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302 results for “plastid”
Data from: Pleistocene climate change and phylogeographic structure of the Gymnocarpos przewalskii (Caryophyllaceae) in the northwest China: Evidence from plastid DNA, ITS sequences, and Microsatellite
Northwestern China has a wealth of endemic species, which has been hypothesized to be affected by the complex paleoclimatic and paleogeographic history during Quaternary. In this paper, we used Gymnocarpos przewalskii as a model to address the evolutionary history and current population genetic structure of species in northwestern China. We employed two chloroplast DNA fragments (rps16 and psbB‐psbI), one nuclear DNA fragment (ITS), and simple sequence repeat (SSRs) to investigate the spatial genetic pattern of G. przewalskii. High genetic diversity (cpDNA: hS = 0.330, hT = 0.866; ITS: hS = 0.458, hT = 0.872) was identified in almost all populations, and most of the population have private haplotypes. Moreover, multimodal mismatch distributions were observed and estimates of Tajima's D and Fu's FS tests did not identify significantly departures from neutrality, indicating that recent expansion of G. przewalskii was rejected. Thus, we inferred that G. przewalskii survived generally in northwestern China during the Pleistocene. All data together support the genotypes of G. przewalskii into three groups, consistent with their respective geographical distributions in the western regions—Tarim Basin, the central regions—Hami Basin and Hexi Corridor, and the eastern regions—Alxa Desert and Wulate Prairie. Divergence among most lineages of G. przewalskii occurred in the Pleistocene, and the range of potential distributions is associated with glacial cycles. We concluded that climate oscillation during Pleistocene significantly affected the distribution of the species.
Data from: Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure
PREMISE OF THE STUDY: There is a misinterpretation in the literature regarding the variable orientation of the small single copy region of plastid genomes (plastomes). The common phenomenon of small and large single copy inversion, hypothesized to occur through intramolecular recombination between inverted repeats (IR) in a circular, single unit-genome, in fact more likely occurs through recombination-dependent replication (RDR) of linear plastome templates. If RDR can be primed through both intra- and intermolecular recombination, then this mechanism could not only create inversion isomers of so-called single copy regions, but also an array of alternative sequence arrangements. METHODS: We used Illumina paired-end and PacBio single-molecule real-time (SMRT) sequences to characterize repeat structure in the plastome of Monsonia emarginata L'Hér. (Geraniaceae). We used OrgConv and inspected nucleotide alignments to infer ancestral nucleotides and identify gene conversion among repeats and mapped long (>1 kb) SMRT reads against the unit-genome assembly to identify alternative sequence arrangements. RESULTS: Although M. emarginata lacks the canonical IR, we found that large repeats (>1 kilobase; kb) represent ~22% of the plastome nucleotide content. Among the largest repeats (>2 kb) we identified GC-biased gene conversion and mapping filtered, long SMRT reads to the M. emarginata unit-genome assembly revealed alternative, substoichiometric sequence arrangements. CONCLUSION: We offer a model based on RDR and gene conversion between long repeated sequences in the M. emarginata plastome, and provide support that both intra-and intermolecular recombination between large repeats, particularly in repeat-rich plastomes, varies unit-genome structure while homogenizing the nucleotide sequence of repeats.
Data from: Strong nuclear differentiation contrasts with widespread sharing of plastid DNA haplotypes across taxa in European purple saxifrages (Saxifraga sect. Porphyrion subsect. Oppositifoliae)
The purple saxifrages, Saxifraga sect. Porphyrion subsect. Oppositifoliae, comprise the closest relatives of the arctic-alpine model plant S. oppositifolia and have a centre of diversity in the central and southern European mountain ranges. A multitude of taxa has been described and taxonomic concepts vary among different treatments. Using amplified fragment length polymorphism (AFLP) fingerprinting we show that some taxa indeed form strongly supported genetic entities best recognized on the species level (S. biflora, S. blepharophylla, S. retusa, S. rudolphiana, S. speciosa), while others (S. murithiana, S. paradoxa) are not genetically divergent at all. Saxifraga oppositifolia s. s. is phylogenetically incoherent. Plastid DNA sequence data show very limited congruence with the predominantly nuclear-derived AFLPs. Several co-distributed taxa (S. biflora, S. blepharophylla, S. oppositifolia s. s., S. retusa) share the same set of haplotypes. In the widespread species S. oppositifolia and S. retusa, highly divergent haplotype lineages were discovered, which exhibit a geographic rather than taxonomic structure. Recent and ancient hybridization and/or lineage sorting are likely responsible for the strong incongruence between data derived from nuclear and plastid genomes. Hybridization, which is known to occur among almost all taxa of this group when growing in sympatry, seems, however, insufficient to break down species barriers.
