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72 results for “plastome”
Plastid introgression and evolution of African miombo woodlands: new insights from the plastome-based phylogeny of Brachystegia trees
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Phylogenomics of mulberries (Morus, Moraceae) inferred from plastomes and single copy nuclear genes
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Data from: Plastome phylogenetics of tribe Eriachneae and evolution of C₄ photosynthesis in subfamily Micrairoideae (Poaceae)
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Data from: Plastome-based subgenus-level phylogenetic backbone of hawthorns: insights into the maternal position and taxonomic synopsis of Crataegus shandongensis (Rosaceae, Maleae)
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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>
Fig. 4 in Complete plastome phylogeny and an update on cox1 intron evolution of Hyoscyameae (Solanaceae)
Fig. 4 An evolutionary scenario for the cox1 intron acquisitions in the tribe Hyoscyameae. Purple dots indicate mitochondrial cox1 intron acquisitions by horizontal gene transfer. The paraphyly of the genus Scopolia is supported by plastid and nuclear markers (see text and Fig. 3)
Fig. 1 in Complete plastome phylogeny and an update on cox1 intron evolution of Hyoscyameae (Solanaceae)
Fig. 1 The chloroplast genome of Scopolia carniolica. Large and small single-copy regions (LSC and SSC, respectively) and inverted repeats (IR) are indicated. Genes inside and outside the circle indicate clockwise and counterclockwise transcription directions, respectively. Gene positions are color-coded according to functional categories of genes. The
Fig. 3 in Complete plastome phylogeny and an update on cox1 intron evolution of Hyoscyameae (Solanaceae)
Fig. 3 Maximum likelihood phylogenetic trees of the tribe Hyoscyameae. A Tree based on the complete chloroplast genomes. The last inverted repeat region was removed to avoid sequence overrepresentation. The alignment length is 134,327 nt. B Tree based on nuclear ITS2 sequences. The seven individuals of Atropa
FIGURE 2 in Phylogenetic position of Vanda coelestis (Rchb.f.) Motes (Orchidaceae; Aeridinae): evidence from complete plastome and combined traditional sequences
FIGURE 2. Maximum likelihood tree for Vanda based on combined nuclear (nrITS) and plastid DNA regions (matK, psbA-trnH, and trnL-trnF). The previously recognized sections from Gardiner et al. (2013) are highlighted by the color of branches and species. The numbers near the nodes are bootstrap percentages and Bayesian posterior probabilities (BP, BP, PP). A dash (-) indicates that a node ML MP is inconsistent between the topology of the MP/ML trees and the Bayesian tree; *node is 100 bootstrap percentage or 1.00 posterior probability.
FIGURE 7 in Plastome data provide insights into intra and interspecific diversity and ndh gene loss in Capparis (Capparaceae)
FIGURE 7. MultiPip analysis showing overall sequence similarity of plastid genomes based on complete plastome alignment using Capparis spinosa var. spinosa as a reference sequence. Levels of sequence similarity are indicated by red (75±100%), green (50±75%), and white (<50%). Arrows indicate gene losses.
FIGURE 6 in Plastome data provide insights into intra and interspecific diversity and ndh gene loss in Capparis (Capparaceae)
FIGURE 6. Nucleotide diversity and hotspot regions in genus Capparis. The X-axis represents the nucleotide position and Y-axis represents nucleotide diversity (Pi). 6a. Interspecific variation among four taxa of Capparis. 6b. Intraspecific variation among two varieties of Capparis spinosa viz. var. spinosa and var. herbacea.
FIGURE 2 in Plastome data provide insights into intra and interspecific diversity and ndh gene loss in Capparis (Capparaceae)
FIGURE 2. Plastome maps of Capparis spinosa var. spinosa and Capparis spinosa var. herbacea. Genes shown outside the circles are transcribed clockwise and those inside are transcribed anticlockwise. Genes belonging to different functional groups are in various colours. The dashed area in inner circles indicates the GC content of plastome. ORF – Open reading frame. Asterisks indicate genes containing introns.
FIGURE 5 in Plastome data provide insights into intra and interspecific diversity and ndh gene loss in Capparis (Capparaceae)
FIGURE 5. Comparison of SSRs in four Capparis taxa viz. C. spinosa var. herbacea, var. spinosa, C. versicolor and C. urophylla. 5a. Types of SSRs; 5b. Size of SSRs; 5c. Number of SSR repeats in LSC, SSC and IRs. Numbers above each bar represents the number of repeats.
