and taxonomy of the apple tribe Maleae (Rosaceae): insights from phylogenomic analyses of 563 plastomes and a taxonomic synopsis of Photinia and its allies in the Old World.
Natural history specimen data linked to collectors and determiners held within, "Refining the phylogeny and taxonomy of the apple tribe Maleae (Rosaceae): insights from phylogenomic analyses of 563 plastomes and a taxonomic synopsis of Photinia and its allies in the Old World". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/aa8d91fe-6fe4-4c59-8831-8103148e66f4">https://bionomia.net/dataset/aa8d91fe-6fe4-4c59-8831-8103148e66f4</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/aa8d91fe-6fe4-4c59-8831-8103148e66f4">https://gbif.org/dataset/aa8d91fe-6fe4-4c59-8831-8103148e66f4</a>. Formatted as a Frictionless Data package.
Pandanaceae Plastome Phylogenetics Project Files
<p>RAxML Tree: PartitionedMLPlastome.tree</p> <p>BEAST Tree: med_Wojahn_Pandanaceae_Plastome_2024.tree</p> <p>Alignment: AlignedRevCompGood.fasta</p>
The chloroplast genomes of Sanicula (Apiaceae): plastome structure, comparative analyses, and phylogenetic relationships
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Data from: Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex
Heterotrophic plants provide excellent opportunities to study the effects of altered selective regimes on genome evolution. Plastid genome (plastome) studies in heterotrophic plants are often based on one or a few highly divergent species or sequences as representatives of an entire lineage, thus missing important evolutionary-transitory events. Here we present the first infraspecific analysis of plastome evolution in any heterotrophic plant. By combining genome skimming and targeted sequence capture, we address hypotheses on the degree and rate of plastome degradation in a complex of leafless orchids (Corallorhiza striata) across its geographic range. Plastomes provide strong support for relationships and evidence of reciprocal monophyly between C. involuta and the endangered C. bentleyi. Plastome degradation is extensive, occurring rapidly over a few million years, with evidence of differing rates of substitution among the two principal clades of the complex. Genome skimming and targeted sequence capture differ widely in coverage depth overall, with depth in targeted sequence capture datasets varying immensely across the plastome as a function of GC content. These findings will help fill a knowledge gap in models of heterotrophic plastid genome evolution, and have implications for future studies in heterotrophs.
Data from: Plastome phylogenetics of tribe Eriachneae and evolution of C₄ photosynthesis in subfamily Micrairoideae (Poaceae)
Tribe Eriachneae in subfamily Micrairoideae is one of the least explored of the ca. 22 C4 lineages in the grass family (Poaceae). Whereas many C4 lineages are more species-rich, more morphologically disparate, and wider ranging than their C3 sisters, Eriachneae has fewer species, less disparity, and covers a far smaller geographical area than its C3 sister tribe Isachneae. Tribe Micraireae, which is C3 and sister to Eriachneae and Isachneae, occupies habitats more similar to C4 Eriachneae than C3 Isachneae. Evolutionary analyses within the subfamily are hindered by the lack of a phylogenetic framework for any substantial sample of species. Additionally, only a handful of members of Micrairoideae have been tested for photosynthetic pathway. This study presents the first well-resolved phylogeny of Eriachneae based on full plastome sequences from almost half of the species in the tribe. Photosynthetic pathway is tested for 47 species representing all three tribes of Micrairoideae using carbon isotopes to test the assumption that C4 is restricted to Eriachneae. Habitat preferences among the tribes are estimated using bioclimatic data, with multivariate analyses showing that habitats of Micraireae and Eriachneae are more similar to each other than either is to Isachneae, and the range of environments is greater in Isachneae than in Eriachneae. All measured Eriachneae are confirmed to be C4, and all Isachneae are C3. Evolutionary interpretation of these results is necessarily preliminary, and greater phylogenetic sampling in Isachneae is needed to estimate diversification rates and ancestral habitats, but subfamily Micrairoideae appears to be an interesting exception to general patterns of C4 evolution in grasses.