Hoarding and horizontal transfer led to an expanded gene and intron repertoire in the plastid genome of the diatom, Toxarium undulatum (Bacillariophyta)
<p>Multiple sequence alignments used to produce Figure 2</p>
Proximity to Photosystem II is necessary for activation of Plastid Terminal Oxidase (PTOX) for photoprotection
<p>TEM and Confocal micrographs images of Arabidopsis thaliana (wt or mutants) and Eutrema salsugineum (wt) plants exposed to control or high light treatments. </p>
FIGURE 5 in The fundamental karyotype and plastid DNA of Alstroemeria piperata (Liliales, Alstroemeriaceae), a species endemic to the Valparaíso Region, Chile
FIGURE 5. Phylogenetic relationships from analyses of three plastid markers (petA-psbJ, trnL-rpl32 and intron rpl16) of Alstroemeria piperata and other Chilean alstroemerias (Baeza et al. 2022). A. Network inferred with TCS. B. Maximum likelihood tree inferred from DNA sequences and indels. The branch lengths in B were modified for aesthetic reasons.
Microsatellite (13 loci) and plastid DNA haplotypes in a population of Antirrhinum charidemi
<p>Genotype matrix of 182 Antirrhinum charidemi individuals sampled in 2007-2009 in the Barranco del Dragoncillo Blanco population in Cabo de Gata, Almería, Spain. Genotypes are given for 13 microsatellite loci and also include 3 plastid DNA haplotypes. Details on loci and genotyping conditions can be found in Forrest et al. 2017, https://doi.org/10.1093/botlinnean/bow002. Each individual is geolocated. Additional information include its corolla colour, its ancestry score in four gene pools obtained in Bayesian genetic cluster analysis (STRUCTURE), and its assignment to geo-genetic subpopulations. Metadata are available in a separate tab in the submitted spreadsheet. The data are analysed in a paper expected to be published in AoB Plants in 2025, titled: "Fine-scale genetic differentiation in the bee-specialized Antirrhinum charidemi covaries more strongly with microenvironment than with corolla colour"</p>
FIGURE. Bayesian tree based on combined plastid (matK, trnL-trnF) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches in Hedysarum sunhangii (Fabaceae, Hedysareae), a new species from Pamir-Alay (Babatag Ridge - Uzbekistan)
FIGURE. Bayesian tree based on combined plastid (matK, trnL-trnF) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches
Plastid genome evolution in subtribe Gentianinae (Gentianaceae)
<p>We investigated plastome evolution in Subtribe Gentianinae of the Gentianaceae, which encompasses ca. 450 species distributed around the world, particularly in alpine and subalpine environments. We sequenced, assembled and annotated the plastomes of 41 species, representing all six genera in subtribe Gentianinae as well as all 14 sections of the species-rich genus <i>Gentiana</i>. Here, we upload (1) original alignments, Gblock alignments and tree topology file in phylogenetic analysis, and (2) results about a 5 kb insertion in <em>Gentiana</em> <i>cuneibarba</i>, including Sanger sequencing results which verified its two boundaries as well as the middle, and annotation results.</p>
Phylogeny of the ingoid clade (Caesalpinioideae, Fabaceae), based on nuclear and plastid data
<p>We investigated generic relationships in the ingoid clade (Fabaceae) (sensu Koenen & al. 2020a), with main focus on genera with a taxonomic history in <i>Calliandra</i> s.l. of the tribe Ingeae (i.e. <i>Afrocalliandra</i>, <i>Calliandra</i> s.s., <i>Sanjappa</i>,<i>Thailentadopsis</i>,<i> Viguieranthus,</i> <i>Zapoteca</i>), and three genera of the tribe Acacieae (i.e., <i>Acacia</i>, <i>Acaciella, Senegalia</i>). The nuclear ribosomal ETS and ITS, and the plastid <i>matK</i>, <i>trnL</i>-<i>trnF </i>and <i>ycf1 </i>DNA-regions were analysed for 246 representatives from 36 genera using maximum likelihood as implemented in IQ-tree. The results show an Ingeae–<i>Acacia </i>clade within the ingoid clade, resolved in three major clades. Clade 1 (<i>Calliandra</i> s.s. and <i>Afrocalliandra</i>) is sister to clades 2 and 3. Clade 2 comprises <i>Faidherbia</i>, <i>Sanjappa</i>, <i>Thailentadopsis</i>, <i>Viguieranthus</i> and <i>Zapoteca</i>. Clade 3 comprises the remaining genera of the Ingeae, plus <i>Acacia</i>. The ingoid genus <i>Senegalia</i> is excluded from the Ingeae–<i>Acacia </i>clade. <i>Acaciella </i>is sister to the remaining ingoid clade when nuclear ribosomal data is included in the analyses, but included in the Ingeae–<i>Acacia</i> clade based on plastid data. <i>Acacia </i>and perhaps also <i>Acaciella </i>are thus nested within Ingeae. Species traditionally referred to <i>Calliandra </i>(<i>Calliandra</i> s.l.) are resolved in two clades, and the "<i>Calliandra</i>-pod" has apparently evolved independently several times.</p>
Untying the Gordian Knot of plastid phylogenomic conflict: a case from ferns