FIGURE 4 in Plastome data provide insights into intra and interspecific diversity and ndh gene loss in Capparis (Capparaceae)
FIGURE 4. Codon usage of four taxa of Capparis viz. Capparis spinosa var. spinosa, var. herbacea, C. versicolor and C. urophylla. Xaxis: Amino acid, Y- axis: codon usage in percentage. * indicates stop codon.
FIGURE 1 in Plastome data provide insights into intra and interspecific diversity and ndh gene loss in Capparis (Capparaceae)
FIGURE 1. Map depicting distribution and altitudinal ranges of seven varieties of Capparis spinosa. (as per Jacobs 1965, Fici 2014, and POWO 2019).
FIGURE 3 in Plastome data provide insights into intra and interspecific diversity and ndh gene loss in Capparis (Capparaceae)
FIGURE 3. Comparison of LSC, SSC and IR borders of Capparaceae with members of Cleomaceae (Tarenaya hassleriana) and Brassicaceae (Aethionema arabicum). Numbers in boxes indicate total length of the particular region; numbers below the arrows show base pair shift or overlapping regions. Gene and IR lengths are not to scale.
Data from: Plastome and nuclear phylogenies of dwarf mistletoes (Arceuthobium: Viscaceae)
<p>Dwarf mistletoes are a group of morphologically-reduced aerial shoot parasites of Pinaceae and Cupressaceae found in the northern hemisphere and equatorial east Africa. Though diagnosable by a suite of morphological traits, phylogenetic knowledge of species relationships has been limited to studies employing either comprehensive sampling of one or two genes, or more sequence data but limited taxonomic sampling. We used genome skimming data to assemble 3kb of the nuclear ribosomal cistron and up to 45kb of the plastome to clarify the phylogenetic root of the genus, species monophyly, and relationships among infraspecific taxa. Genomic differentiation among taxa was variable; however, we found strong support for reciprocally monophyletic New World and Old World lineages and congruent nrDNA and plastome topologies at the species level and below, and most taxonomic sections and at the species level and below. Plastome gene content was stable across the genus with minimal pseudogenization or loss, with the notable exception of <i>cemA</i>. These findings form the basis of our re-evaluation of historical biogeographical hypotheses, species and subspecies-level taxonomy, and plastome evolution in <i>Arceuthobium. </i>More broadly, this work provides a foundation for future clade-focused comparative and biosystematics studies of <i>Arceuthobium.</i></p>
Phylogenomic data of Camellia section Paracamellia based on transcriptomes and plastomes
<p><em>Camellia</em> section <em>Paracamellia</em> of the genus <em>Camellia</em> (Theaceae) includes major woody oil crops in China and relative wild species as valuable genetic resources for breeding. However, the phylogeny and origin of <em>C. oleifera</em> and its relative species are still uncertain. In this study, the transcriptomes of 22 samples and plastomes of 19 samples were sequenced and assembled. Finally, the dataset of phylogenomic matrices was generated, including 982 and 326 single-copy orthologous (SCO) genes generated from transcriptomes data and the plastid matrix used for phylogenetic analysis. Please cite this article as doi: 10.1111/jse.12948.</p>
Phylogenomic data of Litsea complex based on genome-wide single-nucleotide variants (SNVs) and plastomes
<p>In this study, we focus on the Litsea complex (Lauraceae), a key lineage with dominant species of evergreen broadleaved forests (EBLFs) in East Asia to gain insights into how evergreen versus deciduous trait shifted, providing insights into the origin and historical dynamics of EBLFs in East Asia under Cenozoic climate change. We reconstructed a robust phylogeny of the Litsea complex using genome-wide single-nucleotide variants (SNVs) and plastomes. Finally, the dataset of phylogenomic matrices was generated, including five genome-wide SNVs dataset and plastomes matrix used for phylogenetic analysis.</p>
FIGURE 1 in Plastome phylogenomics of Micromeles (Rosaceae)
FIGURE 1. Gene map of 14 Micromeles plastomes. Genes inside and outside the circle are transcribed clockwise and counter-clockwise, respectively. Genes are color-coded indicates the different functional groups. The dark gray in inner circle indicates the GC contents.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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