Plastid introgression and evolution of African miombo woodlands: new insights from the plastome-based phylogeny of Brachystegia trees
<p><strong>Aim</strong>: Miombo woodlands form a characteristic vegetation type covering 2.7 million km<sup>2</sup> in southern and eastern Africa. Despite their wide geographical extent, their origin, floristic and spatial evolution through time remain understudied. To fill this gap, we studied the evolution of <em>Brachystegia</em> trees, one of the most representative genera of these woodlands (20 species), also represented in Guineo-Congolian rain forests (8 species).</p> <p><strong>Location</strong>: Tropical Africa, Guineo-Congolian forests and Zambezian savannahs.</p> <p><strong>Methods</strong>: We used a genome skimming approach to sequence the plastomes of 45 <em>Brachystegia</em> samples, covering 25 of the 29 existing species, and one outgroup (<em>Julbernardia paniculata</em>). The phylogeny of the plastomes was reconstructed and time-calibrated. We tested if the genetic divergence between lineages reflected taxonomic and/or geographic distances using Mantel tests. Finally, we inferred the evolutionary history of <em>Brachystegia</em> based on the age and spatial distribution of its lineages.</p> <p><strong>Results</strong>: Surprisingly, species represented by multiple specimens appear rarely monophyletic while plastid clades display strong geographical structuring, independently of the species. Two main clades separate woodland and rain forest species, which diverged during the late Miocene-Pliocene (95% HPD = 2.78-8.59 Ma). In miombo woodlands, three subclades occur in parapatry along an East-West axis, ranging from Angola to East Africa. Their divergence started from the Plio-Pleistocene (95% HPD = 1.17-3.69 Ma). Divergence dates (TMRCA) within miombo subclades decrease from East Africa (1.53 Ma) to Angola (0.76 Ma).</p> <p><strong>Main Conclusions</strong>: <em>Brachystegia</em> plastomes appear unreliable to identify species, probably due to species introgression leading to recurrent chloroplast captures. However, they prove very informative for tracking the past dynamics of the genus, and suggest a historical westwards expansion of miombo <em>Brachystegia</em>, and possibly of miombo vegetation, during the Plio-Pleistocene. Further investigations using nuclear DNA are needed to assess the species tree as well as speciation and hybridisation events between species. </p>
Data from: Resolution, conflict and rate shifts: Insights from a densely sampled plastome phylogeny for Rhododendron (Ericaceae)
<p><strong>Background and Aims</strong> <em>Rhododendron </em>is a species-rich and taxonomically challenging genus due to recent adaptive radiation and frequent hybridization. A well-resolved phylogenetic tree would help to understand the diverse history of <em>Rhododendron </em>in the Himalaya–Hengduan Mountains where the genus is most diverse.</p> <p><strong>Methods </strong>We reconstructed the phylogeny based on plastid genomes with broad taxon sampling, covering 161 species representing all eight subgenera and all 12 sections, including ~45 % of the <em>Rhododendron </em>species native to the Himalaya–Hengduan Mountains. We compared this phylogeny with nuclear phylogenies to elucidate reticulate evolutionary events and clarify relationships at all levels within the genus. We also estimated the timing and diversification history of <em>Rhododendron</em>, especially the two species-rich subgenera <em>Rhododendron</em> and <em>Hymenanthes </em>that comprise >90 % of <em>Rhododendron </em>species in the Himalaya–Hengduan Mountains.</p> <p><strong>Key Results </strong>The full plastid dataset produced a well-resolved and supported phylogeny of <em>Rhododendron</em>. We identified 13 clades that were almost always monophyletic across all published phylogenies. The conflicts between nuclear and plastid phylogenies strongly suggested that reticulation events may have occurred in the deep lineage history of the genus. Within <em>Rhododendron</em>, subgenus <em>Therorhodion </em>diverged first at 56 Mya, then a burst of diversification occurred from 23.8 to 17.6 Mya, generating ten lineages among the component 12 clades of core <em>Rhododendron</em>. Diversification in subgenus <em>Rhododendron </em>accelerated c. 16.6 Mya and then became fairly continuous. Conversely, <em>Hymenanthes </em>diversification was slow at first, then accelerated very rapidly around 5 Mya. In the Himalaya–Hengduan Mountains, subgenus <em>Rhododendron </em>contained one major clade adapted to high altitudes and another to low altitudes, whereas most clades in <em>Hymenanthes </em>contained both low- and high-altitude species, indicating greater ecological plasticity during its diversification.</p> <p><strong>Conclusions </strong>The 13 clades proposed here may help to identify specific ancient hybridization events. This study will help to establish a stable and reliable taxonomic framework for <em>Rhododendron</em>, and provides insight into what drove its diversification and ecological adaption. Denser sampling of taxa, examining both organelle and nuclear genomes, is needed to better understand the divergence and diversification history of <em>Rhododendron</em>.</p>
The alignment of 163 plastome haplotypes of East Asian Cerris oaks and 29 plastomes of related oak species
<p>This dataset includes the alignment of 163 plastome haplotypes of East Asian Cerris oaks and 29 plastomes of related oak species. The alignment was generated through four steps: (1) We used PhyloSuite v.1.2.2 to extract protein-coding genes (PCGs), tRNA genes, rRNA genes, introns, and intergenic spacers (IGSs) from the plastomes of 761 East Asian Cerris oak trees and 29 accessions of 22 related oak species. (2) The extracted regions were aligned individually with MAFFT v.7.313 and adjusted manually using BioEdit v.7.2.5. Specifically, inversions and length variations in simple sequence repeats were excluded because of their tendency for homoplasy. Eight ambiguously aligned regions in rps16-trnQ, psbM-trnD, ndhF-rpl32, rpl32-trnL, ndhD-psaC, and psaC-ndhE IGSs, and ndhF and ycf1 PCGs were also discarded to reduce phylogenetic noise. (3) The individual alignments were concatenated according to their respective positions in the plastome to generate a whole-plastome alignment with only one inverted repeat (IR) retained. (4) Unique plastome haplotypes were determined by DnaSP v.5.10.01.</p>