<p>Phylogenomic studies based on plastid genome have resolved the recalcitrant relationships among various plants, yet the phylogeny of Dennstaedtiaceae at the taxonomic level remains unresolved due to conflicting plastid genes, limited molecular data and incomplete taxon sampling of previous studies. The present study generated 31 new plastid genomes of Dennstaedtiaceae (9 genera, 30 species) and combined 41 publicly available sequences of plastid genome (including 24 families, 26 genera, 41 species) to solve and explore the evolution of Dennstaedtiaceae. In order to minimize the impact of systematic errors on the resolution of phylogenetic inference, we applied six strategies to generate 30 datasets based on CDS, Spacer, and All datasets, and two tree inference methods (maximum-likelihood, ML; and multispecies coalescent, MSC) to comprehensively analyze the plastome-scale data. Besides, the phylogenetic signal among all loci was quantified for the controversial node using the ML framework, and the phylogenetic hypotheses among all datasets were tested. In the species tree based on different data sets and methods, obvious conflicts were detected at the base of the polypod ferns. Meanwhile, the topology of the "CDS-codon-align-rm3" (CDS removed the third codon) matrix was selected as the primary reference or summary tree due to its analysis results are consistent, and similar to the topological structure of the amino-acid matrix. The final phylogenetic tree supported Dennstaedtiaceae as the sister group to eupolypods, and<em> Dennstaedtia</em> (sen. lat.) can divided into smaller genera, which was also supported by geographical distribution and plastid structure. This robust reconstructed phylogenetic backbone established a framework for future studies on Dennstaedtiaceae classification, evolution and diversification. The present study suggests considering plastid phylogenomic conflict when using plastid genomes. From our results, reducing saturated genes or sites can effectively mitigate the tree conflicts of distantly related taxa. Moreover, amino acid sequences may verify the accuracy of nucleotide-based phylogeny.</p>
Variation in frequency of plastid RNA editing within Adiantum (Pteridaceae) implies rapid evolution in fern plastomes
<p>Premise</p> <p>Recent advances in studies of plant RNA editing have demonstrated that the number of editing sites can vary widely among large taxonomic groups (orders, families). Yet, very little is known about intrageneric variation in frequency of plant RNA editing, and no study has been conducted in ferns.</p> <p>Methods</p> <p>We determined plastid RNA editing counts for two species of Adiantum (Pteridaceae), A. shastense and A. aleuticum, by implementing a pipeline that integrated read mapping and SNP calling software to identify RNA editing sites. We then compared the edits found in A. aleuticum and A. shastense with previously published edits from A. capillus-veneris by generating alignments for each plastid gene.</p> <p>Results</p> <p>We found direct evidence for 505 and 509 plastid RNA editing sites in A. aleuticum and A. shastense, respectively, compared with 350 sites in A. capillus-veneris. We observed striking variation in the number and location of the RNA editing sites among the three species, with reverse (U-to-C) editing sites showing a higher degree of conservation than forward (C-to-U) sites. Additionally, sites involving start and stop codons were highly conserved.</p> <p>Conclusions</p> <p>Variation in RNA editing frequency observed within Adiantum implies that RNA editing sites can be rapidly gained or lost throughout evolution. However, varying degrees of conservation between both C-to-U and U-to-C sites and sites in start or stop codons, versus other codons, hints at the likely independent origin of both types of edits and a potential selective advantage conferred by RNA editing.</p>
Plastid phylogenomics of tribe Perseeae (Lauraceae) yields insights into the evolution of East Asian subtropical evergreen broad-leaved forests
<p><b>Background:</b> The East Asian subtropical evergreen broad-leaved forests (EBLFs) harbor remarkable biodiversity. However, their historical assembly remains unclear. To gain new insights into the assembly of this biome, we generated a molecular phylogeny of one of its essential elements, the tribe Perseeae (Lauraceae).</p> <p><b>Results: </b>Our plastid tree topologies were robust to analyses based on different plastid regions, data partitioning, nucleotide substitution saturation and gap handling strategies. We found that Perseeae comprised six major clades and started to colonize the subtropical EBLFs of east Asia in the early Miocene. The diversification rates of Perseeae accelerated twice in the late Miocene.</p> <p><b>Conclusions: </b>Our findings suggest that the intensified precipitation in East Asia in the early Miocene might have facilitated range expansions of the drought-sensitive subtropical EBLFs and establishment of Perseeae within this biome. By the late Miocene, assembly and diversification within the EBLFs had become rapid.</p>
FIGURE 6 in Miliusa microphylla (Annonaceae), a new species from Thailand as evidenced by morphology and plastid phylogeny, with M. glandulifera, a new record for Thailand
FIGURE 6. Specimen of Miliusa glandulifera collected from Kui Buri National Park, Thailand (Kaitongsuk et al. 241 [SN222215], BKF; = Miliusa glandulifera 1 in Fig. 1).
FIGURE 5 in Miliusa microphylla (Annonaceae), a new species from Thailand as evidenced by morphology and plastid phylogeny, with M. glandulifera, a new record for Thailand
FIGURE 5. Distribution of Miliusa glandulifera (squares), Miliusa microphylla, sp. nov. (triangles) and Miliusa mollis (circles).
FIGURE 3. A–F in Miliusa microphylla (Annonaceae), a new species from Thailand as evidenced by morphology and plastid phylogeny, with M. glandulifera, a new record for Thailand
FIGURE 3. A–F. Floral organs of member in clade CM2 (= Miliusa microphylla, sp. nov.). A. Adaxial side of inner petal. B. Abaxial side of inner petal. C. Back view of flower, showing sepals and outer petals. D. Flower with stamens and carpels enlarged. E. Carpel. F. Adaxial (above) and abaxial (below) sides of stamen. G. Adaxial side of inner petal of member in clade CM1 (= Miliusa mollis). From Chaowasku 172 (CMUB; A–F) and Smitinand 7455 (BKF; G).
FIGURE 1 in Miliusa microphylla (Annonaceae), a new species from Thailand as evidenced by morphology and plastid phylogeny, with M. glandulifera, a new record for Thailand
FIGURE 1. Phylogram derived from Bayesian inference, with support values indicated: PP (posterior probabilities) / BS (maximum likelihood bootstrap values) / SR (parsimony symmetric resampling values). ** = BS and/or SR <50%. Scale bar unit: substitutions per site.
FIGURE 2. A in Miliusa microphylla (Annonaceae), a new species from Thailand as evidenced by morphology and plastid phylogeny, with M. glandulifera, a new record for Thailand
FIGURE 2. A. Flower of member in clade CM2 (= Miliusa microphylla, sp. nov.), apical view. B. Flower of member in clade CM1 (= Miliusa mollis), apical view. C. Flower of Miliusa glandulifera, apical view. D. Mature monocarps of Miliusa glandulifera. Photographs by A. Damthongdee (C, D) and T. Chaowasku (A, B).
FIGURE 21 in A broadly sampled 3-loci plastid phylogeny of Atraphaxis (Polygoneae, Polygonoideae, Polygonaceae) reveals new taxa: III. A. kuvaevii and сryptic species in A. pungens from Southern Siberia and Northern Mongolia
FIGURE 21. Holotype of Atraphaxis ledebourii sp. nov. RUSSIA. Tuva: Tes-Khem Raion, the southern slope of the East Tannu-Ola ridge, dry stone bed of the Khyralyg-Khem river, 1200 m, 03 June 1972, Khanminchun 4821 (holotype MW0061283).
FIGURE 15 in A broadly sampled 3-loci plastid phylogeny of Atraphaxis (Polygoneae, Polygonoideae, Polygonaceae) reveals new taxa: III. A. kuvaevii and сryptic species in A. pungens from Southern Siberia and Northern Mongolia
FIGURE 15. Atraphaxis decipiens (A–F, I–L) and A. pungens × A. decipiens (G–H): leaf blades (A, G), fragment of thyrse (B, I, J), flowers (C, D, K), fruits (D–F, H), and styles (E, L). A–F—(310) RUSSIA. Tuva: Ulug-Khem Raion, Khayyrakan vill., steppe, 01 August 2015, Kostikov & Kostikova (MW). G–H—(309) RUSSIA. Tuva: Barun-Khemchik Raion, Shekpeer vill., 03 August 2015, Kostikov & Kostikova (MW). I–L—RUSSIA. Tuva: Kyzyl Raion, Kara-Khaak vill., 28 July 2015, Kostikov & Kostikova (MW). Scale Bar: = 1 µm (A, B, G, I, K); = 0.5 µm (C, D, F, H, J); = 0.2 µm (E, L).
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.