Genome-scale angiosperm phylogenies based on nuclear, plastome, and mitochondrial datasets
<p>Angiosperms dominate the Earth's ecosystems and provide most of the basic necessities for human life. The major angiosperm clades comprise 64 orders, as recognized by the APG IV classification. However, the phylogenetic relationships of angiosperms remain unclear, as phylogenetic trees with different topologies have been reconstructed depending on the sequence datasets utilized, from targeted genes to transcriptomes. Here, we used currently available <em>de novo</em> genome data to reconstruct the phylogenies of 366 angiosperm species from 241 genera belonging to 97 families across 43 of the 64 orders based on orthologous genes from the nuclear, plastid, and mitochondrial genomes of the same species with compatible datasets. The phylogenetic relationships were largely consistent with previously constructed phylogenies based on sequence variations in each genome type. However, there were major inconsistencies in the phylogenetic relationships of the five Mesangiospermae lineages when different genomes were examined. We discuss ways to address these inconsistencies, which could ultimately lead to the reconstruction of a comprehensive angiosperm tree of life. The angiosperm phylogenies presented here provide a basic framework for further updates and comparisons. These phylogenies can also be used as guides to examine the evolutionary trajectories among the three genome types during lineage radiation. </p>
A plastome phylogeny of Rumex (Polygonaceae) illuminates the divergent evolutionary histories of docks and sorrels
<p>The genus <em>Rumex</em> L. (Polygonaceae) provides a unique system for investigating the evolutionary development of sex determination and molecular rate evolution. Historically, <em>Rumex</em> has been divided, both taxonomically and colloquially into two groups: 'docks' and 'sorrels'. A well-resolved phylogeny can help evaluate a genetic basis for this division. Here we present a plastome phylogeny for 34 species of <em>Rumex</em>, inferred using maximum likelihood criteria. The historical 'docks' (<em>Rumex</em> subgenus <em>Rumex</em>) were resolved as monophyletic. The historical 'sorrels' (<em>Rumex</em> subgenera <em>Acetosa</em> and <em>Acetosella</em>) were resolved together, though not monophyletic due to the inclusion of <em>R. bucephalophorus</em> (<em>Rumex</em> subgenus <em>Platypodium</em>). <em>Emex</em> is supported as its own subgenus within <em>Rumex</em>, instead of resolved as sister taxa. We found remarkably low nucleotide diversity among the docks, consistent with recent diversification in that group, especially as compared to the sorrels. Fossil calibration of the phylogeny suggested that the common ancestor for <em>Rumex</em> (including <em>Emex</em>) has origins in the lower Miocene (22.13 MYA). The sorrels appear to have subsequently diversified at a relatively constant rate. The origin of the docks, however, was placed in the upper Miocene, but with most speciation occurring in the Plio-Pleistocene.</p>
Phylogenomics of mulberries (Morus, Moraceae) inferred from plastomes and single copy nuclear genes
<p><span>Mulberry (genus <em>Morus</em>), belonging to the order Rosales, family Moraceae, is an important woody plant due to its economic value in sericulture as well as for its nutritional benefits and medicinal values. However, the taxonomy and phylogeny of <em>Morus</em> remain challenging due to its wide geographical distribution, morphological plasticity, and interspecific hybridization. To better understand the evolutionary history of <em>Morus</em>, we combined plastomes and a large-scale nuclear gene to investigate their phylogenetic relationships in the present study. We assembled the plastomes and screened 211 single-copy nuclear genes from 14 <em>Morus</em> species and related taxa. The plastomes of <em>Morus</em> species were relatively conserved in terms of genome size, gene content and order, IR boundary and codon usage. Using nuclear data, we yielded completely identical topologies based on coalescent and concatenation methods, and multiple individuals of the same species were intraspecific monophyletic. The genus <em>Morus</em> was supported as a monophyly, and <em>M. notabilis</em> was recovered as the first diverging, and the two North American <em>Morus</em> species, <em>M. celtidifolia</em> and <em>M. rubra</em>, were sister to the other Asian species. However, the relationships of <em>Morus</em> based on plastomes were strongly incongruent with those from nuclear genes, and intraspecific non-monophyly was retrieved in the plastid phylogeny. Comparisons of nuclear and plastid phylogenies, and combining with the result of network inference, hybridization/introgression was regarded as the main cause of the discordance between nuclear and plastid phylogenies in the genus <em>Morus</em>. Overall, the robust phylogenetic relationships of <em>Morus</em> described here will be useful for genetic resources development of this economically important genus and exploitation of sericulture industry.</span></p>
Genome-scale angiosperm phylogenies based on nuclear, plastome, and mitochondrial datasets
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Re-annotated genomes for plastomes and mitogenomes
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Multiple alignment data for diatom plastomes and mitogenomes
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Data from: Resolution, conflict and rate shifts: Insights from a densely sampled plastome phylogeny for Rhododendron (Ericaceae)
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Data from: Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex
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Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages
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A plastome phylogeny of Rumex (Polygonaceae) illuminates the divergent evolutionary histories of docks and sorrels
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Allen Brain Atlas
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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.